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Sethi MK, Hancock WS, Fanayan S. Identifying N-Glycan Biomarkers in Colorectal Cancer by Mass Spectrometry. Acc Chem Res 2016; 49:2099-2106. [PMID: 27653471 DOI: 10.1021/acs.accounts.6b00193] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Colorectal cancer (CRC) is one of the most prevalent cancers worldwide. Delineating biological markers (biomarkers) for early detection, when treatment is most effective, is key to prevention and long-term survival of patients. Development of reliable biomarkers requires an increased understanding of the CRC biology and the underlying molecular and cellular mechanisms of the disease. With recent advances in new technologies and approaches, tremendous efforts have been put in proteomics and genomics fields to deliver detailed analysis of the two major biomolecules, genes and proteins, to gain a more complete understanding of cellular systems at both genomic and proteomic levels, allowing a mechanistic understanding of the human diseases, including cancer, and opening avenues for identification of novel gene and protein based prognostic and therapeutic markers. Although the importance of glycosylation in modulating protein function has long been appreciated, glycan analysis has been complicated by the diversity of the glycan structures and the large number of potential glycosylation combinations. Driven by recent technological advances, LC-MS/MS based glycomics is gaining momentum in cancer research and holds considerable potential to deliver new glycan-based markers. In our laboratory, we investigated alterations in N-glycosylation associated with CRC malignancy in a panel of CRC cell lines and CRC patient tissues. In an initial study, LC-MS/MS-based N-glycomics were utilized to map the N-glycome landscape associated with a panel of CRC cell lines (LIM1215, LIM1899, and LIM2405). These studies were subsequently extended to paired tumor and nontumorigenic CRC tissues to validate the findings in the cell line. Our studies in both CRC cell lines and tissues identified a strong representation of high mannose and α2,6-linked sialylated complex N-glycans, which corroborate findings from previous studies in CRC and other cancers. In addition, certain unique glycan determinants such as bisecting β1,4-GlcNAcylation and α2,3-sialylation, identified in the metastatic (LIM1215) and aggressive (LIM2405) CRC cell lines, respectively, were shown to be associated with epidermal growth factor receptor (EGFR) expression status. In this Account, we will describe the mass spectrometry based N-glycomics approach utilized in our laboratory to accurately profile the cell- and tissue-specific N-glycomes associated with CRC. We will highlight altered N-glycosylation observed by our studies, consistent with findings from other cancer studies, and discuss how the observed alterations can provide insights into CRC pathogenesis, opening new avenues to identify novel disease-associated glycan markers.
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Affiliation(s)
- Manveen K. Sethi
- Department
of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - William S. Hancock
- Barnett
Institute and Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
- Department
of Biomedical Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Susan Fanayan
- Department
of Biomedical Sciences, Macquarie University, North Ryde, NSW 2109, Australia
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Walsh I, Zhao S, Campbell M, Taron CH, Rudd PM. Quantitative profiling of glycans and glycopeptides: an informatics' perspective. Curr Opin Struct Biol 2016; 40:70-80. [PMID: 27522273 DOI: 10.1016/j.sbi.2016.07.022] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 07/25/2016] [Accepted: 07/30/2016] [Indexed: 12/16/2022]
Abstract
Experimental techniques to identify and quantify glycan structures in a given sample are continuously improving. However, as they advance data analysis and annotation seems to become more complex. To address this issue, much progress has been made in developing software for interpretation of quantitative glycan profiles. Here, we focus on these informatics tools for high/ultra performance liquid chromatography (H/UPLC), mass spectrometry (MS), tandem mass spectrometry (MSn) and combinations thereof. Software for biomarker discovery, pathway, genomic and disease analysis and a final note on some future prospects for glycoinformatics are also mentioned.
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Affiliation(s)
- Ian Walsh
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore 138668, Singapore; New England Biolabs, Ipswich, MA, United States
| | - Sophie Zhao
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore 138668, Singapore
| | - Matthew Campbell
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | | | - Pauline M Rudd
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore 138668, Singapore; National Institute for Bioprocessing Research & Training, Dublin, Ireland.
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Bennun SV, Hizal DB, Heffner K, Can O, Zhang H, Betenbaugh MJ. Systems Glycobiology: Integrating Glycogenomics, Glycoproteomics, Glycomics, and Other ‘Omics Data Sets to Characterize Cellular Glycosylation Processes. J Mol Biol 2016; 428:3337-3352. [DOI: 10.1016/j.jmb.2016.07.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Revised: 07/05/2016] [Accepted: 07/07/2016] [Indexed: 12/17/2022]
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54
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Gray C, Thomas B, Upton R, Migas L, Eyers C, Barran P, Flitsch S. Applications of ion mobility mass spectrometry for high throughput, high resolution glycan analysis. Biochim Biophys Acta Gen Subj 2016; 1860:1688-709. [DOI: 10.1016/j.bbagen.2016.02.003] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 02/01/2016] [Accepted: 02/02/2016] [Indexed: 12/21/2022]
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55
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Akune Y, Lin CH, Abrahams JL, Zhang J, Packer NH, Aoki-Kinoshita KF, Campbell MP. Comprehensive analysis of the N-glycan biosynthetic pathway using bioinformatics to generate UniCorn: A theoretical N-glycan structure database. Carbohydr Res 2016; 431:56-63. [PMID: 27318307 DOI: 10.1016/j.carres.2016.05.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 05/23/2016] [Accepted: 05/29/2016] [Indexed: 02/06/2023]
Abstract
Glycan structures attached to proteins are comprised of diverse monosaccharide sequences and linkages that are produced from precursor nucleotide-sugars by a series of glycosyltransferases. Databases of these structures are an essential resource for the interpretation of analytical data and the development of bioinformatics tools. However, with no template to predict what structures are possible the human glycan structure databases are incomplete and rely heavily on the curation of published, experimentally determined, glycan structure data. In this work, a library of 45 human glycosyltransferases was used to generate a theoretical database of N-glycan structures comprised of 15 or less monosaccharide residues. Enzyme specificities were sourced from major online databases including Kyoto Encyclopedia of Genes and Genomes (KEGG) Glycan, Consortium for Functional Glycomics (CFG), Carbohydrate-Active enZymes (CAZy), GlycoGene DataBase (GGDB) and BRENDA. Based on the known activities, more than 1.1 million theoretical structures and 4.7 million synthetic reactions were generated and stored in our database called UniCorn. Furthermore, we analyzed the differences between the predicted glycan structures in UniCorn and those contained in UniCarbKB (www.unicarbkb.org), a database which stores experimentally described glycan structures reported in the literature, and demonstrate that UniCorn can be used to aid in the assignment of ambiguous structures whilst also serving as a discovery database.
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Affiliation(s)
- Yukie Akune
- Department of Chemistry and Biomolecular Sciences, Faculty of Science & Engineering, Macquarie University, Balaclava Road, North Ryde, NSW, 2109, Australia; Department of Bioinformatics, Graduate School of Engineering, Soka University, 1-236, Tangi, Hachioji, 192-8577, Tokyo, Japan
| | - Chi-Hung Lin
- Department of Chemistry and Biomolecular Sciences, Faculty of Science & Engineering, Macquarie University, Balaclava Road, North Ryde, NSW, 2109, Australia
| | - Jodie L Abrahams
- Department of Chemistry and Biomolecular Sciences, Faculty of Science & Engineering, Macquarie University, Balaclava Road, North Ryde, NSW, 2109, Australia
| | - Jingyu Zhang
- Department of Chemistry and Biomolecular Sciences, Faculty of Science & Engineering, Macquarie University, Balaclava Road, North Ryde, NSW, 2109, Australia
| | - Nicolle H Packer
- Department of Chemistry and Biomolecular Sciences, Faculty of Science & Engineering, Macquarie University, Balaclava Road, North Ryde, NSW, 2109, Australia
| | - Kiyoko F Aoki-Kinoshita
- Department of Bioinformatics, Graduate School of Engineering, Soka University, 1-236, Tangi, Hachioji, 192-8577, Tokyo, Japan
| | - Matthew P Campbell
- Department of Chemistry and Biomolecular Sciences, Faculty of Science & Engineering, Macquarie University, Balaclava Road, North Ryde, NSW, 2109, Australia.
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56
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Zhang P, Woen S, Wang T, Liau B, Zhao S, Chen C, Yang Y, Song Z, Wormald MR, Yu C, Rudd PM. Challenges of glycosylation analysis and control: an integrated approach to producing optimal and consistent therapeutic drugs. Drug Discov Today 2016; 21:740-65. [DOI: 10.1016/j.drudis.2016.01.006] [Citation(s) in RCA: 136] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 12/22/2015] [Accepted: 01/14/2016] [Indexed: 12/18/2022]
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57
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Lu H, Zhang Y, Yang P. Advancements in mass spectrometry-based glycoproteomics and glycomics. Natl Sci Rev 2016. [DOI: 10.1093/nsr/nww019] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Abstract
Protein N-glycosylation plays a crucial role in a considerable number of important biological processes. Research studies on glycoproteomes and glycomes have already characterized many glycoproteins and glycans associated with cell development, life cycle, and disease progression. Mass spectrometry (MS) is the most powerful tool for identifying biomolecules including glycoproteins and glycans, however, utilizing MS-based approaches to identify glycoproteomes and glycomes is challenging due to the technical difficulties associated with glycosylation analysis. In this review, we summarize the most recent developments in MS-based glycoproteomics and glycomics, including a discussion on the development of analytical methodologies and strategies used to explore the glycoproteome and glycome, as well as noteworthy biological discoveries made in glycoproteome and glycome research. This review places special emphasis on China, where scientists have made sizeable contributions to the literature, as advancements in glycoproteomics and glycomincs are occurring quite rapidly.
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Affiliation(s)
- Haojie Lu
- Department of Systems Biology for Medicine, School of Basic Medicine and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
- Key Lab of Glycoconjugate of Ministry of Health and Birth Control, Fudan University, Shanghai 200032, China
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Ying Zhang
- Department of Systems Biology for Medicine, School of Basic Medicine and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
- Key Lab of Glycoconjugate of Ministry of Health and Birth Control, Fudan University, Shanghai 200032, China
| | - Pengyuan Yang
- Department of Systems Biology for Medicine, School of Basic Medicine and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
- Key Lab of Glycoconjugate of Ministry of Health and Birth Control, Fudan University, Shanghai 200032, China
- Department of Chemistry, Fudan University, Shanghai 200433, China
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58
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Campbell MP, Packer NH. UniCarbKB: New database features for integrating glycan structure abundance, compositional glycoproteomics data, and disease associations. Biochim Biophys Acta Gen Subj 2016; 1860:1669-75. [PMID: 26940363 DOI: 10.1016/j.bbagen.2016.02.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 02/23/2016] [Accepted: 02/24/2016] [Indexed: 10/22/2022]
Abstract
BACKGROUND UniCarbKB aims to provide a resource for the representation of mammalian glycobiology knowledge by providing a curated database of structural and experimental data, supported by a web application that allows users to easily find and view richly annotated information. The database comprises two levels of annotation (i) global-specific data of oligosaccharides released and characterised from single purified glycoproteins and (ii) information pertaining to site-specific glycan heterogeneity. Additional, contextual information is provided including structural, bibliographic, and taxonomic information for each entry. METHODS Since the launch of UniCarbKB in 2012, we have continued to improve the organisation of our data model. Recently, we have extended our pipeline to collate structural and abundance changes of oligosaccharides in different human disease states and experimental models to extend our coverage of the human glycome. RESULTS In this manuscript, we demonstrate the capability of UniCarbKB to store and query relative glycan abundance data using a set of published colorectal and prostate cancer cell lines as examples. Furthermore, we outline our strategy for managing large-scale glycoproteomics data, site-specific and glycan compositional data, and how this information is adding value to UniCarbKB. Finally, we summarise our efforts to improve the efficient representation of disease terms and associated changes in glycan heterogeneity by integrating the Disease Ontology. CONCLUSIONS Updates and improvements to UniCarbKB have introduced unique features for storing and displaying glycosylation features of mammalian glycoproteins. The integration of site-specific glycosylation data obtained from large-scale glycoproteomics and introduction of cell line studies will improve the analysis of glycoproteins and entire glycomes. GENERAL SIGNIFICANCE Continuing advancements in analytical technologies and new data types are advancing disease-related glycomics. It is increasingly necessary to ensure all the data are comprehensively annotated. UniCarbKB was established with the mission of providing a resource for human glycobiology by capturing a wide range of data with corresponding annotations. This article is part of a Special Issue entitled "Glycans in personalised medicine" Guest Editor: Professor Gordan Lauc.
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Affiliation(s)
- Matthew P Campbell
- Department of Chemistry and Biomolecular Sciences, Biomolecular Frontiers Research Centre, Macquarie University, Sydney 2109, Australia.
| | - Nicolle H Packer
- Department of Chemistry and Biomolecular Sciences, Biomolecular Frontiers Research Centre, Macquarie University, Sydney 2109, Australia
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59
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Mariethoz J, Khatib K, Alocci D, Campbell MP, Karlsson NG, Packer NH, Mullen EH, Lisacek F. SugarBindDB, a resource of glycan-mediated host-pathogen interactions. Nucleic Acids Res 2016; 44:D1243-50. [PMID: 26578555 PMCID: PMC4702881 DOI: 10.1093/nar/gkv1247] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 10/22/2015] [Accepted: 10/31/2015] [Indexed: 12/16/2022] Open
Abstract
The SugarBind Database (SugarBindDB) covers knowledge of glycan binding of human pathogen lectins and adhesins. It is a curated database; each glycan-protein binding pair is associated with at least one published reference. The core data element of SugarBindDB is a set of three inseparable components: the pathogenic agent, a lectin/adhesin and a glycan ligand. Each entity (agent, lectin or ligand) is described by a range of properties that are summarized in an entity-dedicated page. Several search, navigation and visualisation tools are implemented to investigate the functional role of glycans in pathogen binding. The database is cross-linked to protein and glycan-relaled resources such as UniProtKB and UniCarbKB. It is tightly bound to the latter via a substructure search tool that maps each ligand to full structures where it occurs. Thus, a glycan-lectin binding pair of SugarBindDB can lead to the identification of a glycan-mediated protein-protein interaction, that is, a lectin-glycoprotein interaction, via substructure search and the knowledge of site-specific glycosylation stored in UniCarbKB. SugarBindDB is accessible at: http://sugarbind.expasy.org.
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Affiliation(s)
- Julien Mariethoz
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | | | - Davide Alocci
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland Department of Computer Science, University of Geneva, Geneva, Switzerland
| | - Matthew P Campbell
- Biomolecular Frontiers Research Centre, Macquarie University, North Ryde, NSW, Australia
| | - Niclas G Karlsson
- University of Gothenburg, Sahlgrenska Academy, Institute of Biomedicine, Department of Medical Biochemistry and Cell Biology, Gothenburg, Sweden
| | - Nicolle H Packer
- Biomolecular Frontiers Research Centre, Macquarie University, North Ryde, NSW, Australia
| | | | - Frederique Lisacek
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland Department of Computer Science, University of Geneva, Geneva, Switzerland
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60
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Svala E, Jin C, Rüetschi U, Ekman S, Lindahl A, Karlsson NG, Skiöldebrand E. Characterisation of lubricin in synovial fluid from horses with osteoarthritis. Equine Vet J 2015; 49:116-123. [PMID: 26507102 DOI: 10.1111/evj.12521] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 10/14/2015] [Indexed: 12/19/2022]
Abstract
REASON FOR PERFORMING STUDY The glycoprotein lubricin contributes to the boundary lubrication of the articular cartilage surface. The early events of osteoarthritis involve the superficial layer where lubricin is synthesised. OBJECTIVES To characterise the glycosylation profile of lubricin in synovial fluid from horses with osteoarthritis and study secretion and degradation of lubricin in an in vitro inflammation cartilage model. STUDY DESIGN In vitro study. METHODS Synovial fluid samples collected from horses with joints with normal articular cartilage and structural osteoarthritic lesions; with and without osteochondral fragments, were analysed for the lubricin glycosylation profiles. Articular cartilage explants were stimulated with or without interleukin-1β for 25 days. Media samples collected at 3-day intervals were analysed by quantitative proteomics, western blot and enzyme-linked immunosorbent assay. RESULTS O-glycosylation profiles in synovial fluid revealed both Core 1 and 2 O-glycans, with Core 1 O-glycans predominating. Synovial fluid from normal joints (49.5 ± 1.9%) contained significantly lower amounts of monosialylated Core 1 O-glycans compared with joints with osteoarthritis (53.8 ± 7.8%, P = 0.03) or joints with osteochondral fragments (57.3 ± 8.8%, P = 0.001). Additionally, synovial fluid from normal joints (26.7 ± 6.7%) showed higher amounts of disialylated Core 1 O-glycan than from joints with osteochondral fragments (21.2 ± 4.9%, P = 0.03). A C-terminal proteolytic cleavage site in lubricin was found in synovial fluid from normal and osteochondral fragment joints and in media from interleukin-1β stimulated and unstimulated articular cartilage explants. CONCLUSIONS This is the first demonstration of a change in the glycosylation profile of lubricin in synovial fluid from diseased equine joints compared with that from normal joints. We demonstrate an identical proteolytic cleavage site of lubricin both in vitro and in vivo. The reduced sialation of lubricin in synovial fluid from diseased joints may affect the boundary lubricating ability of the superficial layer of articular cartilage and could be one of the early events in the progression of osteoarthritis.
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Affiliation(s)
- E Svala
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska University Hospital, Gothenburg University, Sweden.,Section of Pathology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - C Jin
- Department of Medical Biochemistry, Institute of Biomedicine, University of Gothenburg, Sweden
| | - U Rüetschi
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska University Hospital, Gothenburg University, Sweden
| | - S Ekman
- Section of Pathology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - A Lindahl
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska University Hospital, Gothenburg University, Sweden
| | - N G Karlsson
- Department of Medical Biochemistry, Institute of Biomedicine, University of Gothenburg, Sweden
| | - E Skiöldebrand
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska University Hospital, Gothenburg University, Sweden.,Section of Pathology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
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61
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Sethi MK, Fanayan S. Mass Spectrometry-Based N-Glycomics of Colorectal Cancer. Int J Mol Sci 2015; 16:29278-304. [PMID: 26690136 PMCID: PMC4691109 DOI: 10.3390/ijms161226165] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 11/23/2015] [Accepted: 12/01/2015] [Indexed: 12/19/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most prevalent cancers worldwide. An increased molecular understanding of the CRC pathology is warranted to gain insights into the underlying molecular and cellular mechanisms of the disease. Altered protein glycosylation patterns are associated with most diseases including malignant transformation. Recent advances in mass spectrometry and bioinformatics have accelerated glycomics research and present a new paradigm for cancer biomarker discovery. Mass spectrometry (MS)-based glycoproteomics and glycomics, therefore, hold considerable promise to improve the discovery of novel biomarkers with utility in disease diagnosis and therapy. This review focuses on the emerging field of glycomics to present a comprehensive review of advances in technologies and their application in studies aimed at discovering novel glycan-based biomarkers. We will also discuss some of the challenges associated with using glycans as biomarkers.
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Affiliation(s)
- Manveen K Sethi
- Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia.
| | - Susan Fanayan
- Department of Biomedical Sciences, Macquarie University, North Ryde, NSW 2109, Australia.
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62
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Chaudhury NMA, Proctor GB, Karlsson NG, Carpenter GH, Flowers SA. Reduced Mucin-7 (Muc7) Sialylation and Altered Saliva Rheology in Sjögren's Syndrome Associated Oral Dryness. Mol Cell Proteomics 2015; 15:1048-59. [PMID: 26631508 DOI: 10.1074/mcp.m115.052993] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Indexed: 12/20/2022] Open
Abstract
Sjögren's syndrome is a chronic autoimmune disorder characterized by lymphocytic infiltration and hypofunction of salivary and lacrimal glands. This loss of salivary function leads to oral dryness, impaired swallowing and speech, and increased infection and is associated with other autoimmune diseases and an increased risk of certain cancers. Despite the implications of this prevalent disease, diagnosis currently takes years, partly due to the diversity in patient presentation. Saliva is a complicated biological fluid with major constituents, including heavily glycosylated mucins MUC5B and MUC7, important for its viscoelastic and hydrating and lubricating properties. This study investigated Sjögren's patient's perception of dryness (bother index questionnaires) along with the rheological, protein composition, and glycan analysis of whole mouth saliva and the saliva on the mucosal surface (residual mucosal saliva) to understand the properties that most affect patient wellbeing. Sjögren's patients exhibited a statistically significant reduction in residual mucosal saliva, salivary flow rate, and extensional rheology, spinnbarkeit (stringiness). Although the concentration of mucins MUC5B and MUC7 were similar between patients and controls, a comparison of protein Western blotting and glycan staining identified a reduction in mucin glycosylation in Sjögren's, particularly on MUC7. LC-MS/MS analysis of O-glycans released from MUC7 by β-elimination revealed that although patients had an increase in core 1 sulfation, the even larger reduction in sialylation resulted in a global decline of charged glycans. This was primarily due to the loss of the extended core 2 disialylated structure, with and without fucosylation. A decrease in the extended, fucosylated core 2 disialylated structure on MUC7, residual mucosal wetness, and whole mouth saliva flow rate appeared to have a negative and cumulative effect on the perception of oral dryness. The observed changes in MUC7 glycosylation could be a potential diagnostic tool for saliva quality and taken into consideration for future therapies for this multifactorial syndrome.
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Affiliation(s)
- Nayab M A Chaudhury
- From the ‡Salivary Unit, Mucosal and Salivary Biology, Dental Institute, King's College London, Guy's Hospital, Floor 17, Tower Wing, London SE1 9RT, UK
| | - Gordon B Proctor
- From the ‡Salivary Unit, Mucosal and Salivary Biology, Dental Institute, King's College London, Guy's Hospital, Floor 17, Tower Wing, London SE1 9RT, UK
| | - Niclas G Karlsson
- §Department of Medical Biochemistry, Institute of Biomedicine, University of Gothenburg, Medicinaregatan 9A, 405 30, Gothenburg, Sweden
| | - Guy H Carpenter
- From the ‡Salivary Unit, Mucosal and Salivary Biology, Dental Institute, King's College London, Guy's Hospital, Floor 17, Tower Wing, London SE1 9RT, UK
| | - Sarah A Flowers
- §Department of Medical Biochemistry, Institute of Biomedicine, University of Gothenburg, Medicinaregatan 9A, 405 30, Gothenburg, Sweden
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63
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A review of methods for interpretation of glycopeptide tandem mass spectral data. Glycoconj J 2015; 33:285-96. [PMID: 26612686 DOI: 10.1007/s10719-015-9633-3] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 10/13/2015] [Accepted: 10/21/2015] [Indexed: 12/25/2022]
Abstract
Despite the publication of several software tools for analysis of glycopeptide tandem mass spectra, there remains a lack of consensus regarding the most effective and appropriate methods. In part, this reflects problems with applying standard methods for proteomics database searching and false discovery rate calculation. While the analysis of small post-translational modifications (PTMs) may be regarded as an extension of proteomics database searching, glycosylation requires specialized approaches. This is because glycans are large and heterogeneous by nature, causing glycopeptides to exist as multiple glycosylated variants. Thus, the mass of the peptide cannot be calculated directly from that of the intact glycopeptide. In addition, the chemical nature of the glycan strongly influences product ion patterns observed for glycopeptides. As a result, glycopeptidomics requires specialized bioinformatics methods. We summarize the recent progress towards a consensus for effective glycopeptide tandem mass spectrometric analysis.
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64
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Cabrera G, Salazar V, Montesino R, Támbara Y, Struwe WB, Leon E, Harvey DJ, Lesur A, Rincón M, Domon B, Méndez M, Portela M, González-Hernández A, Triguero A, Durán R, Lundberg U, Vonasek E, González LJ. Structural characterization and biological implications of sulfated N-glycans in a serine protease from the neotropical moth Hylesia metabus (Cramer [1775]) (Lepidoptera: Saturniidae). Glycobiology 2015; 26:230-50. [PMID: 26537504 DOI: 10.1093/glycob/cwv096] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 10/27/2015] [Indexed: 11/13/2022] Open
Abstract
Contact with the urticating setae from the abdomen of adult females of the neo-tropical moth Hylesia metabus gives rise to an urticating dermatitis, characterized by intense pruritus, generalized malaise and occasionally ocular lesions (lepidopterism). The setae contain a pro-inflammatory glycosylated protease homologous to other S1A serine proteases of insects. Deglycosylation with PNGase F in the presence of a buffer prepared with 40% H2 (18)O allowed the assignment of an N-glycosylation site. Five main paucimannosidic N-glycans were identified, three of which were exclusively α(1-6)-fucosylated at the proximal GlcNAc. A considerable portion of these N-glycans are anionic species sulfated on either the 4- or the 6-position of the α(1-6)-mannose residue of the core. The application of chemically and enzymatically modified variants of the toxin in an animal model in guinea pigs showed that the pro-inflammatory and immunological reactions, e.g. disseminated fibrin deposition and activation of neutrophils, are due to the presence of sulfate-linked groups and not on disulfide bonds, as demonstrated by the reduction and S-alkylation of the toxin. On the other hand, the hemorrhagic vascular lesions observed are attributed to the proteolytic activity of the toxin. Thus, N-glycan sulfation may constitute a defense mechanism against predators.
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Affiliation(s)
- Gleysin Cabrera
- Department of Carbohydrates, Center for Genetic Engineering and Biotechnology, PO Box 6162, Havana, Cuba
| | | | - Raquel Montesino
- School of Biological Sciences, Universidad de Concepción, Víctor Lamas 1290, PO Box 160C, Concepción, Chile
| | - Yanet Támbara
- Department of Proteomics, Center for Genetic Engineering and Biotechnology, PO Box 6162, Havana, Cuba
| | - Weston B Struwe
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Evelyn Leon
- Proteomics Unit, Center of Structural Biology
| | - David J Harvey
- Glycobiology Institute, Department of Biochemistry, Oxford University, South Parks Road, Oxford OX1 3QU, UK
| | - Antoine Lesur
- Luxembourg Clinical Proteomics Center, 1A-B, rue Thomas Edison, L-1445 Strassen, Luxembourg
| | | | - Bruno Domon
- Luxembourg Clinical Proteomics Center, 1A-B, rue Thomas Edison, L-1445 Strassen, Luxembourg
| | | | - Madelón Portela
- Unidad de Bioquímica y Proteómica Analíticas, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo, Uruguay
| | - Annia González-Hernández
- Department of Carbohydrates, Center for Genetic Engineering and Biotechnology, PO Box 6162, Havana, Cuba
| | - Ada Triguero
- Department of Carbohydrates, Center for Genetic Engineering and Biotechnology, PO Box 6162, Havana, Cuba
| | - Rosario Durán
- Unidad de Bioquímica y Proteómica Analíticas, Institut Pasteur de Montevideo and IIBCE, Mataojo 2020, Montevideo, Uruguay
| | - Ulf Lundberg
- Unit for Invertebrate Toxins, Venezuelan Institute for Scientific Research (IVIC), PO Box 20632, Caracas 1020A, Venezuela
| | - Eva Vonasek
- Proteomics Unit, Center of Structural Biology
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Jin C, Padra JT, Sundell K, Sundh H, Karlsson NG, Lindén SK. Atlantic Salmon Carries a Range of Novel O-Glycan Structures Differentially Localized on Skin and Intestinal Mucins. J Proteome Res 2015; 14:3239-51. [PMID: 26066491 DOI: 10.1021/acs.jproteome.5b00232] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Aquaculture is a growing industry, increasing the need for understanding host-pathogen interactions in fish. The skin and mucosal surfaces, covered by a mucus layer composed of mucins, is the first point of contact between fish and pathogens. Highly O-glycosylated mucins have been shown to be an important part of the defense against pathogens, and pathogens bind to host surfaces using lectin-like adhesins. However, knowledge of piscine O-glycosylation is very limited. We characterized mucin O-glycosylation of five freshwater acclimated Atlantic salmon, using mass spectrometry. Of the 109 O-glycans found, most were sialylated and differed in distribution among skin, pyloric ceca, and proximal and distal intestine. Skin O-glycans were shorter (2-6 residues) and less diverse (33 structures) than intestinal O-glycans (2-13 residues, 93 structures). Skin mucins carried O-glycan cores 1, 2, 3, and 5 and three types of sialic acids (Neu5Ac, Neu5Gc, and Kdn) and had sialyl-Tn as the predominant structure. Intestinal mucins carried only cores 1, 2, and 5, Neu5Ac was the only sialic acid present, and sialylated core 5 was the most dominant structure. This structural characterization can be used for identifying structures of putative importance in host-pathogen interactions for further testing in biological assays and disease intervention therapies.
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Affiliation(s)
- Chunsheng Jin
- †Department of Medical Chemistry and Cell Biology, ‡Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg SE-405 30, Sweden
| | - János Tamás Padra
- †Department of Medical Chemistry and Cell Biology, ‡Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg SE-405 30, Sweden
| | - Kristina Sundell
- †Department of Medical Chemistry and Cell Biology, ‡Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg SE-405 30, Sweden
| | - Henrik Sundh
- †Department of Medical Chemistry and Cell Biology, ‡Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg SE-405 30, Sweden
| | - Niclas G Karlsson
- †Department of Medical Chemistry and Cell Biology, ‡Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg SE-405 30, Sweden
| | - Sara K Lindén
- †Department of Medical Chemistry and Cell Biology, ‡Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg SE-405 30, Sweden
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66
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Sethi MK, Kim H, Park CK, Baker MS, Paik YK, Packer NH, Hancock WS, Fanayan S, Thaysen-Andersen M. In-depth N-glycome profiling of paired colorectal cancer and non-tumorigenic tissues reveals cancer-, stage- and EGFR-specific protein N-glycosylation. Glycobiology 2015; 25:1064-78. [PMID: 26085185 DOI: 10.1093/glycob/cwv042] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 06/11/2015] [Indexed: 01/01/2023] Open
Abstract
Glycomics may assist in uncovering the structure-function relationships of protein glycosylation and identify glycoprotein markers in colorectal cancer (CRC) research. Herein, we performed label-free quantitative glycomics on a carbon-liquid chromatography-tandem mass spectrometry-based analytical platform to accurately profile the N-glycosylation changes associated with CRC malignancy. N-Glycome profiling was performed on isolated membrane proteomes of paired tumorigenic and adjacent non-tumorigenic colon tissues from a cohort of five males (62.6 ± 13.1 y.o.) suffering from colorectal adenocarcinoma. The CRC tissues were typed according to their epidermal growth factor receptor (EGFR) status by western blotting and immunohistochemistry. Detailed N-glycan characterization and relative quantitation identified an extensive structural heterogeneity with a total of 91 N-glycans. CRC-specific N-glycosylation phenotypes were observed including an overrepresentation of high mannose, hybrid and paucimannosidic type N-glycans and an under-representation of complex N-glycans (P < 0.05). Sialylation, in particular α2,6-sialylation, was significantly higher in CRC tumors relative to non-tumorigenic tissues, whereas α2,3-sialylation was down-regulated (P < 0.05). CRC stage-specific N-glycosylation was detected by high α2,3-sialylation and low bisecting β1,4-GlcNAcylation and Lewis-type fucosylation in mid-late relative to early stage CRC. Interestingly, a novel link between the EGFR status and the N-glycosylation was identified using hierarchical clustering of the N-glycome profiles. EGFR-specific N-glycan signatures included high bisecting β1,4-GlcNAcylation and low α2,3-sialylation (both P < 0.05) relative to EGFR-negative CRC tissues. This is the first study to correlate CRC stage and EGFR status with specific N-glycan features, thus advancing our understanding of the mechanisms causing the biomolecular deregulation associated with CRC.
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Affiliation(s)
| | - Hoguen Kim
- Department of Pathology, Yonsei University College of Medicine, Seoul 120-752, Korea
| | - Cheol Keun Park
- Department of Pathology, Yonsei University College of Medicine, Seoul 120-752, Korea
| | - Mark S Baker
- Department of Biomedical Sciences, Macquarie University, North Ryde NSW 2109, Australia
| | - Young-Ki Paik
- Yonsei Proteome Research Center, Yonsei University, Seoul 120-749, Korea
| | | | - William S Hancock
- Department of Biomedical Sciences, Macquarie University, North Ryde NSW 2109, Australia Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Susan Fanayan
- Department of Biomedical Sciences, Macquarie University, North Ryde NSW 2109, Australia
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67
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Vitiazeva V, Kattla JJ, Flowers SA, Lindén SK, Premaratne P, Weijdegård B, Sundfeldt K, Karlsson NG. The O-Linked Glycome and Blood Group Antigens ABO on Mucin-Type Glycoproteins in Mucinous and Serous Epithelial Ovarian Tumors. PLoS One 2015; 10:e0130197. [PMID: 26075384 PMCID: PMC4468167 DOI: 10.1371/journal.pone.0130197] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 05/16/2015] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Mucins are heavily O-glycosylated proteins where the glycosylation has been shown to play an important role in cancer. Normal epithelial ovarian cells do not express secreted mucins, but their abnormal expression has previously been described in epithelial ovarian cancer and may relate to tumor formation and progression. The cyst fluids were shown to be a rich source for acidic glycoproteins. The study of these proteins can potentially lead to the identification of more effective biomarkers for ovarian cancer. METHODS In this study, we analyzed the expression of the MUC5AC and the O-glycosylation of acidic glycoproteins secreted into ovarian cyst fluids. The samples were obtained from patients with serous and mucinous ovarian tumors of different stages (benign, borderline, malignant) and grades. The O-linked oligosaccharides were released and analyzed by negative-ion graphitized carbon Liquid Chromatography (LC) coupled to Electrospray Ionization tandem Mass Spectrometry (ESI-MSn). The LC-ESI-MSn of the oligosaccharides from ovarian cyst fluids displayed differences in expression of fucose containing structures such as blood group ABO antigens and Lewis-type epitopes. RESULTS The obtained data showed that serous and mucinous benign adenomas, mucinous low malignant potential carcinomas (LMPs, borderline) and mucinous low-grade carcinomas have a high level of blood groups and Lewis type epitopes. In contrast, this type of fucosylated structures were low abundant in the high-grade mucinous carcinomas or in serous carcinomas. In addition, the ovarian tumors that showed a high level of expression of blood group antigens also revealed a strong reactivity towards the MUC5AC antibody. To visualize the differences between serous and mucinous ovarian tumors based on the O-glycosylation, a hierarchical cluster analysis was performed using mass spectrometry average compositions (MSAC). CONCLUSION Mucinous benign and LMPs along with mucinous low-grade carcinomas appear to be different from serous and high-grade mucinous carcinomas based on their O-glycan profiles.
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Affiliation(s)
- Varvara Vitiazeva
- Department of Medical Biochemistry, University of Gothenburg, Gothenburg, Sweden
- * E-mail:
| | - Jayesh J. Kattla
- Department of Medical Biochemistry, University of Gothenburg, Gothenburg, Sweden
| | - Sarah A. Flowers
- Department of Medical Biochemistry, University of Gothenburg, Gothenburg, Sweden
| | - Sara K. Lindén
- Department of Medical Biochemistry, University of Gothenburg, Gothenburg, Sweden
| | - Pushpa Premaratne
- Department of Medical Biochemistry, University of Gothenburg, Gothenburg, Sweden
| | - Birgitta Weijdegård
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Cancer Center, University of Gothenburg, Gothenburg, Sweden
| | - Karin Sundfeldt
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Cancer Center, University of Gothenburg, Gothenburg, Sweden
| | - Niclas G. Karlsson
- Department of Medical Biochemistry, University of Gothenburg, Gothenburg, Sweden
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68
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Struwe WB, Gough R, Gallagher ME, Kenny DT, Carrington SD, Karlsson NG, Rudd PM. Identification of O-glycan Structures from Chicken Intestinal Mucins Provides Insight into Campylobactor jejuni Pathogenicity. Mol Cell Proteomics 2015; 14:1464-77. [PMID: 25776888 DOI: 10.1074/mcp.m114.044867] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Indexed: 01/28/2023] Open
Abstract
The Gram-negative bacteria Campylobactor jejuni is the primary bacteria responsible for food poisoning in industrialized countries, and acute diarrheal illness is a leading cause of mortality among children in developing countries. C. jejuni are commensal in chickens. They are particularly abundant in the caecal crypts, and poultry products are commonly infected as a result of cross-contamination during processing. The interactions between C. jejuni and chicken intestinal tissues as well as the pathogenic molecular mechanisms of colonization in humans are unknown, but identifying these factors could provide potential targets to reduce the incidence of campylobacteriosis. Recently, purified chicken intestinal mucin was shown to attenuate adherence and invasion of C. jejuni in the human colorectal adenocarcinoma cell line HCT-8 in vitro, and this effect was attributed to mucin O-glycosylation. Mucins from different regions of the chicken intestine inhibited C. jejuni binding and internalization differentially, with large intestine>small intestine>caecum. Here, we use LC-MS to perform a detailed structural analysis of O-glycans released from mucins purified from chicken large intestine, small intestine, and caecum. The O-glycans identified were abundantly sulfated compared with the human intestines, and sulfate moieties were present throughout the chicken intestinal tract. Interestingly, alpha 1-2 linked fucose residues, which have a high binding affinity to C. jejuni, were identified in the small and large intestines. Additionally, N-glycolylneuraminic/N-acetylneuraminic acid containing structures present as Sd(a)-like epitopes were identified in large intestine samples but not small intestine or caecum. O-glycan structural characterization of chicken intestinal mucins provides insights into adherence and invasion properties of C. jejuni, and may offer prospective candidate molecules aimed at reducing the incidence of infection.
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Affiliation(s)
- Weston B Struwe
- From the ‡Dublin-Oxford Glycobiology Group, National Institute for Bioprocessing Research and Training (NIBRT), Dublin, Ireland
| | - Ronan Gough
- §School of Agriculture, Food Science and Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Mary E Gallagher
- §School of Agriculture, Food Science and Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Diarmuid T Kenny
- ¶Department of Medical Biochemistry, Gothenburg University, Gothenburg, Sweden
| | - Stephen D Carrington
- §School of Agriculture, Food Science and Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Niclas G Karlsson
- ¶Department of Medical Biochemistry, Gothenburg University, Gothenburg, Sweden
| | - Pauline M Rudd
- §School of Agriculture, Food Science and Veterinary Medicine, University College Dublin, Dublin, Ireland; ¶Department of Medical Biochemistry, Gothenburg University, Gothenburg, Sweden
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69
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Liu J, Jin C, Cherian RM, Karlsson NG, Holgersson J. O-glycan repertoires on a mucin-type reporter protein expressed in CHO cell pools transiently transfected with O-glycan core enzyme cDNAs. J Biotechnol 2015; 199:77-89. [PMID: 25722186 DOI: 10.1016/j.jbiotec.2015.02.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 02/05/2015] [Accepted: 02/09/2015] [Indexed: 02/07/2023]
Abstract
Glyco-engineering of host cells is used to increase efficacy, decrease immunogenicity and increase circulatory half-lives of protein biopharmaceuticals. The effect of transiently expressed O-glycan core chain glycosyltransferases on O-glycan biosynthesis pathways in CHO cells is reported. Liquid chromatography-mass spectrometry and Western blotting were used to map the O-glycome of a mucin-type fusion protein transiently co-transfected with β1,3-N-acetylglucosaminyltransferase 3 (extended C1 β3GnT3), core 2 β1,6-N-acetylglucosaminyltransferase I (C2 β3GnT1) or core 3 β1,3-N-acetylglucosaminyltransferase 6 (C3 β3GnT6) in CHO cells. Extended core 1 (GlcNAcβ1,3Galβ1,3GalNAc) and core 3 (GlcNAcβ1,3GalNAc), and increased expression of core 2 [Galβ1,3(GlcNAcβ1,6)GalNAc], O-glycans were generated on P-selectin glycoprotein ligand-1/mouse IgG2b (PSGL1/mIgG2b). Endogenous poly-N-acetyllactosamine (poly-LacNAc) synthase elongated extended core 1 and core 3 generating O-glycans with up to five LacNAc repeats. Low amounts of core 3 O-glycans appeared upon extended C1 β3GnT3 expression. The α2,6-sialylated type 2 chain was detected upon co-transfection with the β-galactoside α2,6-sialyltransferase I. N-acetylglucosamine-6-O-sulfotransferase 2 transferred sulfate to carbon 6 of GlcNAc in poly-LacNAc sequences. CHO cells with its known O-glycan repertoire can be used to express recombinant mucin-type proteins together with selected glycosyltransferases in order to recreate carbohydrate determinants on defined O-glycan chains. They will become important tools for assessing the core chain-dependent binding activity of carbohydrate-binding proteins.
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Affiliation(s)
- Jining Liu
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-413 45 Gothenburg, Sweden
| | - Chunsheng Jin
- Department of Medical Biochemistry, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-405 30 Gothenburg, Sweden.
| | - Reeja Maria Cherian
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-413 45 Gothenburg, Sweden
| | - Niclas G Karlsson
- Department of Medical Biochemistry, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Jan Holgersson
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-413 45 Gothenburg, Sweden
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70
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Abrahams JL, Packer NH, Campbell MP. Relative quantitation of multi-antennary N-glycan classes: combining PGC-LC-ESI-MS with exoglycosidase digestion. Analyst 2015; 140:5444-9. [DOI: 10.1039/c5an00691k] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
In the search for N-glycan disease biomarkers current glycoanalytical methods may not be revealing a complete picture of precious samples, and we may be missing valuable structural information that fall outside analysis windows.
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Affiliation(s)
- J. L. Abrahams
- Department of Chemistry and Biomolecular Sciences
- Macquarie University
- Sydney
- Australia
| | - N. H. Packer
- Department of Chemistry and Biomolecular Sciences
- Macquarie University
- Sydney
- Australia
| | - M. P. Campbell
- Department of Chemistry and Biomolecular Sciences
- Macquarie University
- Sydney
- Australia
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71
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Venkataraman M, Sasisekharan R, Raman R. Glycan array data management at Consortium for Functional Glycomics. Methods Mol Biol 2015; 1273:181-90. [PMID: 25753711 DOI: 10.1007/978-1-4939-2343-4_13] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Glycomics or the study of structure-function relationships of complex glycans has reshaped post-genomics biology. Glycans mediate fundamental biological functions via their specific interactions with a variety of proteins. Recognizing the importance of glycomics, large-scale research initiatives such as the Consortium for Functional Glycomics (CFG) were established to address these challenges. Over the past decade, the Consortium for Functional Glycomics (CFG) has generated novel reagents and technologies for glycomics analyses, which in turn have led to generation of diverse datasets. These datasets have contributed to understanding glycan diversity and structure-function relationships at molecular (glycan-protein interactions), cellular (gene expression and glycan analysis), and whole organism (mouse phenotyping) levels. Among these analyses and datasets, screening of glycan-protein interactions on glycan array platforms has gained much prominence and has contributed to cross-disciplinary realization of the importance of glycomics in areas such as immunology, infectious diseases, cancer biomarkers, etc. This manuscript outlines methodologies for capturing data from glycan array experiments and online tools to access and visualize glycan array data implemented at the CFG.
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Affiliation(s)
- Maha Venkataraman
- Department of Biological Engineering, Koch Institute of Integrative Cancer Research, Massachusetts Institute of Technology, MIT Building 76, Room 158, 500 Main Street, Cambridge, MA, 02139, USA
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72
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Stavenhagen K, Kolarich D, Wuhrer M. Clinical Glycomics Employing Graphitized Carbon Liquid Chromatography-Mass Spectrometry. Chromatographia 2014; 78:307-320. [PMID: 25750456 PMCID: PMC4346670 DOI: 10.1007/s10337-014-2813-7] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 10/25/2014] [Accepted: 11/13/2014] [Indexed: 12/25/2022]
Abstract
Glycoconjugates and free glycan are involved in a variety of biological processes such as cell-cell interaction and cell trafficking. Alterations in the complex glycosylation machinery have been correlated with various pathological processes including cancer progression and metastasis. Mass Spectrometry (MS) has evolved as one of the most powerful tools in glycomics and glycoproteomics and in combination with porous graphitized carbon-liquid chromatography (PGC-LC) it is a versatile and sensitive technique for the analysis of glycans and to some extent also glycopeptides. PGC-LC-ESI-MS analysis is characterized by a high isomer separation power enabling a specific glycan compound analysis on the level of individual structures. This allows the investigation of the biological relevance of particular glycan structures and glycan features. Consequently, this strategy is a very powerful technique suitable for clinical research, such as cancer biomarker discovery, as well as in-depth analysis of recombinant glycoproteins. In this review, we will focus on how PGC in conjunction with MS detection can deliver specific structural information for clinical research on protein-bound N-glycans and mucin-type O-glycans. In addition, we will briefly review PGC analysis approaches for glycopeptides, glycosaminoglycans (GAGs) and human milk oligosaccharides (HMOs). The presented applications cover systems that vary vastly with regard to complexity such as purified glycoproteins, cells, tissue or body fluids revealing specific glycosylation changes associated with various biological processes including cancer and inflammation.
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Affiliation(s)
- Kathrin Stavenhagen
- Division of BioAnalytical Chemistry, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Daniel Kolarich
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Wissenschaftspark Potsdam-Golm, Am Mühlenberg 1 OT Golm, 14242 Potsdam, Germany
| | - Manfred Wuhrer
- Division of BioAnalytical Chemistry, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands ; Department of Molecular Cell Biology and Immunology, VU University Medical Center, Amsterdam, The Netherlands ; Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
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73
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Gaunitz S, Liu J, Nilsson A, Karlsson N, Holgersson J. Avian influenza H5 hemagglutinin binds with high avidity to sialic acid on different O-linked core structures on mucin-type fusion proteins. Glycoconj J 2014; 31:145-59. [PMID: 24233973 DOI: 10.1007/s10719-013-9503-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 10/04/2013] [Accepted: 10/07/2013] [Indexed: 12/15/2022]
Abstract
The interaction between P-selectin glycoprotein ligand-1/mouse IgG2b (PSGL-1/mIgG(2b)) fusion protein carrying multiple copies of the influenza hemagglutinin receptor Siaα2-3Gal on different O-glycan chains and recombinant human influenza H5N1 A/Vietnam/1203/04 hemagglutinin was investigated with a Biacore biosensor. The fusion protein was produced by stable cell lines in large scale cultures and purified with affinity- and gel filtration chromatography. TheC-P55 and 293-P cell lines were established by transfecting the Chinese hamster ovary (CHO)-K1 and Human embryonic kidney (HEK)-293 cell lines with plasmids encoding the PSGL-1/mIgG(2b) fusion protein, while the C-PSLex cell line was engineered by transfecting CHO-K1 cells with the plasmids encoding the core 2 β1,6GnT-I and FUT-VII glycosyltransferases. Glycosylation was characterized by lectin Western blotting of the proteins and liquid chromatography - mass spectrometry of released non-derivatized O-glycans. Biacore experiments revealed that PSGL-1/mIgG(2b) is a good binding partner of H5. The binding curves displayed a slow dissociation indicating a multivalent binding. The H5 hemagglutinin binds with similar strength to PSGL-1/mIgG(2b) carrying mostly sialylated core 1 (clone C-P55), a mix of sialylated core 1 and sialylated lactosamine (clone 293-P) or mainly sialylated lactosamine (clone C-PSLex) O-glycans, indicating that this hemagglutinin is unable to discriminate between these structures.The potential use of the large, flexible PSGL-1/mIgG(2b) mucin-type fusion protein carrying Siaα2-3Gal as a multivalent inhibitor of influenza virus is discussed.
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74
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Hofmann J, Struwe WB, Scarff CA, Scrivens JH, Harvey DJ, Pagel K. Estimating collision cross sections of negatively charged N-glycans using traveling wave ion mobility-mass spectrometry. Anal Chem 2014; 86:10789-95. [PMID: 25268221 DOI: 10.1021/ac5028353] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Glycosylation is one of the most common post-translational modifications occurring in proteins. A detailed structural characterization of the involved carbohydrates, however, is still one of the greatest challenges in modern glycoproteomics, since multiple regio- and stereoisomers with an identical monosaccharide composition may exist. Recently, ion mobility-mass spectrometry (IM-MS), a technique in which ions are separated according to their mass, charge, and shape, has evolved as a promising technique for the separation and structural analysis of complex carbohydrates. This growing interest is based on the fact that the measured drift times can be converted into collision cross sections (CCSs), which can be compared, implemented into databases, and used as additional search criteria for structural identification. However, most of the currently used commercial IM-MS instruments utilize a nonuniform traveling wave field to propel the ions through the IM cell. As a result, CCS measurements cannot be performed directly and require calibration. Here, we present a calibration data set consisting of over 500 reference CCSs for negatively charged N-glycans and their fragments. Moreover, we show that dextran, already widely used as a calibrant in high performance liquid chromatography, is also a suitable calibrant for CCS estimations. Our data also indicate that a considerably increased error has to be taken into account when reference CCSs acquired in a different drift gas are used for calibration.
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Affiliation(s)
- Johanna Hofmann
- Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society , Faradayweg 4-6, 14195 Berlin, Germany
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75
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Al Jadda K, Porterfield MP, Bridger R, Heiss C, Tiemeyer M, Wells L, Miller JA, York WS, Ranzinger R. EUROCarbDB(CCRC): a EUROCarbDB node for storing glycomics standard data. ACTA ACUST UNITED AC 2014; 31:242-5. [PMID: 25217575 DOI: 10.1093/bioinformatics/btu609] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
MOTIVATION In the field of glycomics research, several different techniques are used for structure elucidation. Although multiple techniques are often used to increase confidence in structure assignments, most glycomics databases allow storing of only a single type of experimental data. In addition, the methods used to prepare a sample for analysis is seldom recorded making it harder to reproduce the analytical data and results. RESULTS We have extended the freely available EUROCarbDB framework to allow the submission of experimental data and the reporting of several orthogonal experimental datasets. The features aim to increase the understandability and reproducibility of the reported data. AVAILABILITY AND IMPLEMENTATION The installation with the glycan standards is available at http://glycomics.ccrc.uga.edu/eurocarb/. The source code of the project is available at https://code.google.com/p/ucdb/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Khalifeh Al Jadda
- Department of Computer Science and Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Melody P Porterfield
- Department of Computer Science and Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Robert Bridger
- Department of Computer Science and Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Christian Heiss
- Department of Computer Science and Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Michael Tiemeyer
- Department of Computer Science and Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Lance Wells
- Department of Computer Science and Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - John A Miller
- Department of Computer Science and Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - William S York
- Department of Computer Science and Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Rene Ranzinger
- Department of Computer Science and Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
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Gotz L, Abrahams JL, Mariethoz J, Rudd PM, Karlsson NG, Packer NH, Campbell MP, Lisacek F. GlycoDigest: a tool for the targeted use of exoglycosidase digestions in glycan structure determination. Bioinformatics 2014; 30:3131-3. [PMID: 25015990 DOI: 10.1093/bioinformatics/btu425] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
UNLABELLED Sequencing oligosaccharides by exoglycosidases, either sequentially or in an array format, is a powerful tool to unambiguously determine the structure of complex N- and O-link glycans. Here, we introduce GlycoDigest, a tool that simulates exoglycosidase digestion, based on controlled rules acquired from expert knowledge and experimental evidence available in GlycoBase. The tool allows the targeted design of glycosidase enzyme mixtures by allowing researchers to model the action of exoglycosidases, thereby validating and improving the efficiency and accuracy of glycan analysis. AVAILABILITY AND IMPLEMENTATION http://www.glycodigest.org.
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Affiliation(s)
- Lou Gotz
- Proteome Informatics Group, Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland, Biomolecular Frontiers Research Centre, Macquarie University, North Ryde, NSW 2109, Australia, National Institute for Bioprocessing Research and Training, GlycoScience Group, Dublin, Ireland, Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 40530 Gothenburg, Sweden and Section of Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Jodie L Abrahams
- Proteome Informatics Group, Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland, Biomolecular Frontiers Research Centre, Macquarie University, North Ryde, NSW 2109, Australia, National Institute for Bioprocessing Research and Training, GlycoScience Group, Dublin, Ireland, Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 40530 Gothenburg, Sweden and Section of Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Julien Mariethoz
- Proteome Informatics Group, Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland, Biomolecular Frontiers Research Centre, Macquarie University, North Ryde, NSW 2109, Australia, National Institute for Bioprocessing Research and Training, GlycoScience Group, Dublin, Ireland, Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 40530 Gothenburg, Sweden and Section of Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Pauline M Rudd
- Proteome Informatics Group, Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland, Biomolecular Frontiers Research Centre, Macquarie University, North Ryde, NSW 2109, Australia, National Institute for Bioprocessing Research and Training, GlycoScience Group, Dublin, Ireland, Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 40530 Gothenburg, Sweden and Section of Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Niclas G Karlsson
- Proteome Informatics Group, Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland, Biomolecular Frontiers Research Centre, Macquarie University, North Ryde, NSW 2109, Australia, National Institute for Bioprocessing Research and Training, GlycoScience Group, Dublin, Ireland, Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 40530 Gothenburg, Sweden and Section of Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Nicolle H Packer
- Proteome Informatics Group, Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland, Biomolecular Frontiers Research Centre, Macquarie University, North Ryde, NSW 2109, Australia, National Institute for Bioprocessing Research and Training, GlycoScience Group, Dublin, Ireland, Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 40530 Gothenburg, Sweden and Section of Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Matthew P Campbell
- Proteome Informatics Group, Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland, Biomolecular Frontiers Research Centre, Macquarie University, North Ryde, NSW 2109, Australia, National Institute for Bioprocessing Research and Training, GlycoScience Group, Dublin, Ireland, Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 40530 Gothenburg, Sweden and Section of Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Frederique Lisacek
- Proteome Informatics Group, Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland, Biomolecular Frontiers Research Centre, Macquarie University, North Ryde, NSW 2109, Australia, National Institute for Bioprocessing Research and Training, GlycoScience Group, Dublin, Ireland, Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 40530 Gothenburg, Sweden and Section of Biology, University of Geneva, 1211 Geneva, Switzerland Proteome Informatics Group, Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland, Biomolecular Frontiers Research Centre, Macquarie University, North Ryde, NSW 2109, Australia, National Institute for Bioprocessing Research and Training, GlycoScience Group, Dublin, Ireland, Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 40530 Gothenburg, Sweden and Section of Biology, University of Geneva, 1211 Geneva, Switzerland
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77
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Anugraham M, Jacob F, Nixdorf S, Everest-Dass AV, Heinzelmann-Schwarz V, Packer NH. Specific glycosylation of membrane proteins in epithelial ovarian cancer cell lines: glycan structures reflect gene expression and DNA methylation status. Mol Cell Proteomics 2014; 13:2213-32. [PMID: 24855066 DOI: 10.1074/mcp.m113.037085] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
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. N-glycans 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 α 2-6 sialylated N-glycans and "N,N'-diacetyl-lactosamine" 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.
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Affiliation(s)
- Merrina Anugraham
- From the ‡Department of Chemistry & Biomolecular Sciences, Biomolecular Frontiers Research Centre, Faculty of Science, Macquarie University, NSW 2109, Sydney, Australia
| | - Francis Jacob
- §Gynaecological Research Group, Department of Biomedicine, Women's University Hospital Basel, University of Basel, Basel 4003, Switzerland; ¶Ovarian Cancer Group, Adult Cancer Program, Lowy Cancer Research Centre, Prince of Wales Clinical School, University of New South Wales, NSW 2052, Sydney, Australia
| | - Sheri Nixdorf
- ¶Ovarian Cancer Group, Adult Cancer Program, Lowy Cancer Research Centre, Prince of Wales Clinical School, University of New South Wales, NSW 2052, Sydney, Australia
| | - Arun Vijay Everest-Dass
- From the ‡Department of Chemistry & Biomolecular Sciences, Biomolecular Frontiers Research Centre, Faculty of Science, Macquarie University, NSW 2109, Sydney, Australia
| | - Viola Heinzelmann-Schwarz
- §Gynaecological Research Group, Department of Biomedicine, Women's University Hospital Basel, University of Basel, Basel 4003, Switzerland; ¶Ovarian Cancer Group, Adult Cancer Program, Lowy Cancer Research Centre, Prince of Wales Clinical School, University of New South Wales, NSW 2052, Sydney, Australia
| | - Nicolle H Packer
- From the ‡Department of Chemistry & Biomolecular Sciences, Biomolecular Frontiers Research Centre, Faculty of Science, Macquarie University, NSW 2109, Sydney, Australia;
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78
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Chik JHL, Zhou J, Moh ESX, Christopherson R, Clarke SJ, Molloy MP, Packer NH. Comprehensive glycomics comparison between colon cancer cell cultures and tumours: implications for biomarker studies. J Proteomics 2014; 108:146-62. [PMID: 24840470 DOI: 10.1016/j.jprot.2014.05.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 04/28/2014] [Accepted: 05/09/2014] [Indexed: 01/27/2023]
Abstract
UNLABELLED Altered glycosylation is commonly observed in colorectal cancer. In vitro models are frequently used to study this cancer but little is known about the differences that may exist between these model cell systems and tumour tissue. We have compared the membrane protein glycosylation of five colorectal cancer cell lines (SW1116, SW480, SW620, SW837, LS174T) with epithelial cells from colorectal tumours using liquid chromatography tandem mass spectrometry. Remarkably, there were five abundant O-glycans in the tumour cells that were undetected in the low-mucin producing cell lines, although two were found in the mucinous LS174T cells. The O-glycans included the well-known glycan cancer marker, sialyl-Tn, which has been associated with mucins. Using qRT-PCR, sialyl-Tn expression was found to be associated with an increase in α2,6-sialyltransferase gene (ST6GALNAC1) and a decrease in core 1 synthase gene (C1GALT1) in LS174T cells. The expression of a subset of mucins (MUC2, MUC6, MUC5B) was also correlated with sialyl-Tn expression in LS174T cells. Overall, the membrane protein glycosylation of the model cell lines was found to differ from each other and from the epithelial cells of tumour tissue. These findings should be noted in the design of biomarker discovery experiments particularly when cell surface targets are being investigated. BIOLOGICAL SIGNIFICANCE The extent of protein glycosylation differences between in vitro cell lines and ex vivo tumours in colorectal cancer research is unknown. Our study expands current knowledge by characterising the membrane protein glycosylation profiles of five different colorectal cancer cell lines and of epithelial cells derived from resected colorectal cancer tumour tissue, using liquid chromatography tandem mass spectrometry. The detailed structural differences found in both N- and O-linked glycan structures on the membrane glycoproteins were determined and correlated with the mRNA expression of the relevant proteins in the cell lines. The glycosylation differences found between cultured cancer cell lines and epithelial cells from tumour tissue have important implications for glycan biomarker discovery.
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Affiliation(s)
- Jenny H L Chik
- Department of Chemistry and Biomolecular Sciences, Faculty of Science, Macquarie University, Sydney, Australia
| | - Jerry Zhou
- School of Molecular Bioscience, University of Sydney, Sydney, Australia
| | - Edward S X Moh
- Department of Chemistry and Biomolecular Sciences, Faculty of Science, Macquarie University, Sydney, Australia
| | | | - Stephen J Clarke
- Department of Medicine, Royal North Shore Hospital, University of Sydney, Australia
| | - Mark P Molloy
- Department of Chemistry and Biomolecular Sciences, Faculty of Science, Macquarie University, Sydney, Australia; Australian Proteome Analysis Facility, Macquarie University, Sydney, Australia
| | - Nicolle H Packer
- Department of Chemistry and Biomolecular Sciences, Faculty of Science, Macquarie University, Sydney, Australia.
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79
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Campbell MP, Ranzinger R, Lütteke T, Mariethoz J, Hayes CA, Zhang J, Akune Y, Aoki-Kinoshita KF, Damerell D, Carta G, York WS, Haslam SM, Narimatsu H, Rudd PM, Karlsson NG, Packer NH, Lisacek F. Toolboxes for a standardised and systematic study of glycans. BMC Bioinformatics 2014; 15 Suppl 1:S9. [PMID: 24564482 PMCID: PMC4016020 DOI: 10.1186/1471-2105-15-s1-s9] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Background Recent progress in method development for characterising the branched structures of complex carbohydrates has now enabled higher throughput technology. Automation of structure analysis then calls for software development since adding meaning to large data collections in reasonable time requires corresponding bioinformatics methods and tools. Current glycobioinformatics resources do cover information on the structure and function of glycans, their interaction with proteins or their enzymatic synthesis. However, this information is partial, scattered and often difficult to find to for non-glycobiologists. Methods Following our diagnosis of the causes of the slow development of glycobioinformatics, we review the "objective" difficulties encountered in defining adequate formats for representing complex entities and developing efficient analysis software. Results Various solutions already implemented and strategies defined to bridge glycobiology with different fields and integrate the heterogeneous glyco-related information are presented. Conclusions Despite the initial stage of our integrative efforts, this paper highlights the rapid expansion of glycomics, the validity of existing resources and the bright future of glycobioinformatics.
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80
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Kailemia MJ, Ruhaak LR, Lebrilla CB, Amster IJ. Oligosaccharide analysis by mass spectrometry: a review of recent developments. Anal Chem 2014; 86:196-212. [PMID: 24313268 PMCID: PMC3924431 DOI: 10.1021/ac403969n] [Citation(s) in RCA: 279] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
| | - L. Renee Ruhaak
- Department of Chemistry, University of California at Davis, Davis, CA 95616
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81
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Campbell MP, Peterson R, Mariethoz J, Gasteiger E, Akune Y, Aoki-Kinoshita KF, Lisacek F, Packer NH. UniCarbKB: building a knowledge platform for glycoproteomics. Nucleic Acids Res 2013; 42:D215-21. [PMID: 24234447 PMCID: PMC3964942 DOI: 10.1093/nar/gkt1128] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The UniCarb KnowledgeBase (UniCarbKB; http://unicarbkb.org) offers public access to a growing, curated database of information on the glycan structures of glycoproteins. UniCarbKB is an international effort that aims to further our understanding of structures, pathways and networks involved in glycosylation and glyco-mediated processes by integrating structural, experimental and functional glycoscience information. This initiative builds upon the success of the glycan structure database GlycoSuiteDB, together with the informatic standards introduced by EUROCarbDB, to provide a high-quality and updated resource to support glycomics and glycoproteomics research. UniCarbKB provides comprehensive information concerning glycan structures, and published glycoprotein information including global and site-specific attachment information. For the first release over 890 references, 3740 glycan structure entries and 400 glycoproteins have been curated. Further, 598 protein glycosylation sites have been annotated with experimentally confirmed glycan structures from the literature. Among these are 35 glycoproteins, 502 structures and 60 publications previously not included in GlycoSuiteDB. This article provides an update on the transformation of GlycoSuiteDB (featured in previous NAR Database issues and hosted by ExPASy since 2009) to UniCarbKB and its integration with UniProtKB and GlycoMod. Here, we introduce a refactored database, supported by substantial new curated data collections and intuitive user-interfaces that improve database searching.
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Affiliation(s)
- Matthew P Campbell
- Biomolecular Frontiers Research Centre, Macquarie University, North Ryde, NSW 2109, Australia, Proteome Informatics Group, Swiss Institute of Bioinformatics, Geneva, Switzerland, Swiss-Prot Group, Swiss Institute of Bioinformatics, Geneva, Switzerland, Department of Bioinformatics, Faculty of Engineering, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo, Japan and Section of Biology, Faculty of Sciences, University of Geneva, Switzerland
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82
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Maria Cherian R, Gaunitz S, Nilsson A, Liu J, Karlsson NG, Holgersson J. Shiga-like toxin binds with high avidity to multivalent O-linked blood group P1 determinants on mucin-type fusion proteins. Glycobiology 2013; 24:26-38. [DOI: 10.1093/glycob/cwt086] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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83
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Everest-Dass AV, Abrahams JL, Kolarich D, Packer NH, Campbell MP. Structural feature ions for distinguishing N- and O-linked glycan isomers by LC-ESI-IT MS/MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:895-906. [PMID: 23605685 DOI: 10.1007/s13361-013-0610-4] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 02/22/2013] [Accepted: 02/28/2013] [Indexed: 05/13/2023]
Abstract
Glycomics is the comprehensive study of glycan expression in an organism, cell, or tissue that relies on effective analytical technologies to understand glycan structure-function relationships. Owing to the macro- and micro-heterogeneity of oligosaccharides, detailed structure characterization has required an orthogonal approach, such as a combination of specific exoglycosidase digestions, LC-MS/MS, and the development of bioinformatic resources to comprehensively profile a complex biological sample. Liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS/MS) has emerged as a key tool in the structural analysis of oligosaccharides because of its high sensitivity, resolution, and robustness. Here, we present a strategy that uses LC-ESI-MS/MS to characterize over 200 N- and O-glycans from human saliva glycoproteins, complemented by sequential exoglycosidase treatment, to further verify the annotated glycan structures. Fragment-specific substructure diagnostic ions were collated from an extensive screen of the literature available on the detailed structural characterization of oligosaccharides and, together with other specific glycan structure feature ions derived from cross-ring and glycosidic-linkage fragmentation, were used to characterize the glycans and differentiate isomers. The availability of such annotated mass spectrometric fragmentation spectral libraries of glycan structures, together with such substructure diagnostic ions, will be key inputs for the future development of the automated elucidation of oligosaccharide structures from MS/MS data.
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Affiliation(s)
- Arun V Everest-Dass
- Biomolecular Frontiers Research Centre, Macquarie University, North Ryde, NSW, Australia
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84
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Everest-Dass AV, Kolarich D, Campbell MP, Packer NH. Tandem mass spectra of glycan substructures enable the multistage mass spectrometric identification of determinants on oligosaccharides. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2013; 27:931-939. [PMID: 23592194 DOI: 10.1002/rcm.6527] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 01/29/2013] [Indexed: 06/02/2023]
Abstract
RATIONALE Glycosylation of proteins and lipids affects many biological processes, such as host-pathogen interactions, cell communication, and initiation of the immune responses. Terminal glycan substructures, or determinants, often govern the function or recognition of the carrier glycoconjugate and modulate these processes. In this study we describe a strategy using multistage mass spectrometry to identify and confirm these glycan substructures. METHODS An online tandem mass spectrometry (MS(2)) spectral fragment library of glycan substructures that typically occur at the non-reducing terminus of glycoconjugates was created to enable the easier identification and confirmation of glycan determinants on oligosaccharides released from glycoproteins. Oligosaccharides were separated by porous graphitized carbon capillary chromatography and analysed by ion trap MS. Candidate product ions that constitute the glycan substructure mass were identified in the MS(2) product ion spectrum, and used as the precursor ion for subsequent MS(3) fragmentation. The resulting MS(3) spectrum was matched against the MS(2) spectral fragment library to identify the glycan substructure(s) that comprise the parent oligosaccharide. RESULTS Thirty biologically important terminal glycan determinants commonly observed on glycoconjugates were fragmented by positive and negative ion mass spectrometry and the MS(2) product ion masses manually annotated and stored in the UniCarb-DB online database. Negative ion tandem mass spectra were especially useful in assigning isobaric glycan structures. We have applied this strategy for the identification of the sulphation, blood group antigens and sialic acid linkages on complex N-and O-glycans released from glycoproteins. CONCLUSIONS We show the potential of these glycan substructure MS(2) spectra in the negative ionization mode to facilitate the assignment of determinants on N- and O-linked glycans released from glycoproteins. Comparing the structural feature ions of known glycan reference substructures assists in the annotation of complex glycan product ion spectra, and can remove the need for other orthogonal confirmation analyses such as sequential glycosidase digestion.
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Affiliation(s)
- Arun V Everest-Dass
- Biomolecular Frontiers Research Centre, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
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85
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Campbell MP, Nguyen-Khuong T, Hayes CA, Flowers SA, Alagesan K, Kolarich D, Packer NH, Karlsson NG. Validation of the curation pipeline of UniCarb-DB: building a global glycan reference MS/MS repository. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1844:108-16. [PMID: 23624262 DOI: 10.1016/j.bbapap.2013.04.018] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 04/01/2013] [Accepted: 04/16/2013] [Indexed: 10/26/2022]
Abstract
The UniCarb-DB database is an emerging public glycomics data repository, containing over 500 tandem mass spectra (as of March 2013) of glycans released from glycoproteins. A major challenge in glycomics research is to provide and maintain high-quality datasets that will offer the necessary diversity to support the development of accurate bioinformatics tools for data deposition and analysis. The role of UniCarb-DB, as an archival database, is to provide the glycomics community with open-access to a comprehensive LC MS/MS library of N- and O- linked glycans released from glycoproteins that have been annotated with glycosidic and cross-ring fragmentation ions, retention times, and associated experimental metadata descriptions. Here, we introduce the UniCarb-DB data submission pipeline and its practical application to construct a library of LC-MS/MS glycan standards that forms part of this database. In this context, an independent consortium of three laboratories was established to analyze the same 23 commercially available oligosaccharide standards, all by using graphitized carbon-liquid chromatography (LC) electrospray ionization (ESI) ion trap mass spectrometry in the negative ion mode. A dot product score was calculated for each spectrum in the three sets of data as a measure of the comparability that is necessary for use of such a collection in library-based spectral matching and glycan structural identification. The effects of charge state, de-isotoping and threshold levels on the quality of the input data are shown. The provision of well-characterized oligosaccharide fragmentation data provides the opportunity to identify determinants of specific glycan structures, and will contribute to the confidence level of algorithms that assign glycan structures to experimental MS/MS spectra. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan.
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Affiliation(s)
- Matthew P Campbell
- Biomolecular Frontiers Research Centre, Macquarie University, Sydney, New South Wales, Australia
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86
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Gaunitz S, Jin C, Nilsson A, Liu J, Karlsson NG, Holgersson J. Mucin-type proteins produced in the Trichoplusia ni and Spodoptera frugiperda insect cell lines carry novel O-glycans with phosphocholine and sulfate substitutions. Glycobiology 2013; 23:778-96. [PMID: 23463814 DOI: 10.1093/glycob/cwt015] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The O-glycans of a recombinant mucin-type protein expressed in insect cell lines derived from Trichoplusia ni (Hi-5) and Spodoptera frugiperda (Sf9) were characterized. The P-selectin glycoprotein ligand-1/mouse IgG2b (PSGL-1/mIgG2b) fusion protein carrying 106 potential O-glycosylation sites and 6 potential N-glycosylation sites was expressed and purified from the Hi-5 and Sf9 cell culture medium using affinity chromatography and gel filtration. Liquid chromatography mass spectrometry (LC-MS) of O-glycans released from PSGL-1/mIgG2b revealed a large repertoire of structurally diverse glycans, which is in contrast to previous reports of only simple glycans. O-Glycans containing hexuronic acid (HexA, here glucuronic acid and galacturonic acid) were found to be prevalent. Also sulfate (Hi-5 and Sf9) and phosphocholine (PC; Sf9) O-glycan substitutions were detected. Western blotting confirmed the presence of O-linked PC on PSGL-1/mIG2b produced in Sf9 cells. To our knowledge, this is the first structural characterization of PC-substituted O-glycans in any species. The MS analyses revealed that Sf9 oligosaccharides consisted of short oligosaccharides (<6 residues) low in hexose (Hex) and with terminating N-acetylhexosamine (HexNAc) units, whereas Hi-5 produced a family of large O-glycans with (HexNAc-HexA-Hex) repeats and sulfate substitution on terminal residues. In both cell lines, the core N-acetylgalactosamine was preferentially non-branched, but small amounts of O-glycan cores with single fucose or hexose branches were found.
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Affiliation(s)
- Stefan Gaunitz
- Division of Clinical Immunology and Transfusion Medicine, Department of Laboratory Medicine, Karolinska Institute, Karolinska University Hospital at Huddinge, SE-141 86 Huddinge, Sweden.
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87
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Flowers SA, Ali L, Lane CS, Olin M, Karlsson NG. Selected reaction monitoring to differentiate and relatively quantitate isomers of sulfated and unsulfated core 1 O-glycans from salivary MUC7 protein in rheumatoid arthritis. Mol Cell Proteomics 2013; 12:921-31. [PMID: 23457413 DOI: 10.1074/mcp.m113.028878] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
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 (Galβ1-3GalNAcol) 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.
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Affiliation(s)
- Sarah A Flowers
- Department of Medical Biochemistry, Institute of Biomedicine, University of Gothenburg, Medicinaregatan 9A, 405 30, Gothenburg, Sweden
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88
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Lindberg L, Liu J, Gaunitz S, Nilsson A, Johansson T, Karlsson NG, Holgersson J. Mucin-type fusion proteins with blood group A or B determinants on defined O-glycan core chains produced in glycoengineered Chinese hamster ovary cells and their use as immunoaffinity matrices. Glycobiology 2013; 23:720-35. [DOI: 10.1093/glycob/cwt011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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89
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Novotny MV, Alley WR, Mann BF. Analytical glycobiology at high sensitivity: current approaches and directions. Glycoconj J 2013; 30:89-117. [PMID: 22945852 PMCID: PMC3586546 DOI: 10.1007/s10719-012-9444-8] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2012] [Revised: 06/29/2012] [Accepted: 08/14/2012] [Indexed: 12/30/2022]
Abstract
This review summarizes the analytical advances made during the last several years in the structural and quantitative determinations of glycoproteins in complex biological mixtures. The main analytical techniques used in the fields of glycomics and glycoproteomics involve different modes of mass spectrometry and their combinations with capillary separation methods such as microcolumn liquid chromatography and capillary electrophoresis. The need for high-sensitivity measurements have been emphasized in the oligosaccharide profiling used in the field of biomarker discovery through MALDI mass spectrometry. High-sensitivity profiling of both glycans and glycopeptides from biological fluids and tissue extracts has been aided significantly through lectin preconcentration and the uses of affinity chromatography.
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Affiliation(s)
- Milos V Novotny
- Department of Chemistry, Indiana University, Bloomington, IN, USA.
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90
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Aoki-Kinoshita KF. Using databases and web resources for glycomics research. Mol Cell Proteomics 2013; 12:1036-45. [PMID: 23325765 DOI: 10.1074/mcp.r112.026252] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Many databases of carbohydrate structures and related information can be found on the World Wide Web. This review covers the major carbohydrate databases that have potential utility for glycoscientists and researchers entering the glycosciences. The first half provides a brief overview of carbohydrate databases and web resources (including a history of carbohydrate databases and carbohydrate notations used in these databases), and the second half provides a guide that can be used as an index to determine which resources provide the data of most interest to the user.
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Affiliation(s)
- Kiyoko F Aoki-Kinoshita
- Department of Bioinformatics, Faculty of Engineering, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo, Japan.
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91
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Abstract
Protein glycosylation is a highly complex and regulated posttranslational modification. In this process several glycosyltransferase families are involved. In cancer this delicate equilibrium is disrupted leading to glycosylation changes on glycoconjugates, namely, glycoproteins. One of the major consequences is the increase of sialylated oligosaccharide chains in glycoproteins. Here we describe an experimental methodology focused in the enrichment and characterization of sialic acid containing glycopeptides by MALDI mass spectrometry and the subsequent data analysis.
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Affiliation(s)
- Hugo Osório
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
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92
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Li F, Glinskii OV, Glinsky VV. Glycobioinformatics: Current strategies and tools for data mining in MS-based glycoproteomics. Proteomics 2012; 13:341-54. [DOI: 10.1002/pmic.201200149] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 10/06/2012] [Accepted: 11/06/2012] [Indexed: 12/18/2022]
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93
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Ali L, Kenny DT, Hayes CA, Karlsson NG. Structural Identification of O-Linked Oligosaccharides Using Exoglycosidases and MSn Together with UniCarb-DB Fragment Spectra Comparison. Metabolites 2012; 2:648-66. [PMID: 24957756 DOI: 10.3390/metabo2040648] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Revised: 09/18/2012] [Accepted: 09/28/2012] [Indexed: 11/16/2022] Open
Abstract
The availability of specific exoglycosidases alongside a spectral library of O-linked oligosaccharide collision induced dissociation (CID) MS fragments, UniCarb-DB, provides a pathway to make the elucidation of O-linked oligosaccharides more efficient. Here, we advise an approach of exoglycosidase-digestion of O-linked oligosaccharide mixtures, for structures that do not provide confirmative spectra. The combination of specific exoglycosidase digestion and MS2 matching of the exoglycosidase products with structures from UniCarb-DB, allowed the assignment of unknown structures. This approach was illustrated by treating sialylated core 2 O-linked oligosaccharides, released from the human synovial glycoprotein (lubricin), with a α2-3 specific sialidase. This methodology demonstrated the exclusive 3 linked nature of the sialylation of core 2 oligosaccharides on lubricin. When specific exoglycosidases were not available, MS3 spectral matching using standards was used. This allowed the unusual 4-linked terminal GlcNAc epitope in a porcine stomach to be identified in the GlcNAc1-4Galb1-3(GlcNAcb1-6)GalNAcol structure, indicating the antibacterial epitope GlcNAca1-4. In total, 13 structures were identified using exoglycosidase and MSn, alongside UniCarb-DB fragment spectra comparison. UniCarb-DB could also be used to identify the specificity of unknown exoglycosidases in human saliva. Endogenous salivary exoglycosidase activity on mucin oligosaccharides could be monitored by comparing the generated tandem MS spectra with those present in UniCarb-DB, showing that oral exoglycosidases were dominated by sialidases with a higher activity towards 3-linked sialic acid rather than 6-linked sialic acid.
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Affiliation(s)
- Liaqat Ali
- Department of Medical Biochemistry, Institute of Biomedicine, University of Gothenburg, 40530 Gothenburg, Sweden.
| | - Diarmuid T Kenny
- Department of Medical Biochemistry, Institute of Biomedicine, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Catherine A Hayes
- Department of Medical Biochemistry, Institute of Biomedicine, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Niclas G Karlsson
- Department of Medical Biochemistry, Institute of Biomedicine, University of Gothenburg, 40530 Gothenburg, Sweden
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94
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Jin C, Ekwall AKH, Bylund J, Björkman L, Estrella RP, Whitelock JM, Eisler T, Bokarewa M, Karlsson NG. Human synovial lubricin expresses sialyl Lewis x determinant and has L-selectin ligand activity. J Biol Chem 2012; 287:35922-33. [PMID: 22930755 DOI: 10.1074/jbc.m112.363119] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Lubricin (or proteoglycan 4 (PRG4)) is an abundant mucin-like glycoprotein in synovial fluid (SF) and a major component responsible for joint lubrication. In this study, it was shown that O-linked core 2 oligosaccharides (Galβ1-3(GlcNAcβ1-6)GalNAcα1-Thr/Ser) on lubricin isolated from rheumatoid arthritis SF contained both sulfate and fucose residues, and SF lubricin was capable of binding to recombinant L-selectin in a glycosylation-dependent manner. Using resting human polymorphonuclear granulocytes (PMN) from peripheral blood, confocal microscopy showed that lubricin coated circulating PMN and that it partly co-localized with L-selectin expressed by these cells. In agreement with this, activation-induced shedding of L-selectin also mediated decreased lubricin binding to PMN. It was also found that PMN recruited to inflamed synovial area and fluid in rheumatoid arthritis patients kept a coat of lubricin. These observations suggest that lubricin is able to bind to PMN via an L-selectin-dependent and -independent manner and may play a role in PMN-mediated inflammation.
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Affiliation(s)
- Chunsheng Jin
- Department of Medical Biochemistry, Institute of Biomedicine, University of Gothenburg, 405 30 Gothenburg, Sweden.
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95
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Schiel JE. Glycoprotein analysis using mass spectrometry: unraveling the layers of complexity. Anal Bioanal Chem 2012; 404:1141-9. [PMID: 22733248 DOI: 10.1007/s00216-012-6185-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Revised: 06/04/2012] [Accepted: 06/07/2012] [Indexed: 12/13/2022]
Abstract
A glycoprotein exists as a heterogeneous mixture of forms due to differential glycosylation, each of which may confer different functionality and/or serve as a biochemical marker for disease. The complex structure of glycans make them a bioanalytical challenge requiring multiple mass spectrometry based approaches to gain different types of information. The following article will briefly describe recently utilized mass spectrometry methods to identify glycosylation sites and measure glycan composition, sequence, branching, and relative quantities. Potential metrological developments are discussed in light of current trends toward complete, reliable glycoanalytical characterization in a high-throughput manner.
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Affiliation(s)
- John E Schiel
- National Institute of Standards and Technology, Analytical Chemistry Division, Gaithersburg, MD 20899, USA.
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96
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Lütteke T. The use of glycoinformatics in glycochemistry. Beilstein J Org Chem 2012; 8:915-29. [PMID: 23015842 PMCID: PMC3388882 DOI: 10.3762/bjoc.8.104] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Accepted: 05/29/2012] [Indexed: 01/10/2023] Open
Abstract
Glycoinformatics is a small but growing branch of bioinformatics and chemoinformatics. Various resources are now available that can be of use to glycobiologists, but also to chemists who work on the synthesis or analysis of carbohydrates. This article gives an overview of existing glyco-specific databases and tools, with a focus on their application to glycochemistry: Databases can provide information on candidate glycan structures for synthesis, or on glyco-enzymes that can be used to synthesize carbohydrates. Statistical analyses of glycan databases help to plan glycan synthesis experiments. 3D-Structural data of protein-carbohydrate complexes are used in targeted drug design, and tools to support glycan structure analysis aid with quality control. Specific problems of glycoinformatics compared to bioinformatics for genomics or proteomics, especially concerning integration and long-term maintenance of the existing glycan databases, are also discussed.
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Affiliation(s)
- Thomas Lütteke
- Justus-Liebig-University Gießen, Institute of Veterinary Physiology and Biochemistry, Frankfurter Str. 100, 35392 Gießen, Germany
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97
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98
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Schulz BL, Cooper-White J, Punyadeera CK. Saliva proteome research: current status and future outlook. Crit Rev Biotechnol 2012; 33:246-59. [DOI: 10.3109/07388551.2012.687361] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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99
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Hayes CA, Nemes S, Karlsson NG. Statistical analysis of glycosylation profiles to compare tissue type and inflammatory disease state. ACTA ACUST UNITED AC 2012; 28:1669-76. [PMID: 22543500 DOI: 10.1093/bioinformatics/bts242] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
MOTIVATION Glycosylation is one of the most important post-translational modifications of proteins and explains some aspects of the diversification of higher organisms not explained by template-driven synthesis. For glycomics to mature as much as genomics and proteomics, the necessary tools need to be developed and tested. Liquid chromatography-mass spectrometry is one of the gold standards for oligosaccharide analysis and leads to large amounts of data, not easily interpreted manually. We present a study on the testing and validation of statistical analysis tools to aid the structural elucidation of these analyses as well as using the results to answer biologically relevant questions. RESULTS We show the usefulness of data reduction and statistical analysis in the interpretation of complex glycosylation data. The reduction does not result in the loss of importance of the glycosylation information as shown by comparison of control and disease samples in two tissue types.
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Affiliation(s)
- Catherine A Hayes
- Department of Medical Biochemistry, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
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100
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Kenny DT, Skoog EC, Lindén SK, Struwe WB, Rudd PM, Karlsson NG. Presence of terminal N-acetylgalactosamineβ1-4N-acetylglucosamine residues on O-linked oligosaccharides from gastric MUC5AC: Involvement in Helicobacter pylori colonization? Glycobiology 2012; 22:1077-85. [DOI: 10.1093/glycob/cws076] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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