Friday, May 17, 2013

Of mice and men: Genes, environment, and whatever

Is the nature/nurture question finally solved? Are we who we are as a consequence of luck?  A paper in Science, Freund et al., "Emergence of Individuality in Genetically Engineered Mice," assesses the effects of the nonshared environment on neural and behavioral development in 40 inbred female mice living in an enriched environment compared with genetically identical mice in a non-enriched environment.  Does the plasticity of the brain in response to environmental stimuli go a long way toward explaining who we are? 

Freund et al. write:
...the emergence of experience-based individual differences within groups of genetically identical animals exposed to the same enriched environment has rarely been addressed. We used a large group of animals and a particularly complex environment to capture the emergence of individual differences in brain and behavior over time. We used exploration as a marker of behavioral development, and adult neurogenesis in the hippocampus as a marker for continued brain development.
  This figure from the paper gives a schematic of the experimental set-up.

Experimental setup and effects on body and brain weight.
(A) Schematic illustration of the large enrichment enclosure housing 40 mice including RFID antenna positions (shown as red rings). Positions of levels, water sources, nesting boxes, and connecting tubes are drawn to scale. (Inset) Schematic illustration of animal tracking; an RFID passive integrated transponder (PIT) is implanted in mouse’s neck. The electromagnetic field issued by the antenna induces the PIT to emit the number identifying the animal. This information is then picked up by the antenna and stored into a database together with spatial and temporal annotations. (B) Experimental time line. (C) Body weight development: weights (in grams) of CTR (blue) and ENR (red) mice at the beginning and end of the experiment. (D) Brain weights at perfusion (in grams). The difference in variance between CTR and ENR missed conventional statistical significance at P = 0.057. Source: Freund et al., 2013, Science.
After 3 months, mice in the enriched environment were heavier, with more variability in brain and body size than the control mice (though, there were only 8 control mice) and more neuronal connections were made in the hippocampus of the enriched adult mice than in the brains of the controls. "This finding supports the idea that the key function of adult neurogenesis is to shape hippocampal connectivity according to individual needs and thereby to improve adaptability over the life course and to provide evolutionary advantage."

While the authors point out a number of ways in which these mice may not in fact be genetically identical, primarily, they suggest, because of epigenetic changes due to such variables as position in the uterus, maternal disease, nutrition and interactions with the mother, maternal imprinting and so on (the 40 mice were randomly picked from different litters of the same strain of inbred mice to minimize these kinds of effects), they still consider them to be "identical."

But...wait a second!  Are they identical?
Much as we like the authors' general conclusion, because it moves away from the excessive level of imputed genetic determinism of our traits, we must add a word of caution.  These mice were actually not even genetically identical. Every time a cell divides, mutation is likely to happen. Based on some estimates from various kinds of data, that can be about 150 changes per cell division.

Such mutational variation accumulates from conception to an animal's sperm or egg production, and is thus transmitted across generations.  This is true, of course, even in inbred laboratory animals.  So even in a litter of 'identical' pup embryos, there is genetic variation.  But the picture is even more complex.

Every cell division during a mouse's (or your) lifetime, mutations occur.  If we assume that the rate is roughly as above, and even a mouse has millions if not billions (and you have billions if not a trillion or so) of cells, there is a lot of genetic variation within an organism.  Once such a somatic (body cell rather than germ cell) mutation occurs, when that cell divides its daughter cells, throughout future  life of the organism, inherit the change.  Thus, the earlier during embryological development that a somatic mutation occurs, the larger the tree of cellular descent--the more organs or larger the part of a developing organ--that will inherit the change.

Now most of these by far will occur in unimportant areas of the genome--not in any actual genes at all, or in genes that aren't used in the tissues in which the mutation has occurred.  But this cannot be assumed as a general fact and one has to consider the nearly inevitable likelihood that whatever trait is being studied, the animals, even inbred lab animals, are not genetically identical in respect to it.

The challenge here is to identify the variation and figure out if it matters to the trait.  To do that one needs to do tissue-specific, if not detailed individual cell-specific genome sequencing, and even then one needs to identify gene expression at the cell level--and maybe (probably) at different times during development or environmental exposure changes--to attempt to identify those genomic elements whose variation might be involved.   This is essentially impossible as a general rule, and certainly only under some unusual circumstances would it even be worth undertaking.  And, of course, you'd kill the animal in the process, so its behavior would be (only) in the mind of the investigator!  Even to justify the cost and effort, without this minor mortal stumbling block, one would once again have to believe that slicing and dicing the genome, cell by cell, minute by minute, will explain complex traits.

Of mice and men....
Is there really such variation in inbred animals?  Well, we used ForSim, a forward evolutionary simulation program developed in my lab by me and Brian Lambert, to simulate a mouse experiment.  Two independent lines of mice were simulated, using many genes and a lot of DNA to get enough statistical stability in the results.  After generating a normal level of variation, as seen in wild animals and people, we simulated selection of some trait in the opposite direction (small trait values in one, large in the other strain), and then inbreeding for a large number of generations (around 200) with the population kept small, roughly as inbred lines are developed.  Then, we examined these simulated animals for sequence variation and we found a substantial amount of it: roughly as many different sites were varying among the animals as had been fixed by selection and inbreeding.  Yet in the usual mapping and experimental approaches such variation is assumed not to exist.  But it does.

Hey, are we against genes or for genes, after all??
Given our predilection for criticizing what we believe are excessive claims of genetic causation, one has to think carefully and avoid oversimplifying.  The argument cuts all ways.  We must therefore also raise similar cautionary questions about excessive dismissal of genomic effects!

Today, our point is that even here, where traits vary to a surprising extent even in putatively identical animals, it cannot really all be attributed to 'chance' (unless that includes mutations), nor to learning, nor environment.  The causal mix is inextricably complex under widespread if not most conditions.

It is for reasons such as revealed by this study in what otherwise is a clear demonstration, that we write so often to try to temper the enthusiasm for genetically deterministic thinking, much less such gene-based predictions of individuals' futures.  But genes do vary, and they vary subtly.  There is no one crystal ball, not even for mice!


Holly Dunsworth said...

This is great, Ken. Can you recommend a good resource/study/reference exploring within-individual genomic variability? Either in one moment of time or across time?

Anne Buchanan said...

Here are a couple, Holly. One Ken published a few years ago, on somatic mutation as a cause of epilepsy, and one recommended by Gholson Lyon in a Twitter exchange. Ken's, "Cryptic causation of human disease: reading between the germ lines", is in Trends in Genetics, here, and the other, "A genomic view of mosaicism in human disease" in Nature Reviews Genetics.

Ken Weiss said...

Somatic variation is just a continuation of evolution within a person (via mitosis not meiosis, but still including some recombination).

But one (even I!) must not go overboard about its effects, because to have an organismal impact the mutation must lead to what I have called 'phenotype amplification' (see my Trends in Genetics paper in about 2005 on 'cryptic causation'). Cancer is the main exemplar but I think there are ways this can happen with mitochondrial mutations accumulating (there is a literature on that), or in epilepsy where I think there is now some accumulating, if sill unclear, evidence.

So it's just one of many causal contributors, and unfortunately of a unique amount to each individual.