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Drug Discovery Protein Profling duction of sample complexity and retention of coverage," he explains. "At the same time, such sample preparation for the pipeline must be cost-effcient and robust." His team from the Center for Proteomics and Metabolomics, headed by Prof. André Deelder, developed two solid-phase peptide extraction protocols that precede an MSbased analysis. The frst is based on magnetic beads functionalized with chromatographic properties, and the second deploys disposable column-like cartridges. Both approaches consistently generate high-quality starting material for identifcation of peptide signatures in biological fuids. To minimize deviations stemming from preanalytical conditions and to focus on biological variations of the specimen fuids, the team standardized operating procedures for each step of the process. "We spent a lot of effort on optimizing our protocol for high-throughput analysis," continues Dr. van der Burgt. Using this method, samples from patients with diagnosed pancreatic cancer were compared to the healthy controls. An automated solid-phase extraction protocol utilized weak cation exchange magnetic beads. The protocol allowed for cleanup and enrichment of certain subsets of peptides and improved sensitivity of the MS assay. "Early detection is paramount for patient NEWS Continued from page 18 Instead of striving to identify as many proteins as possible, we should focus on approaches that analyze just a few proteins but with excellent predictive value. survival," says Dr. van der Burgt. "Imaging technologies provide good tools for this purpose, but can still beneft from additional information such as blood-based serum biomarkers that may pick up the small changes of cellular function." Out of several hundred peptides reproducibly identifed by this profling, a set of seven was found to be suffcient to differentiate pancreatic cancer from normal samples with a sensitivity of 78% and a specifcity of 89%. The validation efforts continue with acquisition of additional samples from other clinical labs. In the future, Dr. van der Burgt sees tremendous diagnostic value for individuals See Protein Profling on page 22 Continued from page 18 milestone and royalty payments. According to Amunix Operating, its eight-month-old research collaboration and licensing agreement with Johnson & Johnson's Janssen Biotech unit will expand now that an option has been exercised for the development of an additional therapeutic molecule that Janssen will select. Amunix will combine its XTEN half-life technology with the molecule. Janssen will be responsible for all preclinical and clinical development as well as commercialization of the product. Amunix will receive an option payment in addition to research funding and will be eligible for future milestone and royalty payments. Amunix and Janssen entered into their collaboration in January. At the time, Amunix said it would assist Janssen in engineering up to three XTEN fusion proteins, in return for Janssen overseeing all preclinical and clinical development as well as manufacturing and commercialization of the resulting products. Under their original agreement, Amunix received an undisclosed initial upfront payment in addition to R&D; funding, and was eligible for future > Roche Pays PTS $10M XTEN Partnership in Spinal Muscular Atrophy Collab PTC Therapeutics just selected a development candidate in its spinal muscular atrophy (SMA) collaboration with Roche and the SMA Foundation, triggering a $10 million payment to PTC from Roche. The SMA program, which PTC had initially been developing solely in partnership with the SMA Foundation, began in 2006 with the aim of identifing and optimizing compounds that increase production of the survival motor neuron (SMN) protein, the lack of which causes SMA. Then in November 2011 Roche gained an exclusive worldwide license to the SMA program, paying PTC $30 million up front and entitling PTC to $10 million based upon the selection of a development candidate. PTC may receive up to an additional $450 million upon successful completion of other development and commercialization milestones, plus royalties on net product sales worldwide. n BMG Monochromator Setup - Method: Fluorescence Intensity / Chromatic scan Set monochromator by typing in center wavelength and bandpass under user defined setting or choose your fluorophore from list. You can also drag & drop the elements in the graph Ex Em 100 90 Relative Intensity (%) > Amunix, Janssen Expand 80 Drag & Drop Monochromator Settings 70 60 50 40 30 20 10 0 300 320 340 360 380 400 420 440 460 480 500 520 540 560 580 600 620 640 Wavelength in nm Select your fluorophore: Scan over: Set monochromator to: Fluoresceine Emission Pacific Blue Stepwidth: Wavelength 1 nm 401 Pacific Blue Pacific Orange Resorufin Rhodamine 110 (R110) Rhodamine Green Rhodamine Red Sulfrhodamine 101 TAMARA Excitation [nm] Emission [nm] Bandpass 44 Wavelength Start: Bandpass 455.0 Stop: 519.5 22 OK Genetic Engineering & Biotechnology News Cancel | GENengnews.com | September 1, 2013 | 21