title: Extraction of leukemia specific glycan motifs in humans by computational glycomics.
abstract: There have been almost no standard methods for conducting computational analyses on glycan structures in comparison to DNA and proteins. In this paper, we present a novel method for extracting functional motifs from glycan structures using the KEGG/GLYCAN database. First, we developed a new similarity measure for comparing glycan structures taking into account the characteristic mechanisms of glycan biosynthesis, and we tested its ability to classify glycans of different blood components in the framework of support vector machines (SVMs). The results show that our method can successfully classify glycans from four types of human blood components: leukemic cells, erythrocyte, serum, and plasma. Next, we extracted characteristic functional motifs of glycans considered to be specific to each blood component. We predicted the substructure alpha-D-Neup5Ac-(2-->3)-beta-D-Galp-(1-->4)-D-GlcpNAc as a leukemia specific glycan motif. Based on the fact that the Agrocybe cylindracea galectin (ACG) specifically binds to the same substructure, we conducted an experiment using cell agglutination assay and confirmed that this fungal lectin specifically recognized human leukemic cells.
authors.affiliation: Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.
authors.forename: Yoshiyuki
authors.initials: Y
authors.lastname: Hizukuri
authors.forename: Yoshihiro
authors.initials: Y
authors.lastname: Yamanishi
authors.forename: Osamu
authors.initials: O
authors.lastname: Nakamura
authors.forename: Fumio
authors.initials: F
authors.lastname: Yagi
authors.forename: Susumu
authors.initials: S
authors.lastname: Goto
authors.forename: Minoru
authors.initials: M
authors.lastname: Kanehisa
mesh_terms: D014408:Biomarkers, Tumor; D019295:Computational Biology / Q000379:methods; D006801:Humans; D007938:Leukemia / Q000378:metabolism*; D011134:Polysaccharides / Q000097:blood / Q000737:chemistry* / Q000145:classification / Q000302:isolation & purification
chemical_list: D014408:Biomarkers, Tumor; D011134:Polysaccharides