Almost two years after signing a landmark $84 million proteomics research deal with Novartis, GeneProt is stepping out on its own. Last week the Geneva-based proteomics factory launched a project to identify biomarkers and protein targets in cerebrospinal fluid (CSF) for degenerative diseases and vascular dementia, with a particular focus on Alzheimer’s disease.
GeneProt ascribed the timing of the new project to two factors: The company has just signed a deal with an unnamed sample supplier to acquire access to two liters of CSF, and secondly, GeneProt needs to collect its own proprietary data using its proteomics platform to demonstrate its capabilities to potential customers. In the past, company officials have said, its confidentiality agreement with Novartis has prevented it from sharing convincing results with other potential partners.
Because GeneProt is interested in generating valuable results rapidly, the new project will differ somewhat from its current project with Novartis. Rather than exhaustively search each fraction of the entire two-liter sample of fluid for potential markers and targets — as the company has attempted for Novartis — the CSF study will involve a preliminary scan of the proteome to generate intellectual property by as early as next year, said Marc Funk, GeneProt’s general counsel and co-chair of the company’s interim management board.
“In terms of the process, we will do it incrementally,” he said. “That means we will do a first sampling run on a smaller scale, immediately. The first collections will be tested and put through our production chain [in order to] have the elements that validate our process,” he added. “Once this is done, we will expand.”
In addition to generating data useful for impressing potential customers, Funk said GeneProt is optimistic the new study will lead to discoveries the company can claim solely as its own. While other companies, such as Pfizer and Oxford Glycosciences, have made efforts to mine the proteome for Alzheimer’s targets, Funk said only GeneProt is studying such large amounts of CSF. The large-volume approach, he said, allows GeneProt to target low abundance proteins that would escape detection when studying smaller volumes, even with the most advanced analytical technology.
“We know that there are [other people studying these diseases],” he said, “but one thing is sure: nobody else is going with large-scale studies with liters [of CSF].”
Part of the reason for GeneProt’s monopoly on the large-volume approach, however, lies in the difficulty in obtaining such large amounts of biological fluids — particularly CSF. In fact, it would be impossible to obtain two liters of CSF in the US, Funk said, because the risks associated with the procedure and the associated insurance costs are more than enough to dissuade US research hospitals from extracting the fluid from many patients.
But even though a sample of this volume would be difficult to procure, others are not so convinced of its value, given that it contains CSF from a large number of patients. The data may not be meaningful, they say, given the differences in protein concentrations between individual patients, even when they are all diagnosed with the same disease.
“It’s a tremendously interesting statistical experiment,” said Leigh Anderson, the former CSO of Large Scale Biology who now heads the Plasma Proteome Institute in Washington, DC. “By having large amounts of sample, you can fractionate down to lower abundance proteins. But by only analyzing pools you miss all the information on the specifics of the patients, and one thing that we and other people have learned in this business is that there’s a lot of variation between patients in the abundance of these proteins.”
Nevertheless, GeneProt claims to have achieved success with its approach for Novartis, which in December of last year accepted for further study six of GeneProt’s synthetic peptides derived from its proteomics research. And Funk said the company is still convinced it’s only a matter of time before the strength of its results overpower the reluctance within big pharma to contract out its proteomics research.
“I would be lying to you if I said there are no discussions [with potential partners], but I would also be lying to you if I said [there is something concrete] that could then be misinterpreted,” Funk said. “We are very cautious. You can understand that we are working hard.”