Hypertext in the book of life
Jul. 10th, 2014 08:05 pm![[personal profile]](https://www.dreamwidth.org/img/silk/identity/user.png){kind=small}
livOr, what an interested lay person should know about epigenetics.
I've been promising a post about epigenetics for ages, because it's one of the most exciting things that's happened in my field in the past decade or so, and it seems like most non-biologists aren't aware of it very much.
Why is it so exciting? Well, to start with there's the older insights which led to the modern field of epigenetics: in a multicellular organism, all cells have exactly the same genome, by definition, but the cells differentiate to take on specialist structures and functions. So there must be something going on beyond (ἐπί, the Greek prefix epi) the sequence of bases forming genes and chromosomes. It turns out that something is that the cell makes a series of chemical marks on the DNA and associated proteins, which turn genes on and off. Those marks are often surprisingly long-lasting, they're not just a short-term response to circumstances, something genes can also do. So you can't take a skin cell and transplant it to the liver, its epigenetic marks make it a permanent skin cell.
It's much more recently that we started to understand that patterns of epigenetic marks don't just follow a set developmental program – they can change in response to external circumstances. And the really mind-blowing thing is that some of these changes can be inherited. This means that a female parent's life circumstances can cause measurable alterations in the genes of offspring and more distant descendants, and there's starting to be evidence for male-line transmission as well, at least in animals and probably in humans too.
The other thing that's cool about epigenetics is that we're getting to the point where we understand it well enough that we can directly manipulate the epigenetic marks. If you change epigenetics, you change the nature of the cell itself, just as much as by directly editing the gene sequence (which can be done but is massively technically difficult, and ethically questionable in humans.) Which is a possible approach for treating cancer, and that's the reason why I got into the epigenetics world, but there's an even more exciting application: we can make stem cells. We can do the thing which was regarded as paradigmatically impossible throughout the twentieth century, we can effectively reverse the direction of development. So it's become possible to take an adult's cells and turn them into the rare kind which, like the cells of an early embryo, have the potential to become any type of tissue, manipulate them more or less at will in the lab, and return them to the same person's body to repair injuries and grow new tissue. In the very last couple of years, this is actually starting to be a treatment for real humans with real diseases.
So how does it work?
I would generally argue that much of the biochemical detail isn't important to know unless you're actually a molecular biologist. I'm going try to give a rough outline, if only to make my descriptions less abstract. One thing that's important about this is informally we're used to thinking of "genes" and "DNA" as pretty much synonymous, and on a biochemical level this is a major simplification. In human cells the actual DNA is in the form of chromatin, so the DNA is wrapped round protein "beads" called histones, and the string of beads is coiled and folded into a compact shape, to a greater or lesser extent depending on the region of the chromosome and the circumstances.
And the whole structure is covered in enzymes which are involved in carrying out the instructions encoded in the DNA sequence. There's a whole fairly complex protein machinery which actually does job of transcribing the DNA to RNA, allowing the gene to be expressed when the RNA does its job in the cell or gets translated into protein which likewise carries out cellular functions. Genes which don't get expressed are inactive; from the point of view of cell structure and function, they might as well not be there, because they're just sequences of DNA that don't do anything. I suppose metaphorically you can see the DNA as an instruction book; if nobody reads the book or carries out the instructions then the instructions themselves don't have any effect, they're just marks on paper.
The key point is that the transcription machinery and the structural proteins of the chromatin occupy the same physical space. So if the DNA is tightly wrapped round its histones and the string of beads coiled up tightly, there's no room for the transcription machinery to get in and the gene remains inactive. The histones and DNA can be modified chemically, changing the relationship of positive and negative charges, so that they repel eachother and the structure partly uncoils. Genes in "open" chromatin regions can potentially be expressed, but will only in fact be expressed if it's appropriate for the cell at that particular moment, because the transcription machinery itself is activated or inactivated by the appropriate combination of signals from inside and outside the cell. The patterns of chemical labels on the chromatin, and thus its open or closed state, can be copied when the DNA is copied, and some of this pattern is retained when gametes are formed and can therefore be passed on to offspring.
Isn't this kind of Lamarckian?
In some ways, yes. In case you're not aware, Lamarck was a nineteenth century scientist who proposed a theory of evolution which was superseded by Darwin's. His idea was that organisms would behave in ways that altered their bodies, and these changes would get passed on to their offspring. I don't know if Lamarck actually said this, but the typical illustration usually given is of the ancestor of the giraffe stretching higher and higher to reach leaves, lengthening its neck and passing on that advantage to its offspring. I want to make clear that Lamarck was not an idiot; Darwin also didn't propose a mechanism by which traits could be inherited, he was just lucky that the genetics discovered decades after he wrote happened to fit exactly with his theory of evolution. The other thing that happened to Lamarck was that Stalin decided that Lamarckian evolution was a better fit for Soviet ideology than Darwinism, and promoted the work of a not really trained horticulturist called Lysenko, who believed that alterations farmers made to plants would be heritable. And, being Stalin, forced everyone to follow Lysenko's wrong ideas and punished everyone who showed any contrary evidence. So Lamarckianism has become associated with the scientific process being corrupted for political ends, and contributing to mass starvation.
So you can imagine that any suggestion that acquired, rather than genetic, characteristics might be heritable met with massive resistance from the scientific community! However, there is more and more evidence accumulating that certain external events in the life of an organism lead to changes in the epigenetic marks, and that these marks can be passed on to offspring.
There's a classic natural experiment in the form of the partition of Germany after WW2: the populations of East Germany and the Bundesrepublik were pretty much genetically homogeneous before partition. In the years after the war, people in West Germany generally had much better diets than those in the Soviet East. The grandchildren and great-grandchildren of people who were pregnant during this era, born since reunification, have different epigenetic marks even though they have pretty much the same genes and nowadays the same lifestyle. As a result of expressing different genes, people with East German ancestry are going to have different physical bodies, different metabolism, different propensity to diseases etc, from people with West German ancestry, because their grandmothers experienced prolonged periods of inadequate nutrition before their mothers were born.
Some skeptics have tried to propose a more respectably Darwinian mechanism for this sort of phenomenon. For example, I don't think it's been completely ruled out that maybe the starving ancestors had some sort of altered womb environment as a result, and random genetic variation meant that some foetuses were able to survive in that altered womb environment. Just coincidentally, the genetic trait that promoted survival happened to correlate with a different epigenetic pattern. Selection against the foetuses that weren't fit to survive in the womb of someone who wasn't adequately nourished changed the overall frequency of which epigenetic patterns showed up in the next generation, enough to make a measurable change in the population.
In my view, the two possibilities are very nearly functionally equivalent. It's pretty clear that events during someone's lifetime can change epigenetic marks; we know smoking does, for example, and there's overwhelming evidence that trauma can change the epigenetics and therefore the gene expression of neurones in the brain. It's probable that other, less extreme experiences also change brain epigenetics, just as part of the normal neurological process of learning, it's just that trauma has such big effects it's more amenable to research. We also know that some epigenetic marks can be passed on; for example, the fact that ligers (with male lion fathers and female tiger mothers) are different from tigons (the offspring of crossing a lioness mother with a male tiger father) is incontrovertibly due to epigenetic differences known as imprinting. So it would almost be more surprising if it were definitively proved that life events couldn't affect future generations' epigenetic heritage, than if the now generally accepted consensus on epigenetic phenomena is true.
The thing is that epigenetics perfectly well follows Darwinian rules, even if it seems conceptually Lamarckian. It's just one more way that genes and environment / experiences can interact. The chemical marks on chromatin aren't made by some magical agent that's outside normal biology, this is epigenetics, not paragenetics. The reason why certain patterns get applied to certain genes is ultimately determined by the DNA sequence, because the DNA itself encodes the enzymes which add or remove the chemical groups. And where the marks get included or omitted also depends on the DNA sequence. It's as if, to extend the instruction book metaphor, the instructions in the book said, if you are more than 6' tall, delete every fifth word in this book. If a tall person happened to use the book, the next person who read it would get a different set of instructions from if the book only passed through the hands of short people (or disobedient people who didn't follow the instructions!) There's nothing magical or mysterious about this.
I'm not putting a lot of references in this, because looking for detailed citations for every single statement was one of the big reasons it's taken me several years to get round to writing this since I first thought of it. But there was a lot of buzz about this paper by Dias & Ressler, published late last year, where they conditioned some mice to fear a particular smell, and then their offspring down to the second generation were born with fear of that same smell. The damn article is paywalled because the Nature group is like that, so I can't give you a detailed analysis. But it seems to have caught the popular imagination in terms of epigenetic trans-generational inheritance. It wasn't especially surprising to me, but I think what may be different about it from the literature in the last five years about inherited effects of trauma is that it goes some way to do experiments to rule out other possible interpretations of why fear of the smell might be inherited. Things like using IVF so that it can't be womb environment, having the pups brought up by non-conditioned mothers so it can't be maternal behaviour affecting the offspring.
We're getting closer and closer to a convergence between animal experiments and observation of humans. Animal work shows a detailed molecular mechanism for how trauma alters the epigenetics of the chromatin in neurones. Because the epigenetically altered neurones express and repress different genes for neurotransmitter receptors, the way those brains respond to stimuli will be different, and quite possibly the brain structure will end up different because brains are plastic. The trauma is also affecting the epigenetics of gametes, so the patterns can be inherited, so the offspring will also have altered brains and therefore altered behaviour. Obviously you don't want to do that kind of experiment on humans, but we do see changed brain epigenetics persisting for several generations after trauma, and it's probably caused by the same kind of mechanism.
I suppose the question I haven't answered is, how does the experience of trauma lead to these epigenetic changes? I can't answer that in a very specific way, but in general, it's a bit like what happens with hormones. If you undergo puberty or start taking exogenous hormones, the chemicals are carried in your blood to the tissues that should be changing under the influence of sex hormones. Those cells will have receptors, proteins which recognize and bind to the hormones. The hormones will activate the receptors and the receptors in turn will activate some genes within the cell and deactivate others, so there might be genes for growing hair in appropriate places, or storing fat in certain parts of the body, or muscle growth, or whatever. Some of the cell factors affected by the hormones will be enzymes which can add or remove chemical marks from the chromatin, leading to permanent or at least long-term changes in gene expression. In the case of sex hormones, the epigenetic changes are not inherited, but it's equally likely that trauma could cause signalling molecules to tell neurones in the brain to turn on or off genes for relevant receptors, and at the same time tell the gamete-producing cells to mark the same genes for an open or closed state.
OK, this post is ridiculously long, I will post it and do one on stem cells another day. Please do ask any questions, whether it's because I've assumed knowledge and explained things with too much jargon and technicalities, or because I've simplified and glossed over something and you want more detail or want to challenge me.
I've been promising a post about epigenetics for ages, because it's one of the most exciting things that's happened in my field in the past decade or so, and it seems like most non-biologists aren't aware of it very much.
Why is it so exciting? Well, to start with there's the older insights which led to the modern field of epigenetics: in a multicellular organism, all cells have exactly the same genome, by definition, but the cells differentiate to take on specialist structures and functions. So there must be something going on beyond (ἐπί, the Greek prefix epi) the sequence of bases forming genes and chromosomes. It turns out that something is that the cell makes a series of chemical marks on the DNA and associated proteins, which turn genes on and off. Those marks are often surprisingly long-lasting, they're not just a short-term response to circumstances, something genes can also do. So you can't take a skin cell and transplant it to the liver, its epigenetic marks make it a permanent skin cell.
It's much more recently that we started to understand that patterns of epigenetic marks don't just follow a set developmental program – they can change in response to external circumstances. And the really mind-blowing thing is that some of these changes can be inherited. This means that a female parent's life circumstances can cause measurable alterations in the genes of offspring and more distant descendants, and there's starting to be evidence for male-line transmission as well, at least in animals and probably in humans too.
The other thing that's cool about epigenetics is that we're getting to the point where we understand it well enough that we can directly manipulate the epigenetic marks. If you change epigenetics, you change the nature of the cell itself, just as much as by directly editing the gene sequence (which can be done but is massively technically difficult, and ethically questionable in humans.) Which is a possible approach for treating cancer, and that's the reason why I got into the epigenetics world, but there's an even more exciting application: we can make stem cells. We can do the thing which was regarded as paradigmatically impossible throughout the twentieth century, we can effectively reverse the direction of development. So it's become possible to take an adult's cells and turn them into the rare kind which, like the cells of an early embryo, have the potential to become any type of tissue, manipulate them more or less at will in the lab, and return them to the same person's body to repair injuries and grow new tissue. In the very last couple of years, this is actually starting to be a treatment for real humans with real diseases.
So how does it work?
I would generally argue that much of the biochemical detail isn't important to know unless you're actually a molecular biologist. I'm going try to give a rough outline, if only to make my descriptions less abstract. One thing that's important about this is informally we're used to thinking of "genes" and "DNA" as pretty much synonymous, and on a biochemical level this is a major simplification. In human cells the actual DNA is in the form of chromatin, so the DNA is wrapped round protein "beads" called histones, and the string of beads is coiled and folded into a compact shape, to a greater or lesser extent depending on the region of the chromosome and the circumstances.
And the whole structure is covered in enzymes which are involved in carrying out the instructions encoded in the DNA sequence. There's a whole fairly complex protein machinery which actually does job of transcribing the DNA to RNA, allowing the gene to be expressed when the RNA does its job in the cell or gets translated into protein which likewise carries out cellular functions. Genes which don't get expressed are inactive; from the point of view of cell structure and function, they might as well not be there, because they're just sequences of DNA that don't do anything. I suppose metaphorically you can see the DNA as an instruction book; if nobody reads the book or carries out the instructions then the instructions themselves don't have any effect, they're just marks on paper.
The key point is that the transcription machinery and the structural proteins of the chromatin occupy the same physical space. So if the DNA is tightly wrapped round its histones and the string of beads coiled up tightly, there's no room for the transcription machinery to get in and the gene remains inactive. The histones and DNA can be modified chemically, changing the relationship of positive and negative charges, so that they repel eachother and the structure partly uncoils. Genes in "open" chromatin regions can potentially be expressed, but will only in fact be expressed if it's appropriate for the cell at that particular moment, because the transcription machinery itself is activated or inactivated by the appropriate combination of signals from inside and outside the cell. The patterns of chemical labels on the chromatin, and thus its open or closed state, can be copied when the DNA is copied, and some of this pattern is retained when gametes are formed and can therefore be passed on to offspring.
Isn't this kind of Lamarckian?
In some ways, yes. In case you're not aware, Lamarck was a nineteenth century scientist who proposed a theory of evolution which was superseded by Darwin's. His idea was that organisms would behave in ways that altered their bodies, and these changes would get passed on to their offspring. I don't know if Lamarck actually said this, but the typical illustration usually given is of the ancestor of the giraffe stretching higher and higher to reach leaves, lengthening its neck and passing on that advantage to its offspring. I want to make clear that Lamarck was not an idiot; Darwin also didn't propose a mechanism by which traits could be inherited, he was just lucky that the genetics discovered decades after he wrote happened to fit exactly with his theory of evolution. The other thing that happened to Lamarck was that Stalin decided that Lamarckian evolution was a better fit for Soviet ideology than Darwinism, and promoted the work of a not really trained horticulturist called Lysenko, who believed that alterations farmers made to plants would be heritable. And, being Stalin, forced everyone to follow Lysenko's wrong ideas and punished everyone who showed any contrary evidence. So Lamarckianism has become associated with the scientific process being corrupted for political ends, and contributing to mass starvation.
So you can imagine that any suggestion that acquired, rather than genetic, characteristics might be heritable met with massive resistance from the scientific community! However, there is more and more evidence accumulating that certain external events in the life of an organism lead to changes in the epigenetic marks, and that these marks can be passed on to offspring.
There's a classic natural experiment in the form of the partition of Germany after WW2: the populations of East Germany and the Bundesrepublik were pretty much genetically homogeneous before partition. In the years after the war, people in West Germany generally had much better diets than those in the Soviet East. The grandchildren and great-grandchildren of people who were pregnant during this era, born since reunification, have different epigenetic marks even though they have pretty much the same genes and nowadays the same lifestyle. As a result of expressing different genes, people with East German ancestry are going to have different physical bodies, different metabolism, different propensity to diseases etc, from people with West German ancestry, because their grandmothers experienced prolonged periods of inadequate nutrition before their mothers were born.
Some skeptics have tried to propose a more respectably Darwinian mechanism for this sort of phenomenon. For example, I don't think it's been completely ruled out that maybe the starving ancestors had some sort of altered womb environment as a result, and random genetic variation meant that some foetuses were able to survive in that altered womb environment. Just coincidentally, the genetic trait that promoted survival happened to correlate with a different epigenetic pattern. Selection against the foetuses that weren't fit to survive in the womb of someone who wasn't adequately nourished changed the overall frequency of which epigenetic patterns showed up in the next generation, enough to make a measurable change in the population.
In my view, the two possibilities are very nearly functionally equivalent. It's pretty clear that events during someone's lifetime can change epigenetic marks; we know smoking does, for example, and there's overwhelming evidence that trauma can change the epigenetics and therefore the gene expression of neurones in the brain. It's probable that other, less extreme experiences also change brain epigenetics, just as part of the normal neurological process of learning, it's just that trauma has such big effects it's more amenable to research. We also know that some epigenetic marks can be passed on; for example, the fact that ligers (with male lion fathers and female tiger mothers) are different from tigons (the offspring of crossing a lioness mother with a male tiger father) is incontrovertibly due to epigenetic differences known as imprinting. So it would almost be more surprising if it were definitively proved that life events couldn't affect future generations' epigenetic heritage, than if the now generally accepted consensus on epigenetic phenomena is true.
The thing is that epigenetics perfectly well follows Darwinian rules, even if it seems conceptually Lamarckian. It's just one more way that genes and environment / experiences can interact. The chemical marks on chromatin aren't made by some magical agent that's outside normal biology, this is epigenetics, not paragenetics. The reason why certain patterns get applied to certain genes is ultimately determined by the DNA sequence, because the DNA itself encodes the enzymes which add or remove the chemical groups. And where the marks get included or omitted also depends on the DNA sequence. It's as if, to extend the instruction book metaphor, the instructions in the book said, if you are more than 6' tall, delete every fifth word in this book. If a tall person happened to use the book, the next person who read it would get a different set of instructions from if the book only passed through the hands of short people (or disobedient people who didn't follow the instructions!) There's nothing magical or mysterious about this.
I'm not putting a lot of references in this, because looking for detailed citations for every single statement was one of the big reasons it's taken me several years to get round to writing this since I first thought of it. But there was a lot of buzz about this paper by Dias & Ressler, published late last year, where they conditioned some mice to fear a particular smell, and then their offspring down to the second generation were born with fear of that same smell. The damn article is paywalled because the Nature group is like that, so I can't give you a detailed analysis. But it seems to have caught the popular imagination in terms of epigenetic trans-generational inheritance. It wasn't especially surprising to me, but I think what may be different about it from the literature in the last five years about inherited effects of trauma is that it goes some way to do experiments to rule out other possible interpretations of why fear of the smell might be inherited. Things like using IVF so that it can't be womb environment, having the pups brought up by non-conditioned mothers so it can't be maternal behaviour affecting the offspring.
We're getting closer and closer to a convergence between animal experiments and observation of humans. Animal work shows a detailed molecular mechanism for how trauma alters the epigenetics of the chromatin in neurones. Because the epigenetically altered neurones express and repress different genes for neurotransmitter receptors, the way those brains respond to stimuli will be different, and quite possibly the brain structure will end up different because brains are plastic. The trauma is also affecting the epigenetics of gametes, so the patterns can be inherited, so the offspring will also have altered brains and therefore altered behaviour. Obviously you don't want to do that kind of experiment on humans, but we do see changed brain epigenetics persisting for several generations after trauma, and it's probably caused by the same kind of mechanism.
I suppose the question I haven't answered is, how does the experience of trauma lead to these epigenetic changes? I can't answer that in a very specific way, but in general, it's a bit like what happens with hormones. If you undergo puberty or start taking exogenous hormones, the chemicals are carried in your blood to the tissues that should be changing under the influence of sex hormones. Those cells will have receptors, proteins which recognize and bind to the hormones. The hormones will activate the receptors and the receptors in turn will activate some genes within the cell and deactivate others, so there might be genes for growing hair in appropriate places, or storing fat in certain parts of the body, or muscle growth, or whatever. Some of the cell factors affected by the hormones will be enzymes which can add or remove chemical marks from the chromatin, leading to permanent or at least long-term changes in gene expression. In the case of sex hormones, the epigenetic changes are not inherited, but it's equally likely that trauma could cause signalling molecules to tell neurones in the brain to turn on or off genes for relevant receptors, and at the same time tell the gamete-producing cells to mark the same genes for an open or closed state.
OK, this post is ridiculously long, I will post it and do one on stem cells another day. Please do ask any questions, whether it's because I've assumed knowledge and explained things with too much jargon and technicalities, or because I've simplified and glossed over something and you want more detail or want to challenge me.
Re: Stem cells
Date: 2014-08-05 11:48 am (UTC)The idea that reducing telomere length with cell division might act to reduce cancer risk is one I had heard of before, but I gather that cancer cells can restore the telomere indefinitely, so I wondered whether the extra risk of one restoration would be unreasonably large. Apparently it is.
Maybe eventually the right solution, if it is ever possible, would be to compare the DNA of multiple cells, probably using some modified bit of cellular machinery to do this, and correct some of the errors. Maybe that would allow telomere reconstruction not to cause significant cancer risk. Or not, maybe the cellular machinery becomes faulty and would need a separate rebuilding for that to work.
The best of my understanding at present is that shortening of telomeres is a cause of at least some of the the unpleasant effects of old age, and personally, I definitely feel like I could benefit from a rebuild from molecular level on up. If it ever becomes possible, I will be long gone, so purely a thought experiment.
Would I be right in surmising that, as far as we can tell so far, lengthening telomeres would be a necessary, but far from sufficient (and from what you say, conuterproductive on its own), step towards much longer healthy life?