Kathryn Lilley tells Michael Smith how curry and beer could be the downfall of biomarkers.     

Kathryn Lilley is director of the Cambridge Centre for Proteomics, located in the Systems Biology Centre, Cambridge, UK. Her group is involved with several important collaborative proteomics projects, in particular involving the model organisms Arabidopsis and Drosophila.

 

What inspired you to become a scientist?

My grandfather was an amateur gardener and my mother picked up his love of plants. I think it was her love and enthusiasm for nature and plants that made me very interested in biology. 

I always had a battle as to whether to become a musician, as that's my other great passion. I suppose I realised that you could be a professional scientist and an amateur musician but it would be very difficult to live your life the other way around! 

Why did you choose to specialise in proteomics?

After my PhD, which involved a lot of protein sequencing, an opportunity came up to run a protein sequencing facility at the University of Leicester. People would send us samples to sequence using Edman degradation, but, rather frustratingly, the majority of proteins are N-terminally blocked and this method of protein sequencing requires you to have a free N-terminal amino group to react with the reagents. 

About that time, there were some major papers published on mass spectrometry of proteins, particularly from Matthias Mann's group at the European Molecular Biology Laboratory in Heidelberg. Julian Ketley, one of my collaborators in Leicester, came to me clutching 2D electrophoresis gels of protein mixtures. I thought it would be wonderful if we could take every spot on the gels and tell him what they were. Although we purchased our own mass spectrometers in Leicester to support peptide and DNA synthesis, they were not the right type to carry out these new methods of protein identification. I was once again frustrated as I really wanted to carry out these wonderful new proteomics technologies.

Next, the opportunity came to move to Cambridge to set up a proteomics laboratory with funding from the BBSRC and with it, the idea that I could do all this wonderful scalable protein identification. After running a core facility for many years in Leicester, in Cambridge I got the opportunity to get back in touch with how to answer interesting biological questions.

What biological questions are you interested in?

In the early days of the facility, most projects centred around knowing the differences in protein abundances between mutant and wild types or treated and untreated states. If we can see which proteins are changing in their expression or post-translational state, it gives us an insight into what's going on inside a cell. 

I got fed up with identifying the same sets of proteins and wanted to probe into the lower abundance fraction of proteins. I also wanted to get information on where they resided in a cell and who with!

What are you working on at the moment?

Organelle proteomics. The first stage of many proteomics experiments is to take the cells and mash them up. Usually you add a healthy dose of detergent. This means you lose all the spatial information about your proteins within a cell. I think this is a very important thing to study because where proteins are and what they associate with is going to give us a huge amount of information that we can't get from just looking at their abundance. 

We are starting to look at components from signalling pathways - how they move around the cell upon signalling events and how this may change under different situations, including development and differentiation. We've spent a few years trying to fine tune the methodologies. We're not there yet but we've gone quite some way to be able to produce technology that is robust both in terms of identifying proteins associated with certain organelles and mapping onto that the position of protein complexes. 

What do you think about biomarkers as an ultimate aim of proteomics?

Proteomics is a very attractive way of finding biomarkers but it is fraught with issues. 

The main issue is the dynamic range of protein concentrations within plasma, which currently no techniques can cover. 

Secondly, if you do find biomarkers in a certain set of proteins that are always up-regulated in someone who is suffering from a cold, how discriminatory is that? I can't see that there is going to be any one biomarker that will tell you which disease is present. 

Finally, blood plasma is really a mirror of your general state of health and what you've been up to in the last day or two. There is a lot of person-in-person variability depending on your health and whether you've had a curry and several beers the night before! In a population set, I think it's going to be very difficult to find an abundance change that is disease-specific. 

What advice would you give to someone considering a career in science?

Looking back on my own career, I became too specialised too soon. What I lost touch with very quickly, and I wish I hadn't, was maths. More and more in biology, we are making quantitative measurements. The way in which we deal with those measurements is controlled by statistical and mathematical tools. We need that know-how to be able to design our experiments properly and to see whether we believe the data that are coming out. My advice is to avoid losing touch with other scientific disciplines. Try and stay broadly focused. 

Are there any particular people who have inspired you?

Cambridge is a fantastic scientific environment. If you have an idea and want someone to help you with it, there is no shortage of people to ask. The mindset is great; collaboration is what it's all about. People are not protective of their patch and they will welcome you. It's very difficult for me to single anybody out, but the person I would mention is a member of the department of genetics, Alfonso Martinez Arias. The great thing about working with him is that no matter how crazy my ideas are, he humours me. He's very enthusiastic and we've had a very successful collaboration. He has encouraged me to think outside of the box, which is essential for what we do.