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.

Kit for kitty: how cats’ genes have changed during their domestication

http://1funny.com/wild-domesticated/

Last year I co-authored why so many domesticated mammals have floppy ears for The Conversation for The Conversation. Since then, a recent paper has tracked down changes in specific genes that are associated with domestication.

As a reminder, the hypothesis was that functional and genetic differences in a specific group of cells – the neural crest – during early development, arose through domestication.

Cells in the neural crest, which forms just under the newly formed neural tube (precursor of the spinal cord), gradually migrate to the upper body where their descendent cells help to shape the brain, face, head, neck, intestine, adrenal glands and skin. Minor defects of neural crest cells, such as slower migration, were hypothesised to unite the main features of domesticated animals: tameness, smaller jaws, curly tails and floppy ears.

Current evidence points to the domestication of wild cats between 5,000 and 9,000 years ago. In the late Stone Age, when we were developing our skills in farming of plants and animals, it is likely that wild cats were attracted by food scraps we left around. They were also likely to be attracted to vermin who fed on stored grain, which you can guess, may have led to a mutually beneficial relationship between cats and us. The ancient Egyptians were so grateful to cats for controlling mice and snakes and so much in admiration of their grace and poise that they elevated them to gods.

In the recent paper, researchers compared the gene sequences of wild cats with a number of different breeds of domesticated cats and the results support the domestication hypothesis. Using stringent criteria, they found over a hundred genetic regions that differed markedly between domesticated and wild cats.

http://catnipsum.com/blog/articles-tips/journey-from-the-wild-evolution-of-the-domestic-cat/757

Looking through these regions, they found genes related to neural crest survival and migration, fear, reward and pigmentation. Most are active in the brain. Fittingly, the gene responsible for the white pigmentation is called KIT, which is essential for the growth and migration of pigmented cells of the skin known as melanocytes. Genetic differences in the KIT gene often result in inefficient migration and maturation of melanocytes during development, resulting in white patches over the body. This condition is known as piebaldism and is seen in humans and in horses (such as pintos), dogs, birds, pigs, cows and even some snakes. In cats, various degrees of white spotting have been produced in the last 200 years by selective breeding. The paper highlights the Birman cat (below), which has quite a high proportion of white fur.

A Birman cat. From http://www.sandswbirmancatclub.co.uk/NEWWWEBSITE/thebirmancat.html

What makes the cat sequencing paper fascinating is how the researchers linked specific genes to specific functions of tissues and organs derived from the neural crest. In addition to taking a guess at a gene’s function from the structure of the protein it produces, they looked at data from animals such as mice and frogs which have been bred in the lab to have one or both copies of a genes either defective or missing altogether (so-called “knockouts”). Comparisons have also come from human medical conditions such as piebaldism, mentioned above, that have had their genetic defects sequenced.

http://pictures-of-cats.org/domestic-cat-to-wildcat-comparison-and-changes.html

The cat sequencing paper also compared cats to other carnivores such as dogs and analysed the genetic differences in a similar way. They identified gene variants that are likely to provide cats with a superior sense of night vision, hearing and sensing of sex hormones, or pheromones.

What the paper did not answer was why do cats NOT have floppy ears? Maybe not all the boxes of domestication syndrome need to be ticked for each animal. Or maybe floppy ears may have been selected against because it would impair cats’ acute sense of hearing?

What all this means is that we are further along the road to understanding how cats and other animals were domesticated. The information gathered from the hundreds of cat genomes sequenced means that we will be better able to understand and treat cats when they get sick. An understanding of early mammalian development will also help us understand our own development and disease predisposition.

http://treesforlife.org.uk/forest/missing-species-rewilding/the-scottish-wildcat/

Blowing the trumpet: a year in review for Dr Chromo

This year, instead of posting disjointed highlights of Facebook, I’ve decided to go back to the old tradition of the “Round Robin” Christmas letter, upgraded to a blog. I still receive Round Robin letters along with Christmas cards from friends and relations and always enjoy reading so why not do something similar but different? Yes, they have been lampooned for being too long and uninteresting so I will keep mine short, and hopefully, interesting.

First up, some trumpet blowing for other people. A large toot for my wife Jane who ran 125 runs this year, most of them around an hour long. I ran the last  one with her this morning and I can tell you, she has definitely overtaken me in the fitness stakes. We’ve also been out to some great restaurants and can tell she has taken note by the standards of her home cooking.

Next, a salute to my parents, who  have remained active despite each going through health scares and coping with the loss of a daughter. It’s hard to imagine what they have been through. A further trumpet to my in-laws who are coping with their own troubles. It was nice to see both sets of parents in November.

A further parp for brother Rod in Canada for suggesting that we brothers swap answers to a Life Questionnaire – around thirty questions on who we are, what we are, what we have achieved and what we like. When our sister Sarah died last year, an outpouring of grief and praise came from her close friends and colleagues past and present and we were all deeply touched by that. Strangely, these people knew better as an adult than did the three of us, mainly because we are scattered to the four winds. A “Big-Up” also to Alex for getting into St Martin’s College in London. I enjoyed a brief visit and a drink or two or three to him in November; I vaguely remember getting my photo taken on King’s cross Station’s Platform Nine the Three Quarters by a pair of Japanese tourists. On the same trip I also met op with Brother-in-law Dfyed, a brilliant art teacher and with his amazing son Matthew, who now goes to high school, where he studies Minecraft among other things 😉 I also had a day out in Leeds (and a drink in Whitelocks) with Brother Jim, who’s also going great guns as a Community Arts Chaplain in Gateshead.

Work trumpets go to my student, now turned Postdoc, Jane Loke, who graduated with a PhD this year. I had a great time at Graduation with Jane and her family. Sadly, I lost Linh Nguyen, to Singapore, and would like to thank her for her excellent work as a student and Research Assistant.  A Herald also for Theme Director Katie Allen and Institute Director Kathy North, for providing ways for me to top up my salary. I will repay in kind in 2015 when I have my whole salary covered, and hopefully beyond. Ana Yap was a great Honours student from MOnash Uni and I was impressed by the quality of all their students.

Next, what are my favourite movies and songs from 2014 (and 2013; sometimes I’m slow to catch on)? First, I filled in a few gaps in my favourite movie genre – time travel. Films I watched included Frequency,  Looper, 12 Monkeys, About Time , all great in their own way, and finally the great but head-scratching  Predestination,  and the even more head-scratching and the low budget Primer. My overall favourite films of the year were the weird Under The Skin (filmed in Glasgow with Scarlett Johannsen in disguise) the brilliantly thrilling  Calvary, Read My Lips, and yes, the “Hollywood” but exhilarating Edge of Tomorrow. Other films worth a mention are Philomena, Boyhood and Lucy. Finally, a special mention to the movie Gabrielle, an uplifting drama/romance whose main characters (and most of the actors) all had intellectual impairments. I say “impairments” but the main character, having Williams Syndrome, was perceptive and super-friendly. Heart-warming.

https://www.southbayfilmsociety.com/wp-content/uploads/2014/05/Gabrielle-poster-low-res.jpg

My favourite albums of the year were “Our Love” by Caribou – brilliant Canadian  electronic artist and very catchy tunes; “Partly Fiction” by Harry Dean Stanton,  such a sweet voice from the veteran actor; “The Island of Dr Electrico” by The Bombay Royale, a great debut album by the Melbourne band with a hot Indian flavour. And a special mention for “All I ever wanted – The Anthology” by the late, great Kirsty MacColl.  So sad that such a talent has been lost.

http://thebombayroyale.com/wp-content/uploads/BR_electrectrico_cover_itunes.jpg

I am finishing with my personal achievements of the year, as, someone once said “if you can’t blow your own trumpet, no-one else will”.  In the garden, I have tended every square metre, with failures and successes, the latter in potatoes, chillies (including the World’s hottest),  silverbeet, lettuce, carrots, zucchinis including the amazing Tromboncino.

After dabbling in slightly cushioned trainers and hurting my ankle, I returned to “barefoot” running with the minimalist Vibram 5 fingers. Despite some controversy as to their effectiveness,  I have been injury free since wearing them, I’ve run a half marathon in them and hope to run a full one in 2015. It was also joy to run again after a few months off due to deep vein thrombosis in late 2013. This year I’ve gone further and run totally barefoot on some great Autralian beaches: Ocean Grove, Rainbow Beach, Noosa, Apollo Bay and Sandy Point.

http://www.barefootfingers.com/trust-store-women-vibram-five-fingers-treksport-champagne-red-shoes-01.jpg

Highlights at work this year have included having lunch with a princess on behalf on the Australian Twin Registry,  of which I was appointed Deputy Director. I was also elected to the Board of the International Society of twin Studies. at the twins conference in Budapest.

As a Chief Investigator,  I was awarded eight research grants of various sizes, the largest being the five-year NHMRC Centre for Research Excellence in twin Research (Chief Investigator B)  and an NHMRC Project grant asking whether we can predict long-term outcomes of preterm birth, and two that give me great pride:  new studies of epigenetic differences within identical twins discordant  for autism or cerebral palsy. Both are collaborations with hospital clinician teams. I now have the best team I have ever had, with whom I am sure I can at least match  our achievements from 2014.

In 2015 I am looking to secure my own salary in the form of an NHMRC Fellowship; hopefully third time lucky; it’s tough.

http://ksoanesresearch.files.wordpress.com/2013/09/slowly-lower-in-the-grant-money.jpg

In 2014 I published 11 peer-reviewed papers, a short chapter about DNA in a crowd-funded book, two articles on twins for the Raising Children Network, and, with colleague Don Newgreen, “Why so many domestic mammals have floppy ears” for The Conversation which, via secondary sites such as IFL Science, was read by over 300,000 people.

After a year of blogging, I have written 15 posts, each one read on average over a thousand times  and posted over 2,500 Tweets in my first year on Twitter as @DrChromo and a few hundred for the Society for the Developmental Origins of Health and Disease Australia and New Zealand and the Murdoch Childrens Research Institute . Social media is getting the message out about medical research quicker than ever, to more people and those researchers who don’t use social media will quickly become dinosaurs. There is also an amazing thrill when you Tweet at a conference as part of a group of Tweeters and get feedback from outside the conference including overseas. Try it.

I’ve had fun trying to get the message across to Uni students and “the public” about epigenetics, twins, the early life origins of chronic disease and medical research in general. This is an obligation for all medical researchers, so why not enjoy it. I lectured (unpaid) in the courses: Genetics; Poetics of The Body; Genetics, Health and Society; Societal Issues and Personal Genomics, all at Melbourne Uni; Nutrition and Dietetics and Monash Uni, and in courses at Victoria and Deakin Universities. I went as far afield as Brisbane and Warrnambool to give talks to GPs and in the latter, discovered a little gem of a place in the South West of Victoria. http://visitwarrnambool.com.au/

I also went out and about to talk to Rotary, GPs, teachers, school kids, an, with colleague Richard Saffery, was filmed for a documentary about twins, recently aired in Canada and got to meet Dr Feelgood on radio station 3AW. Talking of radio, I continued in my role as a monthly panelist on community radio 3RRR’s Einstein A Go-Go science show. I also started listening to an excellent request show – Centrelinked – on community radio station NorthWest FM and even went on as a guest co-presenter on a hair-themed to coincide with shaving all my hair off for the Leukaemia Foundation’s World’s Greatest Shave. And coming soon you will get to see the results of the >30 blogs to be published on the new MCRI web site early in the New Year. I commissioned these from MCRI staff and students and interestingly, found that in general, the younger the writer, the better the quality of blog. These are the small mammals that will soon take over the territory of the dinosaurs when the social media meteor really hits. However, for an example of a well-written blog by a seasoned researcher, see Dr Jenny Martin’s blog Espresso Science.

Ultimately, in many ways I have had a good year and wish you all the best for 2015.

Fact, fudge or fiction: understanding medical research news

Every day we are bombarded with stories of medical “breakthroughs”, cures for cancer and claims that substance X causes disease Y. But how do we know which reports to trust? Are we being fed the truth or has it been bent beyond all recognition by PR departments, journalists and headline writers? Below is a rough guide to getting to the bottom of news stories about medical research.

Cartoon by Jim Borgman, first published by the Cincinnati Inquirer and King Features Syndicate 1997 Apr 27; Forum section: 1 and reprinted in the New York Times, 27 April 1997, E4

Where is the study reported?

Whether the study has been reported on television, radio, print or online, you must first judge the quality of the media outlet on which the story is presented and whether bias may be present. Gone are the days in which “mainstream” media was more reliable than online media but you can still choose a news source you know to be trustworthy. Sites such as Newstrust and mic can help you identify these. Examples of trustworthy sources include the New York Times, Reuters and BBC News. In addition, The Conversation is an independent source of news and analysis written by academics and research scientists. It features topical stories and corrects misinformation emanating from less rigorous media sources. Specific medical research institutes may also have blog posts written by their own experts in the field.

At what stage is the study?

Sometimes researchers may issue a press release before they start their research, when research is in progress or before their work has been reviewed and published. These situations are the least reliable. Ideally we will know whether the researchers are the first to find such results (they will definitely say if this is the case). If so, it’s possible that a single study may not be able to replicated by others. As a research area matures, researchers will spend time writing a “systematic review” or conducting a “meta-analysis”. Systematic reviews are “studies of studies” which identify, appraise, select and synthesize all high quality research evidence relevant to a specific research question and make conclusions about whether sufficient evidence exists to support a research finding. Among the most trusted examples of these are Cochran reviews. New treatments for diseases must go through these processes before entering the clinic.

What organism has been studied?

This may sound like a strange question but medical research often starts with human cells in a dish. Showing that a drug can kill cancer cells in a petri dish does not mean it will kill cancer in a real person. And new drugs require testing on animals before humans and surprisingly, news reports may sometime fail to mention whether the study is of mice or men.

Is sensationalism used?

Studies labelled “breakthrough” and “cure” rarely are. Research takes years and the vast majority of research is achieved in small advances. See also “what stage is the study at” above. Check the language used; researchers often suggest that their research “may lead to” a cure.

How thorough and critical is the news report?

A bonus if an independent expert is quoted; this provides a valuable independent assessment. Lazy news sources may not even speak to the original researchers and will quote the original press release verbatim, so if in doubt look up the study.

Go to the source

Another bonus if the source of the news story is quoted. Journalists may include just the journal name but if you are lucky, the story will link to the article itself. However, there are a couple of barriers to overcome once you have come this far. Firstly, if the study is not freely available, you can search for it. Most journals are, however, still pay-per-view but at least you will be search for and read the summary or “abstract” for free. Once you have done this, there are excellent guides that can help you understand and evaluate research papers.

“But I don’t have time to do all this checking!”

In this case, someone may have already done the checking for you. The searchable Behind the Headlines from the UK National Health Service’s NHS Choices web site is the one site you need. It breaks down each story into sections of where the story came from, what kind of study it is, what the basic results were and how they were interpreted. Each short article ends with a conclusion summarising the strengths and weaknesses of the study followed by links to the original research article and examples of how the mainstream media has covered the story.

Finally, if I were offering two pieces of advice: start skeptical and if you disagree with the way the story is covered, write a comment on the story’s web site or complain about it. After all, every news outlet should share the motto of the New York Times: “All the News That’s Fit to Print”.

 

Acknowledgements

Many thanks to Anne Byrne for proof reading

Science: uncovering Nature’s secrets

It was a wet Saturday afternoon and I was sat in a dark room looking down a microscope. Then I saw it – something that no-one had ever seen before. This was my “Eureka” moment and encapsulated what it’s like being a scientist of the natural world.

The Ancient Greek Homer knew a thing or two about science; he said that it was the knowledge of nature, true for every community, as opposed to local customs and superstitions. Since that time, science has gradually uncovered more of nature’s secrets one by one.

This uncovering of secrets using science is basically detective work. We sit and watch nature for hours, days, and months. Maybe we see nothing for a long time; maybe we see more than we bargained for. And at the end, our equivalent of a defendant being found guilty is the publication of your research findings that results following peer review.

For my first job interview, one of the panel asked me whether I liked to do crosswords. Funny question, I thought, but a lucky one, as I had started to learn about how to crack cryptic crosswords. I said yes and got the job. The interviewer was really asking whether I was patient and did I have the deductive thought processes to progress though a scientific investigation.

You don’t have to be a working scientist to do science. When I was a child I kept mini worm and butterfly farms and made unwritten observations every day. When I was at high school, this came in useful when I had to think of a biology project. I stuck a brick in our garden at home, monitored what I found underneath it every day and called the project “Life Under a Brick”. I won.

The scientific study of nature can take many forms – from chemistry to physics and biology. With medical research, we use all three, but mainly biology, to uncover how humans develop and age and what can go wrong and result in disease. In my area – the early origins of disease – we have found that the time spent in the womb in the most formative part of life because our bodies are at their most vulnerable. Together, those who study our DNA and the proteins that it codes for, work together with doctors who see the patients, collect their samples for study and return the favour by applying newly-discovered treatments.  

A few centuries after Homer, another ancient Greek, Archimedes, stepped into his bath, saw the water rise and realised that he had found a way to measure the volume, and hence the density of a gold crown that a friend of his had suspected wasn’t pure gold. This thought caused him to yell out “Eureka!” (“I have found it”) and promptly ran to see his friend, not realising he was naked. For scientists, the thrill of discovering new things is the same. When I had my microscope moment, I immediately ran (with my clothes on) to tell a colleague down the corridor. Today, I guess, I would have Tweeted it. There are other ways to celebrate a discovery. A colleague wanted to make her mark on the gene she discovered and called it “RING” – short for “Really Interesting New Gene”. This gene is now known to be part of a family of genes all sharing a particular characteristic in their protein called the “RING finger”. Scientists do have sense of humour too.  

Eureka moments can also come before the discovery. They can be the time when you put together your thoughts with those of others and come up with a hypothesis that can be tested. In a way, this was similar to Archimedes’ experience.

Back to my specific area of research. Like all my colleagues at the Murdoch Childrens Research Institute, I want my research to lead to the detection, prevention and treatment of childhood disease. Maybe it was seeing my sister cured of childhood leukaemia that inspired me to start my career in medical research? It certainly made me aware that every step of her journey, from her diagnostic blood tests, right through to her chemotherapy were all products of medical research. In the end, “breakthroughs”, such as the dramatic increase in survival for childhood leukaemia, mostly come from years of work by many researchers. I want to be among the number.