What could phenomics mean?

What questions might phenomics answer?
12 November 2019

Interview with 

Nicola Grey, Luke Wiley, Ruey Leng Loo, Australian National Phenome Centre, Murdoch University


two CGI figures, showing the systems of organs in the body


What sorts of questions might phenomics answer? From inside our bodies to the food we eat, phenomics has the potential to change a lot of things. Chris found out more when he visited the Australian National Phenome Centre and spoke to researchers Nicola Grey, Luke Wiley and Ruey Leng Loo. And to finish, a few closing words from Jeremy Nicholson...

Nicola - So in terms of using these state of the art platforms, we'll be looking initially to develop methodologies, making sure that those methodologies are very robust so that we can use them not only now but in years to come, and they'll be able to run many many thousands of samples and always give us the same reliable data that we need. We rely on that information to then make our inferences as to how a disease is progressing in a particular population. We're also looking at the mechanisms behind why particular diseases occur, why particular populations are more susceptible to developing a disease, and we'll be looking at how environments, how our lifestyle, what we eat, affects that disease risk. By doing that we can hopefully prevent a lot of these diseases from occurring. We're looking at diseases such as dementia, obesity, type 2 diabetes; big global health problems that we know are largely affected by our environment. So it's really trying to pinpoint exactly how the environment increases those risks, enabling us to reduce them and developing better therapies to reduce those disease risks.

Adam - Luke?

Luke - My research is going to be looking at the way people age and the way people have disease through age, in particular looking at how that impacts our cognitive health and our brain health. So what we can do is we can look at people's biological profiles and see if there are any trends in people's aging, and if we can spot trends, perhaps we can give policy advice of what can help healthy aging. Perhaps we can identify things that are causative of neurodegeneration or cognitive problems as people age. So I'm very interested in looking at a variety of samples of tissue, and for example urine and blood samples, and just really trying to understand how people age and how their metabolism changes as people age.

Chris - Because one of the goals is what we call a healthy or a longer health span, rather than just lifespan, because it's more a quality over quantity thing, isn't it? We've become very good in the modern era at making people live for what feels like forever for some people, but unfortunately they spend a significant amount of that time in ill health, and we want to minimise that.

Luke - Yes, exactly. So if we can improve the quality of life - an example would be Alzheimer's disease - if we can understand the disease more and slow down the progression of the disease, people are going to have a higher quality of life for longer, and we can really make real gains in people's enjoyment of life as they age.

Chris - How do you go from a bunch of molecules on a graph, which is what you're going to see from these machines in here, to practical advice for somebody? “You need to eat more bananas, your potassium is a bit low.” How do you actually get those sorts of conclusions out of the cocktail of chemicals that emerge from these machines?

Nicola - It's very complex, and one of the biggest challenges that we will face. So once we've actually identified these molecules, we then would have to validate that. What we would potentially do is to look at that in a more controlled environment. It might potentially be an intervention study where participants would be in a very controlled environment, we would give them a very specific diet and we would look to see how that would affect their metabolites and potentially disease risk markers.

Chris - So you’re hunting through the haystack here, biochemical needles in haystacks, that might be indicative of certain diseases, certain risks for diseases. And then once you think you've found them, then you're going to intervene in people and do a proper controlled experiment. So, “if we change those things, will we change outcomes”.

Luke - Exactly. The initial work that we complete is certainly at the discovery end of the lifespan and as we progress, and as we start to understand more about that metabolism and how metabolic systems are behaving in health and disease, then we can take that forward for validation and for real intervention and make the impact. So, the long term plan is to be involved at all stages of that process.

Adam - Luke Wiley, and before him, Nicola Gray. But it's not just about what goes on inside our bodies. You can point the powerful finger of phenomics at the food we eat too, and explore how different cooking techniques will affect the nutrient quality of a meal.

Ruey - My name is Ruey Leng Loo. I’m the Premier Early to Mid Career Fellow. Currently, we don't know too much about the chemical composition of the food. But when you cook them, how you cook them, that is going to change the chemical composition again. By doing all these different experiments, we can cook it differently before we put it through the instrument, then it can give us the full picture of what’s the kind of vitamin that's lost. If we knew that chemical composition that have a health benefit to us, how we can maintain those molecules, that's what we want to do, really.

Chris - So when I barbecue my chicken leg, we know it has a risk of colon cancer but chemically we don't know why, and you're saying if we feed it into machines like this, we can work out what the molecules are that might be linked to those disease states?

Ruey - Yes, so that we can see what are the changes on the molecule when it’s fresh, when we haven't done anything to that, and compared to if we barbecue the meat, what are the changes on those.

Chris - And going a step further, are you also going to ask the question: if I cook it and eat it, what effect do these different cooking methods have on my biochemistry?

Ruey - That’s right. So because all of us have a very unique set of gut microbacteria, they all have a specific function. If I eat this piece of chicken boiled that’s probably better for me because of my gut bacteria compared to somebody else. That's what we wanted to differentiate so that we can be able to precisely tell you whether you're better off eating a piece of chicken boiled, or maybe a piece of fruit because that would be better for them.

Chris - So you can debunk some of these claims about foods being extra good for you, blueberries being superfoods and all this kind of thing, and actually say “yes, look, I've got plausible scientific evidence” or “actually, this is bunkum, don't waste your money”.

Ruey - Hopefully, that's the goal. We wanted to be able to demythify some of these claims, really.

Chris - And will this enable you to prescribe what actually constitutes a healthy diet one day, then?

Ruey - If I can do that, that would be great. That would be my aim.

Adam - And a laudable and very realistic one at that. So, it's clear we are moving into a very exciting era for medicine. One that will enable us to keep more people living well for longer. But it's also clear that the hard work is only just beginning. We'll leave you with this from Jeremy Nicholson.

Jeremy - Genes and environment come together to create your disease risk. They create you. The things that we want to do is understand how those come together exactly by studying the biochemistry of the body, so that we understand the origins of disease and therefore can inform future healthcare policy. And when somebody becomes ill, we use the same technologies for moving someone from an unhealthy space into a healthy space, which we've already defined by the biochemistry of the whole population.


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