Tag Archives: epigenetics

How going beyond genetics reveals more about autism

Autism spectrum disorder (autism for short) describes a heterogeneous set of conditions characterised by problems with social communication, social interaction and repetitive or restrictive behaviours. It effects approximately one in a hundred people and is four times more common in males than females, although it has been suggested that girls may “hide” their symptoms more than boys.

We do not know what causes autism, but we do know that brain development is different when compared to those without autism, known as ‘neurotypicals’. Recent reports have led us to believe that autism is a genetic disorder. But there is more to life than genetic sequence. We are physiological beings; our genetic instruments are played at different tempos in different individuals and are likely contributing to our individual differences in health and wellbeing.

Our best guess is that genetic sequence accounts for, on average, just over three quarters of each individual’s autism. My team studies the ‘epigenetic’ musicians that play the symphony of life on our genes. Such musicians, in reality tiny molecules, are essential for making each tissue in our body different, despite having identical genes. Epigenetic musicians can often be influenced by environment. As they are often sidelined by genetic researchers, we chose to review what we know about them and to see what came out of the wash.

We first chose to briefly review the hundreds of genes whose sequences have been linked with autism. Luckily, the Simons Foundation had done this for us. They had even ranked the genes based on accumulated evidence. Interestingly, of the sixteen genes that are most strongly associated with autism, half code for proteins that act as epigenetic musicians. Many of these genes also play a role in the brain’s development.

Leaving gene sequences behind, we started at the level of the ‘shop floor’ of the body. We asked what is known about the physiology of people with autism. Among other things, it turns out that their immune systems are more easily disrupted than those in neurotypicals. They are more likely to experience inflammation, both in the blood and the brain, and this may explain why immune suppressants have sometimes been shown to reduce autistic symptoms temporarily.

Moving back one step in the production line, we looked for studies that had measured gene activity in people with autism. Those genes most frequently played too loud or too quiet were associated with brain development and function, and again, with immune state in the blood and brain.

Finally, we focused most of my attention on the epigenetic musicians that play the genes. A few researchers had taken a guess at which genes weren’t being played very well. Looking mostly in the brain, they found four or five genes whose epigenetic musicians weren’t working properly. The clearest evidence was for a gene called the oxytocin receptor, for which two studies showed differences in the blood and brain of those with autism compared with neurotypicals. Oxytocin, often referred to as the ‘love hormone’, regulates many of the behaviours associated with autism, so this is a plausible candidate for causing some of its characteristic features.

However, with almost twenty thousand genes in the genome, the quickest way to find genes is to look everywhere in our genomes, and current technology is advanced enough to do this. So that’s where we went next. One of the problems with this approach is that different researchers use different technologies to search for epigenetic changes to genes, which meant that comparing studies was hard. But surely, any gene identified by two independent studies must be worthy of more attention? So we carefully read through three genome-wide epigenetic studies of the brain, three of blood and one of cheek cells. Again, you can see that researchers look in different places for clues about the causes of autism.

Yet again, genes involved in brain development and the immune system floated to the top. As for specific genes, four emerged for which two independent studies showed a disruption to the epigenetic musicians that played them. None had been indicated previously as strong autism candidates, which may be a surprise to some. For two, very little is known about what they do in the body. The other two are known but not previously associated with autism. The first of these is likely to play a role in the sense of smell. A common feature of autism is a lower sensory threshold – senses, including smelling, working overtime. The second gene codes for an epigenetic musician required for early development and has been shown to be affected in immune cells in children whose mothers had low levels of folate during pregnancy. Interestingly, low folate levels have been linked with autism risk in a small number of studies.

So, what does all this information tell us? Firstly, as Aristotle said may years ago “One swallow does not a summer make, nor one fine day”, which means that we need to gather a lot more evidence that epigenetic changes in such genes are truly associated with autism. Then of course such changes could result from autism rather than cause autism, an idea that also needs testing.

However, there are numerous research teams around the world that can start giving attention to these ‘candidates’ and to the physiological processes such as inflammation that have not been identified in purely genetic studies. Should we be thinking of ways to minimise inflammation during pregnancy to lower the risk of autism? Should we be focusing on raising our children in low inflammatory environments? There is currently not enough evidence available for us to answer these questions and clearly, more research is needed.

Research is likely to lead to the development of tests at birth, which may be able to help (i) predict the likelihood of a child developing autism, and ultimately (ii) develop better informed treatments and (iii) alleviate some of the symptoms of some of the most distressing cases of autism. Interventions that lessen the symptoms of autism are currently being trialled. And to link prediction with treatment would be a great outcome, although as this can be a sensitive area for some in the autism community, we must progress by engagement.

With many thanks to my co-authors Tony Hannan and Jane Loke and to Jeanette Purkis and Dennis Crowley for helpful advice and proofreading.

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Epigenetics 201: the four ‘R’s

Want to know a little more about epigenetic marks; what they are and how they come about? Read on.

Epigenetic marks are all small molecules, some examples being the methyl group (-CH3) and the acetyl group (-COH3). Many different marks can bind to histones – the proteins that are responsible for packaging DNA into the two metres of genetic information found in every nucleus. Histones are shaped like commas and most epigenetic marks bind to the tail of the comma. However, only a single mark – the methyl group – binds to DNA and only then, to one specific sequence – cytosine-guanine (CG) – often referred to as CpG, the ‘p’ denoting the phosphate ‘backbone’ of the DNA double helix. Together with other packaging molecules and RNA, they make a substance called chromatin. Chromatin can come in many flavours depending on how tight it is packed, from ‘open for business’ to ‘closed for the season’ and states in between. At any particular gene, combinations of different epigenetic marks combine to influence its structure and function. Generally speaking, when regions regulating gene activity contain DNA with CpG methylation, the gene is inactive. Conversely, if the CpG methylation is removed, the gene may be activated. This is, however, a very simplistic interpretation because it ignores all the other epigenetic marks but it fits most situations.

NIHepi2

How do epigenetic marks get added and removed from our genes? This is when the ‘four Rs’ come in: epigenetic Recruiters, wRiters, Readers and eRasers. In the figure below, a strand of DNA located at a gene’s control region is illustrated with, for clarity, only four groups of histones.

JC1The first stage of epigenetic change involves the addition of sequence-specific Recruiter proteins or RNA, illustrated by the coloured symbols.

JC2Next, epigenetic wRiters, often called transferases, attracted by the recruiters, add an epigenetic mark, for example, acetyl (Ac), methyl (Me) and phosphoryl (P). Note that the first three marks are added to histones and the final, methyl mark, is added to DNA.

JC3Next, a combination of epigenetic Readers specific for each epigenetic mark bind in tandem in a way analogous to a key in a lock. Each gene or group of genes can have its own specific combination of marks, writers and readers.

JC4This ‘opening of a lock’ is akin to opening up the structure of the gene for it to be expressed.

JC5To reverse this process, a set of molecular eRasers specific for each mark can strip the mark off. An example of such an eraser is the deacteylase group of proteins.

JC6Which, when all marks have been stripped off, brings the gene back to square one.

JC7Further links and a more basic description of epigenetics can be found in my Blog “Epigenetics: from Greeks to geeks and leaks”

Epigenetics: from Greeks to geeks and leaks

Epigenetics, a word that seems to have stirred up disagreement between scientists for so long, is currently experiencing a rebirth and may have applications for the prevention of many different human diseases.

Starting at the beginning, the word ‘epigenesis’ was coined by the Greek philosopher Aristotle over 2,200 years ago because he was sick of the theory current at the time that we all start out as microscopic versions of our adult selves. He believed that all complex creatures grow from a simple fertilised egg or seed though to a mature organism through stages of development and differentiation: out of the simple comes the complex. This idea is widely accepted as true today.

Aristotle Jump forward just over 2,100 years and we come across a man with possibly the longest name in scientific history: Jean-Baptiste Pierre Antoine de Monet, Chevalier de Lamarck. Let’s just call him Lamarck. He proposed that the way an organism adapted to its environment would somehow be passed down the generations. Two generations later, Charles Darwin liked Lamarck’s idea and went further, proposing an idea of his own – ‘gemmules’ – minute granules that are ‘thrown off’ by our tissues. Gemmules, he proposed, could multiply and travel to our eggs or sperm sex cells through which they could be passed on to future generations.

lamarckDarwin

 Step forward another 75 years and followers of Darwin thought they knew it all – evolution occurs by natural selection through random changes in our DNA that have enabled us evolve and adapt over millennia. And that’s that. Then Conrad ‘Hal’ Waddington came along and stirred things up by turning ‘epigenesis’ to ‘epigenetics’, which he used to describe the way in which our genes interact with their environment to make us what we are. In this sense, epigenetics means literally ‘the factors on top of our genes’. Waddington was a man before his time.  Between then and now, arguments have raged about whether nature (genes) or nurture (environment) are more likely to influence our health and behaviour. The truth, exemplified by a recent book by Matt Ridley entitled ‘Nature via Nurture: Genes, experience and what makes us human’ is, like Waddington suggested, a combination of the two.

waddington2Today, epigenetics now describes the set of small molecules that sit ‘on top of our genes’ and choreograph when and how they act. This in turn directs our development from the zygote to the grave. Epigenetic molecules can be encoded by our DNA and they can be added or removed in response to our environment. Nature via nurture. Another way of looking at it is that in the symphony of life, epigenetic molecules are the musicians that play the genes as instruments and together they make up a huge orchestra of thousands of working genes. Alone, genes are silent; they need musicians to play them.

orchestraHowever, controversy still exists about what we can actually label as ‘epigenetic’. Some say that epigenetic changes need to be long-term, lasting for many cell generations, while others have shown that some epigenetic marks can change within a single cell’s lifetime. Some geeks say that the epigenetics should be tightly linked with its molecular definition and others that it should be loosely applied to how an organism adapts to its environment.

Arguments aside, epigenetic changes are most likely lie behind a recently recognised phenomenon call the Developmental Origins of Health and Disease. Known in short as ‘DOHaD’, the idea is that our experiences in the womb and early childhood can ‘program’ our future health. It is likely that epigenetics is part of the programming language involved. An oft-cited example of this in humans is that sixty-year-olds who were in their mother’s womb at the time of the Dutch Famine in the Second World War, not only had poorer heart health than their siblings but also had an epigenetic imprint of this experience stamped on a handful of their genes.

Animal studies reveal a similar story. In rats, a mother’s licking and grooming behaviour influenced subsequent stress levels in the offspring, mediated by an epigenetic change to a gene involved in stress response. Newborn rat pups whose mothers spend time licking and grooming them grow into calmer adults, whilst pups who receive little maternal attention tended to grow into more anxious adults. Grooming altered the pattern of epigenetic marks, which in turn altered gene activity of the stress regulator gene. Critically, when neglected rats were treated with a drug that alters these epigenetic marks, both their anxiety and the accompanying epigenetic changes could be reversed.

Such findings have huge implications for medicine, the largest being that if we can reliably detect epigenetic changes that in early childhood signal a risk for diseases such as cancer, heart disease, autism or diabetes, we can start to prevent these diseases by intervening early. This is the area I find most exciting, but we have a long way to go to the clinic for most of these. However, we can take heart from cancer research, which has already supplied a small number of epigenetic tests that can predict severity or response to treatment in some cancers.

Finally, it seems that in principle, Lamarck and Darwin may also have been on the right track after all. There is accumulating evidence that the environment our mothers and even our fathers encountered before we were a twinkling in their eye may be passed onto us in the form of a risk for conditions such as obesity, diabetes or anxiety. Studies of a remote Swedish village have shown that food abundance in grandparents correlate with the health of their grandchildren. Another found that sons of men who smoked just before puberty were more likely to become obese. However, neither of these has yet been linked with an epigenetic change. Could it be that epigenetic marks can ‘leak though’ to us via eggs and sperm? There is recent evidence that this can happen in animals that has people in some very high places invoking Lamarck.

NN lamarckWe still need to discover how such factors could pass into the eggs and sperm and how these changes would survive two major life stages at which the epigenetic ‘whiteboard’ is wiped almost clean. This usually occurs just after fertilisation when a newly-formed zygote wants to shed its sexual origins and become a new human being and when the opposite happens, when a group of cells early on in development want to put on the sexual cloak and become eggs and sperm. However, I said ‘almost clean’, which leaves the door open in principle for these barriers to be breached. An attractive, emerging idea borrowed originally from plants is that small epigenetic molecules, in form of the “messenger” genetic material – ribonucleic acid (RNA) – can be shuttled into eggs or sperm and be inherited by the next generation, and survive the epigenetic cleaning. Watch this space.

 

Epigenetics resources

Web sites

Epigenetics Genetic Science Learning Center, University of Utah

The Nova documentary on epigenetics originally aired in 2007

Instant expert: epigenetics’ from New Scientist magazine

Epigenetics explained‘ by Scientific American

Awesome animations and short documentaries

The epigenome at a glance‘from the Epigenetics Genetic Science Learning Center, University of Utah (01:46)

Lick your rats‘ interactive game from the Epigenetics Genetic Science Learning Center, University of Utah (takes about 5 mins to lick a couple of rats)

Insights from identical twins‘ from the Epigenetics Genetic Science Learning Center, University of Utah (04:41)

‘X inactivation and Epigenetics’ by Etsuko Uno and Drew Berry from WEHI TV (11:04)

Epigenetics Overview‘ by Cell Signaling Technologies (02:14)

Epigenetics: what makes us who we are?‘ from Begin before Birth (04:10)

What happens in the womb can last a lifetime‘ from Begin before Birth (02:24)

Epigenetics‘ – a short documentary from the Science Show on DNATube (09:26)

Resverlogix movie about epigenetic drug RVX-208 (03:32)

Charlie’s Story – can we improve crime rates by supporting vulnerable women during pregnancy and the first 2 years of their baby’s life?‘ from Begin before Birth

Articles – basic

Epigenetics’ by Brona McVittie (2006)

‘Evolution, Epigenetics, and Maternal Nutrition’ by Asim K. Duttaroy (2006)

‘Why Your DNA isn’t your destiny’ from Time Magazine (2010)

Epigenetics: promising field delivers (2013)

Articles aimed more at undergraduates

Epigenetics: the sins of the father’ from Nature magazine (2006)

‘Taking a chance on epigenetics’ (2014)

Books

epigenetics revolutionorigins2genome generationidenitcally different

Further learning

Marnie Blewitt’s Coursera online course on epigenetics

Epigenetics 201: the four Rs

Catching up with the sun: the consequences of premature birth and how to prevent them

“No one told you when to run, you missed the starting gun/So you run and you run to catch up with the sun but it’s sinking”

Mason, Water and colleagues (1973) could well have been referring to the long-term effects of premature birth, which refers to all babies born before the thirty- seventh week of pregnancy. Globally, around fifteen million babies are born premature every year, and this rate is rising according to the World Health Organisation. Premature birth imposes a huge health burden on individuals, including a four to five times greater likelihood of developing disorders of the heart, lungs and  brain, with the latter costing more than one million dollars to manage over a lifetime.

However, not everyone born premature will get sick, so researchers have for many years been looking for equivalent of a crystal ball to predict future health. Such predictions would lead to treatments specific for early prevention of major illnesses. Doctors can do so many things to keep such babies alive but prediction of future health is incredibly difficult.

That is where my recent research comes in. In a paper published late last year, my colleagues and I showed that premature birth is associated with measurable biological marks, some of which are present at birth and eighteen years later.

The marks are epigenetic – literally “on top of the DNA”. Such marks were predicted over sixty years ago by the British researcher Conrad Hal Waddington who described epigenetics as “the interactions of genes with their environment” that make us what we are. Some years later, researchers discovered the mechanism behind epigenetics: small molecules that can stick to our DNA and change the volume settings on our genes without changing the genetic sequence of the underlying DNA.

One such molecule is the methyl group – one of the simplest molecules in nature, comprising a carbon and three hydrogens. Over the years, this has been the most well-studied epigenetic mark. We have learned that whenever it sticks to the region that controls a gene’s activity, it can act as a dimmer switch to lower the activity of the gene, effectively making it manufacture less of its protein product.

Nowadays we can scan people’s DNA for methyl groups and see which genes have this molecular dimmer switch stuck to them. DNA can be obtained from biological samples such as cheek cells and blood. Researchers can easily obtain such samples from those of us willing to part with them but how can they see what they were like way back when we were born?

In 2008, we answered this question. Within a week after birth, almost all babies have their heels pricked for tests to provide a few drops of blood that are used to screen for major debilitating disease such as cystic fibrosis. After this testing, two or three dried blood spots are left behind and can be stored for a number of years. We showed that the blood spots could be smashed open to yield DNA that could be used for measuring the methyl molecule dimmer switch.

Seven years later, we compared twelve 18-year-olds born premature and twelve 18-year-olds born at the normal time (around 40 weeks). We prepared DNA from blood taken at 18 years with DNA extracted from dried blood spots taken at birth and in both sets of samples, measured the  methyl dimmer switch at almost half a million locations along the subjects’ DNA.

What we found was that at birth, there were huge differences between the two groups of babies, which was understandable because as epigenetic changes drive our development, the babies born at the “right” time will have had more mature setting on their methyl dimmer switches. However, at 18 years of age, a small number of epigenetic differences remained, which showed that our body “remembers” that we were born premature and that this memory is encoded by epigenetics.

But how does knowing that we may have a molecular memory of how far though pregnancy we were born? The answer lies in studies that have shown that our time in the womb can “program” our future health through changing our epigenetics. Although not referring to epigenetics, the Dalai Lama explains the general idea in his book The Art of Happiness: “A certain type of event may have occurred in an earlier period of your life which has left a very strong imprint on your mind which can remain hidden, and then later affect your behaviour”.

We aim to scale up the study to look at hundreds of young adults born premature and ask which memory marks math up with which health problems: heart, lungs of brains? Our ultimate aim is to target the right treatments to the right kids in early childhood, to effectively change their destiny to a healthier one.