The Australian National Phenome Centre (ANPC) uses phenomics to better understand diseases and disease risk. With the help of a $10 million grant from the Medical Research Future Fund, the ANPC was established at Murdoch University in Western Australia (WA) in 2019. It is now helping to solve the COVID-19 puzzle.
Leading COVID research
The ANPC was opened in October 2019. Professor Jeremy Nicholson explains that they rapidly shifted focus to deal with the world’s emerging health crisis.
‘We started to get up and running with various research projects after opening. But in February 2020, I made the decision that the best lab in the world should be working on the biggest health problem in the world – COVID-19’, says Professor Nicholson.
‘The lab is so powerful that we have made huge progress in understanding the disease, based on samples collected from around the world. We now have 15 papers published or accepted for publication on COVID-19 covering novel diagnostics, disease mechanisms and new ways of assessing Post Acute COVID-19 syndrome (also known as Long COVID).’
Professor Nicholson explains that COVID-19 is not really a respiratory disease. ‘We have found that COVID-19 causes microclotting that damages everything, not just the lungs. Brain, heart, liver, kidneys – we haven’t found any organ that it doesn’t attack.
‘And the real problem is that the damage is ongoing. COVID-19 can cause diabetes and heart disease and we now know that some of the damage is not fully reversible.’
This research is very personal for Professor Nicholson.
‘My only symptom was that I had several days where I felt very tired. But my COVID test was positive. Now I have diabetes’, he says.
‘Even if only 10% of COVID patients end up with long-term problems like diabetes or heart disease, this single virus will have enormous implications for our health systems for years to come. It’s vital that we understand what will happen.’
The history of the ANPC
Professor Nicholson set up the world’s first phenome centre in 2012 at Imperial College London. In 2016, he set up the International Phenome Centre Network with 8 centres around the world to harmonise and standardise phenotyping methods. As part of this international outreach, he started work with Australia to set up a phenome centre in WA.
‘Then they said, why don’t you come and run it? I brought some members of the Imperial College team with me, and used the MRFF funding to build arguably the best equipped metabolic lab in the world’, says Professor Nicholson.
With the lab as the starting point, the team received other funding to bring in staff and equipment. The centre now has 30 staff with access to a wealth of metabolic phenotyping techniques. These include mass spectrometry, nuclear magnetic resonance spectroscopy and advanced data modelling.
The study of phenomics
Your environment and lifestyle interact with the expression of your genes to influence your health and risk of disease. Phenomics analyses biological tissue and fluid to find out how genetic, environmental and lifestyle factors interact at a molecular level.
This allows researchers to better understand the causes of disease and to develop personalised treatments for diseases such as cancers and type 2 diabetes. It also helps to predict risk factors for disease in communities and develop preventative programs.
Professor Nicholson believes that Australia should be very pleased with its ANPC investment.
The centre will help to provide the best COVID information and treatment for Australians. For example, our work will develop models to predict Post Acute COVID-19 Syndrome in individuals and to create new mitigation strategies for patients with persistent symptoms. Our models will tell us whether a specific individual will have a mild case or something more severe or long lasting. We are also starting to work on understanding the biochemical actions of the new COVID-19 vaccines.
‘We will start work on other research projects in the longer term. The lab was built to have enormous capacity. We can process hundreds of thousands of assays and generate up to 10 petabytes of metabolic data a year.
‘Our work, and our national and international collaborations, will also build the health research profile of Australia and WA. We have built a world-class facility and our research can help to revolutionise the way we treat so many diseases.’