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Proteomics Heads North of The Border As Canada Launches Funding Efforts


Proteomics researchers who have looked thus far for funding in the US may now want to turn to its friendly neighbor to the North. Fresh from hosting the second annual HUPO Congress, and soon to become the home of the new international HUPO headquarters, Canada is looking to position itself as a major funding body of proteomics research.

Genome Canada — a “hybrid between a granting body and a venture capitalist” — is leading this effort, with over CA$300 million ($230 million) already invested in genomics and proteomics and another CA$65 million on the way come April. According to Genome Quebec’s chief scientific officer Guy Bellemare, Genome Quebec — one of five regional centers that make up Genome Canada — is currently funding 17 large-scale genomics or proteomics-related projects totaling nearly CA$120 million. Approximately 25 percent of that is geared toward proteomics, Bellemare added.

The Canadian Institutes of Health Research also fund several proteomics initiatives, mostly through the Institute of Neurosciences, Mental Health, and Addiction; and the Institute of Genetics — although the numbers are currently far less impressive than their American counterparts at the NIH. “Of course, each [US institute] has a budget of billions,” said IMNHA scientific director Rémi Quirion at the HUPO Congress in Montreal. “We can’t do that in Canada.”

Despite its still relatively small investment, however, this “village” of 33 million people, as Genome Canada’s vice president of communications Anie Perrault termed it, has been receiving international attention recently from genomics and proteomics gurus. Francis Collins, director of the US National Human Genome Research Institute , for example, paid a visit to Genome British Columbia this week. Probably most notable was HUPO council members’ selection of Montreal as the site of the organization’s new international headquarters, and the subsequent appointment of John Bergeron, who leads the Montreal Proteomics Network, as the next HUPO president. According to Bellemare, Genome Quebec is helping the headquarters get off the ground with some modest start-up funds, as well as offering its experience as “another organization that is well-established, has a reputation, stability, and knows how to organize a large activity.” Bellemare emphasized, however, that Genome Canada was “not an organization with a mission to start another organization,” and that HUPO itself would need to raise money beyond initial costs. Still, he added that the presence of HUPO at Genome Quebec’s back door was positive.

Genome Canada’s biggest recent funding push, set to enter the due diligence stage of review in early November, is the Competition in Applied Genomics and Proteomics Research in Human Health (see PM 6-27-03). The competition’s winners will take a share of a CA$65 million pot set aside by the Canadian government for the development of genomics and proteomics tools that can be used in a clinical health care setting within five years of the start of the project — an ambitious timeline for most proteomics researchers. “At first we thought, ‘Oh my God, the scientists will hate us,’ and the pickup was slow at first,” said Roger Foxall, executive vice president of research at Genome BC. “But then the real clinicians got wind of this. … Whether any [of the tools developed under this program] will really be in the health system in five years doesn’t really matter — what matters is, they’re going to be in the health system a heck of a lot earlier than would otherwise have been.” Foxall said that of the 14 projects that Genome BC approved for submission to the competition, “Nine to 10 have a hefty dose of proteomics.” As opposed to de novo drug discovery, which tends to take many years to reach the clinic, the tools that the competition will concentrate on will address the three ‘P’s: prediction, prevention, and personalization, Foxall added. “The issue up here as we try to cut costs is, let’s get better diagnosis and prognosis, because the cost of health care is a major political issue,” he said. Techniques for analyzing differential expression of proteins — including ICAT, 2D-LC, and the use of newer mass specs — have figured most prominently in the proposals that came through Genome BC, he said. Bellemare added protein chips to that list, although he stressed that these were less developed, riskier technologies.

Unlike a pure granting body, Genome Canada requires researchers to provide milestone markers, as well as to raise from other sources matching funds for the money Genome Canada gives them. In further contrast with Canada’s other major source of proteomics funding — the government-run CIHR — Genome Canada also only funds projects that respond to its specific competitions. This can leave scientists with other ambitions out in the dust. “If we had an idea we wanted to pursue, unless Genome Canada had a specific call for projects in that area, we’re out of luck,” said Brenda Andrews, a professor of medical genetics and microbiology at the University of Toronto who has served on advisory boards for the Institute of Genetics.

According to Andrews, Genome Canada’s recent dominance in Canadian genomics and proteomics funding has in some ways clashed with the CIHR’s more general mandate. She cited the case of the CIHR-funded Collaborative Genomics Special Projects Program, which she called “hugely successful,” but which was recently cut due to perceived redundancy with Genome Canada. “The reason [CIHR] cited was because Genome Canada has this mandate, and we have a much broader mandate, and therefore we’re going to cut that program,” she said. “At the surface that makes sense, but they’re very different agencies.” Andrews warned that unless the CIHR and Genome Canada found better ways to work together, “Some very good people are going to be left out in the cold and be tempted to go to the US, where they can always get NIH money to do this kind of stuff.” In order for Canada to get on the international radar in genomics and proteomics, she said, the two groups needed to find more synergy. “I’m not sure that they’re working together as effectively as they could in terms of getting the best genomics research funded at internationally competitive levels,” Andrews said.

Quirion, from his seat at the IMNHA, was also looking for ways to put Canada on the international radar. The IMNHA has recently started funding an initiative in regenerative medicine, which Quirion said would include proteomics in its rubric. “If you have a spinal cord injury … it’s kind of always a ying yang situation — there is a protein that will favor growth, and a protein that will block growth. By using proteomics, we hope we will uncover new ways to facilitate growth,” Quirion said. Quirion hoped that the National Institute of Drug Abuse in the US would help to sponsor further neuroproteomics projects for understanding brain function under disease conditions, and earlier this month he made plans to collaborate with the Human Brain Proteome Project. “I’m interested in collaboration at two levels: one at the level of the CIHR as funders of research in human brain proteomics, and the other at the level of my own personal research — we have a large brain bank and maybe we can find ways to provide tissue to these international networks,” Quirion said.

But it was large-scale domestic collaboration that was more on the mind of the IG’s scientific director, Rod McInnes, during his speech at the HUPO Congress. McInnes expressed his desire to start a national proteomics “big bang” project in Canada that would bring a large number of scientists together in a big collaboration. He said that this month a Canadian scientist had approached both the CIHR and Genome Canada with a “fantastic idea [for the big bang] that you’re all going to hear about in the coming months.”



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