Researchers use our differences to identify our similarities

A key factor in ensuring future equality in health is ensuring that treatment is tailored to the individual – personalised medicine. Although everyone has roughly the same cellular building blocks, small molecular differences can make one type of treatment work better than another for individuals. Researchers have how developed a new method of analysing these minute molecular differences, enabling them to identify novel cellular patterns and interactions with the body’s physiology.

“Phosphorylation is the process by which tiny phosphate groups constantly modify the surfaces of proteins – the body’s building blocks. We combined experimental and computational analysis to link this chemical signalling with the proteins’ biological function and especially with how this affects the physiology of the whole body. The method can both predict individual physiological differences and help to identify new important mechanisms by which these proteins regulate metabolism,” explains Jørgen Wojtaszewski, Professor, August Krogh Section for Molecular Physiology, Department of Nutrition, Exercise and Sports, University of Copenhagen – one of the senior researchers involved in the study.

Tiny enough to vanish

Phosphorylating proteins is one way cells can collect and integrate information from the surrounding environment to control biological processes. The basic structure of proteins is genetically determined, and thus generally unchanged throughout life. However, phosphorylation can help to fine-tune the function of proteins, such as their activity of interactions with other proteins.

“The challenge has been that phosphorylation involves tens of thousands of small chemical changes, so we do not know which ones are the most important and thus crucial for regulating our physiology. This combined with our differences means that biological variation in phosphorylation responses ends up reducing the likelihood of identifying any important responses within a given sample size. Instead of viewing this as an obstacle, we tried to use it to our advantage,” says Elise Needham, PhD candidate and lead author from University of Sydney.

Researchers previously measured the average phosphorylation of a given experimental group on each of the thousands of proteins. This has provided some insight – but the researchers expect to obtain much more and new information by examining data using the novel personalised method.

“The changes in phosphorylation are both individual and sometimes so tiny that they vanished when we just averaged individual phosphorylated proteins. Instead, we focused on how the phosphorylated proteins vary in response to various types of stimuli and linked this with the individual variation in physiological processes. This enabled us to identify important chemical changes that determine physiology even though individuals have different starting-points and react differently,” explains Needham.

Personalised phosphoproteomics

This new method that the researchers call “personalised phosphoproteomics” measures individual phosphoproteome responses to a given physiological intervention, such as exercise and/or insulin stimulation. This is a massive task but produces remarkable results.

“We generated comprehensive phosphoproteomic data on the relationship between exercise and insulin signalling in human skeletal muscle, to determine whether we could narrow the thousands of observed phosphorylation sites to those linked to the uptake of glucose into skeletal muscle. We identified about 130 sites strongly associated with glucose uptake in muscle. Several of these sites are thought to be regulatory and functionally connected. A completely unexpected regulator was the protein mTOR,” says Sean Humphrey, Early Career Researcher at University of Sydney.

Based on previous experiments in model systems, the researchers had expected an almost opposite role for mTOR (mammalian target of rapamycin).

“Our subsequent biochemical analysis identified new regulatory roles for mTOR. For example, we identified unexpected communication between mTOR and AMPK, which previous studies have shown is important in regulating muscle metabolism by improving the muscles’ insulin sensitivity after exercise,” explains Humphrey, who adds that discoveries like this challenge established knowledge and probably would not have been made without the new analytical method.

Using variation to understand similarity

By using this new method to study how exercise enhances insulin signalling in skeletal muscle, the researchers hope to confirm known communication between the proteins involved in glucose metabolism but also to find new links such as the one between mTOR and AMPK (adenosine monophosphate–activated protein kinase).

“We only currently know the function of very few of the thousands of post-translational modifications, so there is great potential in identifying novel sites that are most critical for biological processes, making further research very useful. Future mapping of these fundamental cellular processes may also lay the foundation for developing new effective drugs for many complex metabolic diseases and for cancer,” says Christian Pehmøller, Principal Scientist, previously at Pfizer Global Research and Development, Cambridge, USA.

“This new tool uses human variation to link this key type of signalling with biological function. It will therefore naturally also bring us closer to understanding the molecular basis of how health and treatment vary dynamically between people, so that we can optimise treatments for individuals,” he concludes.