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Big data, muffins and space travel

What do muffins and space travel have in common?
Answer: They affect our genes through altered DNA methylation patterns.
Two researchers who studied this recently met at the public defence of a doctoral thesis at Lund University.

Andrew Feinberg from Johns Hopkins University's School of Medicine in Baltimore, USA, has often been called the "father of epigenetics”.
Andrew Feinberg from Johns Hopkins University's School of Medicine in Baltimore, USA, has often been called the "father of epigenetics”.

Andrew Feinberg from Johns Hopkins University's School of Medicine in Baltimore, USA, has often been called the "father of epigenetics”.  When the US Space Agency NASA decided to send an astronaut into space while his twin brother stayed on the ground, Feinberg thought to take some samples. The analysis showed that time in space, 340 days, caused thousands of changes to DNA methylation on the astronaut’s genes. The results attracted great attention around the world.

When Alexander Perfilyev learned who would be the external reviewer at the public defence of his doctoral thesis, he was intimidated.

“I googled his name and was blown away by his biography and publications in journals such as Nature. He started publishing before I was even born.”

Fluent in Italian

Alexander Perfilyev was born in Russia 35 years ago and studied mathematics at the University of Moscow. After three years of further study in the Italian capital, where he learned to speak Italian fluently, he came to Malmö and the Lund University Diabetes Centre. This was six years ago, and despite that he has not yet learned the Swedish language.

“It has not been needed, everyone here speaks English”, he says.

What, on the other hand, he quickly learned was biology and epigenetics.

“I did not know anything about it earlier. I did not know much about genes.”

Mathematical methods

Now he is talking about methylation patterns and CpG sites (regions in the genome where methylation occurs) as if it were the most natural thing in the world. But he does not want to pretend to be any expert on epigenetics or DNA methylation. His role as bioinformatician in the research group is to use mathematical methods to analyse the enormous amount of data that comes from research and is often referred to as big data.

“Modern technology generates so much data that it is not possible to use simple tools to analyse it. But using these methods allows you to distinguish patterns and other results.”

The methods he uses are also applied in other fields, such as computer technology, to collect and analyse people's behaviour and to evaluate risks, and they are also being used in epigenetic research.

Inheritable

Just as you inherit the genes of your parents, you inherit many of their DNA methylation patterns. The difference is that you can affect some of them with your lifestyle.

The research group to which Alexander Perfilyev belongs has studied the impact of diet and physical activity on the epigenome in different tissues and they have shown that the methylation patterns are influenced by age.“When you exercise, many things happen, not only fat burning or muscle gain; DNA methylation also changes. Diet also influences DNA methylation.”

In the well-published “Muffin study”, participants ate different numbers of muffins baked with different kinds of fat; saturated fat (palm oil) and polyunsaturated fat (sunflower oil). The results from the study were included in Perfilyev’s doctoral thesis, showing that the methylation pattern in the adipose tissue was affected by eating a lot of fat and it differed between those who had eaten muffins baked with saturated fat and polyunsaturated fats.

“Our conclusion is that overeating matters and that different types of fat matter.”

Our conclusion is that overeating matters and that different types of fat matter.

Changes return

An article in the Swedish journal Illustrerad Vetenskap, describing the major changes to astronauts' genes, also reported that the changes soon returned to normal after the astronaut returned to Earth. Does this mean that, in the long run, it does not matter whether you are baking your muffins with saturated or polyunsaturated fats?

“Changes in the methylation pattern depend, inter alia, on how long you have been exposed to a particular factor. When you stop exposing yourself to this particular factor, changes may return to their previous pattern.”

In the future, Alexander Perfilyev plans to continue his work combining mathematics and epigenetics.“I like the research area and, with new technology, we get better opportunities to study new things. There is so much to learn, not just within epigenetics. The more you learn the more you understand you do not know. It's quite overwhelming.”

Text and photo: Sara Liedholm

Facts about epigenetics

Epigenetics is a field studying heritable changes to the genome that do not involve changes in the DNA sequence. Epigenetics might explain how our genes are affected by various lifestyle factors. One example is DNA methylation, a process where a small chemical compound attaches to certain locations in the genome, thus controlling whether genes are on or off. It affects, among other things, the production of proteins that in turn affects the functioning of our tissues and organs and may be important for the onset of diseases such as cancer and type 2 diabetes

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Lund University Diabetes Centre, CRC, SUS Malmö, Jan Waldenströms gata 35, House 91:12. SE-214 28 Malmö. Telephone: +46 40 39 10 00