UniCarb-DB: a database resource for glycomic discovery

Hayes, Catherine A.; Karlsson, Niclas G.; Struwe, Weston B.; Lisacek, Frédérique; Rudd, Pauline M.; Packer, Nicolle H.; Campbell, Matthew P.

doi:10.1093/bioinformatics/btr137

Cited by 132 publications

(86 citation statements)

References 12 publications

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“…Reactions were quenched with 1 l of glacial acetic acid, and samples were desalted and dried for capillary graphitized carbon LC-MS and LC-MS/MS in negative ion mode using an LTQ XL ion trap mass spectrometer (Thermo Scientific) (42). Oligosaccharides were identified from their MS/MS spectra using UniCarb-DB database (2011 version) (43) and validated manually. The annotated structures on lubricin are available on the UniCarb-DB database (available on the World Wide Web).…”

Section: Methodsmentioning

confidence: 99%

Human Synovial Lubricin Expresses Sialyl Lewis x Determinant and Has L-selectin Ligand Activity

Jin

Ekwall

Bylund

et al. 2012

Journal of Biological Chemistry

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Background:Lubricin is an abundant mucin-like glycoprotein in synovial fluid and a major component responsible for joint lubrication. Results: Lewis x and sulfated O-glycans enable lubricin to bind L-selectin. Lubricin binds to polymorphonuclear granulocytes (PMN) in an L-selectin-dependent and -independent manner. Conclusion: PMN isolated from peripheral blood and synovial fluid keep a coat of lubricin. Significance: Lubricin may play a role in PMN-mediated inflammation.

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Section: Methodsmentioning

confidence: 99%

Human Synovial Lubricin Expresses Sialyl Lewis x Determinant and Has L-selectin Ligand Activity

Jin

Ekwall

Bylund

et al. 2012

Journal of Biological Chemistry

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“…The proposed glycan structures were manually assigned and interpreted from the tandem MS fragmentation spectra and further characterized with the GlycoWorkBench software tool (19). In addition, the web-based LC-MS/MS database, UniCarb KB (17), was also utilized to confirm fragmentation and retention time of N-glycans based on previously reported glycan structures that were available in the online library (34 -37). The assignment of sialic acid linkages on the N-glycan structures were carried out through specific exoglycosidase treatment described below.…”

Section: Cell Membrane Preparation and Triton X-114 Phase Partitioninmentioning

confidence: 99%

“…Furthermore, the development of glyco-bioinformatics databases and tools such as UniCarb KB (17), GlycoMod (18), GlycoWorkBench (19), GlycReSoft (20), and Multiglycan (21) have accelerated the pace of glycan characterization. In ovarian cancer, the majority of studies investigating N-glycans have been performed using serum (22)(23)(24)(25), in which significant cancer-associated changes such as increased levels of branching of the N-glycans attached to glycoproteins (24) and increased sialylation of N-glycopeptides (25) have been found.…”

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confidence: 99%

Specific Glycosylation of Membrane Proteins in Epithelial Ovarian Cancer Cell Lines: Glycan Structures Reflect Gene Expression and DNA Methylation Status

Anugraham

Jacob

Nixdorf

et al. 2014

Molecular & Cellular Proteomics

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Epithelial ovarian cancer is the fifth most common cause of cancer in women worldwide bearing the highest mortality rate among all gynecological cancers. Cell membrane glycans mediate various cellular processes such as cell signaling and become altered during carcinogenesis. The extent to which glycosylation changes are influenced by aberrant regulation of gene expression is nearly unknown for ovarian cancer and remains crucial in understanding the development and progression of this disease. To address this effect, we analyzed the membrane glycosylation of non-cancerous ovarian surface epithelial (HOSE 6.3 and HOSE 17.1) and serous ovarian cancer cell lines (SKOV 3, IGROV1, A2780, and OVCAR 3), the most common histotype among epithelial ovarian cancers. Nglycans were released from membrane glycoproteins by PNGase F and analyzed using nano-liquid chromatography on porous graphitized carbon and negative-ion electrospray ionization mass spectrometry (ESI-MS). Glycan structures were characterized based on their molecular masses and tandem MS fragmentation patterns. We identified characteristic glycan features that were unique to the ovarian cancer membrane proteins, namely the "bisecting N-acetyl-glucosamine" type N-glycans, increased levels of ␣ 2-6 sialylated N-glycans and "N,N-diacetyllactosamine" type N-glycans. These N-glycan changes were verified by examining gene transcript levels of the enzymes specific for their synthesis (MGAT3, ST6GAL1, and B4GALNT3) using qRT-PCR. We further evaluated the potential epigenetic influence on MGAT3 expression by treating the cell lines with 5-azacytidine, a DNA methylation inhibitor. For the first time, we provide evidence that MGAT3 expression may be epigenetically regulated by DNA hypomethylation, leading to the synthesis of the unique "bisecting GlcNAc" type N-glycans on the membrane proteins of ovarian cancer cells. Linking the observation of specific N-glycan substructures and their complex association with epigenetic programming of their associated synthetic enzymes in ovarian cancer could potentially be used for the development of novel anti-glycan drug targets and clinical diagnostic tools. Molecular & Cellular

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“…The development of O-glycan resources, such as Unicarb-DB, will aid in this process (47). Unicarb-DB is an LC-MS database of published glycan data.…”

Section: Development Of An Srm Methods For Core 1 O-glycans-mentioning

confidence: 99%

Selected Reaction Monitoring to Differentiate and Relatively Quantitate Isomers of Sulfated and Unsulfated Core 1 O-Glycans from Salivary MUC7 Protein in Rheumatoid Arthritis

Flowers

Ali

Lane³

et al. 2013

Molecular & Cellular Proteomics

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Rheumatoid arthritis is a common and debilitating systemic inflammatory condition affecting up to 1% of the world's population. This study aimed to investigate the immunological significance of O-glycans in chronic arthritis at a local and systemic level. O-Glycans released from synovial glycoproteins during acute and chronic arthritic conditions were compared and immune-reactive glycans identified. The sulfated core 1 O-glycan (Gal␤1-3GalNAcol) was immune reactive, showing a different isomeric profile in the two conditions. From acute reactive arthritis, three isomers could be sequenced, but in patients with chronic rheumatoid arthritis, only a single 3-Gal sulfate-linked isomer could be identified. The systemic significance of this glycan epitope was investigated using the salivary mucin MUC7 in patients with rheumatoid arthritis and normal controls. To analyze this low abundance glycan, a selected reaction monitoring (SRM) method was developed to differentiate and relatively quantitate the core 1 O-glycan and the sulfated core 1 O-glycan Gal-and GalNAc-linked isomers. The acquisition of highly sensitive full scan linear ion trap MS/MS spectra in addition to quantitative SRM data allowed the 3-and 6-linked Gal isomers to be differentiated. The method was used to relatively quantitate the core 1 glycans from MUC7 to identify any systemic changes in this carbohydrate epitope. A statistically significant increase in sulfation was identified in salivary MUC7 from rheumatoid arthritis patients. This suggests a potential role for this epitope in chronic inflammation. This study was able to develop an SRM approach to specifically identify and relatively quantitate sulfated core 1 isomers and the unsulfated structure. The expansion of this method may afford an avenue for the high throughput investigation of O-glycans. Molecular & Cellular

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UniCarb-DB: a database resource for glycomic discovery

Abstract: http://www.unicarb-db.org

Cited by 132 publications

References 12 publications

Human Synovial Lubricin Expresses Sialyl Lewis x Determinant and Has L-selectin Ligand Activity

Human Synovial Lubricin Expresses Sialyl Lewis x Determinant and Has L-selectin Ligand Activity

Specific Glycosylation of Membrane Proteins in Epithelial Ovarian Cancer Cell Lines: Glycan Structures Reflect Gene Expression and DNA Methylation Status

Selected Reaction Monitoring to Differentiate and Relatively Quantitate Isomers of Sulfated and Unsulfated Core 1 O-Glycans from Salivary MUC7 Protein in Rheumatoid Arthritis

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