Covalent Incorporation Of A New Class Of Dye-Based Affinity Baits In Sieving Hydrogel Nanoparticles Overcome Roadblocks To Cancer Biomarker Discovery

Cancer biomarker discovery and clinical application has been seriously hampered by low abundance, instability and complex formation with high abundance proteins (e.g. albumin). N-isopropylacrylamide (NIPA) based hydrogel particles, consisting of a bait-containing core and a protective shell, overcome these major issues associated to biomarker discovery and measurement. Particles perform in one step, in solution, a) total sequestration and concentration, b) size sieving and c) complete protection form degradation of LMW protein biomarkers in blood and urine. In this study, novel dye molecules were selected as affinity ligands for broad classes of biomarkers; dyes were chosen for their ability to bind proteins, glycoproteins and nucleic acid for tissue histology, to bind textile proteins for fabric staining or for their known property to bind allergens. Dyes containing primary amine group (e.g. Acid Black 48, Basic Red 9) were coupled to NIPA/acrylic acid (AAc) particles by condensation of the amine group the carboxylic group. The ability of particles to capture and concentrate analytes was tested against a panel of low abundance, labile tumor relevant biomarker that include angiogenic growth factors (bFGF, VEGF, PDGF), IGF-1 and IGF binding proteins, interleukins (IL-6, IL-8), chemokines (CXCL12, CCL24), pro-apoptotic Bcl-2 proteins (Bak, Bax), and nucleic acids. Technologies used to screen dye functionalized particles include 1 D gel electrophoresis, western blotting, immunoassay, and mass spectrometry. Results showed that dye based baits have extremely high affinity for the target analytes so that particles capture all the analyte present in solution and that the affinity of biomarkers to the bait is unique and specific to the chemical structure of the bait molecule. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 4575.