Wonca, 19/9/2009 (Florianne Koechlin)
I’m a biologist, working at the tiny blueridge-institute and indigenous of Basle. My issues are: a critical look at genetics, investigation on new concepts, with inclusion of ethical and philosophical considerations. So I’m not a family doctor and I’m not doing research in a lab.
In the last years many new studies about epigenetic effects on offspring appeared in scientific journals. Perhaps you remember these headlines: „You are what your mother ate“ – the food a pregnant mother eats can affect not only the phenotype but also the genetic outfit of an embryo – at least in mice.
Or: The rough handling of eggcells and sperms during IVF could be the cause for an enhanced risk for the Angelman syndrome. Persons with an Angelman syndrome are mentally incapacitated, they hardly speak, show uncoordinated movements – and they’re always smiling. It’s supposed to be a wrong epigenetic imprinting on chromosome 15.
The new magic word epigenetic is actually not so new any more, a very exciting research area. Epi means ‚above’ in Greek language – epigenetics being a regulation system above the genome; a system of enzymes and RNA molecules regulating the expression of genes, without changing them.
But before going into this new area let’s have a look at the history of genetics.
The discovery of the DNA structure by Watson and Crick in 1953 led to one of the most successful paradigms in biology – the Central Dogma of the Gene. It was the beginning of a whole new area the philosopher Evelyn Fox Keller called the Century of the Gene.
The Central Dogma of the Gene, as formulated by Watson and Crick, was a beautifully elegant, straight forward and powerful theory to explain heredity. And not only heredity, but also traits, diseases, the way we behave.
The Central Dogma states: 1gene – 1protein – 1function.
The gene contains the blueprint for a protein. Information flows from the gene to the protein, never v.v., it’s a one way street. A gene is perceived as the starting point sending out instructions, as inert and context-independent. In this way genes not only determine structure and functions of an organism, but also its characteristics in linear causal chains.
So for a long time this genetic determinism was prevalent in science. We learned that schizophrenia, obesity, homosexuality, alcoholism or fidelity in marriage were determined by our genes. As human beings we appeared to be determined by our genes, like puppets of our genes.
Even in recent times, with much of the euphoric claims of the pioneer time gone, we read that many cases of depression – not all – can be traced back to a single gene- mutation of the serotonine-receptor gene. Or that many cases of breast cancer, are due to mutations of the 2 breast cancer genes BRCA1 and BRCA2.
These findings were accompanied by fierce struggles for patents on genes. The US firm Myriad Genetics for example owns the patents on BRCA1 and BRCA2, which gives her the right to monopolize all so-called breast cancer tests, and also vast research areas around these genes.
In the meantime the Central Dogma of the Gene was challenged by many scientists. A major blow was one of its most successful achievements: the Decoding of the human genome in 2000, celebrated by Bill Clinton rather pathetically as the decoding of the book of life. But it was also a blow: Scientists expected 130,000 coding genes, but they only found 25,000. Just lately this number was reduced to 19,042, whereas the genome of a mouse contains 20,212 genes. And the sequencing of a tree – the black cottonwood poplar – has revealed that this tree has more than 45,000 genes. A tree over 2 times more genes than a human? Can genes really be the book of life, determining our fates?
First problem: there are many more proteins – the formula 1 gene equals one protein could not be true.
It turns out that several different proteins may be produced from a single strech of DNA. A gene can code for many proteins; A gene from cells from the inner ear of a hen can code for 576 different protein-variants.
The linear dogma was challenged by many more findings. Here only a few:
* Genes are context dependent
I have a date tonight with John
This date-palm looks beautiful
The date is the 18th of september
A gene coding for the protein isomerase is found in bacteria, insects and mammals. In drosophila, this protein is part of building pigments for the sight; in mice the same protein has a function in the immune system. It has different functions in different organisms. The function of a gene depends on the environment.
By a process called alternative splicing genes get spliced and rearrangend, as with TIME, MITE, EMIT, ITEM.
So molecular biology’s concept of DNA as „master molecule“ has given way to a more dynamic system of cellular complexity, a system of complex networks, communicating and interacting with each other. A system which is non-linear, not monocausal and not determined by genes or DNA.
And here epigenetics enters the scene: a whole set of molecules responsible for the regulation of genes. Epigenetics deals with how gene activity is regulated within a cell – which genes are switched on or off, which are dimmed and how, and when and where all this happens. Without – and this is important – changing the DNA-sequence of a gene. You can say the epigenetic system interpretes genes. The question is then, who interpretes and regulates the epigenetic systems, and who the next higher level – an infinite regress where at the end you find the cell. And from there on upwards.
I’m not going deeply into the different, so far known mechanisms of the epigenetic system. As known so far, there are different levels of regulation of gene expression:
One is the DNA Methylation: Methyl groups are added to the DNA, to cytosine and deactivate this region.
Another is histone modification by acetylation. Histones are proteins around which DNA wraps around.
And then there are non-coding RNA possibly involved in epigenetic gene regulation. Different RNA-mocelules, eg the small interfering RNA and others.
What becomes clear is that it is actually the cell, which determines, which gene becomes active at what time and in which place to provide the needed proteins. This is a complete reversal of the hierarchy. Genes are not isolated items but part of a dynamic network.
From this view we have to reconsider some developments. Patents on genes eg seem utterly absurd. Not only because nobody invented a gene, and discoveries cannot be patented, nor that they create vast monopoly control, nor that they are more and more an obstacle for research, but also because nobody knows any more what a gene really is. They are part of a network. By patenting a gene the patentholder gets monopoly control over this whole network.
Add to it that concept of a gene seems to elude more and more, the more we know about it. Defining just what a gene is turns out to be a surprisingly slippery problem... There are overlapping regions; they can be read differently etc.
So, perhaps not so amazingly, most of the claims for one gene-traits turned out to be wrong or at least vastely exaggerated. Except, of course, for monogenetic illnesses, like Huntington’s disease or Cystis Fibrosis.
Take the depression-gene. The finding of the serotonin-transporter gene was celebrated in 2003. Many studies were done. It was said that people most likely to fall into a depression after stress-experience often had a particular variant of this gene regulating serotonin.
But in 2009 a metastudy of all available studies found no evidence of an association between the serotonin gene and the risk of depression. In this metastudy 14 studies with overall more than 14,000 participants were analysed.
Conclusion: „This meta-analysis yielded no evidence that the serotonin transporter genotype alone or in interaction with stressful life events is associated with an elevated risk of depression in men alone, women alone, or in both sexes combined.“
Similar story could be told about the BRCA 1 and 2 genes. Heredity plays a much smaller role than advocated by its proponents. And even though research still knows little, environmental factors seem to play a major role.
And there is no doubt that epigenetic signals play a role in many illnesses. It’s well documented that many cancer cells show epigenetic alterations.
In a second step I want to look at how the environment may influence the expression of genes via epigenetics and how these influences can be inherited – a Non-Darwinian epigenetic inheritance.
Well known example: A diet of royal jelly turns a regular, sterile honeybee into a queen. So it’s the food – the royal jelly which has this influence on the genes of a queen.
See these 2 mice, age one year. Their mothers were clones. The mother of the mouse on the left ate a normal mouse diet while pregnant. In contrast, the mother of the mouse on the right ate a diet supplemented with methyl donors while pregnant- vitamin B 12 and folic acid.
The researchers found that in the second group a gene, so called agouti-gene was silenced by the extra-feed of the mother. So the feed of the mother not only influenced the phenotype, but actually also the genes – or preciser: the expression of the genes of the embryos in the womb.
So the environment can have a direct influence on the genes – which is the contrary of what the Central Dogma of the Gene states.
Many scientists today believe that epigenetics is building a bridge between the genome and the environment, enabling a fast adaptation to a changing environment.
This re-opens an old controversy Lamarck against Darwin. In the beginning of the 19th century the French biologist Jean-Baptiste Lamarck claimed that a living being can inherit its acquired characteristics to its offspring. Famous example: A funny mammal, always stretching its neck to eat branches high up – which turned after many generations into a giraffe.
Then Darwin and Mendel provided a different explanation: some mammals had by pure chance – mutations – longer necks and could survive because of the selection- advantage. Survival of the fittest.
I learned at university that Lamarck’s theory was a famous example of misguided science. Now Lamarck seems to sneek in again, at least partly. And of course genetic mutations and changes are most important – but there are other processes as well.
Some other examples of epigenetic inheritance – since I was asked by Urs Glenck for this workshop many more examples appeared in scientific papers.
One group of new born rats was kept isolated alone, the other group with their mums. They experienced a lot of pup licking and grooming and nursing. The neglected pups grew up to be more frightful and less stress-resistent. Researchers showed that certain genes of the neglected rats were silenced by epigenetic methylation. These genes code for the glucocorticoid-receptor in the hypocampus in the brain. The little rats produced more stress hormones, and they did so during their whole life. So pup-licking has consequences on genes of offspring, on their expression, at least in rats.
Perhaps these changes in epigenetic patterns also occur in humans. Meany and his team examined the history of suicide-victims. They divided them in 2 groups: those who have been abused during childhood and those who have not. In the first group they found that the glucocorticoid receptor gene had significantly more epigenetic marks – they had more ‘methylation caps’ – same as the glcocorticoid-receptor genes of the neglected rats. I want to stress: we’re still at the very beginning oof understanding these phenomena.
Larry Feig at Tufts University and his collegues bred ‚knockout mice’ that lacked a gene causing them to have a memory defect. Normally, if mice in a cage receive an electric shock to their feet, they freeze in fear if they are placed back into the same cage. In contrast, these knockout mice did not associate the cage with fear.
The team kept these knockout mice in a cage filled with toys and other mice for 2 weeks. The mice could compensate for their memory defect; they also associated the shock with the cage, like normal mice.
Surprisingly, all their offspring, which all had the memory defect, could associate the shock with the cage – what their mothers learned during therapy was inherited to their offsprings.
Barbara Hohns team from the FMI here in Basel could show that arabidopsis, when stressed by damaging UV-light, showed many mutations in special regions of their genome. Interestingly, these genetic changes – all probably due to epigenetics – were still observed in the F-5 generation, although the next generations were not stressed by UV. It was, she told me, as if the genes of these plants remembered the stress their great-, great-, great parents experienced.
* Humans: experiments naturally much more difficult, so mostly only soft evidence.
The example I mentioned in the beginning: Ariane Giacobino from the University hospital Geneva studies epigenetic effects of hormone treated eggcells in mice. She found epigenetic marks even in sperm cells of the offspring. There are clinical indications that a hormonal treatment of human eggcells during IVF could lead to defective epigenetic markings. This could result in an enhanced risk for Angelman-syndrome. The scientist assumes that the rough treatment of eggcells and sperms is responsible for these epigenetic changes.
*A few months ago psycologist Terry Moffit from the Duke University, Durham, received the renowned Grawe-price in Zürich. Her research shows, she says, that „abuse and traumatic experiences can damage the genes of offspring“, causing epigenetic alternations of certain genes.
And so on. You’ll find new evidence for this kind of epigenetic inheritance nearly every week, if you look for it. In June scientist Eva Jablonka published a comprehensive overview of over 200 examples of epigenetic inheritance – of microorganisms, plants, animals, humans…
The question is: Why only now? Why are these studies only now entering the realm of main stream science? Why was the Central Dogma of the Gene so long so dominant?
One reason might be commercial interests. You cannot patent a complex interaction as easily as a single gene. The whole area of genetic testing seems to have a huge economic potential, even though experts warn that they are probably rather unnecessary. But here also the Thomas theorem seems to be true: What science defines as real is real in its consequences.
Another reason seems to be the reluctance to get anywhere near the realm of esoterics. Lamarck’s theory was long time connected with esoterics – and probably still is. Barbara Hohn told me that she had troubles getting her experiments financed because they were thought to be dangerously near esoteric waters. I talked to Eva Jablonka who did this survey and she also gave this reason. Sidetrack: Epigenetic inheritance could play a role in evolution. And its not random, bud semi-directed. So that’s a challenge to the NeoDarwinian Theory of Evolution …
Epigenetics and epigenetic inheritance really DO challenge the gene-dogma in a fundamental way – we experience a paradigm change. From a linear, monocausal and quite inflexible theory of the gene to a theory of highly dynamic, complex and multifunctional networks – where genes are important, but by no means the „book of life“.
Let me end with a citation from Steve Jones, one of GB’s top geneticists. He and other experts just made a surway of population studies relating to disease-genes. They concluded that in most cases there was no clinical relevance and are leading to a blind alley, also because of the neglect of epigenetic effects.
„In most cases, hundreds of genes are responsible, and often they have less effect than other factors such as diet, lifestyle and the environment.“
Transgenerational Epigenetic Inheritance: Prevalence, Mechanisms, and Implications for the Study of Heredity and Evolution
Eva Jablonka, The Quarterly Review of Biology, June 2009, vol. 84, no. 2
Conclusion: “This meta-analysis yielded no evidence that the serotonin transporter genotype alone or in interaction with stressful life events is associated with an elevated risk of depression in men alone, women alone, or in both sexes combined.”
N. Risch et al., 2009, JAMA, 301, 23, 2462
Effects of nutrition on the epigenome of viable yellow agouti (Avy) mice. These female one year old Avy mice are isogenic. The mother of the mouse on the left ate a normal mouse diet while pregnant. In contrast, the mother of the mouse on the right ate a diet supplemented with methyl donors while pregnant [1]. The marked differences in the coat color and weight of these offspring resulted from a dissimilarity in the level of DNA methylation at the Agouti locus.
Randy L. Jirtle, I, 2008; 299: 1249-1250
One group of new born rats was kept isolated alone, the other group with their mums. They experienced a lot of pup licking and grooming and nursing. The neglected pups grew up to be more frightfull and less stress resistent. Researchers showed that certain genes were silenced by methylation. These genes code for the glucocorticoid-receptor in the brain. The little rats produced more stress hormones, and they did so during their whole life.
Epigenetic Programming of Stress Responses through Variations in Maternal Care, E.W. Fish et al., Ann. N.Y.Acad.Sci. 1036: 167-180 (2004)
Larry Feig at Tufts University and his collegues bred ‚knockout mice’ that lacked a gene causing them to have a memory defect.
The team kept these knockout mice in a cage filled with toys and other mice for 2 weeks. They could compensate for their memory defect; they also associated the shock with the cage, like normal mice.
Surprisingly, all their offspring, which all had the memory defect, reacted normally – what their mothers learned during therapy was inherited to their offsprings.
J.A. Arai et al., Journal of Neuroscience, 2009, 29 (5), 1496-1502
Arabidoptis-plants , when stressed by UV-light, showed many mutations in special regions in their genome. Interestingly, these genetic changes – all probably due to epigenetics – were still observed in the F-5 generation, although the next generations were not stressed by UV. It was, as if the genes of these plants remembered the stress their great-, great-, great-parents experienced.
Molinier et al., 2006, Transgenerational memory of stress in plants. Nature, 442, 1046-1049
Hormone stimulated eggcells for IVF seem to have an enhanced risk for Angelman-syndrome. Hypothesis: the rough treatment of eggcells and sperms can lead to epigenetic changes.
Paoloni - Giacobino, 2007, Pedriatic Research, 61,5
Terry Moffitt states that abuse and traumatic experiences can damage the genes of offspring, causing epigenetic alternations of certain genes.
A. Caspi and T.E. Moffitt, Nature Reviews/Neuroscience, 2006, 7, 583-590