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Bedside to bench
April 2009
by Lloyd Dunlap  |  Email the author
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MADISON, Wis.—Extending the use of its ProteoSep 2D liquid fractionation system, Eprogen is producing whole-proteome microarrays for probing with antibodies and partnering with Gentel Biosciences to create products for the discovery of new autoantibody biomarkers using their whole-proteome microarray technology.

By collecting the liquid phase output from the second dimension analysis, discrete fractions containing small subsets of "intact" proteins contained in cell lysates (or subcellular fractions and biofluids) can be arrayed in a unique 3D format to serve as "bait" for probing with sera for autoantibody response (serological assays) or with known antibodies to mine for specific proteins, says company president Tim Barder.

"Simply stated," Barder says, "we take well-established cell lines or tissue samples for a particular disease of interest, lyse them and, after a 2D liquid phase separation using ProteoSep, we print microarrays on Gentel slides of the approximately 1000 discrete fractions containing subsets of the 'intact' proteins fractionated from the lysate. The slides are then probed with sera or known antibodies for intact proteins (spots) of interest. This 'bedside-to-bench' methodology is a novel approach to combine analytical proteomics techniques with antibody detection techniques to mine for new clinically relevant biomarkers at the patient level."

Dr. Dan Clutter, who recently joined Gentel as VP of commercial development, says he believes that the company is well-positioned to be a leader in high-throughput biomarker discovery and screening.

"Our expertise in quantitative multiplexed protein assays—coupled with some amazing new profiling applications—gives us the ability to screen for biomarkers that no one could screen for previously." he adds. "I started out my career as a protein biochemist using 2D chromatography with silver stain. Twenty years later, it has become MS, which will not move into the clinic easily. Now Eprogen, with our assistance, is preparing proteomics for an overdue leap in technology."

The agreement couples technology from Eprogen with Gentel's portfolio of nitrocellulose-based protein microarray surface chemistries. As part of the agreement, partitioned whole proteome arrays will be offered for fluorescence detection on PATH protein microarray slides and chromogenic detection on Gentel's APiX Array System. Additionally, Gentel will process samples on whole proteome arrays for customers through its Symphony Array Services group.

"This microarray platform eliminates the MS bottleneck and makes discovery and prioritization of new candidate biomarkers for further analysis and characterization by MS or Western Blots significantly easier," Barder says. "It uses everything researchers are used to using to discover things they don't know in order to characterize pre-malignancies, malignancies and early- to late-stage markers. When the question is, 'Does my drug work?' we can discriminate between responders and non-responders, pointing to protein pathways you would never have discovered otherwise."

Gentel arrived on the scene when Eprogen was working on commercializing their process and "looking at every platform we could think of," in Barder's words. Since researchers do not know the quantity of each protein, he says they must "take what the lysate gives you." To optimize the signal-to-noise in the whole-proteome arrays, Eprogen selected Gentel's nitrocellulose-based surface chemistry.

"The combination of protein partitioning using Eprogen's ProteoSep technology coupled with Gentel's technology is powerful," Barder says. "It should have a significant impact on clinically relevant biomarker discovery."
ProteoSep, PATH, APiX and whole-proteome partitioning technology are covered by a suite of issued and pending US and international patents.
 
 
Code: E040917

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