A Proteomics Upstart Tries to Outrun the Competition
Robert F. Service
By assembling an arsenal of technology, GeneProt aims to identify proteins associated with disease
GENEVA, SWITZERLAND--"Proteomics is something you either do in a big way or putter around in a corner," says Keith Rose. He should know. Last year, along with fellow proteomics pioneers Denis Hochstrasser, Amos Bairoch, Ron Appel, and Robin Offord, Rose launched GeneProt, the biggest proteomics test-bed to date in this young field. Armed with 51 mass spectrometers--protein sequencing machines that can cost over $150,000 each--and a massive supercomputer, the company is already a proteomics powerhouse.
And that's just for starters. In addition to the research lab here in the outskirts of Geneva, the company is constructing an even bigger facility in North Brunswick, New Jersey, slated to open next year. Moreover, it's considering plans to open a third site in Japan. All this for a deceptively simple goal: finding proteins involved in disease.
The company is banking that these proteins will produce a string of lucrative drugs aimed at top killers such as cancer and heart disease. GeneProt will use the proteins either as drugs themselves--like Amgen's top-selling protein therapeutic erythropoietin--or as targets for making their own small-molecule drugs.
GeneProt is sprinting out of the blocks, says Rose, because drugs, patents, and profits will go to those who are first with discoveries or can fish out the most important disease-related proteins. And GeneProt execs are convinced that the technology for analyzing proteins en masse has finally come of age. "You can either drop a line in or drain the whole area and see what is on the bottom," Rose says. The company, obviously, is taking the second tack.
Despite GeneProt's fast start, fellow proteomics firms Oxford GlycoSciences (OGS) in the United Kingdom and Large Scale Biology Corp. (LSBC) in Vacaville, California, are already in hot pursuit. OGS has protein-hunting collaborations with Pfizer, Bayer, GlaxoSmithKline, and the agricultural firm Pioneer Hi-Bred; LSBC has teamed up with Proctor & Gamble and Dow AgroSciences, among others. Celera's footsteps are also getting louder. This genomics powerhouse in Rockville, Maryland, raised nearly $1 billion in a March 2000 stock offering, much of it slated for proteomics. The company is now completing a seperate proteomics research center. And it recently formed a joint venture with equipment dynamo Applied Biosystems--which helped Celera sequence the human genome--giving it early access to the latest mass spectrometers, among other tools. To stay ahead, concedes GeneProt president Cédric Loiret-Bernal, the company will have to cut several deals with firms willing to have GeneProt be their primary proteomics source. He says the company is in discussions with 11 possible partners, six of which are "very interested."
--------------------------------------------------------------------------------
Gamblers. GeneProt execs including Keith Rose (middle) and Denis Hochstrasser are betting that banks of high-speed mass spec machines and supercomputing power will put them ahead of the pack.
CREDITS: (LAB) GENEPROT; (ROSE) MARY RITCHIE; (HOCHSTRASSER) COURTESY OF DENIS HOCHSTRASSER
--------------------------------------------------------------------------------
GeneProt's moves have inspired both awe and skepticism among other proteomics researchers. "They are going to industrialize the process," says David Hachey, a proteomics expert at Vanderbilt University in Nashville, Tennessee. "I think it will work." Ruedi Aebersold of the Institute for Systems Biology in Seattle, Washington, gives them a shot as well. The expertise of GeneProt's founders in proteomics is "very, very good," he says.
But John Yates, a proteomics researcher at the Scripps Research Institute in La Jolla, California, wonders whether the company is starting too fast with talk of three research centers: "It seems like a lot given that proteomics is still unknown as a business strategy." Hochstrasser's response: "If you want to place a satellite in orbit, you have to have a rocket of a certain size."
Hochstrasser concedes, however, that "there are not that many customers" for his business--perhaps 40 pharmaceutical companies that would be willing to strike deals. But he thinks they will, because to maintain their recent run of strong returns to investors, they must discover an ever larger number of blockbuster drugs: "The drug industry is ready because they want to go faster and can't do everything internally."
GeneProt has already lured one big customer. Last October, while its labs were still under construction, the company struck an $84 million deal with Novartis Pharmaceuticals. Backed by these resources, the company plans to work its way through a series of "twin proteome" studies, which can take up to 6 months apiece. Each will carefully analyze a pair of tissues--such as normal lung tissue and tissue from a lung cancer--and look for changes in expressed proteins that correlate with disease. For its investment, Novartis will receive three twin proteome studies, on diseases the company declines to specify.
GeneProt plans to keep its lead, says Rose, by producing a better product faster. He claims that GeneProt can analyze several hundred thousand proteins a year. That's on par with numbers by competitors such as OGS. But when GeneProt's new U.S. facility comes on line next year, its output will double, the company claims. At the Geneva site alone, this stream of proteins is expected to generate a torrent of some 40 terabytes, or 40 trillion bytes, of data per year. To handle that flood, the company has teamed up with Compaq to create one of the largest civilian supercomputers in the world, comprising 1400 separate processors capable of carrying out 2 trillion operations per second.
And GeneProt will offer its partners something its competitors don't: synthesized proteins. Not only will this strategy help jump-start drugmaking efforts, asserts Rose, but it may also help GeneProt researchers dodge patent disputes. Companies such as Incyte Genomics in Palo Alto, California, and Human Genome Sciences in Rockville, Maryland, claim rights to certain genes that can be used to make proteins in bacteria. By synthesizing proteins directly, Rose asserts, GeneProt can navigate around those claims. "The genomics companies thought they would stake out acres of virgin land," Rose asserts. "I'm not sure that will cover chemical protein synthesis."
If GeneProt's technology is as powerful as its executives claim, the first drug targets, and even drug candidates, should show up over the next year. "Expectations are very high," says Loiret-Bernal. "People are really looking at us to see if we are going to be successful or fail." Whatever the outcome, it's likely to serve as a bellwether for other firms looking to cash in on industrial protein analysis.
sciencemag.org |
