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In this study, we characterized a series of antibodies generated in C57BL/6 mice (Mus musculus) using the Tic (JCRB1331) human induced pluripotent cell (hiPSC) line as an antigen. This report describes the isolation and characterization of two new antibodies, R-6C (IgM) and R-13E (IgM), and their comparisons with two existing antibodies, R-10G (IgG1) and R-17F (IgG1). Their epitopes were studied by Western blotting after various glycosidase digestions, binding analyses using enzyme-linked immunosorbent assays (ELISAs) and microarrays with various synthetic oligosaccharides. The minimum epitope structures identified were: Siaα2-3Galβ1-3GlcNAc(6S)β1-3Galβ1-4GlcNAc(6S)β1 (R-6C), Fucα1-2Galβ1-3GlcNAcβ1-3Galβ1 (R-13E), Galβ1-4GlcNAc(6S)β1-3Galβ1-4GlcNAc(6S)β1 (R-10G), and Fucα1-2Galβ1-3GlcNAβ1-3Galβ1-4Glc (lacto-N-fucopentaose I) (R-17F) (shown in Fig. 11 using symbol nomenclature). Most glycoprotein epitopes are expressed as O-glycans on podocalyxin, a mucin-type glycoprotein. The common feature of these epitopes is the presence of an N-acetyllactosamine type 1 structure (Galβ1-3GlcNAc) at their nonreducing termini, followed by a type 2 structure (Galβ1-4GlcNAc); this arrangement comprises a type 1-type 2 motif. This motif is also shared by TRA-1-60, a traditional onco-fetal antigen. In contrast, the R-10G epitope has a type 2-type 2 motif. Among these antibodies, R-17F and R-13E exhibit cytotoxic activity toward hiPSCs. R-17F and R-13E exhibit extremely high similarity in the amino acid sequences in their complementarity-determining regions (CDRs), which is consistent with their highly similar glycan recognition. These antibodies are excellent tools for investigating the biological functions of glycoconjugates in hiPSCs/hESCs; they could be useful for the selection, isolation and selective killing of such undifferentiated pluripotent stem cells.

Aim: Tumorigenicity of residual undifferentiated induced pluripotent stem cells (iPSCs) is a major concern. The purpose of this study was to investigate the optimal conditions for removal of iPSCs using R-17F antibody, which recognizes specific glycosphingolipids glycans on undifferentiated iPSCs and exhibits selective cytotoxicity to iPSCs. Materials & methods: After adding of R-17F and secondary antibody to co-cultured iPSCs and chondrocytes, residual iPSCs were quantitatively evaluated by iPS specific glycome analysis. Results: Undifferentiated iPSCs were sufficiently removed using R-17F in combination with an equal amount of a secondary antibody. Furthermore, teratomas were not observed upon transplantation of co-cultured cells pretreated under the same conditions into testes of immunodeficient mice. Conclusion: This removal method incorporating R-17F may be useful for regenerative medicine using iPSCs.

R-10G antigen of human iPS and ES cells has been assigned as a unique mono-sulfated glycan. We highlight its relationship to a known bioactive glycan sequence, the ligand on high endothelial venules for the lymphocyte homing receptor, L-selectin. Details of the sequences of four other glycan antigens on the podocalyxin are re-evaluated and ambiguities resolved. Regulation of biosynthesis and possible involvements of these glycans in podocalyxin-signaling in stem cells are discussed., Graphical Abstract Highlights R-10G is a mono-sulfated glycan antigen of human iPS and ES cells on podocalyxin. R-10G and nonsulfated i are reciprocal antigens on type 2 glycan backbones. TRA-1–60 and -81 and FC10.2 are antigens expressed on unsulfated type 1 backbones. These assignments open the way to probing their roles in podocalyxin-signaling., Glycan antigens recognized by monoclonal antibodies have served as stem cell markers. To understand regulation of their biosynthesis and their roles in stem cell behavior precise assignments are required. We have applied state-of-the-art glycan array technologies to compare the glycans bound by five antibodies that recognize carbohydrates on human stem cells. These are: FC10.2, TRA-1–60, TRA-1–81, anti-i and R-10G. Microarray analyses with a panel of sequence-defined glycans corroborate that FC10.2, TRA-1–60, TRA-1–81 recognize the type 1-(Galβ-3GlcNAc)-terminating backbone sequence, Galβ-3GlcNAcβ-3Galβ-4GlcNAcβ-3Galβ-4GlcNAc, and anti-i, the type 2-(Galβ-4GlcNAc) analog, Galβ-4GlcNAcβ-3Galβ-4GlcNAcβ-3Galβ-4GlcNAc, and we determine substituents they can accommodate. They differ from R-10G, which requires sulfate. By Beam Search approach, starting with an antigen-positive keratan sulfate polysaccharide, followed by targeted iterative microarray analyses of glycan populations released with keratanases and mass spectrometric monitoring, R-10G is assigned as a mono-sulfated type 2 chain with 6-sulfation at the penultimate N-acetylglucosamine, Galβ-4GlcNAc(6S)β-3Galβ-4GlcNAcβ-3Galβ-4GlcNAc. Microarray analyses using newly synthesized glycans corroborate the assignment of this unique determinant raising questions regarding involvement as a ligand in the stem cell niche.

We developed two human-induced pluripotent stem cell (hiPSC)/human embryonic stem cell (hESC)-specific glycan-recognizing mouse antibodies, R-10G and R-17F, using the Tic (JCRB1331) hiPSC line as an antigen. R-10G recognizes a low-sulfate keratan sulfate, and R-17F recognizes lacto-N-fucopentaose-1. To evaluate the general characteristics of stem cell glycans, we investigated the hiPSC line 201B7 (HPS0063), a prototype iPSC line. Using an R-10G affinity column, an R-10G-binding protein was isolated from 201B7 cells. The protein yielded a single but very broad band from 480 to 1236 kDa by blue native gel electrophoresis. After trypsin digestion, the protein was identified as podocalyxin by liquid chromatography/mass spectrometry. According to Western blotting, the protein reacted with R-10G and R-17F. The R-10G-positive band was resistant to digestion with glycan-degrading enzymes, including peptide N-glycanase, but the intensity of the band was decreased significantly by digestion with keratanase, keratanase II, and endo-β-galactosidase, suggesting the R-10G epitope to be a keratan sulfate. These results suggest that keratan sulfate-type epitopes are shared by hiPSCs. However, the keratan sulfate from 201B7 cells contained a polylactosamine disaccharide unit (Galβ1-4GlcNAc) at a significant frequency, whereas that from Tic cells consisted mostly of keratan sulfate disaccharide units (Galβ1-4GlcNAc(6S)). In addition, the abundance of the R-10G epitope was significantly lower in 201B7 cells than in Tic cells.

Cartilage damage may eventually lead to osteoarthritis because it is difficult to repair. Human-induced pluripotent stem cell (iPSC)-derived chondrocytes may potentially be used to treat cartilage damage, but the tumorigenicity of iPSCs is a major concern for their application in regenerative medicine. Many glycoconjugates serve as stem cell markers, and glycosphingolipids (GSLs) including H type 1 antigen (Fuc&alpha, 1-2Gal&beta, 1-3GlcNAc) have been expressed on the surface of iPSCs. The purpose of the present study was to investigate whether GSL-glycome analysis is useful for quality control of residual iPSCs in chondrocytes. We performed GSL-glycome analysis of undifferentiated iPSCs in chondrocytes by combining glycoblotting and aminolysis-sialic acid linkage-specific alkylamidation (SALSA) method, enabling the detection of small quantities of iPSC-specific GSL-glycans from 5 &times, 104 cells. Furthermore, we estimated the residual amount of iPSCs using R-17F antibody, which possesses cytotoxic activity toward iPSCs that is dependent on the Lacto-N-fucopentaose I (LNFP I) of GSL. Moreover, we could detect a small number of LNFP I during mesenchymal stem cells (MSCs) differentiation from iPSCs. This is the first demonstration that GSL-glycome analysis is useful for detecting undifferentiated iPSCs, and can thereby support safe regenerative medicine.

This is the first report of the crystal structure of mukhinite, V-analogue clinozoisite, on the join Ca2Al3Si3O12(OH)–Ca2Al2V3+Si3O12(OH) synthesized at 1.5 GPa and 800 °C. The study was performed to clarify the distribution of V3+ among structurally independent octahedral M1, M2, and M3 sites, and the effect of V3+ on the crystal structure. Mukhinite and V3+-bearing clinozoisite in all run products are associated with zoisite, and also coexist with V-bearing phases such as vanadomalayaite, goldmanite, V-oxides, and unidentified Ca–Al-bearing vanadates. Mukhinite and V3+-bearing clinozoisite crystallized in the Run 20 product show a compositional gap between 0.33 and 0.74 V atoms per formula unit (apfu), and the V content attains 1.14 apfu. The coexistence of low V3+- and high V3+-clinozoisites indicates the presence of a miscibility gap at 1.5 GPa and 800 °C. Two mukhinite crystals with 0.75 and 0.83 V3+ apfu were used for X-ray single-crystal structure analysis. The unit-cell parameters are a = 8.8995(2), b = 5.6299(1), c = 10.1532(2) A, β = 115.327(1)°, and V = 459.81(2) A3 for the former, and a = 8.8999(1), b = 5.6357(1), c = 10.1499(1) A, β = 115.306(1)°, and V = 460.24(2) A3 for the latter. The resulting V3+ occupancies among the octahedral sites are M1(Al0.894(6)V0.106)M2(Al0.976(6)V0.024)M3(V0.621(6)Al0.379) for the former and M1(Al0.868(4)V0.132)M2(Al0.957(4)V0.043)M3(V0.652(2)Al0.348) for the latter. Site preference of V3+ at the octahedral sites is M3 > M1 > M2 as that of Fe3+ and Mn3+. The intracrystalline partition coefficient of V3+ and Al3+ between the M1 and M3 sites, KD = (V3+/Al)M1/(V3+/Al)M3, is 0.07–0.08, which is greater than those of Fe3+ and Al3+ (0.03–0.05) and of Mn3+ and Al3+ (0.04–0.06). Variations of the unit-cell parameters are strongly related to the variations of the M3−Oi and M1−Oi distances.

Recently, we established a mouse monoclonal antibody specific to hiPS/ hES cells, R-10G, which recognizes a type of keratan sulfate. Keratan sulfates (KS) comprise a family of glycosaminoglycans consisting of the repeating unit of [Gal-GlcNAc(6S)]. However, there is a diversity in the degree of sulfation at Gal and GlcNAc residues, and also in the mode of linkage, Galβ1 − 3GlcNAc (type 1) or Galβ1 − 4GlcNAc (type 2). To gain more insight into the binding specificity of R-10G, we carried out an ELISA test on avidin-coated plates using polyethylene glycol (PEG)3-biotinylated derivatives of a series of N-acetyllactosamine tetrasaccharides (keratan sulfates (KSs)). The results suggested that the minimum epitope structure is Galβ1 − 4GlcNAc(6S)β1 − 3Galβ1 − 4GlcNAc(6S)β1 (type 2- type 2 keratan sulfate). Removal of sulfate from GlcNAc(6S) or addition of sulfate to Gal abolished the binding activity almost completely. We also examined the binding specificity of TRA-1-60/81 in the same assay system. The minimum epitope structure was shown to be Galβ1 − 3GlcNAcβ1 − 3Galβ1 − 4GlcNAcβ1 in agreement with the previous study involving glycan arrays (Natunen et al., Glycobiology, 21, 1125–1130 (2011)). Interestingly, however, TRA-1-60/81 was shown to bind to Galβ1 − 3GlcNAc(6S)β1 − 3Galβ1 − 4GlcNAc(6S)β1 (type 1- type 2 keratan sulfate) dose-dependently, being more than one-third the binding activity toward Galβ1 − 3GlcNAcβ1 − 3Galβ1 − 4GlcNAcβ1 than in the case of TRA-1-60. In addition, a substrate specificity study on keratanase II revealed that keratanase II degraded not only “type 2-type 2 keratan sulfate” but also “type 1-type 2 keratan sulfate”, significantly.

Summary The Integrated Life Science Database Project of Japan funded a group of glycoscientists to carry out a project to integrate glycoscience databases using Semantic Web technologies. As a continuation of the previous project period, the Japan Consortium for Glycobiology and Glycotechnology Database (JCGGDB) developed several glycoscience-related databases. The GlycoProtDB database is among those being integrated, providing an important resource to understand protein glycosylation. Another database being integrated is GlycoEpitope, a comprehensive database of carbohydrate epitopes and antibodies. In the current project period, we started the development of GlyTouCan, the international glycan structure repository providing unique accession numbers to all glycan structures. Although such databases are sufficiently important in and of themselves, their integration with other—omics data such as the protein information in UniProt will be crucial to bring glycosciences to the forefront of life sciences. However, to integrate such disparate sets of data among different fields in a way such that future maintenance costs are minimal, standardized ontologies and formats must be established. Our latest project has attempted to define the minimal standards that are necessary to enable this integration. The technical challenges to integrate all these databases and the technologies to overcome these challenges will be described.

Recently, we established two mouse monoclonal antibodies (R-10G and R-17F). The R-17F antibody (IgG1 subtype) exhibited a strong cytotoxic effect on hiPS/ES cells. The R-17F antigen isolated from a total lipid extract of hiPS (Tic) cells was identified as LNFP I (Fucα1-2Galβ1-3GlcNAcβ1-3Galβ1-4Glc). In the present study, R-17F binding proteins were isolated from hiPS (Tic) cell lysates with an affinity column of R-17F. They gave one major R-17F positive band around 250 kDa, and several minor bands between 150 kDa and 25 kDa. The former band was identified as podocalyxin by LC/MS/MS after SDS-PAGE. Hapten inhibition studies on R-17F binding to R-17F column-purified proteins with various synthetic oligosaccharides revealed that the blood group H type 1 triaose structure (Fucα1-2Galβ1-3GlcNAc) was the predominant epitope on all the R-17F binding proteins. These bands disappeared completely on digestion with α1-2 fucosidase, but not with α1-3/4 fucosidase. Upon PNGase F digestion, the R-17F positive band around and above 250 kDa did not show any change, while the minor bands between 150 kDa and 25 kDa disappeared completely, suggesting that the epitope is expressed on N-glycans in the latter and probably on O-glycans in the former. These results, together with those obtained in our previous studies on R-10G (Kawabe et al. Glycobiology, 23, 322-336 (2013)), indicated that both R-10G and R-17F epitopes are carried on the same podocalyxin molecule. The R-17F epitopes on these glycoproteins expressed on hiPS cells could be associated with the molecular mechanism underlying the carbohydrate-mediated cytotoxic activity of R-17F.

A class of glycoproteins such as carcinoembryonic antigen (CEA)/CEA-related cell adhesion molecule 1(CEACAM1), CD26 (DPPIV), and mac-2 binding protein (Mac-2BP) harbor tumor-associated glycans in colorectal cancer. In this study, we identified type II transmembrane mosaic serine protease large-form (MSPL) and its splice variant transmembrane protease serine 13 (TMPRSS13) as ligands of Dendritic cell-specific intercellular adhesion molecule-3-grabbing nonintegrin (DC-SIGN) on the colorectal cancer cells. DC-SIGN is a C-type lectin expressed on dendritic cells, serves as a pattern recognition receptor for numerous pathogens such as human immunodeficiency virus (HIV) and M. tuberculosis. DC-SIGN recognizes these glycoproteins in a Ca2+ dependent manner. Meanwhile, we found that MSPL proteolytically cleaves DC-SIGN in addition to the above glycan-mediated recognition. DC-SIGN was degraded more efficiently by MSPL when treated with ethylenediaminetetraacetic acid (EDTA), suggesting that glycan-dependent interaction of the two molecules partially blocked DC-SIGN degradation. Our findings uncovered a dual recognition system between DC-SIGN and MSPL/TMPRSS13, providing new insight into the mechanism underlying colorectal tumor microenvironment.

We have experimentally confirmed that the solubility of SiO2 in clinopyroxene at ultrahigh-pressure metamorphic conditions is buffered by coesite and kyanite. The present findings were derived from high-pressure experiments on metapelite glass, powdered andesite and eclogite glass under anhydrous conditions. The metapelite glass and powdered andesite were recrystallised in boron nitride capsules at 8 GPa and 1100–1500 °C. The eclogite glass was heated in an AuPd capsule, both ends of which were welded, at 3 GPa and 1000 °C. Clinopyroxene nucleated from metapelite glass, the bulk composition of which is saturated in both SiO2 and Al2SiO5 components plotting within the Jd (Na,K)(Al,Cr)(Si,Ti)2O6−Qtz (Si,Ti)O2−Grt M3(Al,Cr)2(Si,Ti)3O12−Als (Al,Cr)2(Si,Ti)O5 tetrahedron (M = Fe, Mn, Mg, Ni, Zn, Ca), coexists with garnet, coesite and kyanite. The average excess silica content of the clinopyroxene ranges from 23.4 to 35.4 mol%. In contrast, an andesite experiment saturated in SiO2 but undersaturated in Al2SiO5 within the Jd–Qtz–Aug M(Si,Ti)O3–Grt tetrahedron produced clinopyroxene, garnet and coesite but no kyanite. The average excess silica in the clinopyroxene was 9.7–15.5 mol%, which is comparable to previous experimental data. Experiment on the eclogite glass with similar composition to andesite yielded clinopyroxene, garnet and coesite. An average excess silica content in clinopyroxene counts 6.4 mol%, which is much lower than that obtained from the andesite. The SiO2 content of clinopyroxene coexisting with garnet, coesite and kyanite is much higher than that of clinopyroxene coexisting with garnet and coesite without kyanite. Although the temperature dependence is unclear, the SiO2 solubility increases with pressure and Fe/(Fe+Mg). Clinopyroxene forms the solid solution series Jd–Es □0.5M0.5Al(Si,Ti)2O6 and Aug–Es, rather than Jd–Ts MAl2(Si,Ti)O6 and Es–Ts joins. Our experimental data suggest the probable existence of octahedral Si which may accompany the M2 vacancies in clinopyroxene.

Induced pluripotent stem cells (iPSCs) offer an invaluable tool for biological research and regenerative medicine. We report establishment of rat iPSCs (riPSCs) using a plasmid vector encoding four transcription factors, Oct3/4, Sox2, c-Myc and Klf4. Although all riPSC clones were generated and cultured under the same conditions, expressed hallmark pluripotency markers and differentiated successfully in vitro, the expression of a keratan sulfate glycan epitope with unique properties defined by R-10G antibody varied in the riPSC clones. In contrast, tumor rejection antigen (TRA)-1-81 epitope expression was comparable. A clone highly reactive to R-10G antibody formed teratomas in vivo consisting of cells from all three germ layers. However, clones expressing a lower level of the epitope defined by R-10G resulted in tumors with rapid growth consisting of undifferentiated cells. Additionally, riPSCs could be successfully differentiated into a neuronal lineage including glutamate neurons that responded to agonist stimulation. These observations demonstrate a glycophenotypic difference that may potentially serve as a useful probe for riPSC evaluation and to study the role of glycans in pluripotency and carcinogenesis in these cells.

Glycans are known as the third major class of biopolymers, next to DNA and proteins. They cover the surfaces of many cells, serving as the 'face' of cells, whereby other biomolecules and viruses interact. The structure of glycans, however, differs greatly from DNA and proteins in that they are branched, as opposed to linear sequences of amino acids or nucleotides. Therefore, the storage of glycan information in databases, let alone their curation, has been a difficult problem. This has caused many duplicated efforts when integration is attempted between different databases, making an international repository for glycan structures, where unique accession numbers are assigned to every identified glycan structure, necessary. As such, an international team of developers and glycobiologists have collaborated to develop this repository, called GlyTouCan and is available at http://glytoucan.org/, to provide a centralized resource for depositing glycan structures, compositions and topologies, and to retrieve accession numbers for each of these registered entries. This will thus enable researchers to reference glycan structures simply by accession number, as opposed to by chemical structure, which has been a burden to integrate glycomics databases in the past.

Proteoglycans play important roles in regulating the development and functions of the brain. They consist of a core protein and glycosaminoglycans, which are long sugar chains of repeating disaccharide units with sulfation. A recent study demonstrated that the sulfation pattern of chondroitin sulfate on proteoglycans contributes to regulation of the critical period of experience-dependent plasticity in the mouse visual cortex. In the present study, we investigated the role of keratan sulfate (KS), another glycosaminoglycan, in critical period plasticity in the mouse visual cortex. Immunohistochemical analyses demonstrated the presence of KS containing disaccharide units of N-acetylglucosamine (GlcNAc)-6-sulfate and nonsulfated galactose during the critical period, although KS containing disaccharide units of GlcNAc-6-sulfate and galactose-6-sulfate was already known to disappear before that period. The KS chains were distributed diffusely in the extracellular space and densely around the soma of a large population of excitatory and inhibitory neurons. Electron microscopic analysis revealed that the KS was localized within the perisynaptic spaces and dendrites but not in presynaptic sites. KS was mainly located on phosphacan. In mice deficient in GlcNAc-6-O-sulfotransferase 1, which is one of the enzymes necessary for the synthesis of KS chains, the expression of KS was one half that in wild-type mice. In the knockout mice, monocular deprivation during the critical period resulted in a depression of deprived-eye responses but failed to produce potentiation of nondeprived-eye responses. In addition, T-type Ca(2+) channel-dependent long-term potentiation (LTP), which occurs only during the critical period, was not observed. These results suggest that regulation by KS-phosphacan with a specific sulfation pattern is necessary for the generation of LTP and hence the potentiation of nondeprived-eye responses after monocular deprivation.