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Antibody Outfit ProteomeBinders Seeking Funding to Jumpstart Benchwork in 2008

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The headline of this article has been updated from a previous version, which inaccurately characterized the project's current cash position.
 
An international consortium designed to catalog and ultimately produce all binding molecules for the detection of human proteins is in search of additional funding that can help it move into the next phase of its mission.
 
Founded in early 2006 with 26 European and two US partners, ProteomeBinders has operated solely with €1.8 million in seed money from the EC, which has been enough for the group’s mostly European members to hold meetings, set goals, plan, and write reports.
 
But in order to do the actual scientific work it was created for, it will need to find additional funds. While the consortium has funded some database development, overall “the problem is that the current ProteomeBinder money does not allow us to do bench work,” said Mike Taussig, coordinator of ProteomeBinders.
 
The group is awaiting word from the European Commission on a proposal that could net it €3 million [$4.4 million]. It also is preparing to file a proposal with the EC that could result in an additional €15 million in funding.
 
Taussig said he hopes to begin setting up a gold standard for binder quality and create a center or centers that perform standardized testing on the binders. Those centers, Taussig said, could eventually become “future hubs for binder storage and distribution.”
 
When ProteomeBinders was created, its mission was to identify all binding molecules against the human proteome [See PM 03/22/07]. In the effort to map the proteome, the creation of binding molecules that enable researchers to detect proteins has become a crucial step to achieving that goal.
 
Despite this, researchers have been able to identify only between 5 and 20 percent of the antibodies related to the 100,000 proteins specified by the human genome.
 
In addition to ProteomeBinders, other efforts underway to build up the base of information include the Human Protein Atlas, a ProteomeBinders partner, which has so far profiled and characterized 3,015 antibodies.
 
The US National Cancer Institute has also embarked on an initiative to create an antibody-characterization laboratory. It is now in the process of rounding up antibody manufacturers to produce three monoclonal antibodies for each of 42 antigens [See PM 11/29/07].
 
The potential scope of ProteomeBinders, however, exceeds both the HPA and NCI’s antibody initiative. In addition to the sheer number of molecules it wants to identify, ProteomeBinders is looking to improve the quality of antibodies being produced, a common complaint among researchers. It also wants to produce renewable antibodies, including monoclonal antibodies and recombinant binders.
 
While its partners are almost exclusively made up of academics and researchers, ProteomeBinders has gotten the interest of commercial vendors, Taussig said, naming Sigma-Aldrich, Applied Biosystems, and Invitrogen specifically.
 
“I think the thing is that they need a handle on what’s coming up, what’s the discovery potential on such a project,” he said. ProteomeBinders is not interested in competing with commercial antibody manufacturers, he stressed.
 

“The problem is that the current ProteomeBinder money does not allow us to do bench work.”

“Unless there’s an obvious, clear need for new reagents,” ProteomeBinders will not duplicate what is already available from vendors, Taussig said. “We may want to quality-control some of the stuff [that] is out there. But there’s no point in making perhaps another set of anti-p53’s, for example, when there are already 950 on the market,” he said.
 
David Smoller, president of the Research Biotech business unit at Sigma-Aldrich, said he was unfamiliar with ProteomeBinders, but said that the company is interested in any collaborative effort to increase the number of antibodies.
 
“To make a binder for every protein in the human body is a task that is outside the resources abilities of any one group, that’s for sure,” he said. “Any time that I see consortia or collaborative efforts, I applaud them because it’s a monumental task to have a reagent to every protein in the human body.”
 
An official at Invitrogen did not respond to a request for comment. Officials at ABI could not be reached for comment.
 
Seeking Funds
 
The main priority now for ProteomeBinders administrators is finding the cash to pay for the science.
 
In the spring, the EC turned down a request for a grant of up to €3 million that would have paid for a quality-control project aimed at benchmarking binding molecules. According to Taussig, the proposal was rejected because it “didn’t address all the ins and outs of running an infrastructure.”
 
In the fall, Taussig and his colleagues applied for a grant from the EC to fund an offshoot project of ProteomeBinders, dubbed AffinityProteome, to develop high-throughput methods of producing molecular binders. The EC is expected to make a decision soon.
 
“The project is to bring together eight or nine partners … to develop binders against kinases and other signaling targets as a sort of model,” Taussig said. “If we can do that, we [are] going to use them in applications like proximity ligation and intrabody use, and high-resolution imaging, and we were going to compare them for those purposes.”
 
He and his colleagues are also writing the EC a funding request for up to €15 million that would help the group make the binders, create technologies, and develop and apply standards and quality controls, Taussig said.
 
Last week, Taussig gave a plenary speech at EuroBioForum 2007 in Lisbon, a meeting held expressly to give scientists and European funders a chance to discuss funding opportunities.
 
Because of its cash crunch, the only benchwork the consortium has been able to do has been to develop a database to store the molecular binders it hopes one day to identify. Three groups are involved in that project: the Royal Institute of Technology in Stockholm, Sweden; the European Bioinformatics Institute; and the University of Bordeaux in France.
 
“We want to have a comprehensive database of publicly available affinity binders, together with quality control and validation data,” Taussig said.
 
While he said that he isn’t unhappy about where ProteomeBinders is today, he acknowledged that the lack of funding has made the future of the organization unclear.
 
“I would have been happier if we had seen clearly how to fund the actual production,” he said. “I would be reassured if I saw the longer-term future in terms of funding, because I think once we got that sorted out, we would be able to do the project. I don’t think there’s any problem doing it so much, or organizing it. It’s more the funding aspect.”

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