Is cancer just bad luck? Part I. Known risk factors are poor predictors

Cancers are a highly unpredictable set of diseases, representing a fundamental problem in understanding causation that Tomasetti and Vogelstein address in a recent paper in Science ("Variation in cancer risk among tissues can be explained by the number of stem cell divisions", 2 Jan 2015, Vol 347 Issue 217).  This paper has gotten a lot of notice, both approving and not.  A bit of history might be helpful.

Cancers are due to cell proliferation gone wrong, that is, not obeying the constraints on division and differentiation of their particular tissue.  The idea has been that this is due either to exposure to some environmental risk factor, including something to do with lifestyle, or to genetic predisposition.  Both seem to be true at the population level, with, for example, breast cancer associated with age at first birth or whether women breast feed or not, number of children, alcohol consumption, and so forth, and with clear genetic risk factors, like some BRCA1 and 2 risk alleles.  In populations, people who smoke are more likely to get lung and other cancers, people with HPV cervical cancer, and so on.  But this doesn't mean that everyone who smokes, or has particular genetic risk allele, will get cancer, and that's the issue.  

Even if a risk factor is know, that doesn't explain the immediate cause of a tumor, at the cell level.  That cause is gene(s) misbehaving, causing the cell to divide at an inappropriate time.  So the idea for decades had been that environmental agents that stimulated cell division put cells at risk of incurring a mutation, and environmental mutagens caused those changes, which were the ultimate or final causes of cancer.  Hence, the search for 'cancer' genes.  

In the old days (the 1990s!), direct searches for genes were generally not possible, with a few exceptions where viruses seemed to change genes in a cancer-causing way.  But some cancers seemed to be clearly familial, that is, inherited in a Mendelian way in families.  They were statistically predictable, but with the problem that the risk depended on whether you inherited a risk gene, and we could only make a probabilistic statement about that.  A few lucky breaks showed that finding such genetic mutations was possible.  Specific inherited cancer risk-genes was first and most clearly demonstrated for a couple of childhood tumors.  Most notably, perhaps, was the eye cancer, retinoblastoma.  A fortuitous chromosomal deletion allowed the responsible gene to be identified, which was rare at that time for biomedical genetics, that was largely confined to predicting risk with no understanding of nor ability to test the actual causal gene.  There were a few others with similarly lucky discovery.

However, when genotyping on a genome-wide scale became possible, the idea was clearly that we could search the entire genome for locations that were co-transmitted or associated with a given type of cancer.  There have been many different methods, and a few clear successes.  The hallmark, and indeed one of the first genomewide screens to yield a major risk factor, was the finding that the BRCA1 and BRCA2 genes could, when experiencing one of several particular mutations, lead to a very high lifetime risk of cancer.  This was done in large, multi-generational families, but the success spurred methods to search more generally in populations (that we now call GWAS or other types of searches).  The BRCA discovery led to the rampant genomewide approach that we have seen in the recent 15-20 years.  The idea underlying this work has been the idea of finding risk variants that are strong enough, if not to be transmitted clearly in families, at least consistently affect risk, and this has been extended to basically every trait someone could get a grant to study.

But even when BRCA causation was found, there were important questions.  Those inheriting a high-risk BRCA mutation and who did in fact get breast (or ovarian) cancer, did not get those diseases until mid- to late life.  The lifetime risk was very high indeed, and some unfortunately got separate cancers in each breast.  Yet this was not the rule.  So, if the gene 'caused' the cancer, why did it take so long to do it?  An obvious answer is that it was environmental factors.  Also, by far most cancers do not segregate in families in Mendelian fashion the way BRCA mutation effects can, and indeed relatives only share slightly excess risk.  Even cases are at only slightly elevated risk than controls for most cancer-related gene mapping results.  One would think that the final risk might be due to the additional contribution of environmental factors.

Epidemiological studies of environmental risk factors for cancer have identified the major ones -- smoking, asbestos, exposure to UV light and X-rays, exposure to some chemicals used in agriculture and so on.  So, many (especially environmental epidemiologists who don't have a stake in the competition for genomic funding) have argued that if genomic variation isn't a good predictor, environmental variation must be!  But after extensive work, environmental factors don't explain all causes of any given cancer, either, nor can exposure history reliably predict cancers -- only a small minority even of smokers goes on to develop lung cancer, e.g.  And, indeed, unlike smoking and a few others, most environmental associations and candidate factors aren't clear mutagens or promoters.  So what's going on??

Why don't environmental or genetic risk factors explain all the risk?
This is the problem Cristian Tomasetti, a mathematician, and Bert Vogelstein addressed.  Vogelstein was one of the pioneers of the search for somatic mutation. That is, the mutational change that makes a cell misbehave need not have been inherited, but have been generated during the person's life. Vogelstein years ago applied a particular technique to show that tumor cells contained a particular kind of mutation (called 'loss of heterozygosity') that was not found in non-cancer cells from the same individual, but often was found in particular genome regions for a given type of cancer (in particular, colorectal cancer).  That was rather clear evidence (and there was evidence from a growing number of other researchers, too) that cancer was indeed a 'genetic' disease, but not just due to inherited variants.

Tomasetti and Vogelstein point out that current data suggest that only 5-10% of cancers are caused by heritable factors, and environmental factors can't explain the wide disparities in risk of cancer in different tissues.  They wondered how much cancer is caused by chance and how much by environmental factors.  By "chance" they mean things that just happen to go wrong during the DNA copying that occurs during cell division, which is when a tumor gets started.  Their analysis suggests that these changes are just inherent molecular copying errors, that don't have to be induced by environmental factors.

Writing in the same issue of Science in which the paper appears, Jennifer Couzin-Frankel describes the work:

In a paper published...this week in Science, Vogelstein and Cristian Tomasetti, who joined the biostatistics department at Hopkins in 2013, put forth a mathematical formula to explain the genesis of cancer. Here’s how it works: Take the number of cells in an organ, identify what percentage of them are long-lived stem cells, and deter- mine how many times the stem cells divide. With every division, there’s a risk of a cancer- causing mutation in a daughter cell. Thus, Tomasetti and Vogelstein reasoned, the tissues that host the greatest number of stem cell divisions are those most vulnerable to cancer. When Tomasetti crunched the numbers and compared them with actual cancer statistics, he concluded that this theory explained two-thirds of all cancers.

Tomasetti and Vogelstein estimate the stochastic, or chance effects "associated with the lifetime number of stem cell divisions within each tissue."  These effects can be mathematically distinguished from environmental risk factors.  They predicted "that there should be a strong, quantitative correlation between the lifetime number of divisions among a particular class of cells within each organ (stem cells) and the lifetime risk of cancer arising in that organ."  And this is what they found, and how they determined that two-thirds of all cancers are due to chance; the changes that occur just by bad luck during DNA replication.

There are also life-history aspects of cell division that are generally consistent with this.  For example, neurons stop or at least slow down their division rates as the brain matures, while glial (supporting) cells keep dividing, and most brain cancers in adults are gliomas.  Retinoblastoma (eye cancer) risk is mainly at birth or early childhood, and retinal cells have stopped dividing after that.  But radiation treatment (an environmental mutagen) for RB has been found in the past, at least, to lead to later bone cancer, when bones are rapidly growing.

This has generated some attempts at rebuttal, which is not surprising, because many hopes as well as vested interests among geneticists and environmental epidemiologists are threatened by the finding.  But in fact, based on work and then-current ideas we ourselves were involved in back in the 1970s and 80s, the current kerfuffle is a reflection both of culpable misunderstanding, ignoring of long-standing evidence, wishful thinking, and looking away from some facts that raise challenges even for the 'new' explanation of cancer causation.  We'll discuss that tomorrow.

Genomic medicine reality check

Dumping cold water on personalized genomic medicine
A news focus piece in last week's Science about cancer geneticist Bert Vogelstein is right up our alley. The piece begins, "Their lab helped reveal how faulty genes cause cancer, but Bert Vogelstein and [laboratory co-director] Kenneth Kinzler sometimes irk colleagues with their “reality check” comments on genomic medicine." Their point? Whole genome sequencing is not going to be useful for predicting who will and who won't get cancer. And they back this up with a study of disease risk in identical twins, described in an April Science Translational Medicine paper ("The predictive capacity of personal genome sequencing").

Vogelstein has long been interested in characterizing genes that are mutated in tumors, long ago identifying genes associated with the development of colorectal cancer. He and Kinzler when the latter was a student in Vogelstein's lab, showed how the slow accumulation of mutations in previously identified genes, including tumor repressor genes that no longer do their job when mutated, lead to tumor growth.

In the last decade, Vogelstein and Kinzler were the first lab to publish an extensive tumor exome sequence, all the coding regions of breast and colorectal cancers. They identified both known and novel genes involved in tumorigenesis. The work was done in the days before high-throughput sequencing was commonplace, however, and their work was criticized as not having been thorough enough or well-analyzed statistically. Though, their results were subsequently confirmed by others.

Whole genome tumor sequencing is much easier and more complete now, but Vogelstein and Kinzler don't see much more to be gained with it, and they've moved on. Their recent work has involved looking at identical twins to determine whether what they call the "genometype" would allow prediction of disease risk. That is, based on the assumption that monozygotic twins share essentially the same genotype, is it possible to predict risk of disease to a second twin if the first one has it? This of course depends on the extent to which the disease is genetically determined.

This basic observation, that monozygotic twins of a pair are not always afflicted by the same maladies, combined with extensive epidemiologic studies of twins and statistical modeling, allows us to estimate upper- and lower- bounds of the predictive value of whole-genome sequencing.

On the negative side, our results show that the majority of tested individuals would receive negative tests for most diseases. Moreover, the predictive value of these negative tests would generally be small, as the total risk for acquiring the disease in an individual testing negative would be similar to that of the general population.

The authors go on to point out that this is consistent with what has been found with GWAS -- many genes explain little risk. 

Thus, our results suggest that genetic testing, at its best, will not be the dominant determinant of patient care and will not be a substitute for preventative medicine strategies incorporating routine checkups and risk management based on the history, physical status and life style of the patient.

The story is different, they point out, for rare monogenic diseases, where whole genome sequencing has already been shown to be informative -- but then, so have association studies and the like.

Why the cold water is warranted

The first point one would make is that most genetic disease susceptibility seems to be due to what is known as the constitutive genome, that is, the DNA sequence you inherited when you were just a single cell, a fertilized egg. As they divide and divide during life, all your cells have a copy of the same genotype--almost. Each time they divide, some DNA copying errors are made, and the descendant 'daughter' cells are slightly different. Since you're made of billions upon billions of cells you have just as many different genotypes.

Most such somatic mutations are never seen clinically. Whether they help or harm, they're just in a single cell, and their effects are swamped by the sea of surrounding cells in the same tissue, that basically have your constitutive genotype at genes relevant to that tissue. If the constitutive genotype confers risk, then basically all cells in that tissue are at risk.

The difference with regard to cancer is that when a bad combination of mutations occurs in a single cell, it doesn't just die or stagger along doing no harm to you, but it proliferates, amplifying the signal of that mutation. It takes many different mutations to transform a cell from normal to cancerous. This is why cancer risk is poorly predictive from your constitutive genotype: most of the changes that lead to disease occur somatically in this or that cell until a bad combo arises in one of billions of cells.

So you'd think at least looking at the tumor cells would show what mutations were important. To some extent that's true, and though it isn't much use in predicting cancer (since the mtuations are found after you already have cancer!), this may provide ideas on how to target the cancer cells. The problem with even that is that a cancer in a single person is continually evolving, rapidly accumulating even more mutations, so that not all cells in the same tumor are cancerous for the same reasons.

You'd have to sample many different parts of the tumor to identify the different variants. And some recent studies have done just that, and shown that different secondary tumors--descendants of the primary tumor, within one patient's body--are genetically different. In part, at least, this is what enables cancer to metastasize, to colonize different parts of the body from the tissue they started in.

But if cancer is therefore not well predicted from your constitutive genome, one might expect that diabetes and heart disease would be predictable because they aren't the same kind of proliferating disorder. But despite what the genome-selling companies would like you to believe, that is turning out not to be true, either, and we have discussed this countless times before, in the context of GWAS and other studies.

Evolutionary implications

This is all consistent with evolution as well. The same genomic complexity that makes your traits, but makes finding single genes 'for' the trait difficult, is exactly what means that natural selection is not working very closely on one or a small number of specific genes. If GWAS can't find causal genes for a trait, even if you have the trait, natural selection can't do that either.

This means that traits can evolve adaptively via natural selection in the way Darwin explained, without this being very tractably understood at specific single genes, and indeed the indirect genomic effects of selection that is merely screening traits is what led causation to be so complex in the first place.

There are many parallels between what happens among cells in your body, and individuals in a species, and Ken wrote about that in 2005 in Trends In Genetics, where he discussed ways in which diseases other than cancer might be caused by somatic mutations whose effect could somehow be amplified so you would notice it at the organism level. Diseases like epilepsy were examples discussed there.

Causation may be genetic in the trait or evolutionary sense, but the specific genotypes that are responsible may be difficult or impossible to detect, or so variable among cases and individuals that by and large it's not worth taking that approach--something roughly consistent with what Vogelstein was saying in the story about him.

Is cancer just bad luck? Part II. It's a genetic, but usually unpredictable, disease

Yesterday, we discussed some history of research on the cause and predictability of cancer.  Today, we'll try to raise some questions that seem to have been overlooked in the recent Tomasetti and Vogelstein paper in Science that argues that much or most cancer, with a few notable and clear exceptions, does not arise from inherited genetic mutations, nor from lifestyle exposures, but arises just by bad luck during the countless cell divisions that occur during our lives.  Much reaction to the paper has overlooked these issues as well.

In the usual use of the term, cancer is not genetic because there are only a few types of cancer that are clearly due to inherited variations in known individual genes. Even these are usually only a subset of all instances of cancer of the particular organ in question.  Most breast cancer does not involve inherited variation in the BRCA1 or BRCA2 genes, for example.

At the same time, some cancers, most notably breast but also colorectal and some other cancers, show family correlations of risk, suggesting that multiple contributing inherited variants might be involved. By far the bulk of cancers are 'sporadic' in the sense that they arise without detectable genetic risk factors.  Even large-scale GWAS type studies find very few genome sites that contribute more than individually very small, barely detectable, risk.

Before the frenetic genome mapping era began around 20 years ago, it seemed clear that with few exceptions (those perhaps mainly due to viruses) cancer was the archetype of a lifestyle-related disease.  Smoking caused a very clear risk of lung cancer.  Some viral exposures caused cancers. Colorectal cancers were largely due to low-roughage western diets, and various things like hormone drugs, coffee, and you-name-it, were suspects.  In addition, we knew clearly that ionizing radiation such as in x-rays and in uranium miners caused cancer risk.

The genome-wielders largely took over, of course, but that was as much a sociopolitical coup as it was based on any serious level science.  DNA was fashionable, sequencers were fancy (and expensive), and we could search the whole genome to find the culprit variants.  This turned out largely to be a big low-payoff bust, though not all geneticists are candid enough to admit it. Still, to many, with the few known exceptions, cancer has been seen as not a genetic disease.

But it's 'genetic' nonetheless!
This may all be true--it certainly is so empirically.  It gives the impression cancer is not really a genetic disease, in the usual sense of the word, meaning due to inherited risk.  But another sense of the word refers to mechanism, and cancer generally does seem clearly to be genetic in that sense.  It's just that the source of the variation is among cells within the body rather than among people (really, conceptuses) in a population.  Or, more properly it's a mix.  In fact if it were really genetic in the inherited sense the fetus would not develop properly, so one should never expect a really deterministic variant to 'cause' cancer by itself.  In this sense, cancer really is, if anything, the archetype of a genetic disease.  Here's why.

Diseases all must arise in some way or other in the behavior of cells.  Usually, it will be some collective aspect of cells, say, the pancreas's cells, as a whole, just don't make enough insulin,  Or by the way diets and other factors affect them, the blood stream produces too much of the wrong kinds of fats and they clog arteries.

But cancer is a disease of a single cell that then goes awry, and its cellular descendants.  The reason is that its genes are not responding in the usually self-restrained way for their local tissue environment. The genes could be induced by viral insertions, or by somatic mutations (that is, mutations occurring in body cells but that were not in the sequences inherited by the individual at his/her conception). The mutations cause the cells to divide without the usual orderly constraints.

Somatic mutations are not in the germ line and are not transmitted from parents to offspring.  They don't generate family risk correlations.  They can't be found by GWAS or other studies based on sequencing inherited genomes.  But they are genetic changes nonetheless, and many studies have shown that tumor cells do share mutational changes not found in normal tissue from the same person, and that as a tumor grows, spreads, develops drug resistance the cells in different descendant parts of the cancer have acquired even further mutational changes.

So that most cancer is not predictable from inherited genotypes is a disappointment, at least for genetic epidemiologists, it's a genetic disease nonetheless.  It's just hard or impossible to detect individual cells with a combination of the 'wrong' changes so as to found a tumor lineage.

At the same time, there is no reason to doubt that countless genetic variants that are inherited can affect risk, and make a cell more vulnerable to transformative somatic mutations.  It's just that, as GWAS types of research shows, the majority of these have individually very small effects--that's because they only have an effect when some other unlucky mutation(s) happen to arise in the same cell during the person's life.  But there can be uncountedly many such heritable weak-effect genome-types that simply can't be found by the current mapping techniques, and that's why such techniques don't find them.

And, yes, it's 'environmental'

Yesterday, we started this series stimulated by the Tomasetti and Vogelstein paper, in which they related the number of dividing cells in a person and the risk and age of onset of cancers of that organ.  They showed statistically that with the few known exceptions such as smoking and lung cancer, that cancer rates correlated pretty well with these considerations.  Since we ourselves were working with cancer site-specific and worldwide age-patterns of cancer, and formulating somatic-mutational models in those pre-genetic days, these ideas were already rather well-established, so the new paper uses newer data and seems very good and apt, but the idea isn't as new as the headlines and attention made it seem.  If anything, the profession at large should never have got to the point of expecting better tumor predictability than was at hand.

Still, environmental risk factors are not ruled out by that analysis.  Environmental or life-history risk factors, like diet or reproductive history and so on, stimulate cell divisions and in that way can affect the risk of mutations arising in the way Tomasetti and Vogelstein suggested: simply the normal errors in DNA copying.  Since the exposure has to affect a cell in a given tissue and in a particular relevant gene being used by that tissue, it is no surprise that the exposure's net effect, and hence predictability, is usually very small.  Still, exposure to environmental agents must contribute to mutations if the agent is known to be mutagenic or to stimulate cell-division.  So epidemiologists may be right that mutagenic or mitogenic exposures can have carcinogenic effect, but Tomasetti and Vogelstein are right that this will be essentially undetectable.  In no way does their analysis relate to the carcinogenic effect per se, just to the net magnitude.  Indeed, we know that such predictions, except relating to a few risk factors like smoking and UV light and HPV virus, haven't proven to be very powerful or reliable.  So there's nothing new here, except to the extent that genetic or environmental epidemiologists are in denial.

But actually, there are very clear environmental factors related to cancer risk.  They have to do with the subtle concept of competing causes.  If mutations arising by chance during cell division ultimately lead to transforming genotypes in some cell, the longer one lives the more likely such changes are likely to arise in at least one such cell in the person.  This is generally why most cancer rates rise with age in ways correlated with rates of cell division.

So, if we were to obtain wonderful preventive measures to eliminate heart disease and stroke, cancer rates would go dramatically up!  That is simply because those who now no longer died from the former would be alive to await the latter.  That is environmental causation, even if indirect!  Likewise, if we really want to reduce the risk of cancer, all we need do is keep eating McBurgers in greater and greater amounts, start some wars, or continue to over-use antibiotics: then we'll all die off of other causes, before we're old enough to get cancer.

Among many things that were said, unaccredited now, by many people including myself, because of the somatic mutational nature of cancer, if you were to live long enough you would get cancer of every organ you have.

Yes, luck is involved!
Indeed, even in inheritors of risk alleles, it need not be that if they get the cancer involved that their case is due to that allele--this is obvious in the sense that the same tumor can arise in people without the allele, usually the vast majority of cases.  So other factors are involved, and the natural occurrence of mutations in cell division, as well as environmental mutagenic or promoter agents doesn't change the fact that which exposed person has the wrong mutations in the vulnerable cells is simply a matter of luck.  An environmental mutagen has to hit the wrong set of genes in the wrong cell.  Naturally and fortunately, the odds are against such bad luck.

Tomasetti and Vogelstein essentially are saying that only the internal luck of mis-copying by DNA causes cancer. But environmental factors contribute to those errors, even if any individual exposure has very weak effects relative to a given type of cancer.  Relative to all cancers, it's harder to say, because through most of history few have lived long enough for there to be the kind of data needed, and since the risk per cell per cell division is small, and cell division generally slows with age, the newer evidence in an aging population will be statistically weak; cancer rates taper off, cancers grow more slowly, and the elderly have more urgent problems to deal with, as a rule.

But even if these findings are true but not revolutionary, not so fast!
The idea that risks per at-risk cell per cell-division that Tomasetti and Vogelstein based their analysis on makes sense, even if it's something that was essentially known decades ago.  We ourselves built multi-hit mutation-accumulation models that seemed to provide reasonably good fits to the known age-onset patterns of specific cancers.  These were based on somatic mutations.  But the T and V paper's analysis actually raises some issues that suggest maybe the authors have given too 'pat' of an explanation.

Even in the mid-20th century it was known that different species of animal also got a similar array of cancers, but that their accelerating age-specific risks, in principle related to the relative number of cells, were correlated with the species' typical lifespan.  And this had little if anything to do with environmental exposures, since the animals involved were typically those we managed or that had rather uniform environments.  This is not a trivial observation!

For example, inbred animals tell the tale as to tissues with a particular life-history of mitosis.  Mice housed in essentially identical conditions, develop an array of tumors at age-specific rates.  But mice get them in months, while we get them in decades.  This problem was raised around 1970 by prominent epidemiologist Richard Peto, but seems to have basically just been (conveniently) ignored. There are also strain-specific cancer risks in mice and other animals (including dogs and cats) that suggest that inherited vulnerability genotypes may be involved, but not single-gene variants.  If the number of cells at risk, or their division rates, are responsible for the just-bad-luck theory, then tiny mice should never get cancer!  And elephants or cows should be dropping over with huge tumors very early in life.

This raises another interesting issue about theory vs data in understanding cancer.  Among the transformative ideas in the late 1900s was that cancer is a 'multistage' disorder, that arises only after several events have occurred in some unlucky cell lineage in the body (or are inherited).  Early results suggested that only 2 events might be responsible.  A number of biostatistical epidemiologists began fitting, or I'd say 'forcing', 2 or 3-stage models to the data.  That is, they had their a specific theory, based on the fragmentary evidence then available, and fit the data to it, to estimate, for example, the rates at which the events occurred.  Then they had to explain what those events were, say, a cell-division inducer and a mutation.  But there was very little substantial evidence that that was the general story of cancer, and the evidence was far weaker than the commitment to the model.

Ranajit Chakraborty and I took a different approach.  We applied a more open multiple hit model and let the data speak for themselves; that is, we estimated (rather than pre-specified) the number of hits required.  We got, I think, better fits and better explanations.  The number of hits was higher, though at the time nothing was known about what they were.  Around 1990 Adam Connor and I suggested that the age pattern of cancer could be accounted for by the age-related probability that some individual cell would acquire some critical set of changes as a function of age, here we didn't specify the number.  This, too, seemed to fit the age-patterns and both approaches suggested that cancers were as a group due to similar genetic processes (whether or not they affected different genes in each instance--there was no useful data at the time), but left open the number of events involved. Since then, it has become clear that many different genes, and different combinations in different instances of cancer in the same organ (lung, stomach, etc.) are involved.  In all, these facts and findings account for the complexity of cancer (and, indeed, many other common normal or abnormal traits).

But if 'luck' means that some individual cell has, for whatever reason, acquired an initiating set of mutations or growth stimuli, then we can expect that to a great extent, each transformed cell is transformed for a different genotypic reason, and no one gene need be involved, or is sufficient.  You just get a bad roll of the mutational dice in one of your cells, regardless of whether the mutation is only due to DNA copying or has been affected by external agents.  The difference would be rather slight, and the main correlation (as in Tomasetti and Vogelstein) related to how many cell-turnovers are at risk.

But the species differences show that something other than just 'luck', or luck affected by lifestyle factors, is involved, and what that is, is basically not known.  That suggests that the Tomasetti and Vogelstein interpretation is itself missing something important (though it won't change the empirical fact that neither inherited genotypes nor most environmental exposures do not have highly predictive effects).

In sum
Cancer is more, and less, than pure luck.  And its causes are still poorly understood.  We think as we've said that the Tomasetti and Vogelstein paper points to many things that are shown by new data--but little if anything that wasn't known, shown, and understood for the right reasons a generation ago.  The love affair with inherited genotypes, enabled, encouraged, and funded by a variety of enthusiasms, opportunities, and vested interests, has distracted attention from working from what we knew.  The problem is that the somatic mutational nature of cancer doesn't lead to tidy prediction, prevention or interventions, at least not with current thinking.  But that's where future thinking should be going.

The (bad) luck of the draw; more evidence

A while back, Vogelstein and Tomasetti (V-T) published a paper in Science in which it was argued that most cancers cannot be attributed to known environmental factors, but instead were due simply to the errors in DNA replication that occur throughout life when cells divide.  See our earlier 2-part series on this.

Essentially the argument is that knowledge of the approximate number of at-risk cell divisions per unit of age could account for the age-related pattern of increase in cancers of different organs, if one ignored some obviously environmental causes like smoking.  Cigarette smoke is a mutagen and if cancer is a mutagenic disease, as it certainly largely is, then that will account for the dose-related pattern of lung and oral cancers.

This got enraged responses from environmental epidemiologists whose careers are vested in the idea that if people would avoid carcinogens they'd reduce their cancer risk.  Of course, this is partly just the environmental epidemiologists' natural reaction to their ox being gored--threats to their grant largesse and so on.  But it is also true that environmental factors of various kinds, in addition to smoking, have been associated with cancer; some dietary components, viruses, sunlight, even diagnostic x-rays if done early and often enough, and other factors.

Most associated risks from agents like these are small, compared to smoking, but not zero and an at least legitimate objection to V-T's paper might be that the suggestion that environmental pollution, dietary excess, and so on don't matter when it comes to cancer is wrong.  I think V-T are saying no such thing.  Clearly some environmental exposures are mutagens and it would be a really hard-core reactionary to deny that mutations are unrelated to cancer.  Other external or lifestyle agents are mitogens; they stimulate cell division, and it would be silly not to think they could have a role in cancer.  If and when they do, it is not by causing mutations per se.  Instead mitogenic exposures in themselves just stimulate cell division, which is dangerous if the cell is already transformed into a cancer cell.  But it is also a way to increase cancer by just what V-T stress: the natural occurrence of mutations when cells divide.

There are a few who argue that cancer is due to transposable elements moving around and/or inserting into the genome where they can cause cells to misbehave, or other perhaps unknown factors such as of tissue organization, which can lead cells to 'misbehave', rather than mutations.

These alternatives are, currently, a rather minor cause of cancer.  In response to their critics, V-T have just published a new multi-national analysis that they suggest supports their theory.  They attempted to correct for the number of at-risk cells and so on, and found a convincing pattern that supports the intrinsic-mutation viewpoint.  They did this to rebut their critics.

This is at least in part an unnecessary food-fight.  When cells divide, DNA replication errors occur.  This seems well-documented (indeed, Vogelstein did some work years ago that showed evidence for somatic mutation--that is, DNA changes that are not inherited--and genomes of cancer cells compared to normal cells of the same individual.  Indeed, for decades this has been known in various levels of detail.  Of course, showing that this is causal rather than coincidental is a separate problem, because the fact of mutations occurring during cell division doesn't necessarily mean that the mutations are causal. However, for several cancers the repeated involvement of specific genes, and the demonstration of mutations in the same gene or genes in many different individuals, or of the same effect in experimental mice and so on, is persuasive evidence that mutational change is important in cancer.

The specifics of that importance are in a sense somewhat separate from the assertion that environmental epidemiologists are complaining about.  Unfortunately, to a great extent this is a silly debate. In essence, besides professional pride and careerism, the debate should not be about whether mutations are involved in cancer causation but whether specific environmental sources of mutation are identifiable and individually strong enough, as x-rays and tobacco smoke are, to be identified and avoided.  Smoking targets particular cells in the oral cavity and lungs.  But exposures that are more generic, but individually rare or not associated with a specific item like smoking, and can't be avoided, might raise the rate of somatic mutation generally.  Just having a body temperature may be one such factor, for example.

I would say that we are inevitably exposed to chemicals and so on that will potentially damage cells, mutation being one such effect.  V-T are substantially correct, from what the data look like, in saying that (in our words) namable, specific, and avoidable environmental mutations are not the major systematic, organ-targeting cause of cancer.  Vague and/or generic exposure to mutagens will lead to mutations more or less randomly among our cells (maybe, depending on the agent, differently depending on how deep in our bodies the cells are relative to the outside world or other means of exposure).  The more at-risk cells, the longer they're at risk, and so on, the greater the chance that some cell will experience a transforming set of changes.

Most of us probably inherit mutations in some of these genes from conception, and have to await other events to occur (whether these are mutational or of another nature as mentioned above).  The age patterns of cancers seem very convincingly to show that.  The real key factor here is the degree to which specific, identifiable, avoidable mutational agents can be identified.  It seems silly or, perhaps as likely, mere professional jealousy, to resist that idea.

These statements apply even if cancers are not all, or not entirely, due to mutational effects.  And, remember, not all of the mutations required to transform a cell need be of somatic origin.  Since cancer is mostly, and obviously, a multi-factor disease genetically (not a single mutation as a rule), we should not have our hackles raised if we find what seems obvious, that mutations are part of cell division, part of life.

There are curious things about cancer, such as our large body size but delayed onset ages relative to the occurrence of cancer in smaller, and younger animals like mice.  And different animals of different lifespans and body sizes, even different rodents, have different lifetime cancer risks (some may be the result of details of their inbreeding history or of inbreeding itself).  Mouse cancer rates increase with age and hence the number of at-risk cell divisions, but the overall risk at very young ages despite many fewer cell divisions (yet similar genome sizes) shows that even the spontaneous mutation idea of V-T has problems.  After all, elephants are huge and live very long lives; why don't they get cancer much earlier?

Overall, if if correct, V-T's view should not give too much comfort to our 'Precision' genomic medicine sloganeers, another aspect of budget protection, because the bad luck mutations are generally somatic, not germline, and hence not susceptible to Big Data epidemiology, genetic or otherwise, that depends on germ-line variation as the predictor.

Related to this are the numerous reports of changes in life expectancy among various segments of society and how they are changing based on behaviors, most recently, for example, the opiod epidemic among whites in depressed areas of the US.  Such environmental changes are not predictable specifically, not even in principle, and can't be built into genome-based Big Data, or the budget-promoting promises coming out of NIH about such 'precision'.  Even estimated lifetime cancer risks associated with mutations in clear-cut risk-affecting genes like BRCA1 mutations and breast cancer, vary greatly from population to population and study to study.  The V-T debate, and their obviously valid point, regardless of the details, is only part of the lifetime cancer risk story.

ADDENDUM 1
Just after posting this, I learned of a new story on this 'controversy' in The Atlantic.  It is really a silly debate, as noted in my original version.  It tacitly makes many different assumptions about whether this or that tinkering with our lifestyles will add to or reduce the risk of cancer and hence support the anti-V-T lobby.  If we're going to get into the nitty-gritty and typically very minor details about, for example, whether the statistical colon-cancer-protective effect of aspirin shows that V-T were wrong, then this really does smell of academic territory defense.

Why do I say that?  Because if we go down that road, we'll have to say that statins are cancer-causing, and so is exercise, and kidney transplants and who knows what else.  They cause cancer by allowing people to live longer, and accumulate more mutational damage to their cells.  And the supposedly serious opioid epidemic among Trump supporters actually is protective, because those people are dying earlier and not getting cancer!

The main point is that mutations are clearly involved in carcinogenesis, cell division life-history is clearly involved in carcinogenesis, environmental mutagens are clearly involved in carcinogenesis, and inherited mutations are clearly contributory to the additional effects of life-history events.  The silly extremism to which the objectors to V-T would take us would be to say that, obviously, if we avoided any interaction whatsoever with our environment, we'd never get cancer.  Of course, we'd all be so demented and immobilized with diverse organ-system failures that we wouldn't realize our good fortune in not getting cancer.

The story and much of the discussion on all sides is also rather naive even about the nature of cancer (and how many or of which mutations etc it takes to get cancer); but that's for another post sometime.

ADDENDUM 2
I'll add another new bit to my post, that I hadn't thought of when I wrote the original.  We have many ways to estimate mutation rates, in nature and in the laboratory.  They include parent-offspring comparison in genomewide sequencing samples, and there have been sperm-to-sperm comparisons.  I'm sure there are many other sets of data (see Michael Lynch in Trends in Genetics 2010 Aug; 26(8): 345–352.  These give a consistent picture and one can say, if one wants to, that the inherent mutation rate is due to identifiable environmental factors, but given the breadth of the data that's not much different than saying that mutations are 'in the air'.  There are even sex-specific differences.

The numerous mutation detection and repair mechanisms, built into genomes, adds to the idea that mutations are part of life, for example that they are not related to modern human lifestyles.  Of course, evolution depends on mutation, so it cannot and never has been reduced to zero--a species that couldn't change doesn't last.  Mutations occur in plants and animals and prokaryotes, in all environments and I believe, generally at rather similar species-specific rates.

If you want to argue that every mutation has an external (environmental) cause rather than an internal molecular one, that is merely saying there's no randomness in life or imperfection in molecular processes.  That is as much a philosophical as an empirical assertion (as perhaps any quantum physicist can tell you!).  The key, as  asserted in the post here, is that for the environmentalists' claim to make sense, to be a mutational cause in the meaningful sense, the force or factor must be systematic and identifiable and tissue-specific, and it must be shown how it gets to the internal tissue in question and not to other tissues on the way in, etc.

Given how difficult it has been to chase down most environmental carcinogenic factors, to which exposure is more than very rare, and that the search has been going on for a very long time, and only a few have been found that are, in themselves, clearly causal (ultraviolet radiation, Human Papilloma Virus, ionizing radiation, the ones mentioned in the post), whatever is left over must be very weak, non tissue-specific, rare, and the like.  Even radiation-induced lung cancer in uranium minors has been challenging to prove (for example, because miners also largely were smokers).

It is not much of a stretch to simply say that even if, in principle, all mutations in our body's lifetime were due to external exposures, and the relevant mutagens could be identified and shown in some convincing way to be specifically carcinogenic in specific tissues, in practice if not ultra-reality, then the aggregate exposures to such mutations are unavoidable and epistemically random with respect to tissue and gene.  That I would say is the essence of the V-T finding.

Quibbling about that aspect of carcinogenesis is for those who have already determined how many angels dance on the head of a pin.

Food-Fight Alert!! Is cancer bad luck or environment? Part I: the basic issues

Not long ago Vogelstein and Tomasetti stirred the pot by suggesting that most cancer was due to the bad luck of inherent mutational events in cell duplication, rather than to exposure to environmental agents.  We wrote a pair of posts on this at the time. Of course, we know that many environmental factors, such as ionizing radiation and smoking, contribute causally to cancer because (1) they are known mutagens, and (2) there are dose or exposure relationships with subsequent cancer incidence. However, most known or suspected environmental exposures do not change cancer risk very much or if they do it is difficult to estimate or even prove the effect.  For the purposes of this post we'll simplify things and assume that what transforms normal cells into cancer cells is genetic mutations; though causation isn't always so straightforward, that won't change our basic storyline here.

Vogelstein and Tomasetti upset the environmental epidemiologists' apple cart by using some statistical analysis of cancer risks related, essentially, to the number of cells at risk, their normal time of renewal by cell division, and age (time as correlated with number of cell divisions).  Again simplifying, the number of at-risk actively dividing cells is correlated with the risk of cancer, as a function of age (reflecting time for cell mutational events), and with a couple of major exceptions like smoking, this result did not require including data on exposure to known mutagens.  V and T suggested that the inherently imperfect process of DNA replication in cell division could, in itself, account for the age- and tissue-specific patterns of cancer.  V and T estimated that except for the clear cases like smoking, a large fraction of cancers were not 'environmental' in the primary causal sense, but were just due, as they said, to bad luck: the wrong set of mutations occurring in some line of body cells due to inherent mutation when DNA is copied before cell division, and not detected or corrected by the cell.  Their point was that, excepting some clear-cut environmental risks such as ionizing and ultraviolet radiation and smoking, cancer can't be prevented by life-style changes, because its occurrence is largely due to the inherent mutations arising from imperfect DNA replication.

Boy, did this cause a stink among environmental epidemiologists!  Now one we think undeniable factor in this food fight is that environmental epidemologists and the schools of public health that support them (or, more accurately, that the epidemiologists support with their grants) would be put out of business if their very long, very large, and very expensive studies of environmental risk (and the huge percent of additional overhead that pays the schools' members meal-tickets) were undercut--and not funded and the money went elsewhere.  In a sense of lost pride, which is always a factor in science because it's run by humans, all that epidemiological work would go to waste, to the chagrin of many, if it was based on misunderstanding the basic nature of the mutagenic and hence carcinogenic processes.

So naturally the V and T explanation has been heavily criticized from within the industry.  But they will also raise the point, and it's a valid one, that we clearly are exposed to many different agents and chemicals that are the result of our culture and not inevitable and are known to cause mutations in cell culture, and these certainly must contribute to cancer risk.  The environmentalists naturally want the bulk of causation to be due to such lifestyle factors because (1) they do exist, and (2) they are preventable at least in principle.  They don't in principle object to the reality that inherent mutations do arise and can contribute to cancer risk, but they assert that most cancer is due to bad behavior rather than bad luck and hence we should concentrate on changing our behavior.

Now in response, a paper in Nature ("Substantial contribution of extrinsic risk factors to cancer development," Wu et al.) provides a statistical analysis of cancer data that is a rebuttal to V and T's assertions.  The authors present various arguments to rebut V and T's assertion that most cancer can be attributed to inherent mutation, and argue instead that external factors account for 70 to 90% of risk.  So there!

In fact, these are a variety of technical arguments, and you can judge which seem more persuasive (many blog and other commentaries are also available as this question hits home to important issues--including vested interests).  But nobody can credibly deny that both environment and inherent DNA replication errors are involved.  DNA replication is demonstrably subject to uncorrected mutational change, and that (for example) is what has largely driven evolution--unless epidemiologists want to argue that for all species in history, lifestyle factors were the major mutagens, which is plausible but very hard to prove in any credible sense.  

At the same time, environmental agents do include mutational effects of various sorts and higher doses generally mean more mutations and higher risk.  So the gist of the legitimate argument (besides professional pride or territoriality and preservation of public health's mega-studies) is really the relative importance of environment vs inherent processes.  The territoriality component of this is reminiscent of the angry assertion among geneticists, about 30 years ago, that environmental epidemiologists and their very expensive studies were soaking up all the money so geneticists couldn't get much of it.  That is one reason geneticists were so delighted when cheap genome sequencing and genetic epidemiological studies (like GWAS) came along, promising to solve problems that environmental epidemiology wasn't answering--to show that it's all in the genes (and so that's where the funding should go).  

But back to basic biology 
Cells in each of our tissues have their own life history.  Many or most tissues are comprised of specialized stem cells that divide and one of the daughter cells differentiates into a mature cell of that tissue type.  This is how, for example, the actively secreting or absorbing cells in the gut are produced and replaced during life.  Various circumstances inherent and environmentally derived can affect the rate of such cell division. Stimulating division is not the same as being a direct mutagen, but there is a confounding because more cell division means more inherent mutational accumulation.  That is, an environmental component can increase risk without being a mutagen and the mutation is due to inherent DNA replication error.  Cell division rates among our different tissues vary quite a lot, as some tissues are continually renewing during life, others less so, some renew under specific circumstances (e.g., pregnancy or hormonal cycles), and so on.

As we age, cell divisions slow down, also in patterned ways.  So mutations will accumulate more slowly and they may be less likely to cause an affected cell to divide rapidly.  After menopause, breast cells slow or stop dividing.  Other cells, as in the gut or other organs, may still divide, but less often.  Since mutation, whether caused by bad luck or by mutagenic agents, affects cells when they divide and copy their DNA, mutation rates and hence cancer rates often slow with advancing age.  So the rate of cancer incidence is age-specific as well as related to the size of organs and lifestyle stimulates to growth or mutation.  These are at least a general characteristics of cancer epidemiology.

It would be very surprising if there were no age-related aspect to cancer (as there is with most degenerative disease).  The absolute risk might diminish with lower exposure to environmental mutagens or mitogens, but the replicability and international consistency of basic patterns suggests inherent cytological etiology.  It does not, of course, in any sense rule out environmental factors working in concert with normal tissue activity, so that as noted above it's not easy to isolate environment from inherent causes.

Wu et al.'s analysis makes many assumptions, the data (on exposures and cell-counts) are suspect in many ways, and it is difficult to accept that any particular analysis is definitive.  And in any case, since both types of causation are clearly at work, where is the importance of the particular percentages of risk due to each?  Clearly strong avoidable risks should be avoided, but clearly we should not chase down every miniscule risk or complex unavoidable lifestyle aspect, when we know inherent mutations arise and we have a lot of important diseases to try to understand better, not just cancer.

Given this, and without discussing the fine points of the statistical arguments, the obvious bottom line that both camps agree on is that both inherent and environmental mutagenic factors contribute to cancer risk. However, having summarized these points generally, we would like to make a more subtle point about this, that in a sense shows how senseless the argument is (except for the money that's at stake). As we've noted before, if you take into account the age-dependency of risk of diseases of this sort, and the competing causes that are there to take us away, both sides in this food fight come away with egg on their face.  We'll explain what we mean, tomorrow.

Cancer--luck or environment? Part II: Nothing to food-fight over

Yesterday we commented on the 'controversy' over whether cancer is mainly due to environmentally (lifestyle) or inherently (randomly) arising mutations.  This is a tempest in a teaspoon.

Mutations, whatever their individual cause, must accumulate among dividing cells until one cell has the bad luck to accumulate a set of changes that 'transforms' it into a misbehaving cancer cell.  The set of changes varies even among tumors of the same organ, because many different genes and their expression-regulation contribute to the growth, or restraint of growth, even within the same tissue. That is, not all breast, colon, or lung cancers are caused by the same set of mutations.   It then proliferates, rapidly dividing and thus indubitably acquiring more mutational changes that enable it to do things like metastasize to other parts of the body, or develop resistance to drug treatment.  The more rapidly it grows and spreads, the more rapidly such things can happen.

Even if the first transformational cause were due entirely to environmentally-induced mutations, the real dangers that ensue during the tumor's lifespan are relatively rapid additions to the original tumorigenesis process, and so in a sense the main dangers of cancer are primarily, if not nearly exclusively, due to inherent mutation among cancer cells.  If you get lung cancer and then stop smoking, your lung cancer will still evolve. Indeed, if environment contributes, it may make things worse--if that "environment" is radiation or chemotherapy: radiation definitely causes mutations, and chemotherapy weeds out cells that haven't experienced resistance mutations, leaving or even making room for tumor lineage cells that do have resistance mutations.  Finally, things that stimulate cell division can facilitate new mutations or even just make a tumor spread more rapidly.

So clearly cancer is not all due to environmental, nor to inherently occurring changes.  These and other factors comprise multiple, interacting causative effects.  Attributing cause to environment or inherency is misleading.  But what if cancer were in fact even entirely due to lifestyle factors that stimulate cell division or directly cause mutation?  Of course this would be very good for the Big Data epidemiologists and their studies, and threatening to industries and so on that produce mutagenic waste or products etc.  But suppose epidemiologists were to continue to find major carcinogenic environmental factors (that is, that the major ones, like smoking, aren't already known). Let us further suppose that avoidance behavior were to follow the announcement of the risks (not an obvious thing to assume, actually; the tobacco industry is still thriving, after all).  Then what?

Epidemiologists would say their work has prevented cancer and would claim victory over the to-them strange idea that cancer is due to inherent mistakes in DNA replication and is inevitable if one were to live long enough.  A lifestyle-change-based reduction in cancer would be clearly a very good thing.  But in fact, it would not be an unalloyed victory: one thing it would do is keep the non-exposed person alive (because s/he didn't get cancer!) and that in turn means that s/he would be at higher risk of (1) other age-related deteriorative diseases that dying of cancer would have precluded, many of which are waiting in the wings at ages when cancers arise, and (2) eventually getting cancer at some older age.  In the first case, the rates of other diseases like stroke and diabetes etc. would necessarily go up.  The risk of slowly petering out in increasingly bad shape in an intensive nursing unit would go up.  That would, of course, lower the lifetime cancer risk, but not in a very pleasant way.

In other words, lifestyle changes can delay cancer, but even assuming that the per-year exposure to environmental mutagens were reduced, the consequently longer exposure to those mutagens might mean their lifetime total would go up), so whether or not it decreased the lifetime risk of cancer would be an open question.  However, what this would do would be, by removing environmental causes, to raise the fraction of cancers that are due to inherent mutation, strengthening the fraction of Vogelstein-Tomasetti cases!

It's undoubtedly good to get cancer later rather than earlier in life, but not an unalloyed good.  In any case, what these points show is that the argument over the particular fraction of cancers that are due to environment vs inherent mutation is rather needless.  At most it might be relevant to ask how much of funding investment in big epidemiological studies is going to pay off, rather than spending on some other clearer issues (especially if the major environmental mutagens are already known).  There have already been scads of massive long-term studies of almost anything you can name, to identify carcinogenic exposures. With some very important exceptions, that are by now well known, these studies have largely come up empty, or with now-it-is/now-it-isn't conclusions, in the sense that risk factors are either weak, or if strong are rare and hard to find embedded in the broad mix of chronic disease risk factors.  Environments are always changing with new possible carcinogenic exposures arising, but basically those with strong effects usually show up on their own such as by multiple cases of a particular cancer type in some specific location or among workers in a particular industry or in vitro mutagenesis studies and the like.

If causation is too generic, don't get your hopes up
If comparisons among countries, for example, show that the same cancer can have very different age patterns or incidence rates, this may suggest lifestyles as major risk differences. But that's far from saying that the causal elements are individually strong or simple enough to be enumerated by the usual Big Study epidemiological approach. One can be extremely doubtful that this would be the case.

Saying something is 'environmental' because, for example, it varies among populations is like saying something is 'genetic' because it varies among relatives.  If it's like genetic factors as documented by countless GWAS studies, there are many different, correlated or even independent contributors, then each person's cancer will be due to a different set or complex set of experiences and the luck of the mutational draw.  As with GWAS and related approaches, it is far from clear that large, long-term environmental studies, more mega than we've already had for decades, will be the appropriate way to approach the problem.

Indeed, to a considerable extent, if each case is causally unique, by some different combination of factors and their respective strengths in that individual, then it's epistemologically not very different from saying that cancer occurs randomly, which, though for a different sort of reason, is what V and T said.  There won't, for example, be a specific environmental change you can make, any more than a specific gene you can re-engineer, to make the disease go away or even to change much in frequency or age of onset.

Food fights like this one are normal in science and often have to do with egos, investment in one 'paradigm' or another, how research is supported or advice from experts are conveyed to the public.  But such disputes, though very human, are rather off the point.  We often basically ignore risks we know, as in the proliferation of CT and other radiation-based scanning and medical testing which can be carcinogenic.  Life is mutagenic, one way or another.  So while you have life, enjoy your food--don't waste it by throwing it at each other!  There are better questions to argue about.

The Elephant (not) in the Cancer Ward

Recently, Tomasetti and Vogelstein (the latter a senior and highly regarded cancer geneticist) suggested that most cancer is due just to bad luck.  We discussed that study here.  When cells divide, DNA is copied, but that is a molecular process that isn't perfect (see discussion of Wednesday's Nobel Prize in Chemistry, e.g., for the discovery of DNA repair mechanisms and their association with cancer).  There are mutation detection mechanisms of various sorts (the BRCA1 gene whose mutations are associated with breast and some other cancers, is one with that sort of function).  The more at-risk cell divisions, the more mutations, and the higher the likelihood that one cell will experience a combination of mutations that (along with inherited variation) transforms the cell into the founder of a cancer.  T and V's assertion based on statistical analysis of numbers of cells at risk, their division rate for given tissues, and age of onset patterns, was that random mutation was a major contributor to cancer, rather than inherited genotype or environmental exposures, which they argue would account for this substantial fraction of cases.

Naturally, those whose grant fortunes depending on the idea that cancer is 'genetic' and/or 'environmental' roared in opposition to an idea that could threaten their perspective (and empires). Some of the T and V paper's statistical methods were questioned, and perhaps their paper was over-stated or less definitive than claimed.  Nobody can doubt that genetic variation and environmental exposures that could cause cells to be more likely to experience mutations, play a role in cancer.  But in any practical sense, it is hard to deny that luck plays a role (even with environmental exposures, because if they cause mutations, they basically strew them randomly across the genome, rather than causing them in any particular gene, etc.).

But we mentioned an important issue then that had been raised 40 years ago by epidemiologist Richard Peto.  Essentially it is that other mammals, like mice, experience a similar array of cancer types, with similarly increasing risk with age....but that increase is roughly calibrated with their life span. In fact, mice have far fewer stem cells in, say, their intestine or blood than humans, but their risk of cancer in these tissues increases far more rapidly (in years) than does human risk, though we have orders of magnitude more at risk cells and cell divisions.  This became known as Peto's Paradox.  It has not really been answered though there are some attempts to determine how it is that different species, of different sizes, calibrate their cancer risk in relation to their observed typical lifespan.

"Elephas maximus (Bandipur)" by Yathin S Krishnappa - Own work. Licensed under CC BY-SA 3.0 via Commons - 

For example a 2014 paper in Nature Reviews Genetics by Gorbunova et al. documents the very different typical lifespans of rodent species, and suggests some plausible genetic mechanisms that may protect the longer-lived species from cancer.  There must be some such mechanism, or else we misunderstand something very important in the carcinogenesis process.

Now a new commentary has been discussed in the NY Times of a JAMA paper, that makes similar genetic arguments for the very out-of-line cancer-free longevity of elephants.  Based on their numbers of at-risk cells, elephants should drop over with cancer at a very young age, but instead they typically live for a very long time.  How can this be?

The JAMA authors, Abegglen et al., found that a gene, called TP53, that is clearly related (when mutated) to cancer susceptibility in humans and in experimental assays, at least in part because it detects and effectively kills misbehaving mutated cells.  The study included humans with Li Fraumeni syndrome (LFS), a genetic disorder that greatly increases the risk of developing cancer, susceptibility to which has long been known to be associated with variants in TP53, and blood samples from Asian and African elephants.  

The study needs close scrutiny for methodological issues, but the authors make what they feel, reasonably, is a relevant finding.  There is only one copy of the TP53 gene in humans, but in elephants there are 20.  In blood cell assays this gene's activity was higher than in humans.  The inference is that elephants' longevity relative to cancer is due to this gene. If that is indeed the (or at least, an) explanation for the elephants' cancer-related longevity, it raises some other important questions, which should at least raise eyebrows and the need for ever-present skepticism.

Questions raised by the results
As in the rodent paper cited above, single-gene mechanisms for complex traits are appealing and publication-worthy, but in a sense such claims raise questions about themselves.  Elephants live long lives relative to other diseases that essentially have little if anything to do with cancer.  One can think of heart disease, dementia, stroke, kidney failure, liver disease, neuromuscular and joint disease, and waning immune systems.  Are these traits all due to having more TP53?  That seems unlikely.  

Alternatively, apparently whales are known not to have multiple TP53 duplicates, and I don't know about other very large animals like rhinos, giraffes, and so on.  A standard argument would be that in ecological circumstances when natural selection favors longer lives for some species, it uses whatever mechanism happens to be available--that is, selection has no foresight and can't just choose genes to duplicate.  Each species will have experienced the longevity advantage in its own local time, place, and ecosystem.  Just as the genes whose mutation yields resistance to malaria in humans vary from continent to continent, so will longevity-related genes favored by selection

So, Peto's Paradox remains curious.  If each species has its own protective mechanism (and perhaps several for its different organ and physiological systems), then we can account in a reasonable way for longevity patterns.  There is no need to find, or even to expect the same thing in all species' evolution: variation in response to selection can vary by organ system, species, and location even among species.  This is exactly the sort of thing that we should expect when we think of the complexity of genomic mechanisms--and what has consistently been found by genome mapping studies (GWAS) of late onset traits (and, for that matter, even early onset ones).

In turn, that means that each paper that claims subtly or overtly to have found 'the' or even a widespread important mechanism related to aging needs to be taken circumspectly.  Aging and lifespans are complex phenomena.  We will learn from each example we document, as with GWAS results, that a simple anti-aging strategy can't be inferred.  It's not likely to be a single magic bullet.

What is 'your' genotype? There's no answer because you have millions of them!

No one has a single genotype.  We begin life as a single cell, a fertilized egg containing two human genome copies, one inherited from each parent.  It also contains hundreds or thousands of mitochondrial DNA molecules that were in the egg cell.  They will not all be identical.  Then the initial cell divides to begin the process by which we formed an embryo that grew its many tissues and organs.  This involved billions of cell divisions.

Human blastocyst; Wikimedia

Each time a cell divides, some mutations occur.  These are not germline (sperm or egg) mutations, differences between your parents and you, the usual notion of mutation.  Instead, they are somatic (body cell) mutations.  The embryo forms a tree of cell descent (and, in that sense, so do you), and mutational changes in a cell are inherited when it divides into two daughter cells and their descendant cells throughout the rest of your life.  So that the earlier a mutation occurs in the embryo the greater the number of cells that will have that change.

As a result, each person is a genotypic mosaic.  When people talk about a genotype, they usually and sloppily refer to what would be sequenced in a sample of blood or cheek cells.  Most of this will be the inherited sequence but there will be a mix of cells with rarer changes (that the sequence-reading software may regard as sequencing errors and ignore), and mutations that may be common in other tissues from different embryonic cell branches will not be seen.

Somatic mutations can have no effect or great effect depending on when and where they occur.  You can have a BRCA1 mutation that arose during your development but that was not inherited and/or isn't in the sample that was sequenced to determine 'your' genotype.  Since your cells are always dying and dividing, you don't really have 'a' genotype!

A recent commentary in Science points out the potential importance of somatic mutations and the complexities they introduce into trying to infer genetic causation in medicine.  This is quite important, and is well-explained.  But there is a deeper history to this than covered in the piece.

Indeed, people had realized by the 1970s that somatic mutation was probably a contributor to cancer, because one transformed cell that had misbehaving behavior as a result of mutant genes could grow into a life-threatening tumor.  The idea was bruited in a wonderful and famous paper by Al Knudsen at the University of Texas in Houston (my Dean, where I was at the time) in the early '70s, in relation to the eye cancer retinoblastoma.  He showed the potential joint impact of inherited and somatic variation.  That conceptually led various people to pursue the idea of multistage somatically based tumorigenesis, and work largely by Bert Vogelstein and colleagues at Johns Hopkins established early ways of genomic screens to compare tumor cells with the patient's normal cells to show this.

Many of us were writing about the implications of somatic mutation at that time.  It was explicit in articles, book chapters, and books.  I myself attempted to awaken people to the potentially broader and challenging impact of somatic mutation (e.g., in Trends in Genetics in 2005).  Ranajit Chakraborty and I wrote many papers in the '80s about the way somatic mutation might explain why cancer is not usually present at birth and to account for the age of onset patterns of cancer, and in my 1993 book Genetic Variation and Human Disease (20 years ago!) and elsewhere I provided a speculative account of how this could apply to age-related diseases (most diseases) more widely.

There were and are many other examples and instances of the importance of somatic mutation, in humans and other animals (and plants).  But the bemused human genetics establishment, anchored in early 20th century concepts of simple inheritance, established its juggernaut of GWAS and the idea of relating 'the' genome of a person to his/her fate, paying conveniently little attention to somatic mutation.

Because the situation is so clear in regard to cancer, cancer research has gone to great lengths to understand somatic mutation, as has some smattering of other work here and there, such as attempts to account for some effects of aging in terms of mitochondrial somatic mutation.  In a way, the idea of genomewide 'expression profiling'--looking for cell-specific gene expression in specific tissues--is related to the idea that you can't describe a person from an inherited genotype.

The challenge is outlined well in the current paper, even if the author decided or neglected to cite the earlier literature or note that somatic mutation has been widely ignored out of convenience or culpable unawareness (pick your favorite explanation).  Until we face up to the problem, we will be wastefully pouring funds down the GWAS and sequence database drain. 

The issues are complex.  We know now that the same inherited mutation has variable effects depending on the rest of a person's genotype--and that's why the effectiveness of personalized genomic medicine is heavily misrepresented by various hopeful and/or vested interests.  Similarly, a person's somatic mutations will interact with each other, and with his/her inherited genotype to produce resulting traits, normal as well as disease.  That two-set pattern 'squares' the amount of complication we have to deal with.

Working out how to handle what we know about genotypic variation will not be easy, but we should slow down the train while we try to work out a useful strategy, or at least stop over-promising.  However, the likelihood is that most people who read the article (or, indeed, this post!) will say "Hmm, that's interesting," and then, feeling satisfied about their new awareness, finish their coffee....and go back to business as usual.

Do we still not know what causes cancer? Part IV. The classic case returns....

We have had a series of posts (starting here) stimulated by a debate in BioEssays about whether one major idea about cancer, that it is due to somatic mutations (SMT), is correct, or whether a very different local-tissue-environment model (TOFT) explains the disease.

Given what it seems that we know, we should expect a spectrum of causation to apply, and we think that's what's been observed.  Clearly cancer is a disease of clonal expansion of cells, typically descendants of a single transformed founder cell.  The job of cells is to behave--express subsets of the genes in their genome--in ways that suit their local signaling (inter-cellular communication) environment. Gene expression is how this works, so clearly either mutant genes or mistaken interpretation of the environment, can trigger misbehavior.

First, the SMT, the idea that cancer is entirely due to somatic mutations, should be tempered, because it is manifestly clear that inherited mutations play a role, not just somatic mutations (that occur in body cells but were not inherited from the patient's parents).  As an overall generalization, cancers show mutations in many genes, but some of these have been inherited. Typically those are mutations that are 'recessive': if you get one 'bad' copy from one parent, but a good copy from your other parent, you're generally OK, unless you inherit deficient variants at other genes.  You get cancer if the good copy is somatically mutated in a cell, as well perhaps as other mutations in other genes or changes in the cellular environment.  Such genes are known as 'antioncogenes' or tumor supressor genes, because on their own they don't cause--and might function to hold back--abnormal cell behavior.  These are the main known genes in which inherited mutations lead to cancer. TP53, a gene that encodes the tumor-suppressor protein p53, is an example.

Oncogenes are those than can actively lead a cell astray, 'causing' cancer on their own (probably other factors  have to be present as well).  Mutations in these genes are rarely inherited, because the affected embryo doesn't make its 0th birthday.  If you suffer a somatic mutation in one of these (probably also if the cell has variants in additional genes, or the cell environment is changed somehow), you get cancer.

In either case, SMT argues that somatic mutations must contribute because, after all, you are born normal which means your inherited genotype didn't prevent proper tissue differentiation when you were an embryo. Debate was about how many or what or what types of genes were mutated somatically before someone got cancer. The age and rate of onset (age-specific 'hazard' function) seemed to reflect the number of changes that were needed to transform a cell, the number of cells at risk, and their cell-division rate.

The type of cancer that started us off on the path to the discovery of these aspects of cancer was the rare cancer of the retina (light perceiving layer inside the eye), retinoblastoma, or RB.  RB mainly occurs by birth or in early childhood.  It's rare, but one of the most stunning and influential discoveries--a true rather than hyped 'breakthrough'--was made in the early '70s by Al Knudson.  He observed that in sporadic RB only one eye was affected and usually with only one primary tumor.  But in the rare instance of inherited RB, both eyes were often affected, and by multiple independent tumors.

The idea struck Knudson that if some gene caused the tumor, then if no mutant copies of this gene were inherited, it would be very unlikely that any given retinal cell would be so unlucky as to experience mutations in both copies of the gene: hence sporadic RB is rare and unsually unilateral.  But if one bad copy were inherited, the fetus would only need to 'wait' for the other copy to be hit.  In the millions of newly forming retinal cells, it was reasonably likely that one or even many such cells would indeed be hit by another mutation.

The fact that RB occurred at birth rather than decades later, along with this idea about causation, suggested that there really was only one gene that needed to go bad.  By luck, a group involving Bob Ferrell, who was in Houston with Al Knudson (as was yours truly), discovered a chromosome change that was associated with RB in a family or two, and this led to the discovery of the gene, which was named RB1.

This opened many doors!  Knudson is widely honored, though he should in our opinion have been awarded a Nobel prize for his very insightful work (and he's a very nice person to boot!).  Anyway, to continue the story of the door he opened, soon other childhood tumors (esp. Wilm's tumor of the kidney) were found to have similar genetic epidemiology.  Then others, notably Bert Vogelstein and Ken Kinzler at Johns Hopkins, developed tests to see how often this phenomenon of somatic loss of a good copy of a tumor-suppressor gene occurred in people who had inherited one bad copy.  They found evidence that led to the discovery of other tumor suppressor genes, the most famous of which had to do with colon cancer (and the Tp53 gene that's involved in cell behavior).

Most tumors take decades to develop, even breast cancer in people inheriting mutations in BRCA genes (which is also in the suppressor category).  And this knitted tissue environmental factors (such as exposure to things including menstrual cycling and lactation that stimulated breast cell division) with genetic factors.  Each patient may have a unique set of many different mutations in other genes, some perhaps inherited others acquired somatically, and these were not terrible in themselves but carcinogenic in combination.  The idea of 'waiting' for these events to occur is strengthened by the discovery that BRCA works in a mutation-repair pathway.  So if you can't repair mutations, you're more likely to collect a bad set of them in some cell.

A generally consistent picture emerged, of complex, multifactorial genetic and histological processes that accounted for much of the epidemiology and genetics of cancer.  There are many aspects of this picture that require particular study and explanation.  It seemed that we had a pretty good understanding of the causal landscape, even if the specifics were complex or elusive.

But a new paper in Nature raises questions about even the simple RB model that are challenging to answer, in light of the above ideas.  That will be in Part V of this series on the causation of this dreaded disease--and what it tells us about basic cell biology.