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.

Somatic mutation beyond neurological traits. Part IV: the big mistake in genetics

The previous posts in this series were about the potential relevance of somatic mutation to neurologically relevant traits.  I commented about ideas I've long had about the possible genetic etiology of epilepsies, but then about the more general relevance of somatic mutation for behavior and other less clinical traits, indeed, to positively beneficial traits.  But the issues go much farther!

Fundamental units as the basis of science
Every science has fundamental units at the bottom of their causal scale, whose existence and properties can be assumed and tested, but below which we cannot go.  The science is about the behavior or consequences of these units and their interactions.  The fundamental unit's nature and existence per se are simply assumed.  Physicists generally don't ask what is inside a photon or electron or neutron (or they say that these 'particles' are really 'waves').   In that sense, fundamental 'causes' are also defined but not internally probed.  They don't really attempt to define 'force' except empirically or, for that matter, 'curved space-time'. You simply don't go there!  Or, more precisely, if and when you venture into the innards of fundamental units, you do that by defining other even more fundamental units.  When string theory tries to delve into unreal dimensions, they leave most other physicists, certainly the day-to-day ones behind.  Generally, I think, physicists are usually more clear about this than biologists.  The same in mathematics: we have fundamental axioms and the like that are accepted, not proven or tested.

Why is somatic mutation considered to be some sort of side-show in genetics?
What are biology's fundamental units?  For historical reasons, evolutionary biology, which became much of the conceptual and theoretical foundation for biology, was about organisms.  Before the molecular age, we simply didn't have the technology to think of organisms in the more detailed way we do now, but thought of them instead as a kind of unit in and of themselves.

Thus, the origins of ecology and phylogeny (before as well as after Darwin) were about whole organisms.   Of course, it was long known that plants had leaves and animals had organs, and these and their structures and behavior (and pathologies) were studied in a way that was known to involve dissecting the system from its normal context. That is, organs were just integral parts of otherwise fundamental units.  This was true even after microscopes were developed, Virchow and others had established the cell theory of life.  Even after Pasteur and others began studying bacteria in detail, the bacterium itself was a fundamental unit.

Eukaryotic cell; figure from The Mermaid's Tale, Weiss and Buchanan, 2009

But this was a major mistake.  Dissecting organs to understand them did, when considered properly, allow the identification of digestion, circulation, muscle contraction, and the like.  But the focus then, and still today in the genetic age, on the whole organism as a basically fundamental unit has had some unfortunate consequences.  We know that genes in some senses 'cause' biological traits, but we treat an organism as a fundamental unit with a genotype, and that is where much trouble lies.

The cell theory made it obvious that you and I are not not just an indivisible fundamental unit, with a genotype as its fundamental characteristic.  Theories of organisms, embryology, and evolution largely rest on that assumption, but it is a mistake, and somatic mutation is a major reason why.

The cell theory, or cell fact, really, makes it clear that you and I are clearly not indivisible causal units with a genotype.  We know beyond dispute that cell division typically involves at least some DNA replication errors--'errors', that is, if you think life's purpose is to replicate faithfully.  That itself is a bit strange, because life is an evolutionary phenomenon that is fundamentally about variation.  Perhaps like most things in the physical world, the important issues have to do with the amount of variation.

Mitotic spindle during cell division; from Wikipedia, Public Domain

The number of cell-divisions from conception through adulthood in humans is huge.  It is comparable to the number of generations in a species, or even a species' lifespan.  Modern humans have been around for, say, 100,000 generations (2 million years), far fewer than the number of cell divisions in a lifetime.  In addition, the number of cells in a human body at any given time is in the many billions, and many or even most cells continue to renew throughout life.  This is comparable to the species size of many organisms.  The point is that the amount of somatically generated variation among cells in any given individual is comparable to the amount of germline variation in a species or even a species' history.  And I have not included the ecological diversity of each individual organism, including the bacteria and viruses and other small organisms on, in, and through a larger organism.

By assuming that somatic mutational variation doesn't exist or is trivially unimportant--that is, by assuming that a whole organism is the fundamental unit of life, we are entirely ignoring this rich, variable, dynamic ecology.  Somatic mutation is hard to study.  There are many ways that a body can detect and rid itself of 'mutant' cells--that is, that differ from the parent cell at their bodily time and place.  But to treat each person as if s/he has 'the' genotype of his/her initial zygote is a rash assumption or, perhaps a bit more charitably, a convenient approximation.

Oversimplification, deeper and deeper
In the same way that we can understand the moon's orbit around the earth by ignoring the innards of both bodies, so long as we don't care about small orbital details, we can understand an organism's life and relations to others including its kin, by ignoring the internal dynamics that life is actually mainly about.  But much of what the whole organism is or does is determined by the aggregate of its nature and the distribution of its genotypes over its large collections of cells.  We have been indulging in avoiding inconvenient facts for several decades now.  Before any real reason to think or know much about somatic mutation (except, for example, rearrangements in adaptive the immune system), the grossness of approximation was at least more excusable.  But those days should be gone.

Geneomewide mapping is one example, of course.  It can find those things which, when inherited in the germline and hence present in all other cells (except where it's been mutated), affect particular traits.  Typically, traits of interest are found by mapping studies to be affected by tens, hundreds, or even thousands of 'genes' (including transcribed RNAs, regulatory regions etc.).  Each individual inherits one diploid genotype, unique to every person, and then around this is a largely randomly generated distribution of mutant cells.  When hundreds of genes contribute, it just makes no sense to think that what you inherit is what you are.

It should also be noted that we have no real way even to identify the 'constitutive' genome of an organism like a person.  We must use some tissue sample, like blood or a cheek swab.  But those will contain somatic mutations that arose subsequent to conception.  We basically don't look for them and indeed each cell in the sample will be different.  Sequencing will generally identify the common nucleotide(s) at each site, and that generally will be the inherited one(s), but that doesn't adequately characterize the variation among the cells; indeed, I think it largely ignores it as technical error.

The roles and relevance of somatic mutation might be studiable in comparing large-bodied, long-lived species with small ones in which not many cell divisions occur. They might be predicted to be more accurately described by constitutive (inherited) genomes, than larger species.  Likewise plants with diverse 'germ lines', such as the countless meristems in trees that generate seeds, compared to simpler plants, might be illuminating.

How to understand and deal with these realities, is not easy to suggest.  But it is easy to say that for every plausible reason somatic mutation must have substantial effects on traits good, bad, and otherwise.  And that means that we have been wrong to consider the individual to be a fundamental unit of life.

Somatic mutation and neurological traits. Part II. Relevant Somatic Mutation discovered?

The first installment of this brief series discussed some possible manifestations of somatic mutation in helping to account for the biology and epidemiology of epilepsies.  From a cellular point of view, epilepsies seem to be functionally close to gene action, but mostly have eluded gene mapping in families, GWAS, or mouse models.  Yesterday, I referred to a paper that I published in 2005 which mused about the possibility that some epilepsies and other behavioral traits might be due to genetic effects that arose through somatic mutation rather than being inherited in the parents' germline, and I tried to suggest reasons why that idea seems plausible  But finding direct evidence for relevant somatic mutation in relevant neural (brain) tissue, just a subset of cells, would have been technically very challenging.  That was then, however, and technology marches on.

A new paper by Wei et al. in the February 2016 issue of Cell ("Long Neural Genes Harbor Recurrent DNA Break Clusters in Neural Stem/Progenitor Cells") may suggest that we're getting to a point where it might be possible to address my speculation directly--and perhaps go far beyond that to understand epilepsies much better but, even more, to address variation in normal behavior and abnormal psychological function in general.

Wei et  al. report using a clever, sophisticated, if very technical method to make a systematic search for a class of somatic mutations in neural cells.  The experiments are done in mouse cell culture and, basically, Wei et al looked genomewide for chromosomal changes or rearrangements that arise out of double-strand chromosomal breaks.  The detail is far beyond what I could competently describe here, and would be out of place in a blog.  However, the upshot of their work is that the authors expanded on what had been known, that there are very large mutational rearrangements detectable in repeatable locations in the genomes of early neural precursor cells.

As shown in the figure below, the rearranged locations are found genomewide, and on most chromosomes. The changes varied among cells tested.  I am not qualified either to defend or critique the method itself, but have no reason to doubt the findings, and if anything it must be fair to assert that because the method only finds one sort of mutation, the finding implies that other methods would find expanded evidence for somatic mutation of various sorts in these cells, as are clearly known to happen in other cell types. The authors used methods that have passed muster before, they cite ample other literature on somatic rearrangements generally.  Experiments like this are artificial in various ways, and theirs doesn't prove that the mutations they detected do in fact have phenotypic effects in vivo, but the case for that is certainly and strongly plausible.

Neural and other genes undergoing SoMu in (mouse) brain. Circle numbers are chromosomes  From Wei et al., Cell, 2016

The importance of this finding, and what justifies its being published in Cell in my view, is that it shows not just tolerance of somatic mutation, but perhaps even active genomic modification in the early mouse brain. Moreover, the authors find that a major fraction if perhaps even preponderance, of the genes altered in this process, whatever other roles they may serve, are involved in neural cell adhesion and synapse formation and/or function.  One can be properly skeptical about assigning function to genes (gene ontologies are often quite shaky and genes typical serve many functions), but even if there is a sort of after-the-fact bias in interpretation, the involvement in the modified genes in synapse function seems well established.

For a partial summary of the approach, the original authors as well as a short, cogent and somewhat more digestible accompanying commentary by Weissman and Gage ("A Mechanism for Somatic Brain Mosaicism"), explain the potential this may have for the determination of individuality. This is speculation in detail, naturally, but the proto-neurons develop into relevant areas of the adult brain, and the authors note that the affected cells are, or reasonably may be, involved in a variety of higher functions.  They mention learning and mental functions such as autism, bipolar depressive disorders, schizophrenia, and intellectual disability.  They also speculate that the somatic changes could be relevant to various forms of cancers of brain cells.  And, perhaps an artifact of the way science is done these days, I saw no mention of the obvious likely fact, that if these changes can be involved in disease they can also be involved in any other psychological traits.

The authors also did not mention epilepsies, nor whether genes known or suspected of being involved in some epilepsies were detected in any of these rearranged regions. I'm not any sort of expert on that, but on a very cursory check, I did not spot any specific known epilepsy related genes in the above figure, but one can hardly take that as in any way definitive. Since epilepsy is itself relatively rare, only rare somatic mutational changes need be involved, for epilepsy to be an occasional consequence and to help account for the variation in the types and parts of the brain affected, the seriousness, age of onset, and so on.  We'll see.

Phenotype amplification
In the previous post, I referred to to means of phenotypic amplification, a process by which mutations in a single or small subset of cells could reach organismal (whole-person) detectability or effect.  One means would be if a somatic mutation happens early enough in development for a large enough set of descendant cells to be affected, almost as if the mutation were inherited in the germ line.  Given the n numbers of at-risk embryonic cells and the number of people produced each year, and the surely large number of genes that could have an effect on epilepsy (or any other psychological trait), this simply must occur!  Depending on when in development the somatic mutation occurred, its descendant set could be general and bilateral, or could be restricted to a small part of the brain on just one side, depending on the way these tissues differentiate during development.  That is, the types of epilepsy that are focal, affecting only a restricted, identifiable part of the brain, might be susceptible to genomic analysis to identify the mutations (illustrated in the figure in yesterday's post).  That is, the rest of the person's neural cells would not be mutated.

The other method of phenotype amplification I mentioned yesterday could occur when one or just a few mutant, misfiring neurons misfires, and that then induces a cascade of firing in the many other neurons to which it synapses.  This kind of phenotype amplification might not be easily detectable, because the single or few mutant culpable neurons might be invisible in sequences of the entire affected brain region, because most of the misfiring cells would, themselves, be genetically normal. That is, their misbehavior would be induced by the abnormal neuron(s) to which they were synapsed.

The variable and usually highly restricted, focal nature of epilepsies (i.e., suggested in yesterday's figure) cries out for explanation that involves the unique features of these small areas.  The methods in the Cell paper are very complex, technical, and certainly nothing I ever did in my lab, so I must acknowledge that my thoughts could be off the speculative mark.  Still, the paper and others it cites show that the ideas have more than totally circumstantial support.  There are lots of mutations in neural cells, as indeed, there are in any set of somatic cells.  They affect the individual in which they occur but are not transmitted in the germ line and hence not discoverable by GWAS and family studies.

No matter what one may think of the idea, a point worth making is that there is now at least one major study systematically documenting the pervasive frequency of somatic mutation of particular types (rearrangements),  that is active, common, and genomewide in developing neural precursor cells (and the authors cite other relevant results).  How or even whether a role of somatic mutation in epilepsy can be shown in real mice, much less humans, and not just cell culture or sequencing of the brains of deceased patients, is of course an open question.

However, unlike 2005 when I wrote my speculations, high throughput and even single-cell sequencing are now at least beginning to be practicable in mouse models and deceased humans who had epilepsies of known focality and expression.  If the ideas are cogent, investigators may find them compelling subjects to study.

Searching for somatic mutational causes of traits that seem to have specific tissue locations, seems now at least more possible, inroads might be possible and could, in principle at least, lead to substantial advances in understanding the mechanisms involved, as well as the epidemiology and phenotypes of epilepsy.