Lisa Imrie is a Proteomics Specialist at the University of Edinburgh and a graduate of Edinburgh Napier University with a degree in microbiology and biotechnology. She has recently started her PhD studies taking a unique perspective in the analysis of biosamples from the VISICORT Foundation Biobank.
Danielle Nicholson, Pintail Limited caught up with Lisa Imrie after the latest plenary meeting in Galway to pose a few questions about her PhD research. In this interview (1 of 2), Lisa discusses her PhD project, how new techniques in the lab and with the data set analyses will carry the results of VISICORT forward and contribute to the field of proteomics.
What is the main focus of your PhD project?
To characterise different eye tissues and identify clinically relevant biomarkers in both keratoconus and Fuch’s Endothelial Corneal Dystrophy (FECD) using a multi-omics approach.
Why have you focussed on that in particular? What is it that interests you about it?
Until recently my career has been very technically orientated as I currently provide a proteomics service for a mass spectrometry core facility within the University of Edinburgh. This has allowed me a brief snapshot of other researcher’s work however I’ve never had any biological research of my own to focus on. In 2015 I was charged with helping the groups postdoc, Khadar Dudekula, with her proteomics profiling of eye tissue samples from the VISICORT project. This area of research piqued my interest and from becoming more involved in the sample analysis and also attending the plenary meetings it became apparent that there was massive scope to carry this research forward in any number of directions. Within my facility, I have a number of high-end mass spectrometers that can carry out various “omics” analyses so this PhD project seemed like a golden opportunity to utilise them to analyse the large number of samples available to me within Biostor Ireland. There are thousands of samples within this biobank so it was sensible to narrow down my thesis question and focus on looking at a couple of conditions to start with (keratoconus and FECD).
“It is really gratifying to see how the VISICORT project has led to the development of a new and exciting approach for analysing the invaluable collection of our biological samples. We can look forward to being able to identify important new and medically important Biomarkers from Lisa’s VISICORT-inspired PhD.”Professor Malcolm Walkinshaw, University of Edinburgh
What big questions do you want to answer?
I want to characterise keratoconus and FECD using a multi-omic approach combining proteomic, metabolomic and lipidomic analyses. This will include developing a method for the efficient extraction of lipids, metabolites and proteins from a single sample, enabling the targeted and untargeted analyses of each eye tissue. Extracting multiple “omes” in one step will ensure like for like comparisons and give a genuine snapshot of the biological status of the system. This will result in much better correlations between differences in metabolites/proteins and we can obtain greater insights into the metabolic pathways comparing healthy and disease states through interrogation and integration of the different omics datasets. This method will be unique in eye tissue omics studies to date.
What are the biggest obstacles to answering these questions?
My biggest challenges in this project will be all the sample prep method development. I’ve seen a similar one-step extraction method used before on plant material but never on the eye tissues that I’ll be working with. All the different tissues, e.g. tears, aqueous humor, cornea, all have very different compositions so it’ll be interesting to see if the one method works with all sample types.
Another challenge I’ll face is the data integration and interpretation. To date, I have only ever run single omics experiments which require just one software analysis approach. I’ll now have to find a way to integrate all the data generated from the proteomics, metabolomics and lipidomics analyses. Fortunately, there’s a symposium towards the end of the year which deals with Multiomics data integration that I’ll be attending so hopefully this will give me some idea of the best way to deal with these large datasets.
How has VISICORT contributed to your project concept and research?
Without VISICORT it may never have occurred to me to embark on my own PhD project. Because the subject matter interested me so much and due to the large number of samples available in the Biostór it was an easy jump to design a project to expand on the profiling data already generated by mass spectrometry. The challenge was distilling it down to look at a couple of biological questions as there were a large number of avenues we could have pursued. The two plenary meetings I have presented at, the first in Berlin to pitch the idea of the PhD project and the second in Galway to present a more definite structure, have been invaluable to me. Getting advice and suggestions from experts in the field has definitely shaped my work going forward.