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Proteomics Scientists Take Stake In Genome Canada Competition

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Genome Canada awarded CA$61.5 million ($46 million) in matching funding this week to 14 recipients for its Applied Genomics and Proteomics Research in Human Health program. Of the recipients, one group — receiving CA$6.1 million in total — will focus primarily on proteomics techniques, while at least two others will heavily incorporate proteomics along with other methods.

In total, the 14 groups received CA$123 million, including funds that they have secured on their own from matching partners.

The Genome Canada competition, first announced a year ago (see PM 6-27-03), supports the development of genomics and proteomics-based tools that can be used in a clinical health care setting within five years of the start of the project (see PM 10-31-03). To that end, all the funded projects have a strong connection to the clinic — including the proteomics-focused heart disease biomarker discovery program, headed up by Andrew Emili, Richard Lewar, and Peter Liu of the University of Toronto. The heart project, which received its matching funds primarily from Roche — with “a smaller amount” coming from the Heart and Stroke Foundation of Canada — has as its ultimate goal the delivery of candidate biomarkers to Roche for their potential development into a heart failure diagnostic, Emili told ProteoMonitor.

“We would identify candidate protein markers that we think are highly elevated at early stages of heart failure, or patterns of proteins for that matter, and some of those we’re hoping we’ll be able to detect in blood,” he said. “The flip side is I think we’ll be learning a lot about the basic biology of heart failure.” Emili said that his group chose to study heart failure because of the strength of heart programs at the university, which assured that the proteomics researchers would have access to high quality heart tissue samples. The researchers will initially use primarily mouse tissue for the project, and will profile the tissue at various stages of the disease, looking for changes in expression, he said. They will employ MudPIT analysis on subcellular fractions of tissue, using capillary-scale LC tandem mass spec.

Other funded projects slated to significantly employ proteomics techniques in addition to other techniques include a CA$16.1 million study on type 2 diabetes led by Marc Prentki at the University of Montreal and Barry Posner at McGill University; and a CA$9.1 million study on biomarkers for organ rejection in transplantation patients, led by Bruce McManus, Paul Keown, and Robert McMaster at the University of British Columbia.

The diabetes project, which received its matching funds from the Quebec government — as well as from mass spec companies — seeks to identify molecules involved in insulin signaling or beta cell growth, according to Posner. “We hope that by looking at these molecules, we’ll be able to pick out from them … key candidates that are potential sites of abnormality in type 2 diabetes,” he said. The proteomics data, which will be obtained by some combination of LC-Q-TOF mass spec with 1D or 2D gel analysis, will be combined with microarray data to select candidates. The genes that code for the selected proteins will then be genotyped to look for mutations that may code for diabetes susceptibility. The ultimate goal, Posner said, will be the development of diagnostics and therapeutics for the disease.

— KAM

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