Core C: GAGomics and Proteomics

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Core C – Project Summary/Abstract Glycosaminoglycans (GAGs) are linear O-linked polysaccharides that modify serine residues for a select number of membrane proteins (e.g., glypicans: GPC1-GPC6, syndecans: SDC1-SDC4), secretory proteins (serglycin), and extracellular proteins (e.g., perlecan). GAGs are synthesized in a non-template directed fashion producing large heterogeneous structures that cannot be predicted in an analogous way that we can use the genome to predict transcriptional (RNA) and translational (proteins) structures/sequences. Consequently these structures are exceedingly difficult to structurally characterize. Furthermore, assigning biological function to these structures such as protein-GAG interactions adds to the glycoanalytical challenges. High-performance mass spectrometry (LC-MS/MS) combined with advanced sample preparation strategies is the leading technology for structural characterization and quantification of GAG structures. The Proteoglycomics-Core C (PG-Core C) fills a critical technologically need for the Program Project which have been outlined in three Specific Aims. In SPECIFIC AIM 1, the PG-Core C will perform comparative structural analysis of heparan and chondroitin sulfate glycosaminoglycans derived from the bone marrow niche. This aim, which we have termed GAGomics, will provide a global measure of GAG modifications, cellular regulation, and protein-GAG interactions for all three Projects. In SPECIFIC AIM 2, the PG-Core C will perform in-depth proteomics analysis of protein-GAG interactions in the bone marrow niche which we've termed GAGactomics or the identification of proteins that differentially bind cellular or extracellular GAG structures. In SPECIFIC AIM 3, or the aim focused solely on Proteomics, the PG-Core C will perform global and targeted quantitative proteomics analysis of protein expression in the bone marrow niche. Our overall goal is to support the innovative hypotheses of all three Projects with the highest quality LC-MS/MS data to elucidate GAG structures, GAG-protein interactions, and protein expression levels in the bone marrow niche.