The Fred Hutchinson Cancer Research Center and Korean firm NSB Postech will be working together to use NSB’s technology with the goal of building antibody microarrays for proteomics research.
Announced last week, the deal represents Fred Hutchinson’s first collaboration in the antibody microarray field, which while gaining traction in proteomics for biomarker research work, still remains something of a supporting technology.
The collaboration will last six months. NSB Postech — spun out of the Pohang University of Science and Technology in South Korea in 2006 — will bear the full cost of the collaboration and pay Fred Hutchinson to develop its slides using the company’s Nanocones technology for use with antibodies. The center told ProteoMonitor it did not want the amount of the payments to be disclosed.
The NanoCones technology has, to date, been used for DNA microarray applications, and while it has worked with DNA, “it’s not as clear how antibodies will work,” said Paul Lampe, associate program head of molecular diagnostics at the Hutch. “Basically what we’re going to do is print antibodies onto [the slides], try them in our own group here and then also send them printed slides for them to try.”
The center will be testing whether the antibodies bind well and covalently link to the surface, and whether the reactivity of the antibody is retained, as well as the background of the slides.
“We’ve put labeled serum on the array and some brands of slides will give us high background, and won’t wash easily,” Lampe said. “Basically, in the end it’s what gives us high signal-to-noise [ratio].”
The work will be directed at four cancers: breast, lung, ovarian, and colon. Because the center has done extensive work in these areas, it has “great patient sample sets,” Lampe said.
The center currently makes its own antibody arrays using slides from an undisclosed vendor. The center, Lampe said, is reluctant to partner with industry, but in this case, it saw promise in the NanoCones technology.
Initially, Lee Hartwell, president and director of the Hutch, was at Pohang University when he met representatives from NSB Postech who told him about their technology and plan to adopt it for protein research. Eventually, the company sent the center its slides with some antibodies printed on them, and preliminary testing of the slides “looked good,” Lampe said.
“My personal bias is that microarrays is going to go further and faster [than mass specs].”
While NSB Postech would retain any IP and commercialization rights for products resulting from the collaboration, Fred Hutchinson hopes that the company will supply the slides to the center for free, Lampe said.
John Woon Park, president of NSB Postech, did not respond to requests for comment. On its website, the company describes NanoCones as a cone-shaped dendron with a “well-defined three-dimensional structure [whose] shape can be changed precisely. When this monodisperse molecule is coated on a surface, branches of the NanoCones form stable chemical bonds with the surface of a substrate, and a functional group at its apex is utilized for immobilization of a bioactive molecule.”
Among the advantages resulting from the NanoCones technology, according to the company, is its well-defined probe spacing and density; high hybridization efficiency and mimicry of solution phase behavior; and “very low” non-specific binding of various biomolecules on the surface of the assay.
The partnership addresses technology that while slowly gaining in proteomics still lags far behind the use of mass spectrometry. Use of protein microarrays, specifically antibody arrays, is hindered by two bottlenecks — the lack of antibodies, and for those antibodies that exist, poor characterization.
The field has moved to try to address the issues. Late last year, the National Institutes of Cancer said it was setting up a laboratory in its Frederick, Md., site to characterize antibodies manufactured by the private sector [see PM 11/29/07].
Last month, Sigma-Aldrich and Atlas Antibodies partnered to sell antibodies that have been highly characterized by the Human Protein Atlas. Atlas Antibodies is the commercial arm of HPA [see PM 02/14/08].
While antibody microarrays today may be something of a fetish technology, Lampe said that may change with improving technology.
“My personal bias is that microarrays is going to go further and faster,” than mass specs, he said. “If microarrays are done well, they give you the ability to do thousands of ELISAs at once, and ELISAs are the gold standard. The number of antibodies is daily increasing, and all one needs to do is the ability to get enough antibodies on an array, and you get the coverage you need. In a sense you’re almost validating right when you’re doing the experiment.”
The two things that are needed to do a microarray experiment correctly are arrays with a good signal-to-noise ratio, and good samples.
“That combination is not so very easy to obtain in a lot of respects,” Lampe said.
The Hutch has been using a library of about 1,600 full-length antibodies purchased from about 10 vendors to make its own antibody microarrays, Lampe said. It will use the same antibodies for the collaboration with NSB Postech although not all 1,600 will probably be used.
“We’ll be able to tell by using 200 antibodies whether they work or not,” he said.