TY - JOUR
T1 - Extraction of leukemia specific glycan motifs in humans by computational glycomics
AU - Hizukuri, Yoshiyuki
AU - Yamanishi, Yoshihiro
AU - Nakamura, Osamu
AU - Yagi, Fumio
AU - Goto, Susumu
AU - Kanehisa, Minoru
PY - 2005/10/17
Y1 - 2005/10/17
N2 - 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 α-d-Neup5Ac-(2→3)-β-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.
AB - 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 α-d-Neup5Ac-(2→3)-β-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.
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U2 - 10.1016/j.carres.2005.07.012
DO - 10.1016/j.carres.2005.07.012
M3 - Article
C2 - 16095580
AN - SCOPUS:24644454168
VL - 340
SP - 2270
EP - 2278
JO - Carbohydrate Research
JF - Carbohydrate Research
SN - 0008-6215
IS - 14
ER -