Scientists, software developers and artists have begun using VR to visualise genes and predict disease

A group of scientists, software developers and artists have taken to using virtual reality (VR) technology to visualise complex interactions between genes and their regulatory elements.

The team, which comprises of members from Oxford University, Universita’ di Napoli and Goldsmiths, University of London, have been using VR to visualise simulations of a composite of data from genome sequencing, data on the interactions of DNA and microscopy data.

When all this data is combined the team are provided with an interactive, 3D image that shows where different regions of the genome sit relative to others, and how they interact with each other.

“Being able to visualise such data is important because the human brain is very good at pattern recognition – we tend to think visually,” said Stephen Taylor, head of the Computational Biology Research Group at Oxford’s MRC Weatherall Institute of Molecular Medicine (WIMM).

“It began at a conference back in 2014 when we saw a demonstration by researchers from Goldsmiths who had used software called CSynth to model proteins in three dimensions. We began working with them, feeding in seemingly incomprehensible information derived from our studies of the human alpha globin gene cluster and we were amazed that what we saw on the screen was an instantly recognisable model.”

The team believe that being able to visualise the interactions between genes and their regulatory elements will allow them to understand the basis of human genetic diseases, and are currently applying their techniques to study genetic diseases such as diabetes, cancer and multiple sclerosis.

“Our ultimate aim in this area is to correct the faulty gene or its regulatory elements and be able to re-introduce the corrected cells into a patient’s bone marrow: to perfect this we have to fully understand how genes and their regulatory elements interact with one another” said Professor Doug Higgs, a principal researcher at the WIMM.

“Having virtual reality tools like this will enable researchers to efficiently combine their data to gain a much broader understanding of how the organisation of the genome affects gene expression, and how mutations and variants affect such interactions.”

There are around 37 trillion cells in the average adult human body, and each cell contains two meters of DNA tightly packed into its nucleus.

While the technology to sequence genomes is well established, it has been shown that the manner in which DNA is folded within each cell affects how genes are expressed.

“There are more than three billion base pairs in the human genome, and a change in just one of these can cause a problem. As a model we’ve been looking at the human alpha globin gene cluster to understand how variants in genes and their regulatory elements may cause human genetic disease,” said Prof Jim Hughes, associate professor of Genome Biology at Oxford University.

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Stronger in old age: Stem cell research paves way for muscle-building medication

It could in the future be possible to take medication that will allow you to build muscle, even when you are in old age.

This is due to the findings of research at the Karolinska Institutet in Sweden, which found that large, and wholly unexpected, amounts of mutations in muscle stem cells blocks their ability to regenerate cells.

“What is most surprising is the high number of mutations. We have seen how a healthy 70-year-old has accumulated more than 1,000 mutations in each stem cell in the muscle, and that these mutations are not random but there are certain regions that are better protected,” said Maria Eriksson, professor at the Department of Biosciences and Nutrition at Karolinska Institutet.

With this knowledge, researchers could develop therapies that would encourage such regeneration, and so allow older people to rebuild lost muscle.

“We can demonstrate that this protection diminishes the older you become, indicating an impairment in the cell’s capacity to repair their DNA. And this is something we should be able to influence with new drugs,” explained Eriksson.

The landmark research, which is published today in the journal Nature Communications, involved the use of single stem cells, which were cultivated to provide enough DNA for whole genome sequencing – a medical first for this part of the body.

“We achieved this in the skeletal muscle tissue, which is absolutely unique. We have also found that there is very little overlap of mutations, despite the cells being located close to each other, representing an extremely complex mutational burden,” said study first author Irene Franco, a postdoc in Eriksson’s research group.

While a significant step, the research is now being expanded to look at whether exercise affects the number of mutations – a potentially vital factor in understand why and how these mutations occur.

“We aim to discover whether it is possible to individually influence the burden of mutations. Our results may be beneficial for the development of exercise programmes, particularly those designed for an ageing population,” said Eriksson.

The research is one of a host of projects being conducted across the world that have potential impacts on ageing, an area that was long ignored by much of the scientific community, but is now garnering increased support.

If many – or even a fair minority – of these findings eventually become the basis of therapeutics, it could be transformative for old age in the future, allowing people to remain healthier for far later in life and potentially even leading to longer life expectancies.