title: Glycosaminoglycanomics: where we are.
abstract: Glycosaminoglycans regulate numerous physiopathological processes such as development, angiogenesis, innate immunity, cancer and neurodegenerative diseases. Cell surface GAGs are involved in cell-cell and cell-matrix interactions, cell adhesion and signaling, and host-pathogen interactions. GAGs contribute to the assembly of the extracellular matrix and heparan sulfate chains are able to sequester growth factors in the ECM. Their biological activities are regulated by their interactions with proteins. The structural heterogeneity of GAGs, mostly due to chemical modifications occurring during and after their synthesis, makes the development of analytical techniques for their profiling in cells, tissues, and biological fluids, and of computational tools for mining GAG-protein interaction data very challenging. We give here an overview of the experimental approaches used in glycosaminoglycomics, of the major GAG-protein interactomes characterized so far, and of the computational tools and databases available to analyze and store GAG structures and interactions.
authors.affiliation: Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, UMR 5246 CNRS - Université Lyon 1, INSA Lyon, CPE Lyon, 69622, Villeurbanne Cedex, France. sylvie.ricard-blum@univ-lyon1.fr.
authors.forename: Sylvie
authors.initials: S
authors.lastname: Ricard-Blum
authors.affiliation: SIB Swiss Institute of Bioinformatics, 1 Rue Michel-Servet, 1211, Geneva, Switzerland.|Computer Science Department, University of Geneva, Geneva, Switzerland.
authors.forename: Frédérique
authors.initials: F
authors.lastname: Lisacek
mesh_terms: D000818:Animals; D002450:Cell Communication; D002845:Chromatography / Q000295:instrumentation / Q000379:methods; D019295:Computational Biology / Q000379:methods; D062126:Databases, Chemical; D005057:Eukaryotic Cells / Q000737:chemistry* / Q000378:metabolism; D005109:Extracellular Matrix / Q000737:chemistry* / Q000378:metabolism; D054794:Glycomics / Q000295:instrumentation / Q000379:methods / Q000639:trends*; D006497:Heparan Sulfate / Q000737:chemistry* / Q000378:metabolism; D054884:Host-Pathogen Interactions; D006801:Humans; D036341:Intercellular Signaling Peptides and Proteins / Q000737:chemistry / Q000378:metabolism; D009682:Magnetic Resonance Spectroscopy / Q000295:instrumentation; D013058:Mass Spectrometry / Q000295:instrumentation / Q000379:methods; D011485:Protein Binding
chemical_list: D006497:Heparan Sulfate; D036341:Intercellular Signaling Peptides and Proteins
keywords: Bioinformatics; Databases; Glycosaminoglycan-protein interaction; Glycosaminoglycomics; Heparanome; Interaction networks