Final Activity Report Summary - DIAGNOMICS (Proteomics and functional genomics in diagnostic target discovery) There is an ever increasing need for new and improved diagnostic markers in the clinical and veterinary arenas to enable earlier and more effective disease diagnosis and monitoring and prediction of therapeutic efficacy. The recent rapid worldwide expansion of the bioscience industry has also created a demand for the identification of quality and safety markers for the biological raw material or end product to confer competitive advantage. Proteomic and functional genomic technologies, combined with powerful bio-informatic systems, are central to the discovery of key differences between biological samples under defined conditions and, ultimately, to the identification of new diagnostic targets for assay development and validation. They also lead to a greater understanding of the function of the many new genes being described by entire genome projects. The goal of this project was to gain expertise in these technologies, and thereby complement ongoing research activities in diagnostic assay development in the University. Through this project, the proteomic techniques of two-dimensional electrophoresis of a range of sample types and mass spectrometric analysis of the isolated proteins were established in our laboratories. The development of novel methods for specific analysis of the glycoprotein fraction in these samples was undertaken to enable more convenient identification of glycoprotein markers of interest. Expertise was increased in microarray based gene expression analysis and, through a visit of one of our researchers to our partner institution, also in methods for manipulation of the resulting data. To increase knowledge transfer, fellows were integrated into specific research teams in the host laboratory and worked on aspects of ongoing projects alongside laboratory personnel. Comparison of protein profiles of a melanocyte cell line with two melanoma cell lines using two-dimensional electrophoresis and mass spectrometry led to the identification of at least three proteins that were expressed only in the melanoma cell lines. The diagnostic potential of these candidate markers needed to be further explored. Differences in some metabolic pathways were also identified but had to be further validated and significance determined. Progress was made in the development of a novel glyco-profiling platform for the recognition of glycoprotein differences between biological samples. This would greatly facilitate the discovery of glycoprotein markers of biological events, including diagnostic and therapeutic targets for many diseases. A panel of candidate genes involved in the stress resistance of certain strains of trout were also discovered in microarray expression analysis experiments using different data analysis approaches. These genes could be useful in selecting resistant strains for trout farming that would have commercial advantage. Thus, the new technologies brought into the University facilitated advances on a number of research fronts. Manuscripts describing these research outputs were in preparation by the time of the project completion and several strands of the work were continuing, both in the University and through ongoing collaborations with some of the incoming fellows. In addition, the research carried out under this programme resulted in new collaborative grant opportunities, with both academia and industry, for the teams involved.
