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Urban J, Jin C, Thomsson KA, Karlsson NG, Ives CM, Fadda E, Bojar D. Predicting glycan structure from tandem mass spectrometry via deep learning. Nat Methods 2024; 21:1206-1215. [PMID: 38951670 PMCID: PMC11239490 DOI: 10.1038/s41592-024-02314-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 05/17/2024] [Indexed: 07/03/2024]
Abstract
Glycans constitute the most complicated post-translational modification, modulating protein activity in health and disease. However, structural annotation from tandem mass spectrometry (MS/MS) data is a bottleneck in glycomics, preventing high-throughput endeavors and relegating glycomics to a few experts. Trained on a newly curated set of 500,000 annotated MS/MS spectra, here we present CandyCrunch, a dilated residual neural network predicting glycan structure from raw liquid chromatography-MS/MS data in seconds (top-1 accuracy: 90.3%). We developed an open-access Python-based workflow of raw data conversion and prediction, followed by automated curation and fragment annotation, with predictions recapitulating and extending expert annotation. We demonstrate that this can be used for de novo annotation, diagnostic fragment identification and high-throughput glycomics. For maximum impact, this entire pipeline is tightly interlaced with our glycowork platform and can be easily tested at https://colab.research.google.com/github/BojarLab/CandyCrunch/blob/main/CandyCrunch.ipynb . We envision CandyCrunch to democratize structural glycomics and the elucidation of biological roles of glycans.
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Affiliation(s)
- James Urban
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Chunsheng Jin
- Proteomics Core Facility at Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Kristina A Thomsson
- Proteomics Core Facility at Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Niclas G Karlsson
- Section of Pharmacy, Department of Life Sciences and Health, Faculty of Health Sciences, Oslo Metropolitan University, Oslo, Norway
| | - Callum M Ives
- Department of Chemistry and Hamilton Institute, Maynooth University, Maynooth, Ireland
| | - Elisa Fadda
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Daniel Bojar
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden.
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2
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Safferthal M, Bechtella L, Zappe A, Vos GM, Pagel K. Labeling of Mucin-Type O-Glycans for Quantification Using Liquid Chromatography and Fluorescence Detection. ACS MEASUREMENT SCIENCE AU 2024; 4:223-230. [PMID: 38645579 PMCID: PMC11027200 DOI: 10.1021/acsmeasuresciau.3c00071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 04/23/2024]
Abstract
O-glycosylation is a common post-translational modification that is essential for the defensive properties of mucus barriers. Incomplete and altered O-glycosylation is often linked to severe diseases, such as cancer, cystic fibrosis, and chronic obstructive pulmonary disease. Originating from a nontemplate-driven biosynthesis, mucin-type O-glycan structures are very complex. They are often present as heterogeneous mixtures containing multiple isomers. Therefore, the analysis of complex O-glycan mixtures usually requires hyphenation of orthogonal techniques such as liquid chromatography (LC), ion mobility spectrometry, and mass spectrometry (MS). However, MS-based techniques are mainly qualitative. Moreover, LC separation of O-glycans often lacks reproducibility and requires sophisticated data treatment and analysis. Here we present a mucin-type O-glycomics analysis workflow that utilizes hydrophilic interaction liquid chromatography for separation and fluorescence labeling for detection and quantification. In combination with mass spectrometry, a detailed analysis on the relative abundance of specific mucin-type O-glycan compositions and features, such as fucose, sialic acids, and sulfates, is performed. Furthermore, the average number of monosaccharide units of O-glycans in different samples was determined. To demonstrate universal applicability, the method was tested on mucins from different tissue types and mammals, such as bovine submaxillary mucins, porcine gastric mucins, and human milk mucins. To account for day-to-day retention time shifts in O-glycan separations and increase the comparability between different instruments and laboratories, we included fluorescently labeled dextran ladders in our workflow. In addition, we set up a library of glucose unit values for all identified O-glycans, which can be used to simplify the identification process of glycans in future analyses.
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Affiliation(s)
- Marc Safferthal
- Fritz
Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany
- Department
of Biology, Chemistry, Pharmacy, Freie Universität
Berlin, Altensteinstraße
23a, 14195 Berlin, Germany
| | - Leïla Bechtella
- Fritz
Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany
- Department
of Biology, Chemistry, Pharmacy, Freie Universität
Berlin, Altensteinstraße
23a, 14195 Berlin, Germany
| | - Andreas Zappe
- Fritz
Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany
- Department
of Biology, Chemistry, Pharmacy, Freie Universität
Berlin, Altensteinstraße
23a, 14195 Berlin, Germany
| | - Gaël M. Vos
- Fritz
Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany
- Department
of Biology, Chemistry, Pharmacy, Freie Universität
Berlin, Altensteinstraße
23a, 14195 Berlin, Germany
| | - Kevin Pagel
- Fritz
Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany
- Department
of Biology, Chemistry, Pharmacy, Freie Universität
Berlin, Altensteinstraße
23a, 14195 Berlin, Germany
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3
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Austin BK, Firooz A, Valafar H, Blenda AV. An Updated Overview of Existing Cancer Databases and Identified Needs. BIOLOGY 2023; 12:1152. [PMID: 37627037 PMCID: PMC10452211 DOI: 10.3390/biology12081152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/26/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023]
Abstract
Our search of existing cancer databases aimed to assess the current landscape and identify key needs. We analyzed 71 databases, focusing on genomics, proteomics, lipidomics, and glycomics. We found a lack of cancer-related lipidomic and glycomic databases, indicating a need for further development in these areas. Proteomic databases dedicated to cancer research were also limited. To assess overall progress, we included human non-cancer databases in proteomics, lipidomics, and glycomics for comparison. This provided insights into advancements in these fields over the past eight years. We also analyzed other types of cancer databases, such as clinical trial databases and web servers. Evaluating user-friendliness, we used the FAIRness principle to assess findability, accessibility, interoperability, and reusability. This ensured databases were easily accessible and usable. Our search summary highlights significant growth in cancer databases while identifying gaps and needs. These insights are valuable for researchers, clinicians, and database developers, guiding efforts to enhance accessibility, integration, and usability. Addressing these needs will support advancements in cancer research and benefit the wider cancer community.
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Affiliation(s)
- Brittany K. Austin
- Department of Biomedical Sciences, School of Medicine Greenville, University of South Carolina, Greenville, SC 29605, USA;
| | - Ali Firooz
- Department of Computer Science and Engineering, College of Engineering and Computing, University of South Carolina, Columbia, SC 29208, USA;
| | - Homayoun Valafar
- Department of Computer Science and Engineering, College of Engineering and Computing, University of South Carolina, Columbia, SC 29208, USA;
| | - Anna V. Blenda
- Department of Biomedical Sciences, School of Medicine Greenville, University of South Carolina, Greenville, SC 29605, USA;
- Prisma Health Cancer Institute, Prisma Health, Greenville, SC 29605, USA
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4
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Lisacek F, Tiemeyer M, Mazumder R, Aoki-Kinoshita KF. Worldwide Glycoscience Informatics Infrastructure: The GlySpace Alliance. JACS AU 2023; 3:4-12. [PMID: 36711080 PMCID: PMC9875223 DOI: 10.1021/jacsau.2c00477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/04/2022] [Accepted: 11/07/2022] [Indexed: 06/18/2023]
Abstract
The GlySpace Alliance was formed in 2018 among the principal investigators of three major glycoscience portals: Glyco@Expasy, GlyCosmos, and GlyGen, representing Europe, Asia, and the United States, respectively. While each of these portals has its unique user interface, the aim is to provide the same basic data set of glycan-related omics data. These portals will be introduced with the aim to enable users to find their target information in the most efficient manner, in particular, in terms of the chemical structures of glycans and their functions.
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Affiliation(s)
- Frederique Lisacek
- Proteome
Informatics Group, SIB Swiss Institute of Bioinformatics, University of Geneva, Geneva CH-1227, Switzerland
- Computer
Science Department & Section of Biology, University of Geneva, Geneva CH-1227, Switzerland
| | - Michael Tiemeyer
- Complex
Carbohydrate Research Center, University
of Georgia, Athens, Georgia 30602, United States
| | - Raja Mazumder
- George
Washington University, Washington, District of Columbia 20037, United States
| | - Kiyoko F. Aoki-Kinoshita
- Glycan
and Life Systems Integration Center (GaLSIC), Soka University, Hachioji, Tokyo 192-8577, Japan
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5
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Benktander J, Sundh H, Sharba S, Teneberg S, Lindén SK. Aeromonas salmonicida binds α2-6 linked sialic acid, which is absent among the glycosphingolipid repertoires from skin, gill, stomach, pyloric caecum, and intestine. Virulence 2022; 13:1741-1751. [PMID: 36205522 PMCID: PMC9553145 DOI: 10.1080/21505594.2022.2132056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Carbohydrates can both protect against infection and act as targets promoting infection. Mucins are major components of the slimy mucus layer covering the fish epithelia. Mucins can act as decoys for intimate pathogen interaction with the host afforded by binding to glycosphingolipids in the host cell membrane. We isolated and characterized glycosphingolipids from Atlantic salmon skin, gill, stomach, pyloric caeca, and intestine. We characterized the glycosphingolipids using liquid chromatography – mass spectrometry and tandem mass spectrometry and the glycan repertoire was compared with the glycan repertoire of mucins from the same epithelia. We also investigated Aeromonas salmonicida binding using chromatogram and microtiter well based binding assays. We identified 29 glycosphingolipids. All detected acid glycans were of the ganglio-series (unless shorter) and showed a high degree of polysialylation. The non-acid glycans were mostly composed of the neolacto, globo, and ganglio core structures. The glycosphingolipid repertoire differed between epithelia and the proportion of the terminal moieties of the glycosphingolipids did not reflect the terminal moieties on the mucins from the same epithelia. A. salmonicida did not bind the Atlantic salmon glycosphingolipids. Instead, we identified that A. salmonicida binding to sialic acid occurred to α2–6 Neu5Ac but not to α2–3 Neu5Ac. α2–6 Neu5Ac was present on mucins whereas mainly α2–3 Neu5Ac was found on the glycosphingolipids, explaining the difference in A. salmonicida binding ability between these host glycoconjugates. A. salmonicida´s ability to bind to Atlantic salmon mucins, but not the glycosphingolipids, is likely part of the host defence against this pathogen.
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Affiliation(s)
- John Benktander
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Henrik Sundh
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Sinan Sharba
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Susann Teneberg
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Sara K Lindén
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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A Complex Connection Between the Diversity of Human Gastric Mucin O-Glycans, Helicobacter pylori Binding, Helicobacter Infection and Fucosylation. Mol Cell Proteomics 2022; 21:100421. [PMID: 36182101 PMCID: PMC9661725 DOI: 10.1016/j.mcpro.2022.100421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 09/25/2022] [Accepted: 09/26/2022] [Indexed: 01/18/2023] Open
Abstract
Helicobacter pylori colonizes the stomach of half of the human population. Most H. pylori are located in the mucus layer, which is mainly comprised by glycosylated mucins. Using mass spectrometry, we identified 631 glycans (whereof 145 were fully characterized and the remainder assigned as compositions) on mucins isolated from 14 Helicobacter spp.-infected and 14 Helicobacter spp.-noninfected stomachs. Only six identified glycans were common to all individuals, from a total of 60 to 189 glycans in each individual. An increased number of unique glycan structures together with an increased intraindividual diversity and larger interindividual variation were identified among O-glycans from Helicobacter spp.-infected stomachs compared with noninfected stomachs. H. pylori strain J99, which carries the blood group antigen-binding adhesin (BabA), the sialic acid-binding adhesin (SabA), and the LacdiNAc-binding adhesin, bound both to Lewis b (Leb)-positive and Leb-negative mucins. Among Leb-positive mucins, H. pylori J99 binding was higher to mucins from Helicobacter spp.-infected individuals than noninfected individuals. Statistical correlation analysis, binding experiments with J99 wt, and J99ΔbabAΔsabA and inhibition experiments using synthetic glycoconjugates demonstrated that the differences in H. pylori-binding ability among these four groups were governed by BabA-dependent binding to fucosylated structures. LacdiNAc levels were lower in mucins that bound to J99 lacking BabA and SabA than in mucins that did not, suggesting that LacdiNAc did not significantly contribute to the binding. We identified 24 O-glycans from Leb-negative mucins that correlated well with H. pylori binding whereof 23 contained α1,2-linked fucosylation. The large and diverse gastric glycan library identified, including structures that correlated with H. pylori binding, could be used to select glycodeterminants to experimentally investigate further for their importance in host-pathogen interactions and as candidates to develop glycan-based therapies.
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7
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Chahal G, Quintana-Hayashi MP, Gaytán MO, Benktander J, Padra M, King SJ, Linden SK. Streptococcus oralis Employs Multiple Mechanisms of Salivary Mucin Binding That Differ Between Strains. Front Cell Infect Microbiol 2022; 12:889711. [PMID: 35782137 PMCID: PMC9247193 DOI: 10.3389/fcimb.2022.889711] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 04/20/2022] [Indexed: 11/13/2022] Open
Abstract
Streptococcus oralis is an oral commensal and opportunistic pathogen that can enter the bloodstream and cause bacteremia and infective endocarditis. Here, we investigated the mechanisms of S. oralis binding to oral mucins using clinical isolates, isogenic mutants and glycoconjugates. S. oralis bound to both MUC5B and MUC7, with a higher level of binding to MUC7. Mass spectrometry identified 128 glycans on MUC5B, MUC7 and the salivary agglutinin (SAG). MUC7/SAG contained a higher relative abundance of Lewis type structures, including Lewis b/y, sialyl-Lewis a/x and α2,3-linked sialic acid, compared to MUC5B. S. oralis subsp. oralis binding to MUC5B and MUC7/SAG was inhibited by Lewis b and Lacto-N-tetraose glycoconjugates. In addition, S. oralis binding to MUC7/SAG was inhibited by sialyl Lewis x. Binding was not inhibited by Lacto-N-fucopentaose, H type 2 and Lewis x conjugates. These data suggest that three distinct carbohydrate binding specificities are involved in S. oralis subsp. oralis binding to oral mucins and that the mechanisms of binding MUC5B and MUC7 differ. Efficient binding of S. oralis subsp. oralis to MUC5B and MUC7 required the gene encoding sortase A, suggesting that the adhesin(s) are LPXTG-containing surface protein(s). Further investigation demonstrated that one of these adhesins is the sialic acid binding protein AsaA.
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Affiliation(s)
- Gurdeep Chahal
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | | | - Meztlli O. Gaytán
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children´s Hospital, Columbus, OH, United States
| | - John Benktander
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | - Medea Padra
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | - Samantha J. King
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children´s Hospital, Columbus, OH, United States
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, United States
- Infectious Diseases Institute, The Ohio State University, Columbus, OH, United States
- *Correspondence: Sara K. Linden, ; Samantha J. King,
| | - Sara K. Linden
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
- *Correspondence: Sara K. Linden, ; Samantha J. King,
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Integrated N- and O-Glycomics of Acute Myeloid Leukemia (AML) Cell Lines. Cells 2021; 10:cells10113058. [PMID: 34831278 PMCID: PMC8616353 DOI: 10.3390/cells10113058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/03/2021] [Accepted: 11/04/2021] [Indexed: 12/19/2022] Open
Abstract
Acute myeloid leukemia (AML) is characterized by a dysregulated expansion of poorly differentiated myeloid cells. Although patients are usually treated effectively by chemotherapy, a high rate of relapsed or refractory disease poses a major hurdle in its treatment. Recently, several studies have proposed implications of protein glycosylation in the pathobiology of AML including chemoresistance. Accordingly, associations have been found between specific glycan epitopes and the outcome of the disease. To advance this poorly studied field, we performed an exploratory glycomics study characterizing 21 widely used AML cell lines. Exploiting the benefits of porous graphitized carbon chromatography coupled to tandem mass spectrometry (PGC nano-LC-MS2), we qualitatively and quantitatively profiled N- and O-linked glycans. AML cell lines exhibited distinct glycan fingerprints differing in relevant glycan traits correlating with their cellular phenotype as classified by the FAB system. By implementing transcriptomics data, specific glycosyltransferases and hematopoietic transcription factors were identified, which are candidate drivers of the glycan phenotype of these cells. In conclusion, we report the varying expression of glycan structures across a high number of AML cell lines, including those associated with poor prognosis, identified underlying glycosyltransferases and transcription factors, and provide insights into the regulation of the AML glycan repertoire.
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Almhöjd U, Cevik-Aras H, Karlsson N, Chuncheng J, Almståhl A. Stimulated saliva composition in patients with cancer of the head and neck region. BMC Oral Health 2021; 21:509. [PMID: 34627217 PMCID: PMC8501675 DOI: 10.1186/s12903-021-01872-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 09/30/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND To analyse over time changes in stimulated whole saliva regarding total protein, Immunoglobulin A (IgA), and mucin type O-glycans (mostly MUC5B and MUC7) in head and neck cancer patients. METHODS 29 dentate patients (20 men and 9 women, 59 ± 8 years) treated with curative radiation therapy and chemotherapy for cancer of the head and neck region were included. The stimulated whole salivary secretion rate was determined and saliva collected at four time-points: at pretreatment, and at 6 months, 1 and 2 years post treatment. The total protein concentration was determined spectrophotometrically by using Bicinchoninic Acid assay and Immunoglobulin A (IgA) by using ELISA technique. Glycosylation pattern of salivary mucins was determined in samples collected pre- and post treatment by using LC/MS electrospray and mucin content quantified using SDS-AgPAGE gels and PAS staining. RESULTS Compared with pretreatment, the total protein concentration was increased already at 6 months post treatment (p < 0.01), and continued to increase up to 2 years post treatment (p < 0.001). During that period no significant changes in IgA concentration was detected. At pretreatment, the output/min of both total protein and IgA was significantly higher than at all time-points post treatment. Saliva from the cancer patients showed a low abundance/no detectable MUC7, while the MUC5B level remained, compared to saliva from a healthy control. The glycomic analysis showed that the percentage of core 2 O-glycans was increased as core 1, 3 and 4 O-glycans were decreased. The level of sialylation was higher at 6 months post treatment, while sulfation was lower. CONCLUSION A decreased output per minute of proteins at decreased salivary secretion rate, as well as reduced sulfation of MUC5B at 6 months post treatment tended to correlate with the patients' experience of sticky saliva and oral dryness. At 2 years post treatment, the decreased amount of IgA combined with a lowered salivary secretion rate indicate a reduced oral defense with increased risk of oral infections.
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Affiliation(s)
- Ulrica Almhöjd
- Department of Cariology, Institute of Odontology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Hulya Cevik-Aras
- Department of Oral Pathology and Medicine, Institute of Odontology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,NÄL Hospital, Trollhättan, Sweden
| | - Niclas Karlsson
- BioMS, Institute of Odontology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Jin Chuncheng
- BioMS, Institute of Odontology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Annica Almståhl
- Department of Oral Microbiology and Immunology, Institute of Odontology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
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10
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Glycoinformatics Tools for Comprehensive Characterization of Glycans Enzymatically Released from Proteins. Methods Mol Biol 2021. [PMID: 34611862 DOI: 10.1007/978-1-0716-1685-7_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Glycosylation is important in biology, contributing to both protein conformation and function. Structurally, glycosylation is complex and diverse. This complexity is reflected in the topology, composition, monosaccharide linkages, and isomerism of each oligosaccharide. Glycoanalytics is a discipline that addresses the understanding and characterization of this complexity and its correlation with biology. It includes analytical steps such as sample preparation, instrument measurements, and data analyses. Of these, data analysis has emerged as a critical bottleneck because data collection has increasingly become high-throughput. This has resulted in data-rich workflows that lack rapid and automated data analytics. To address this issue, the field has been developing software for interpretation of quantitative glycomics studies. Here, we describe a protocol using available informatics tools for analysis of data from analysis of released glycans using high-/ultraperformance liquid chromatography (H/UPLC) coupled with mass spectrometry (MS).
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11
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Luis AS, Jin C, Pereira GV, Glowacki RWP, Gugel SR, Singh S, Byrne DP, Pudlo NA, London JA, Baslé A, Reihill M, Oscarson S, Eyers PA, Czjzek M, Michel G, Barbeyron T, Yates EA, Hansson GC, Karlsson NG, Cartmell A, Martens EC. A single sulfatase is required to access colonic mucin by a gut bacterium. Nature 2021; 598:332-337. [PMID: 34616040 PMCID: PMC9128668 DOI: 10.1038/s41586-021-03967-5] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 08/26/2021] [Indexed: 12/29/2022]
Abstract
Humans have co-evolved with a dense community of microbial symbionts that inhabit the lower intestine. In the colon, secreted mucus creates a barrier that separates these microorganisms from the intestinal epithelium1. Some gut bacteria are able to utilize mucin glycoproteins, the main mucus component, as a nutrient source. However, it remains unclear which bacterial enzymes initiate degradation of the complex O-glycans found in mucins. In the distal colon, these glycans are heavily sulfated, but specific sulfatases that are active on colonic mucins have not been identified. Here we show that sulfatases are essential to the utilization of distal colonic mucin O-glycans by the human gut symbiont Bacteroides thetaiotaomicron. We characterized the activity of 12 different sulfatases produced by this species, showing that they are collectively active on all known sulfate linkages in O-glycans. Crystal structures of three enzymes provide mechanistic insight into the molecular basis of substrate specificity. Unexpectedly, we found that a single sulfatase is essential for utilization of sulfated O-glycans in vitro and also has a major role in vivo. Our results provide insight into the mechanisms of mucin degradation by a prominent group of gut bacteria, an important process for both normal microbial gut colonization2 and diseases such as inflammatory bowel disease3.
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Affiliation(s)
- Ana S Luis
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA.
- Department of Medical Biochemistry, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
| | - Chunsheng Jin
- Department of Medical Biochemistry, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | | | - Robert W P Glowacki
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Sadie R Gugel
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Shaleni Singh
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Dominic P Byrne
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Nicholas A Pudlo
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - James A London
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Arnaud Baslé
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
| | - Mark Reihill
- Centre for Synthesis and Chemical Biology, University College Dublin, Belfield, Dublin, Ireland
| | - Stefan Oscarson
- Centre for Synthesis and Chemical Biology, University College Dublin, Belfield, Dublin, Ireland
| | - Patrick A Eyers
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Mirjam Czjzek
- Sorbonne Université, Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Roscoff, Bretagne, France
| | - Gurvan Michel
- Sorbonne Université, Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Roscoff, Bretagne, France
| | - Tristan Barbeyron
- Sorbonne Université, Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Roscoff, Bretagne, France
| | - Edwin A Yates
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Gunnar C Hansson
- Department of Medical Biochemistry, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Niclas G Karlsson
- Department of Medical Biochemistry, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Alan Cartmell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK.
| | - Eric C Martens
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA.
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12
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Towards a more complete glycome: Advances in ion chromatography-mass spectrometry (IC-MS) for improved separation and analysis of carbohydrates. J Chromatogr B Analyt Technol Biomed Life Sci 2021; 1175:122719. [PMID: 34020151 DOI: 10.1016/j.jchromb.2021.122719] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 04/06/2021] [Accepted: 04/10/2021] [Indexed: 11/23/2022]
Abstract
To date, few tools are available for the analysis of the glycome without derivatization, a process which is known to introduce issues such as differential loss of sialic acid and incomplete labeling. We have previously reported the use of ion chromatography-mass spectrometry (IC-MS) to analyze native sialylated and sulfated glycans. Here, we introduce improvements to IC column technology, enabling the separation of neutral glycans while maintaining charge separation capabilities. When implemented in an IC-MS workflow, this enables the structural characterization of a broad array of chemically distinct glycans. With the newly developed IC column and modified IC-MS instrumentation configuration, we qualitatively investigated O-glycome profiles in bovine fetuin and porcine gastric mucins. The improved chromatographic resolution in combination with high-resolution MS data present a powerful tool for glycan structural identification.
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13
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Importance of evaluating protein glycosylation in pluripotent stem cell-derived cardiomyocytes for research and clinical applications. Pflugers Arch 2021; 473:1041-1059. [PMID: 33830329 PMCID: PMC8245383 DOI: 10.1007/s00424-021-02554-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 03/01/2021] [Accepted: 03/06/2021] [Indexed: 01/21/2023]
Abstract
Proper protein glycosylation is critical to normal cardiomyocyte physiology. Aberrant glycosylation can alter protein localization, structure, drug interactions, and cellular function. The in vitro differentiation of human pluripotent stem cells into cardiomyocytes (hPSC-CM) has become increasingly important to the study of protein function and to the fields of cardiac disease modeling, drug testing, drug discovery, and regenerative medicine. Here, we offer our perspective on the importance of protein glycosylation in hPSC-CM. Protein glycosylation is dynamic in hPSC-CM, but the timing and extent of glycosylation are still poorly defined. We provide new data highlighting how observed changes in hPSC-CM glycosylation may be caused by underlying differences in the protein or transcript abundance of enzymes involved in building and trimming the glycan structures or glycoprotein gene products. We also provide evidence that alternative splicing results in altered sites of glycosylation within the protein sequence. Our findings suggest the need to precisely define protein glycosylation events that may have a critical impact on the function and maturation state of hPSC-CM. Finally, we provide an overview of analytical strategies available for studying protein glycosylation and identify opportunities for the development of new bioinformatic approaches to integrate diverse protein glycosylation data types. We predict that these tools will promote the accurate assessment of protein glycosylation in future studies of hPSC-CM that will ultimately be of significant experimental and clinical benefit.
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14
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Yamada I, Campbell MP, Edwards N, Castro LJ, Lisacek F, Mariethoz J, Ono T, Ranzinger R, Shinmachi D, Aoki-Kinoshita KF. The glycoconjugate ontology (GlycoCoO) for standardizing the annotation of glycoconjugate data and its application. Glycobiology 2021; 31:741-750. [PMID: 33677548 PMCID: PMC8351504 DOI: 10.1093/glycob/cwab013] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 12/31/2020] [Accepted: 01/01/2021] [Indexed: 01/19/2023] Open
Abstract
Recent years have seen great advances in the development of glycoproteomics protocols and methods resulting in a sustainable increase in the reporting proteins, their attached glycans and glycosylation sites. However, only very few of these reports find their way into databases or data repositories. One of the major reasons is the absence of digital standard to represent glycoproteins and the challenging annotations with glycans. Depending on the experimental method, such a standard must be able to represent glycans as complete structures or as compositions, store not just single glycans but also represent glycoforms on a specific glycosylation side, deal with partially missing site information if no site mapping was performed, and store abundances or ratios of glycans within a glycoform of a specific site. To support the above, we have developed the GlycoConjugate Ontology (GlycoCoO) as a standard semantic framework to describe and represent glycoproteomics data. GlycoCoO can be used to represent glycoproteomics data in triplestores and can serve as a basis for data exchange formats. The ontology, database providers and supporting documentation are available online (https://github.com/glycoinfo/GlycoCoO).
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Affiliation(s)
- Issaku Yamada
- Research Department, The Noguchi Institute, 1-9-7 Kaga, Itabashi, Tokyo 173-0003, Japan
| | - Matthew P Campbell
- Institute for Glycomics, Griffith University at Gold Coast, Southport, QLD 4215, Australia
| | - Nathan Edwards
- Department of Biochemistry, Molecular and Cellular Biology, Georgetown University Medical Center, Washington, D.C. 20007, USA
| | - Leyla Jael Castro
- ZB MED Information Centre for Life Sciences, Gleueler Str. 60, 50931 Cologne, Germany
| | - Frederique Lisacek
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Computer Science Department, University of Geneva, route de Drize 7, CH - 1227 Geneva Switzerland, and also Section of Biology, University of Geneva, Geneva, Switzerland
| | - Julien Mariethoz
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, 7 Route de Drize, 1227 Geneva, Switzerland
| | - Tamiko Ono
- Faculty of Science and Engineering, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan
| | - Rene Ranzinger
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Rd, Athens, Georgia 30602, USA
| | - Daisuke Shinmachi
- R&D Department, SparqLite LLC., 1615-22 Ishikawamachi, Hachioji, Tokyo 192-0032, Japan
| | - Kiyoko F Aoki-Kinoshita
- Glycan & Life Science Integration Center (GaLSIC), Faculty of Science and Engineering, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan
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15
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Benktander J, Sundh H, Sundell K, Murugan AVM, Venkatakrishnan V, Padra JT, Kolarevic J, Terjesen BF, Gorissen M, Lindén SK. Stress Impairs Skin Barrier Function and Induces α2-3 Linked N-Acetylneuraminic Acid and Core 1 O-Glycans on Skin Mucins in Atlantic Salmon, Salmo salar. Int J Mol Sci 2021; 22:ijms22031488. [PMID: 33540792 PMCID: PMC7867331 DOI: 10.3390/ijms22031488] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 02/07/2023] Open
Abstract
The skin barrier consists of mucus, primarily comprising highly glycosylated mucins, and the epithelium. Host mucin glycosylation governs interactions with pathogens and stress is associated with impaired epithelial barrier function. We characterized Atlantic salmon skin barrier function during chronic stress (high density) and mucin O-glycosylation changes in response to acute and chronic stress. Fish held at low (LD: 14–30 kg/m3) and high densities (HD: 50-80 kg/m3) were subjected to acute stress 24 h before sampling at 17 and 21 weeks after start of the experiment. Blood parameters indicated primary and secondary stress responses at both sampling points. At the second sampling, skin barrier function towards molecules was reduced in the HD compared to the LD group (Papp mannitol; p < 0.01). Liquid chromatography–mass spectrometry revealed 81 O-glycan structures from the skin. Fish subjected to both chronic and acute stress had an increased proportion of large O-glycan structures. Overall, four of the O-glycan changes have potential as indicators of stress, especially for the combined chronic and acute stress. Stress thus impairs skin barrier function and induces glycosylation changes, which have potential to both affect interactions with pathogens and serve as stress indicators.
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Affiliation(s)
- John Benktander
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Box 440, Medicinaregatan 9C, 405 30 Gothenburg, Sweden; (J.B.); (A.V.M.M.); (V.V.); (J.T.P.)
| | - Henrik Sundh
- Department of Biological and Environmental Sciences, University of Gothenburg, 405 30 Gothenburg, Sweden; (H.S.); (K.S.)
| | - Kristina Sundell
- Department of Biological and Environmental Sciences, University of Gothenburg, 405 30 Gothenburg, Sweden; (H.S.); (K.S.)
| | - Abarna V. M. Murugan
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Box 440, Medicinaregatan 9C, 405 30 Gothenburg, Sweden; (J.B.); (A.V.M.M.); (V.V.); (J.T.P.)
| | - Vignesh Venkatakrishnan
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Box 440, Medicinaregatan 9C, 405 30 Gothenburg, Sweden; (J.B.); (A.V.M.M.); (V.V.); (J.T.P.)
| | - János Tamás Padra
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Box 440, Medicinaregatan 9C, 405 30 Gothenburg, Sweden; (J.B.); (A.V.M.M.); (V.V.); (J.T.P.)
| | | | | | - Marnix Gorissen
- Radboud University, Institute for Water and Wetland Research, Department of Animal Ecology & Physiology, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands;
| | - Sara K. Lindén
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Box 440, Medicinaregatan 9C, 405 30 Gothenburg, Sweden; (J.B.); (A.V.M.M.); (V.V.); (J.T.P.)
- Correspondence: ; Tel.: +46-(0)-31-786-3057
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16
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Lisacek F, Alagesan K, Hayes C, Lippold S, de Haan N. Bioinformatics in Immunoglobulin Glycosylation Analysis. EXPERIENTIA SUPPLEMENTUM (2012) 2021; 112:205-233. [PMID: 34687011 DOI: 10.1007/978-3-030-76912-3_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Analytical methods developed for studying immunoglobulin glycosylation rely heavily on software tailored for this purpose. Many of these tools are now used in high-throughput settings, especially for the glycomic characterization of IgG. A collection of these tools, and the databases they rely on, are presented in this chapter. Specific applications are detailed in examples of immunoglobulin glycomics and glycoproteomics data processing workflows. The results obtained in the glycoproteomics workflow are emphasized with the use of dedicated visualizing tools. These tools enable the user to highlight glycan properties and their differential expression.
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Affiliation(s)
- Frédérique Lisacek
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland.
- Computer Science Department, University of Geneva, Geneva, Switzerland.
- Section of Biology, University of Geneva, Geneva, Switzerland.
| | | | - Catherine Hayes
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
- Computer Science Department, University of Geneva, Geneva, Switzerland
| | - Steffen Lippold
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Noortje de Haan
- Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, Denmark
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17
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Insights into Bioinformatic Applications for Glycosylation: Instigating an Awakening towards Applying Glycoinformatic Resources for Cancer Diagnosis and Therapy. Int J Mol Sci 2020; 21:ijms21249336. [PMID: 33302373 PMCID: PMC7762546 DOI: 10.3390/ijms21249336] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/26/2020] [Accepted: 12/01/2020] [Indexed: 01/10/2023] Open
Abstract
Glycosylation plays a crucial role in various diseases and their etiology. This has led to a clear understanding on the functions of carbohydrates in cell communication, which eventually will result in novel therapeutic approaches for treatment of various disease. Glycomics has now become one among the top ten technologies that will change the future. The direct implication of glycosylation as a hallmark of cancer and for cancer therapy is well established. As in proteomics, where bioinformatics tools have led to revolutionary achievements, bioinformatics resources for glycosylation have improved its practical implication. Bioinformatics tools, algorithms and databases are a mandatory requirement to manage and successfully analyze large amount of glycobiological data generated from glycosylation studies. This review consolidates all the available tools and their applications in glycosylation research. The achievements made through the use of bioinformatics into glycosylation studies are also presented. The importance of glycosylation in cancer diagnosis and therapy is discussed and the gap in the application of widely available glyco-informatic tools for cancer research is highlighted. This review is expected to bring an awakening amongst glyco-informaticians as well as cancer biologists to bridge this gap, to exploit the available glyco-informatic tools for cancer.
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18
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Gill Mucus and Gill Mucin O-glycosylation in Healthy and Amebic Gill Disease-Affected Atlantic Salmon. Microorganisms 2020; 8:microorganisms8121871. [PMID: 33256221 PMCID: PMC7768351 DOI: 10.3390/microorganisms8121871] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/23/2020] [Accepted: 11/24/2020] [Indexed: 01/17/2023] Open
Abstract
Amoebic gill disease (AGD) causes poor performance and death in salmonids. Mucins are mainly comprised by carbohydrates and are main components of the mucus covering the gill. Since glycans regulate pathogen binding and growth, glycosylation changes may affect susceptibility to primary and secondary infections. We investigated gill mucin O-glycosylation from Atlantic salmon with and without AGD using liquid chromatography–mass spectrometry. Gill mucin glycans were larger and more complex, diverse and fucosylated than skin mucins. Confocal microscopy revealed that fucosylated mucus coated sialylated mucus strands in ex vivo gill mucus. Terminal HexNAcs were more abundant among O-glycans from AGD-affected Atlantic salmon, whereas core 1 structures and structures with acidic moieties such as N-acetylneuraminic acid (NeuAc) and sulfate groups were less abundant compared to non-infected fish. The fucosylated and NeuAc-containing O-glycans were inversely proportional, with infected fish on the lower scale of NeuAc abundance and high on fucosylated structures. The fucosylated epitopes were of three types: Fuc-HexNAc-R, Gal-[Fuc-]HexNAc-R and HexNAc-[Fuc-]HexNAc-R. These blood group-like structures could be an avenue to diversify the glycan repertoire to limit infection in the exposed gills. Furthermore, care must be taken when using skin mucus as proxy for gill mucus, as gill mucins are distinctly different from skin mucins.
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19
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Bagdonas H, Ungar D, Agirre J. Leveraging glycomics data in glycoprotein 3D structure validation with Privateer. Beilstein J Org Chem 2020; 16:2523-2533. [PMID: 33093930 PMCID: PMC7554661 DOI: 10.3762/bjoc.16.204] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 10/06/2020] [Indexed: 12/20/2022] Open
Abstract
The heterogeneity, mobility and complexity of glycans in glycoproteins have been, and currently remain, significant challenges in structural biology. These aspects present unique problems to the two most prolific techniques: X-ray crystallography and cryo-electron microscopy. At the same time, advances in mass spectrometry have made it possible to get deeper insights on precisely the information that is most difficult to recover by structure solution methods: the full-length glycan composition, including linkage details for the glycosidic bonds. The developments have given rise to glycomics. Thankfully, several large scale glycomics initiatives have stored results in publicly available databases, some of which can be accessed through API interfaces. In the present work, we will describe how the Privateer carbohydrate structure validation software has been extended to harness results from glycomics projects, and its use to greatly improve the validation of 3D glycoprotein structures.
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Affiliation(s)
- Haroldas Bagdonas
- York Structural Biology Laboratory, Department of Chemistry, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Daniel Ungar
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Jon Agirre
- York Structural Biology Laboratory, Department of Chemistry, University of York, Wentworth Way, York, YO10 5DD, UK
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20
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Flowers SA, Thomsson KA, Ali L, Huang S, Mthembu Y, Regmi SC, Holgersson J, Schmidt TA, Rolfson O, Björkman LI, Sundqvist M, Karlsson-Bengtsson A, Jay GD, Eisler T, Krawetz R, Karlsson NG. Decrease of core 2 O-glycans on synovial lubricin in osteoarthritis reduces galectin-3 mediated crosslinking. J Biol Chem 2020; 295:16023-16036. [PMID: 32928962 DOI: 10.1074/jbc.ra120.012882] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 09/11/2020] [Indexed: 11/06/2022] Open
Abstract
The synovial fluid glycoprotein lubricin (also known as proteoglycan 4) is a mucin-type O-linked glycosylated biological lubricant implicated to be involved in osteoarthritis (OA) development. Lubricin's ability to reduce friction is related to its glycosylation consisting of sialylated and unsialylated Tn-antigens and core 1 and core 2 structures. The glycans on lubricin have also been suggested to be involved in crosslinking and stabilization of the lubricating superficial layer of cartilage by mediating interaction between lubricin and galectin-3. However, with the spectrum of glycans being found on lubricin, the glycan candidates involved in this interaction were unknown. Here, we confirm that the core 2 O-linked glycans mediate this lubricin-galectin-3 interaction, shown by surface plasmon resonance data indicating that recombinant lubricin (rhPRG4) devoid of core 2 structures did not bind to recombinant galectin-3. Conversely, transfection of Chinese hamster ovary cells with the core 2 GlcNAc transferase acting on a mucin-type O-glycoprotein displayed increased galectin-3 binding. Both the level of galectin-3 and the galectin-3 interactions with synovial lubricin were found to be decreased in late-stage OA patients, coinciding with an increase in unsialylated core 1 O-glycans (T-antigens) and Tn-antigens. These data suggest a defect in crosslinking of surface-active molecules in OA and provide novel insights into OA molecular pathology.
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Affiliation(s)
- Sarah A Flowers
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Kristina A Thomsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Liaqat Ali
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Shan Huang
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Yolanda Mthembu
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Suresh C Regmi
- Faculty of Kinesiology, University of Calgary, Calgary, Alberta, Canada
| | - Jan Holgersson
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Tannin A Schmidt
- Biomedical Engineering Department, University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Ola Rolfson
- Department of Orthopaedics, Institute of Clinical Sciences, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Lena I Björkman
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Martina Sundqvist
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anna Karlsson-Bengtsson
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Chalmers University of Technology, Gothenburg, Sweden
| | - Gregory D Jay
- Department of Emergency Medicine, Warren Alpert Medical School and Division of Biomedical Engineering, School of Engineering, Brown University, Providence, Rhode Island, USA
| | - Thomas Eisler
- Department of Clinical Sciences, Danderyd Hospital, Karolinska Institute, Stockholm, Sweden
| | - Roman Krawetz
- Department of Cell Biology and Anatomy, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, Alberta, Canada
| | - Niclas G Karlsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
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21
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Choudhary P, Nagar R, Singh V, Bhat AH, Sharma Y, Rao A. ProGlycProt V2.0, a repository of experimentally validated glycoproteins and protein glycosyltransferases of prokaryotes. Glycobiology 2020; 29:461-468. [PMID: 30835791 DOI: 10.1093/glycob/cwz013] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 02/22/2019] [Accepted: 03/01/2019] [Indexed: 01/05/2023] Open
Abstract
Knowledge of glycosylation status and glycan-pattern of proteins are of considerable medical, academic and application interest. ProGlycProt V2.0 (www.proglycprot.org) therefore, is conceived and maintained as an exclusive web-resource providing comprehensive information on experimentally validated glycoproteins and protein glycosyltransferases (GTs) of prokaryotic origin. The second release of ProGlycProt features a major update with a 191% increase in the total number of entries, manually collected and curated from 607 peer-reviewed publications, on the subject. Protein GTs from prokaryotes that catalyze a varied range of glycan linkages are amenable glycoengineering tools. Therefore, the second release presents content that is greatly expanded and reorganized in two sub-databases: ProGPdb and ProGTdb. While ProGPdb provides information about validated glycoproteins (222 entries), ProGTdb catalogs enzymes/proteins that are instrumental in protein glycosylation, directly (122) or as accessory proteins (182). ProGlycProt V2.0 remains highly cross-referenced yet exclusive and complementary in content to other related databases. The second release further features enhanced search capability, a "compare" entries option and an innovative geoanalytical tool (MapView) facilitating location-assisted search-cum filtering of the entries using geo-positioning information of researchers/groups cited in the ProGlycProt V2.0 databases. Thus, ProGlycProt V2.0 continues to serve as a useful one-point web-resource on various evidence-based information on protein glycosylation in prokaryotes.
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Affiliation(s)
| | - Rupa Nagar
- CSIR-Institute of Microbial Technology, Sector 39 A, Chandigarh, India
| | - Vaidhvi Singh
- CSIR-Institute of Microbial Technology, Sector 39 A, Chandigarh, India
| | | | - Yogita Sharma
- CSIR-Institute of Microbial Technology, Sector 39 A, Chandigarh, India
| | - Alka Rao
- CSIR-Institute of Microbial Technology, Sector 39 A, Chandigarh, India
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22
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Dyukova I, Carrascosa E, Pellegrinelli RP, Rizzo TR. Combining Cryogenic Infrared Spectroscopy with Selective Enzymatic Cleavage for Determining Glycan Primary Structure. Anal Chem 2020; 92:1658-1662. [PMID: 31898462 DOI: 10.1021/acs.analchem.9b04776] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Given the biological relevance and intrinsic structural complexity of glycans, increasing efforts are being directed toward developing a general glycan database that includes information from different analytical methods. As recently demonstrated, cryogenic infrared (IR) spectroscopy is a promising technique for glycan analysis, as it provides unique vibrational fingerprints of specific glycan isomer ions. One of the main goals of a glycan database is the identification and detailed characterization of unknown species. In this work, we combine enzymatic digestion with cryogenic IR-spectroscopy and demonstrate how it can be used for glycan identification. We measured the IR-spectra of a series of cationic glycan standards of increasing complexity and compared them with spectra of the same species after enzymatic cleavage of larger glycans. We show that the cryogenic IR spectra of the cleaved glycans are highly structured and virtually identical to those of standards after both single and multiple cleavages. Our results suggest that the combination of these methods represents a potentially powerful and specific approach for the characterization of unknown glycans.
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Affiliation(s)
- Irina Dyukova
- Laboratoire de Chimie Physique Moléculaire , École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM , Station 6, CH-1015 Lausanne , Switzerland
| | - Eduardo Carrascosa
- Laboratoire de Chimie Physique Moléculaire , École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM , Station 6, CH-1015 Lausanne , Switzerland
| | - Robert P Pellegrinelli
- Laboratoire de Chimie Physique Moléculaire , École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM , Station 6, CH-1015 Lausanne , Switzerland
| | - Thomas R Rizzo
- Laboratoire de Chimie Physique Moléculaire , École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM , Station 6, CH-1015 Lausanne , Switzerland
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23
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Abrahams JL, Taherzadeh G, Jarvas G, Guttman A, Zhou Y, Campbell MP. Recent advances in glycoinformatic platforms for glycomics and glycoproteomics. Curr Opin Struct Biol 2019; 62:56-69. [PMID: 31874386 DOI: 10.1016/j.sbi.2019.11.009] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 11/05/2019] [Accepted: 11/15/2019] [Indexed: 12/16/2022]
Abstract
Protein glycosylation is the most complex and prevalent post-translation modification in terms of the number of proteins modified and the diversity generated. To understand the functional roles of glycoproteins it is important to gain an insight into the repertoire of oligosaccharides present. The comparison and relative quantitation of glycoforms combined with site-specific identification and occupancy are necessary steps in this direction. Computational platforms have continued to mature assisting researchers with the interpretation of such glycomics and glycoproteomics data sets, but frequently support dedicated workflows and users rely on the manual interpretation of data to gain insights into the glycoproteome. The growth of site-specific knowledge has also led to the implementation of machine-learning algorithms to predict glycosylation which is now being integrated into glycoproteomics pipelines. This short review describes commercial and open-access databases and software with an emphasis on those that are actively maintained and designed to support current analytical workflows.
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Affiliation(s)
- Jodie L Abrahams
- Institute for Glycomics, Griffith University, Gold Coast, QLD, Australia
| | - Ghazaleh Taherzadeh
- School of Information and Communication Technology, Griffith University, Gold Coast, QLD, Australia
| | - Gabor Jarvas
- Translational Glycomics Research Group, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, Veszprém, Hungary; Horváth Csaba Laboratory of Bioseparation Sciences, Research Centre for Molecular Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Andras Guttman
- Translational Glycomics Research Group, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, Veszprém, Hungary; Horváth Csaba Laboratory of Bioseparation Sciences, Research Centre for Molecular Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary; SCIEX, Brea, CA, USA
| | - Yaoqi Zhou
- School of Information and Communication Technology, Griffith University, Gold Coast, QLD, Australia
| | - Matthew P Campbell
- Institute for Glycomics, Griffith University, Gold Coast, QLD, Australia.
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24
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Chernyshov IY, Toukach PV. REStLESS: automated translation of glycan sequences from residue-based notation to SMILES and atomic coordinates. Bioinformatics 2019; 34:2679-2681. [PMID: 29547883 DOI: 10.1093/bioinformatics/bty168] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Accepted: 03/13/2018] [Indexed: 11/12/2022] Open
Abstract
Motivation Glycans and glycoconjugates are usually recorded in dedicated databases in residue-based notations. Only a few of them can be converted into chemical (atom-based) formats highly demanded in conformational and biochemical studies. In this work, we present a tool for translation from a residue-based glycan notation to SMILES. Results The REStLESS algorithm for translation from the CSDB Linear notation to SMILES was developed. REStLESS stands for ResiduEs as Smiles and LinkagEs as SmartS, where SMARTS reaction expressions are used to merge pre-encoded residues into a molecule. The implementation supports virtually all structural features reported in natural carbohydrates and glycoconjugates. The translator is equipped with a mechanism for conversion of SMILES strings into optimized atomic coordinates which can be used as starting geometries for various computational tasks. Availability and implementation REStLESS is integrated in the Carbohydrate Structure Database (CSDB) and is freely available on the web (http://csdb.glycoscience.ru/csdb2atoms.html). Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ivan Yu Chernyshov
- All-Russia Research Institute of Agricultural Biotechnology, Laboratory of Plant Stress Tolerance, Russian Academy of Sciences, Moscow, Russia
| | - Philip V Toukach
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Laboratory of Complex and Nano-scaled Catalysts, Moscow, Russia
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25
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Rojas-Macias MA, Mariethoz J, Andersson P, Jin C, Venkatakrishnan V, Aoki NP, Shinmachi D, Ashwood C, Madunic K, Zhang T, Miller RL, Horlacher O, Struwe WB, Watanabe Y, Okuda S, Levander F, Kolarich D, Rudd PM, Wuhrer M, Kettner C, Packer NH, Aoki-Kinoshita KF, Lisacek F, Karlsson NG. Towards a standardized bioinformatics infrastructure for N- and O-glycomics. Nat Commun 2019; 10:3275. [PMID: 31332201 PMCID: PMC6796180 DOI: 10.1038/s41467-019-11131-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 06/24/2019] [Indexed: 12/21/2022] Open
Abstract
The mass spectrometry (MS)-based analysis of free polysaccharides and glycans released from proteins, lipids and proteoglycans increasingly relies on databases and software. Here, we review progress in the bioinformatics analysis of protein-released N- and O-linked glycans (N- and O-glycomics) and propose an e-infrastructure to overcome current deficits in data and experimental transparency. This workflow enables the standardized submission of MS-based glycomics information into the public repository UniCarb-DR. It implements the MIRAGE (Minimum Requirement for A Glycomics Experiment) reporting guidelines, storage of unprocessed MS data in the GlycoPOST repository and glycan structure registration using the GlyTouCan registry, thereby supporting the development and extension of a glycan structure knowledgebase.
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Affiliation(s)
- Miguel A Rojas-Macias
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 40530, Sweden
| | - Julien Mariethoz
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva, 1211, Switzerland
- Computer Science Department, University of Geneva, Geneva, 1227, Switzerland
| | - Peter Andersson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 40530, Sweden
| | - Chunsheng Jin
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 40530, Sweden
| | - Vignesh Venkatakrishnan
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 40530, Sweden
| | - Nobuyuki P Aoki
- Soka University, Hachioji, 192-8577, Tokyo, Japan
- SparqLite LLC., Hachioji, 192-0032, Tokyo, Japan
| | - Daisuke Shinmachi
- Soka University, Hachioji, 192-8577, Tokyo, Japan
- SparqLite LLC., Hachioji, 192-0032, Tokyo, Japan
| | - Christopher Ashwood
- Department of Molecular Sciences, Macquarie University, Sydney, 2109, Australia
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | | | - Tao Zhang
- Leiden University Medical Center, Leiden, 2333ZA, Netherlands
| | - Rebecca L Miller
- Copenhagen Centre for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, København, DK-2200, Denmark
| | - Oliver Horlacher
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva, 1211, Switzerland
| | - Weston B Struwe
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK
| | - Yu Watanabe
- Graduate School of Medical and Dental Sciences, Niigata University, 950-2181, Niigata, Japan
| | - Shujiro Okuda
- Graduate School of Medical and Dental Sciences, Niigata University, 950-2181, Niigata, Japan
| | - Fredrik Levander
- National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Department of Immunotechnology, Lund University, Lund, 22387, Sweden
| | - Daniel Kolarich
- Institute for Glycomics, Gold Coast Campus, Griffith University, Gold Coast, QLD, QLD 4222, Australia
- ARC Centre for Nanoscale BioPhotonics, Macquarie University and Griffith University, North Ryde and Gold Coast, NSW and QLD, NSW 2109 and QLD 4222, Australia
| | - Pauline M Rudd
- Bioprocessing Technology Institute, AStar, Singapore, 138668, Singapore
| | - Manfred Wuhrer
- Leiden University Medical Center, Leiden, 2333ZA, Netherlands
| | | | - Nicolle H Packer
- Department of Molecular Sciences, Macquarie University, Sydney, 2109, Australia
- Institute for Glycomics, Gold Coast Campus, Griffith University, Gold Coast, QLD, QLD 4222, Australia
- ARC Centre for Nanoscale BioPhotonics, Macquarie University and Griffith University, North Ryde and Gold Coast, NSW and QLD, NSW 2109 and QLD 4222, Australia
| | | | - Frédérique Lisacek
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva, 1211, Switzerland
- Computer Science Department, University of Geneva, Geneva, 1227, Switzerland
- Section of Biology, University of Geneva, Geneva, 1211, Switzerland
| | - Niclas G Karlsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 40530, Sweden.
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26
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Jin C, Harvey DJ, Struwe WB, Karlsson NG. Separation of Isomeric O-Glycans by Ion Mobility and Liquid Chromatography–Mass Spectrometry. Anal Chem 2019; 91:10604-10613. [DOI: 10.1021/acs.analchem.9b01772] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Chunsheng Jin
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - David J. Harvey
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Weston B. Struwe
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
- Chemistry Research laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Niclas G. Karlsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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27
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Flowers SA, Lane CS, Karlsson NG. Deciphering Isomers with a Multiple Reaction Monitoring Method for the Complete Detectable O-Glycan Repertoire of the Candidate Therapeutic, Lubricin. Anal Chem 2019; 91:9819-9827. [PMID: 31246420 DOI: 10.1021/acs.analchem.9b01485] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Glycosylation is a fundamental post-translational modification, occurring on half of all proteins. Despite its significance, our understanding is limited, in part due to the inherent difficulty in studying these branched, multi-isomer structures. Accessible, detailed, and quantifiable methods for studying glycans, particularly O-glycans, are needed. Here we take a multiple reaction monitoring (MRM) approach to differentiate and relatively quantify all detectable glycans, including isomers, on the heavily O-glycosylated protein lubricin. Lubricin (proteoglycan 4) is essential for lubrication of the joint and eye. Given the therapeutic potential of lubricin, it is essential to understand its O-glycan repertoire in biological and recombinantly produced samples. O-Glycans were released by reductive β-elimination and defined, showing a range of 26 neutral, sulfated, sialylated, and both sulfated and sialylated core 1 (Galβ1-3GalNAcα1-) and core 2 (Galβ1-3(GlcNAcβ1-6)GalNAcα1-) structures. Isomer-specific MRM transitions allowed effective differentiation of neutral glycan isomers as well as sulfated isomeric structures, where the sulfate was retained on the fragment ions. This strategy was not as effective with labile sialylated structures; instead, it was observed that the optimal collision energy for the m/z 290.1 sialic acid B-fragment differed consistently between sialic acid isomers, allowing differentiation between isomers when fragmentation spectra were insufficient. This approach was also effective for purchased Neu5Acα2-3Galβ1-4Glc and Neu5Acα2-6Galβ1-4Glc and for Neu5Acα2-3Galβ1-4GlcNAc and Neu5Acα2-6Galβ1-4GlcNAc linkage isomers with the Neu5Acα2-6 consistently requiring more energy for optimal generation of the m/z 290.1 fragment. Overall, this method provides an effective and easily accessible approach for the quantification and annotation of complex released O-glycan samples.
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Affiliation(s)
- Sarah A Flowers
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy , University of Gothenburg , Medicinaregatan 9A , 40530 Gothenburg , Sweden.,Department of Neuroscience , Georgetown University , 3970 Reservoir Road NW, New Research Building EP20 , Washington, D.C. , United States
| | - Catherine S Lane
- SCIEX , Phoenix House, Lakeside Drive, Centre Park , Warrington WA1 1RX , United Kingdom
| | - Niclas G Karlsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy , University of Gothenburg , Medicinaregatan 9A , 40530 Gothenburg , Sweden
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28
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Benktander J, Venkatakrishnan V, Padra JT, Sundh H, Sundell K, Murugan AVM, Maynard B, Lindén SK. Effects of Size and Geographical Origin on Atlantic salmon, Salmo salar, Mucin O-Glycan Repertoire. Mol Cell Proteomics 2019; 18:1183-1196. [PMID: 30923042 PMCID: PMC6553937 DOI: 10.1074/mcp.ra119.001319] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 03/27/2019] [Indexed: 11/29/2022] Open
Abstract
Diseases cause ethical concerns and economic losses in the Salmonid industry. The mucus layer comprised of highly O-glycosylated mucins is the first contact between pathogens and fish. Mucin glycans govern pathogen adhesion, growth and virulence. The Atlantic salmon O-glycome from a single location has been characterized and the interindividual variation was low. Because interindividual variation is considered a population-based defense, hindering the entire population from being wiped out by a single infection, low interindividual variation among Atlantic salmon may be a concern. Here, we analyzed the O-glycome of 25 Atlantic salmon from six cohorts grown under various conditions from Sweden, Norway and Australia (Tasmania) using mass spectrometry. This expanded the known Atlantic salmon O-glycome by 60% to 169 identified structures. The mucin O-glycosylation was relatively stable over time within a geographical region, but the size of the fish affected skin mucin glycosylation. The skin mucin glycan repertoires from Swedish and Norwegian Atlantic salmon populations were closely related compared with Tasmanian ones, regardless of size and salinity, with differences in glycan size and composition. The internal mucin glycan repertoire also clustered based on geographical origin and into pyloric cecal and distal intestinal groups, regardless of cohort and fish size. Fucosylated structures were more abundant in Tasmanian pyloric caeca and distal intestine mucins compared with Swedish ones. Overall, Tasmanian Atlantic salmon mucins have more O-glycan structures in skin but less in the gastrointestinal tract compared with Swedish fish. Low interindividual variation was confirmed within each cohort. The results can serve as a library for identifying structures of importance for host-pathogen interactions, understanding population differences of salmon mucin glycosylation in resistance to diseases and during breeding and selection of strains. The results could make it possible to predict potential vulnerabilities to diseases and suggest that inter-region breeding may increase the glycan diversity.
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Affiliation(s)
- John Benktander
- From the ‡Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Box 440, Medicinaregatan 9A, 405 30 Gothenburg, Sweden
| | - Vignesh Venkatakrishnan
- From the ‡Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Box 440, Medicinaregatan 9A, 405 30 Gothenburg, Sweden
| | - János T Padra
- From the ‡Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Box 440, Medicinaregatan 9A, 405 30 Gothenburg, Sweden
| | - Henrik Sundh
- §Department of Biological and Environmental Sciences, University of Gothenburg, Sweden
| | - Kristina Sundell
- §Department of Biological and Environmental Sciences, University of Gothenburg, Sweden
| | - Abarna V M Murugan
- From the ‡Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Box 440, Medicinaregatan 9A, 405 30 Gothenburg, Sweden
| | - Ben Maynard
- ¶The Commonwealth Scientific and Industrial Research Organisation, Hobart, Australia
| | - Sara K Lindén
- From the ‡Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Box 440, Medicinaregatan 9A, 405 30 Gothenburg, Sweden;
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29
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Ashwood C, Pratt B, MacLean BX, Gundry RL, Packer NH. Standardization of PGC-LC-MS-based glycomics for sample specific glycotyping. Analyst 2019; 144:3601-3612. [PMID: 31065629 DOI: 10.1039/c9an00486f] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Porous graphitized carbon (PGC) based chromatography achieves high-resolution separation of glycan structures released from glycoproteins. This approach is especially valuable when resolving structurally similar isomers and for discovery of novel and/or sample-specific glycan structures. However, the implementation of PGC-based separations in glycomics studies has been limited because system-independent retention values have not been established to normalize technical variation. To address this limitation, this study combined the use of hydrolyzed dextran as an internal standard and Skyline software for post-acquisition normalization to reduce retention time and peak area technical variation in PGC-based glycan analyses. This approach allowed assignment of system-independent retention values that are applicable to typical PGC-based glycan separations and supported the construction of a library containing >300 PGC-separated glycan structures with normalized glucose unit (GU) retention values. To enable the automation of this normalization method, a spectral MS/MS library was developed of the dextran ladder, achieving confident discrimination against isomeric glycans. The utility of this approach is demonstrated in two ways. First, to inform the search space for bioinformatically predicted but unobserved glycan structures, predictive models for two structural modifications, core-fucosylation and bisecting GlcNAc, were developed based on the GU library. Second, the applicability of this method for the analysis of complex biological samples is evidenced by the ability to discriminate between cell culture and tissue sample types by the normalized intensity of N-glycan structures alone. Overall, the methods and data described here are expected to support the future development of more automated approaches to glycan identification and quantitation.
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Affiliation(s)
- Christopher Ashwood
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia. and ARC Centre of Excellence for Nanoscale Biophotonics, Macquarie University, Sydney, NSW, Australia and Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Brian Pratt
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Brendan X MacLean
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Rebekah L Gundry
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA and Center for Biomedical Mass Spectrometry Research, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Nicolle H Packer
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia. and ARC Centre of Excellence for Nanoscale Biophotonics, Macquarie University, Sydney, NSW, Australia
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30
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Dang L, Jia L, Zhi Y, Li P, Zhao T, Zhu B, Lan R, Hu Y, Zhang H, Sun S. Mapping human N-linked glycoproteins and glycosylation sites using mass spectrometry. Trends Analyt Chem 2019; 114:143-150. [PMID: 31831916 PMCID: PMC6907083 DOI: 10.1016/j.trac.2019.02.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
N-linked glycoprotein is a highly interesting class of proteins for clinical and biological research. Over the last decade, large-scale profiling of N-linked glycoproteins and glycosylation sites from biological and clinical samples has been achieved through mass spectrometry-based glycoproteomic approaches. In this paper, we reviewed the human glycoproteomic profiles that have been reported in more than 80 individual studies, and mainly focused on the N-glycoproteins and glycosylation sites identified through their deglycosylated forms of glycosite-containing peptides. According to our analyses, more than 30,000 glycosite-containing peptides and 7,000 human glycoproteins have been identified from five different body fluids, twelve human tissues (or related cell lines), and four special cell types. As the glycoproteomic data is still missing for many organs and tissues, a systematical glycoproteomic analysis of various human tissues and body fluids using a uniform platform is still needed for an integrated map of human N-glycoproteomes.
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Affiliation(s)
- Liuyi Dang
- College of Life Sciences, Northwest University, Xi’an, Shaanxi province 710069, China
| | - Li Jia
- College of Life Sciences, Northwest University, Xi’an, Shaanxi province 710069, China
| | - Yuan Zhi
- College of Life Sciences, Northwest University, Xi’an, Shaanxi province 710069, China
| | - Pengfei Li
- College of Life Sciences, Northwest University, Xi’an, Shaanxi province 710069, China
| | - Ting Zhao
- College of Life Sciences, Northwest University, Xi’an, Shaanxi province 710069, China
| | - Bojing Zhu
- College of Life Sciences, Northwest University, Xi’an, Shaanxi province 710069, China
| | - Rongxia Lan
- College of Life Sciences, Northwest University, Xi’an, Shaanxi province 710069, China
| | - Yingwei Hu
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland 21287, USA
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland 21287, USA
| | - Shisheng Sun
- College of Life Sciences, Northwest University, Xi’an, Shaanxi province 710069, China
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31
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Mariethoz J, Alocci D, Gastaldello A, Horlacher O, Gasteiger E, Rojas-Macias M, Karlsson NG, Packer NH, Lisacek F. Glycomics@ExPASy: Bridging the Gap. Mol Cell Proteomics 2018; 17:2164-2176. [PMID: 30097532 PMCID: PMC6210229 DOI: 10.1074/mcp.ra118.000799] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 07/15/2018] [Indexed: 12/28/2022] Open
Abstract
Glycomics@ExPASy (https://www.expasy.org/glycomics) is the glycomics tab of ExPASy, the server of SIB Swiss Institute of Bioinformatics. It was created in 2016 to centralize web-based glycoinformatics resources developed within an international network of glycoscientists. The hosted collection currently includes mainly databases and tools created and maintained at SIB but also links to a range of reference resources popular in the glycomics community. The philosophy of our toolbox is that it should be {glycoscientist AND protein scientist}-friendly with the aim of (1) popularizing the use of bioinformatics in glycobiology and (2) emphasizing the relationship between glycobiology and protein-oriented bioinformatics resources. The scarcity of data bridging these two disciplines led us to design tools as interactive as possible based on database connectivity to facilitate data exploration and support hypothesis building. Glycomics@ExPASy was designed, and is developed, with a long-term vision in close collaboration with glycoscientists to meet as closely as possible the growing needs of the community for glycoinformatics.
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Affiliation(s)
- Julien Mariethoz
- From the ‡Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
- §Computer Science Department, University of Geneva, Geneva, Switzerland
| | - Davide Alocci
- From the ‡Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
- §Computer Science Department, University of Geneva, Geneva, Switzerland
| | - Alessandra Gastaldello
- From the ‡Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
- §Computer Science Department, University of Geneva, Geneva, Switzerland
| | - Oliver Horlacher
- From the ‡Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Elisabeth Gasteiger
- ¶Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Miguel Rojas-Macias
- ‖Glyco Inflammatory Group, Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Niclas G Karlsson
- ‖Glyco Inflammatory Group, Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Nicolle H Packer
- **Institute for Glycomics, Gold Coast Campus, Griffith University, Southport, QLD, Australia
- ‡‡Biomolecular Discovery & Design Research Centre, Macquarie University, North Ryde, NSW, Australia
| | - Frédérique Lisacek
- From the ‡Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland;
- §Computer Science Department, University of Geneva, Geneva, Switzerland
- §§Section of Biology, University of Geneva, Geneva, Switzerland
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32
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Mirgorodskaya E, Karlsson NG, Sihlbom C, Larson G, Nilsson CL. Cracking the Sugar Code by Mass Spectrometry : An Invited Perspective in Honor of Dr. Catherine E. Costello, Recipient of the 2017 ASMS Distinguished Contribution Award. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1065-1074. [PMID: 29644549 PMCID: PMC6003999 DOI: 10.1007/s13361-018-1912-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 02/06/2018] [Accepted: 02/07/2018] [Indexed: 06/08/2023]
Abstract
The structural study of glycans and glycoconjugates is essential to assign their roles in homeostasis, health, and disease. Once dominated by nuclear magnetic resonance spectroscopy, mass spectrometric methods have become the preferred toolbox for the determination of glycan structures at high sensitivity. The patterns of such structures in different cellular states now allow us to interpret the sugar codes in health and disease, based on structure-function relationships. Dr. Catherine E. Costello was the 2017 recipient of the American Society for Mass Spectrometry's Distinguished Contribution Award. In this Perspective article, we describe her seminal work in a historical and geographical context and review the impact of her research accomplishments in the field.8 ᅟ Graphical abstract.
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Affiliation(s)
- Ekaterina Mirgorodskaya
- Proteomics Core Facility, University of Gothenburg, Sahlgrenska Academy, Box 413, SE-405 30, Gothenburg, Sweden
| | - Niclas G Karlsson
- Department of Medical Biochemistry, University of Gothenburg, Sahlgrenska Academy, Box 440, SE-405 30, Gothenburg, Sweden
| | - Carina Sihlbom
- Proteomics Core Facility, University of Gothenburg, Sahlgrenska Academy, Box 413, SE-405 30, Gothenburg, Sweden
| | - Göran Larson
- Department of Clinical Chemistry and Transfusion Medicine, University of Gothenburg, Sahlgrenska Academy, Institute of Biomedicine, SE-413 45, Gothenburg, Sweden
| | - Carol L Nilsson
- Department of Experimental Medical Science, Lund University, SE-223 62, Lund, Sweden.
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33
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Everest-Dass AV, Moh ESX, Ashwood C, Shathili AMM, Packer NH. Human disease glycomics: technology advances enabling protein glycosylation analysis - part 1. Expert Rev Proteomics 2018; 15:165-182. [PMID: 29285957 DOI: 10.1080/14789450.2018.1421946] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
INTRODUCTION Protein glycosylation is recognized as an important post-translational modification, with specific substructures having significant effects on protein folding, conformation, distribution, stability and activity. However, due to the structural complexity of glycans, elucidating glycan structure-function relationships is demanding. The fine detail of glycan structures attached to proteins (including sequence, branching, linkage and anomericity) is still best analysed after the glycans are released from the purified or mixture of glycoproteins (glycomics). The technologies currently available for glycomics are becoming streamlined and standardized and many features of protein glycosylation can now be determined using instruments available in most protein analytical laboratories. Areas covered: This review focuses on the current glycomics technologies being commonly used for the analysis of the microheterogeneity of monosaccharide composition, sequence, branching and linkage of released N- and O-linked glycans that enable the determination of precise glycan structural determinants presented on secreted proteins and on the surface of all cells. Expert commentary: Several emerging advances in these technologies enabling glycomics analysis are discussed. The technological and bioinformatics requirements to be able to accurately assign these precise glycan features at biological levels in a disease context are assessed.
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Affiliation(s)
- Arun V Everest-Dass
- a Biomolecular Discovery and Design Research Centre, Faculty of Science and Engineering , Macquarie University , Sydney , Australia.,b Institute for Glycomics , Griffith University , Gold Coast , Australia.,c ARC Centre for Nanoscale BioPhotonics , Macquarie University , Sydney , Australia
| | - Edward S X Moh
- a Biomolecular Discovery and Design Research Centre, Faculty of Science and Engineering , Macquarie University , Sydney , Australia.,c ARC Centre for Nanoscale BioPhotonics , Macquarie University , Sydney , Australia
| | - Christopher Ashwood
- a Biomolecular Discovery and Design Research Centre, Faculty of Science and Engineering , Macquarie University , Sydney , Australia.,c ARC Centre for Nanoscale BioPhotonics , Macquarie University , Sydney , Australia
| | - Abdulrahman M M Shathili
- a Biomolecular Discovery and Design Research Centre, Faculty of Science and Engineering , Macquarie University , Sydney , Australia.,c ARC Centre for Nanoscale BioPhotonics , Macquarie University , Sydney , Australia
| | - Nicolle H Packer
- a Biomolecular Discovery and Design Research Centre, Faculty of Science and Engineering , Macquarie University , Sydney , Australia.,b Institute for Glycomics , Griffith University , Gold Coast , Australia.,c ARC Centre for Nanoscale BioPhotonics , Macquarie University , Sydney , Australia
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34
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Adamczyk B, Jin C, Polom K, Muñoz P, Rojas-Macias MA, Zeeberg D, Borén M, Roviello F, Karlsson NG. Sample handling of gastric tissue and O-glycan alterations in paired gastric cancer and non-tumorigenic tissues. Sci Rep 2018; 8:242. [PMID: 29321476 PMCID: PMC5762837 DOI: 10.1038/s41598-017-18299-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 12/07/2017] [Indexed: 12/13/2022] Open
Abstract
Sample collection, handling and storage are the most critical steps for ensuring the highest preservation of specimens. Pre-analytical variability can influence the results as protein signatures alter rapidly after tissue excision or during long-term storage. Hence, we evaluated current state-of-the-art biobank preservation methods from a glycomics perspective and analyzed O-glycan alterations occurring in the gastric cancer tissues. Paired tumor and adjacent normal tissue samples were obtained from six patients undergoing gastric cancer surgery. Collected samples (n = 24) were either snap-frozen or heat stabilized and then homogenized. Glycans were released from extracted glycoproteins and analyzed by LC-MS/MS. In total, the relative abundance of 83 O-glycans and 17 derived structural features were used for comparison. There was no statistically significant difference found in variables between snap frozen and heat-stabilized samples, which indicated the two preservation methods were comparable. The data also showed significant changes between normal and cancerous tissue. In addition to a shift from high sialylation in the cancer area towards blood group ABO in the normal area, we also detected that the LacdiNAc epitope (N,N'-diacetyllactosamine) was significantly decreased in cancer samples. The O-glycan alterations that are presented here may provide predictive power for the detection and prognosis of gastric cancer.
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Affiliation(s)
- Barbara Adamczyk
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Chunsheng Jin
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Karol Polom
- Department General Surgery and Surgical Oncology, University of Siena, Siena, Italy
- Department of Surgical Oncology, Medical University of Gdansk, Gdansk, Poland
| | - Pedro Muñoz
- Department of Biochemistry and Molecular Biology III, School of Medicine, Complutense University of Madrid, Madrid, Spain
| | - Miguel A Rojas-Macias
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | | | - Mats Borén
- Denator AB, Uppsala Science Park, Uppsala, Sweden
| | - Franco Roviello
- Department of Medicine, Surgery and Neurosciences, University of Siena, Siena, Italy
| | - Niclas G Karlsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
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35
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Rabus JM, Simmons DR, Maître P, Bythell BJ. Deprotonated carbohydrate anion fragmentation chemistry: structural evidence from tandem mass spectrometry, infra-red spectroscopy, and theory. Phys Chem Chem Phys 2018; 20:27897-27909. [DOI: 10.1039/c8cp02620c] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We investigate the gas-phase structures and fragmentation chemistry of deprotonated carbohydrate anions using combined tandem mass spectrometry, infrared spectroscopy, regioselective labelling, and theory.
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Affiliation(s)
- Jordan M. Rabus
- Department of Chemistry and Biochemistry
- University of Missouri-St. Louis
- St. Louis
- USA
| | - Daniel R. Simmons
- Department of Chemistry and Biochemistry
- University of Missouri-St. Louis
- St. Louis
- USA
| | - Philippe Maître
- Laboratoire de Chimie Physique (UMR8000)
- CNRS
- Univ. Paris-Sud
- Université Paris-Saclay
- Orsay
| | - Benjamin J. Bythell
- Department of Chemistry and Biochemistry
- University of Missouri-St. Louis
- St. Louis
- USA
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36
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Tiemeyer M, Aoki K, Paulson J, Cummings RD, York WS, Karlsson NG, Lisacek F, Packer NH, Campbell MP, Aoki NP, Fujita A, Matsubara M, Shinmachi D, Tsuchiya S, Yamada I, Pierce M, Ranzinger R, Narimatsu H, Aoki-Kinoshita KF. GlyTouCan: an accessible glycan structure repository. Glycobiology 2017; 27:915-919. [PMID: 28922742 PMCID: PMC5881658 DOI: 10.1093/glycob/cwx066] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 07/06/2017] [Accepted: 07/07/2017] [Indexed: 11/12/2022] Open
Abstract
Rapid and continued growth in the generation of glycomic data has revealed the need for enhanced development of basic infrastructure for presenting and interpreting these datasets in a manner that engages the broader biomedical research community. Early in their growth, the genomic and proteomic fields implemented mechanisms for assigning unique gene and protein identifiers that were essential for organizing data presentation and for enhancing bioinformatic approaches to extracting knowledge. Similar unique identifiers are currently absent from glycomic data. In order to facilitate continued growth and expanded accessibility of glycomic data, the authors strongly encourage the glycomics community to coordinate the submission of their glycan structures to the GlyTouCan Repository and to make use of GlyTouCan identifiers in their communications and publications. The authors also deeply encourage journals to recommend a submission workflow in which submitted publications utilize GlyTouCan identifiers as a standard reference for explicitly describing glycan structures cited in manuscripts.
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Affiliation(s)
- Michael Tiemeyer
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Rd, Athens, Georgia 30602, USA
| | - Kazuhiro Aoki
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Rd, Athens, Georgia 30602, USA
| | - James Paulson
- The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Richard D Cummings
- Harvard Medical School, 330 Brookline Ave, Room SL-0408, Boston, MA 02115, USA
| | - William S York
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Rd, Athens, Georgia 30602, USA
| | | | - Frederique Lisacek
- Swiss Institute of Bioinformatics, CUI - 7, route de Drize, CH-1211 Geneva, Switzerland
| | - Nicolle H Packer
- Institute for Glycomics, Gold Coast Campus, Griffith University, Parklands Drive, Gold Coast, QLD 4222, Australia
- Macquarie University, Balaclava Road, North Ryde, NSW 2109, Australia
| | - Matthew P Campbell
- Institute for Glycomics, Gold Coast Campus, Griffith University, Parklands Drive, Gold Coast, QLD 4222, Australia
| | - Nobuyuki P Aoki
- Soka University, 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan
| | - Akihiro Fujita
- Soka University, 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan
| | - Masaaki Matsubara
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Rd, Athens, Georgia 30602, USA
| | | | | | - Issaku Yamada
- The Noguchi Institute, 1-9-7, Kaga, Itabashi-ku, Tokyo 173-0003, Japan
| | - Michael Pierce
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Rd, Athens, Georgia 30602, USA
| | - René Ranzinger
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Rd, Athens, Georgia 30602, USA
| | - Hisashi Narimatsu
- National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-0046, Japan
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37
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Anugraham M, Jacob F, Everest-Dass AV, Schoetzau A, Nixdorf S, Hacker NF, Fink D, Heinzelmann-Schwarz V, Packer NH. Tissue glycomics distinguish tumour sites in women with advanced serous adenocarcinoma. Mol Oncol 2017; 11:1595-1615. [PMID: 28853212 PMCID: PMC5663998 DOI: 10.1002/1878-0261.12134] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Revised: 08/06/2017] [Accepted: 08/11/2017] [Indexed: 11/08/2022] Open
Abstract
In the era of precision medicine, the tailoring of cancer treatment is increasingly important as we transition from organ‐based diagnosis towards a more comprehensive and patient‐centric molecular diagnosis. This is particularly the case for high‐grade serous adenocarcinomas of the ovary and peritoneum, which are commonly diagnosed at an advanced stage, and collectively treated and managed similarly. We characterized the N‐ and O‐glycome of serous ovarian (OC) and peritoneal cancer (PC) tissues using PGC‐LC‐ESI‐IT‐MS/MS profiling and validated the discriminatory glycans and their corresponding glyco‐gene expression levels using cell lines and transcriptomic data from 232 patients. Overall, the N‐ and O‐glycan repertoires of both cancer types were found to comprise mostly of α2,6‐sialylated glycan structures, with the majority of N‐glycans displaying the biantennary mono‐ and disialylation as well as bisecting‐type biantennary glycans. The MS profiling by PGC‐LC also revealed several glycan structural isomers that corresponded to LacdiNAc‐type (GalNAcβ1‐4GlcNAc) motifs that were unique to the serous ovarian cancers and that correlated with elevated gene expression of B4GALNT3 and B4GALNT4 in patients with serous cancer. Statistical evaluation of the discriminatory glycans also revealed 13 N‐ and 3 O‐glycans (P < 0.05) that significantly discriminated tumour‐sampling sites, with LacdiNAc‐type N‐glycans (m/z 1205.02− and m/z 1059.42−) being associated with ovarian‐derived cancer tissue and bisecting GlcNAc‐type (m/z 994.92−) and branched N‐glycans (m/z 1294.02− and m/z 1148.42−) upregulated at the metastatic sites. Hence, we demonstrate for the first time that OC and PC display distinct molecular signatures at both their glycomic and transcriptomic levels. These signatures may have potential utility for the development of accurate diagnosis and personalized treatments.
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Affiliation(s)
- Merrina Anugraham
- Department of Chemistry & Biomolecular Sciences, Biomolecular Discovery & Design Research Centre, Faculty of Science and Engineering, Macquarie University, North Ryde, NSW, Australia.,Glyco-oncology, Ovarian Cancer Research, Department of Biomedicine, University Hospital Basel, University of Basel, Switzerland
| | - Francis Jacob
- Glyco-oncology, Ovarian Cancer Research, Department of Biomedicine, University Hospital Basel, University of Basel, Switzerland
| | - Arun V Everest-Dass
- Department of Chemistry & Biomolecular Sciences, Biomolecular Discovery & Design Research Centre, Faculty of Science and Engineering, Macquarie University, North Ryde, NSW, Australia.,Australian Research Council Centre of Excellence in Nanoscale Biophotonics, Macquarie University, North Ryde, NSW, Australia.,Glycomics Institute, Griffith University, Gold Coast, Queensland, Australia
| | - Andreas Schoetzau
- Ovarian Cancer Research, Department of Biomedicine, University Hospital Basel, University of Basel, Switzerland
| | - Sheri Nixdorf
- Gynecological Research, Adult Cancer Program, Lowy Cancer Research Centre, University of New South Wales, Sydney, Australia
| | - Neville F Hacker
- Royal Hospital for Women, Gynecological Cancer Centre, School of Women's and Children's Health, University of New South Wales, Sydney, Australia
| | - Daniel Fink
- Department of Gynecology, University Hospital Zurich, Switzerland
| | - Viola Heinzelmann-Schwarz
- Ovarian Cancer Research, Department of Biomedicine, University Hospital Basel, University of Basel, Switzerland.,Hospital for Women, Department of Gynecology and Gynecological Oncology, University Hospital Basel, University of Basel, Switzerland
| | - Nicolle H Packer
- Department of Chemistry & Biomolecular Sciences, Biomolecular Discovery & Design Research Centre, Faculty of Science and Engineering, Macquarie University, North Ryde, NSW, Australia.,Australian Research Council Centre of Excellence in Nanoscale Biophotonics, Macquarie University, North Ryde, NSW, Australia.,Glycomics Institute, Griffith University, Gold Coast, Queensland, Australia
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38
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Horlacher O, Jin C, Alocci D, Mariethoz J, Müller M, Karlsson NG, Lisacek F. Glycoforest 1.0. Anal Chem 2017; 89:10932-10940. [PMID: 28901741 DOI: 10.1021/acs.analchem.7b02754] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Tandem mass spectrometry, when combined with liquid chromatography and applied to complex mixtures, produces large amounts of raw data, which needs to be analyzed to identify molecular structures. This technique is widely used, particularly in glycomics. Due to a lack of high throughput glycan sequencing software, glycan spectra are predominantly sequenced manually. A challenge for writing glycan-sequencing software is that there is no direct template that can be used to infer structures detectable in an organism. To help alleviate this bottleneck, we present Glycoforest 1.0, a partial de novo algorithm for sequencing glycan structures based on MS/MS spectra. Glycoforest was tested on two data sets (human gastric and salmon mucosa O-linked glycomes) for which MS/MS spectra were annotated manually. Glycoforest generated the human validated structure for 92% of test cases. The correct structure was found as the best scoring match for 70% and among the top 3 matches for 83% of test cases. In addition, the Glycoforest algorithm detected glycan structures from MS/MS spectra missing a manual annotation. In total 1532 MS/MS previously unannotated spectra were annotated by Glycoforest. A portion containing 521 spectra was manually checked confirming that Glycoforest annotated an additional 50 MS/MS spectra overlooked during manual annotation.
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Affiliation(s)
- Oliver Horlacher
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics , Geneva, 1211, Switzerland.,University of Geneva , Geneva, 1211, Switzerland
| | - Chunsheng Jin
- Glyco Inflammatory Group, Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg , Gothenburg, SE405 30, Sweden
| | - Davide Alocci
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics , Geneva, 1211, Switzerland.,University of Geneva , Geneva, 1211, Switzerland
| | - Julien Mariethoz
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics , Geneva, 1211, Switzerland.,University of Geneva , Geneva, 1211, Switzerland
| | - Markus Müller
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics , Geneva, 1211, Switzerland.,University of Geneva , Geneva, 1211, Switzerland
| | - Niclas G Karlsson
- Glyco Inflammatory Group, Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg , Gothenburg, SE405 30, Sweden
| | - Frederique Lisacek
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics , Geneva, 1211, Switzerland.,University of Geneva , Geneva, 1211, Switzerland
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39
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An J, Jin C, Dėdinaitė A, Holgersson J, Karlsson NG, Claesson PM. Influence of Glycosylation on Interfacial Properties of Recombinant Mucins: Adsorption, Surface Forces, and Friction. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:4386-4395. [PMID: 28431467 DOI: 10.1021/acs.langmuir.7b00030] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Interfacial properties of two brush-with-anchor mucins, C-P55 and C-PSLex, have been investigated at the aqueous solution/poly(methyl methacrylate) (PMMA) interface. Both are recombinant mucin-type fusion proteins, produced by fusing the glycosylated mucin part of P-selectin glycoprotein ligand-1 (PSLG-1) to the Fc part of a mouse immunoglobulin in two different cells. They are mainly expressed as dimers upon production. Analysis of the O-glycans shows that the C-PSLex mucin has the longer and more branched side chains, but C-P55 has slightly higher sialic acid content. The adsorption of the mucins to PMMA surfaces was studied by quartz crystal microbalance with dissipation. The sensed mass, including the adsorbed mucin and water trapped in the layer, was found to be similar for these two mucin layers. Atomic force microscopy with colloidal probe was employed to study surface and friction forces between mucin-coated PMMA surfaces. Purely repulsive forces of steric origin were observed between mucin layers on compression, whereas a small adhesion was detected between both mucin layers on decompression. This was attributed to chain entanglement. The friction force between C-PSLex-coated PMMA is lower than that between C-P55-coated PMMA at low loads, but vice versa at high loads. We discuss our results in terms of the differences in the glycosylation composition of these two mucins.
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Affiliation(s)
- Junxue An
- Department of Chemistry, Division of Surface and Corrosion Science, School of Chemical Science and Engineering, KTH Royal Institute of Technology , Drottning Kristinas väg 51, SE-100 44 Stockholm, Sweden
| | - Chunsheng Jin
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg , SE-405 30 Gothenburg, Sweden
| | - Andra Dėdinaitė
- Department of Chemistry, Division of Surface and Corrosion Science, School of Chemical Science and Engineering, KTH Royal Institute of Technology , Drottning Kristinas väg 51, SE-100 44 Stockholm, Sweden
- Chemistry, Materials and Surfaces, SP Technical Research Institute of Sweden , P.O. Box 5607, SE-114 86 Stockholm, Sweden
| | - Jan Holgersson
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Sahlgrenska University Hospital , Vita stråket 13, SE-413 45 Gothenburg, Sweden
| | - Niclas G Karlsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg , SE-405 30 Gothenburg, Sweden
| | - Per M Claesson
- Department of Chemistry, Division of Surface and Corrosion Science, School of Chemical Science and Engineering, KTH Royal Institute of Technology , Drottning Kristinas väg 51, SE-100 44 Stockholm, Sweden
- Chemistry, Materials and Surfaces, SP Technical Research Institute of Sweden , P.O. Box 5607, SE-114 86 Stockholm, Sweden
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40
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Jin C, Kenny DT, Skoog EC, Padra M, Adamczyk B, Vitizeva V, Thorell A, Venkatakrishnan V, Lindén SK, Karlsson NG. Structural Diversity of Human Gastric Mucin Glycans. Mol Cell Proteomics 2017; 16:743-758. [PMID: 28461410 DOI: 10.1074/mcp.m116.067983] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Indexed: 01/16/2023] Open
Abstract
The mucin O-glycosylation of 10 individuals with and without gastric disease was examined in depth in order to generate a structural map of human gastric glycosylation. In the stomach, these mucins and their O-glycosylation protect the epithelial surface from the acidic gastric juice and provide the first point of interaction for pathogens such as Helicobacter pylori, reported to cause gastritis, gastric and duodenal ulcers and gastric cancer. The rational of the present study was to map the O-glycosylation that the pathogen may come in contact with. An enormous diversity in glycosylation was found, which varied both between individuals and within mucins from a single individual: mucin glycan chain length ranged from 2-13 residues, each individual carried 34-103 O-glycan structures and in total over 258 structures were identified. The majority of gastric O-glycans were neutral and fucosylated. Blood group I antigens, as well as terminal α1,4-GlcNAc-like and GalNAcβ1-4GlcNAc-like (LacdiNAc-like), were common modifications of human gastric O-glycans. Furthemore, each individual carried 1-14 glycan structures that were unique for that individual. The diversity and alterations in gastric O-glycosylation broaden our understanding of the human gastric O-glycome and its implications for gastric cancer research and emphasize that the high individual variation makes it difficult to identify gastric cancer specific structures. However, despite the low number of individuals, we could verify a higher level of sialylation and sulfation on gastric O-glycans from cancerous tissue than from healthy stomachs.
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Affiliation(s)
- Chunsheng Jin
- From the ‡Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Box 440, Medicinaregatan 9A, 405 30 Gothenburg, Sweden
| | - Diarmuid T Kenny
- From the ‡Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Box 440, Medicinaregatan 9A, 405 30 Gothenburg, Sweden
| | - Emma C Skoog
- From the ‡Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Box 440, Medicinaregatan 9A, 405 30 Gothenburg, Sweden
| | - Médea Padra
- From the ‡Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Box 440, Medicinaregatan 9A, 405 30 Gothenburg, Sweden
| | - Barbara Adamczyk
- From the ‡Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Box 440, Medicinaregatan 9A, 405 30 Gothenburg, Sweden
| | - Varvara Vitizeva
- From the ‡Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Box 440, Medicinaregatan 9A, 405 30 Gothenburg, Sweden
| | - Anders Thorell
- §Karolinska Institute, Department for Clinical Science and Department of Surgery, Ersta Hospital, Stockholm, Sweden
| | - Vignesh Venkatakrishnan
- From the ‡Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Box 440, Medicinaregatan 9A, 405 30 Gothenburg, Sweden
| | - Sara K Lindén
- From the ‡Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Box 440, Medicinaregatan 9A, 405 30 Gothenburg, Sweden
| | - Niclas G Karlsson
- From the ‡Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Box 440, Medicinaregatan 9A, 405 30 Gothenburg, Sweden;
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41
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Adua E, Russell A, Roberts P, Wang Y, Song M, Wang W. Innovation Analysis on Postgenomic Biomarkers: Glycomics for Chronic Diseases. ACTA ACUST UNITED AC 2017; 21:183-196. [DOI: 10.1089/omi.2017.0035] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Eric Adua
- School of Medical and Health Sciences, Edith Cowan University, Perth, Australia
| | - Alyce Russell
- School of Medical and Health Sciences, Edith Cowan University, Perth, Australia
| | - Peter Roberts
- School of Medical and Health Sciences, Edith Cowan University, Perth, Australia
| | - Youxin Wang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China
| | - Manshu Song
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China
| | - Wei Wang
- School of Medical and Health Sciences, Edith Cowan University, Perth, Australia
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42
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Jin C, Kenny DT, Skoog EC, Padra M, Adamczyk B, Vitizeva V, Thorell A, Venkatakrishnan V, Lindén SK, Karlsson NG. Structural diversity of human gastric mucin glycans. Mol Cell Proteomics 2017; 16:mcp.M117.067983. [PMID: 28289177 PMCID: PMC5417818 DOI: 10.1074/mcp.m117.067983] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 03/13/2017] [Indexed: 01/14/2023] Open
Abstract
The mucin O-glycosylation of 10 individuals with and without gastric disease was examined in depth in order to generate a structural map of human gastric glycosylation. In the stomach, these mucins and their O-glycosylation protect the epithelial surface from the acidic gastric juice and provide the first point of interaction for pathogens such as Helicobacter pylori, reported to cause gastritis, gastric and duodenal ulcers and gastric cancer. The rational of the present study was to map the O-glycosylation that the pathogen may come in contact with. An enormous diversity in glycosylation was found, which varied both between individuals and within mucins from a single individual: mucin glycan chain length ranged from 2-13 residues, each individual carried 34-103 O-glycan structures and in total over 258 structures were identified. The majority of gastric O-glycans were neutral and fucosylated. Blood group I antigens, as well as terminal α1,4-GlcNAc-like and GalNAcβ1-4GlcNAc-like (LacdiNAc-like), were common modifications of human gastric O-glycans. Furthemore, each individual carried 1-14 glycan structures that were unique for that individual. The diversity and alterations in gastric O-glycosylation broaden our understanding of the human gastric O-glycome and its implications for gastric cancer research and emphasize that the high individual variation makes it difficult to identify gastric cancer specific structures. However, despite the low number of individuals, we could verify a higher level of sialylation and sulfation on gastric O-glycans from cancerous tissue than from healthy stomachs.
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Affiliation(s)
- Chunsheng Jin
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy,, Sweden
| | - Diarmuid T Kenny
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy,, Sweden
| | - Emma C Skoog
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy,, Sweden
| | - Medéa Padra
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy,, Sweden
| | - Barbara Adamczyk
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy,, Sweden
| | - Varvara Vitizeva
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy,, Sweden
| | - Anders Thorell
- Karolinska Institute, Department for Clinical Science and Department of Surgery, Ersta Hospital, Sweden
| | - Vignesh Venkatakrishnan
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy,, Sweden
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43
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Karlsson NG, Jin C, Rojas-Macias MA, Adamczyk B. Next Generation O-Linked Glycomics. TRENDS GLYCOSCI GLYC 2017. [DOI: 10.4052/tigg.1602.1e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Niclas G. Karlsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg
| | - Chunsheng Jin
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg
| | - Miguel A. Rojas-Macias
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg
| | - Barbara Adamczyk
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg
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44
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Campbell MP. A Review of Software Applications and Databases for the Interpretation of Glycopeptide Data. TRENDS GLYCOSCI GLYC 2017. [DOI: 10.4052/tigg.1601.1e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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45
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Campbell MP, Peterson RA, Gasteiger E, Mariethoz J, Lisacek F, Packer NH. Navigating the Glycome Space and Connecting the Glycoproteome. Methods Mol Biol 2017; 1558:139-158. [PMID: 28150237 DOI: 10.1007/978-1-4939-6783-4_7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
UniCarbKB ( http://unicarbkb.org ) is a comprehensive resource for mammalian glycoprotein and annotation data. In particular, the database provides information on the oligosaccharides characterized from a glycoprotein at either the global or site-specific level. This evidence is accumulated from a peer-reviewed and manually curated collection of information on oligosaccharides derived from membrane and secreted glycoproteins purified from biological fluids and/or tissues. This information is further supplemented with experimental method descriptions that summarize important sample preparation and analytical strategies. A new release of UniCarbKB is published every three months, each includes a collection of curated data and improvements to database functionality. In this Chapter, we outline the objectives of UniCarbKB, and describe a selection of step-by-step workflows for navigating the information available. We also provide a short description of web services available and future plans for improving data access. The information presented in this Chapter supplements content available in our knowledgebase including regular updates on interface improvements, new features, and revisions to the database content ( http://confluence.unicarbkb.org ).
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Affiliation(s)
- Matthew P Campbell
- Department of Chemistry and Biomolecular Sciences, Research Drive, Building E8C, Macquarie University, North Ryde, Sydney, 2109, NSW, Australia
| | - Robyn A Peterson
- Department of Chemistry and Biomolecular Sciences, Research Drive, Building E8C, Macquarie University, North Ryde, Sydney, 2109, NSW, Australia
| | - Elisabeth Gasteiger
- Swiss-Prot group, SIB Swiss Institute of Bioinformatics, Battelle - Building A7, Route de Drize, 1227 Carouge, Switzerland
| | - Julien Mariethoz
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Battelle - Building A7, Route de Drize, 1227 Carouge, Switzerland
| | - Frederique Lisacek
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Battelle - Building A7, Route de Drize, 1227 Carouge, Switzerland
- Computer Science Department, University of Geneva, Battelle - Building A7, Route de Drize, 1227 Carouge, Switzerland
| | - Nicolle H Packer
- Department of Chemistry and Biomolecular Sciences, Research Drive, Building E8C, Macquarie University, North Ryde, Sydney, 2109, NSW, Australia.
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Lisacek F, Mariethoz J, Alocci D, Rudd PM, Abrahams JL, Campbell MP, Packer NH, Ståhle J, Widmalm G, Mullen E, Adamczyk B, Rojas-Macias MA, Jin C, Karlsson NG. Databases and Associated Tools for Glycomics and Glycoproteomics. Methods Mol Biol 2017; 1503:235-264. [PMID: 27743371 DOI: 10.1007/978-1-4939-6493-2_18] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The access to biodatabases for glycomics and glycoproteomics has proven to be essential for current glycobiological research. This chapter presents available databases that are devoted to different aspects of glycobioinformatics. This includes oligosaccharide sequence databases, experimental databases, 3D structure databases (of both glycans and glycorelated proteins) and association of glycans with tissue, disease, and proteins. Specific search protocols are also provided using tools associated with experimental databases for converting primary glycoanalytical data to glycan structural information. In particular, researchers using glycoanalysis methods by U/HPLC (GlycoBase), MS (GlycoWorkbench, UniCarb-DB, GlycoDigest), and NMR (CASPER) will benefit from this chapter. In addition we also include information on how to utilize glycan structural information to query databases that associate glycans with proteins (UniCarbKB) and with interactions with pathogens (SugarBind).
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Affiliation(s)
- Frederique Lisacek
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Julien Mariethoz
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Davide Alocci
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Pauline M Rudd
- NIBRT GlycoScience Group, NIBRT-The National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Co., Dublin, Ireland
| | - Jodie L Abrahams
- Biomolecular Frontiers Research Centre, Macquarie University, North Ryde, NSW, Australia
| | - Matthew P Campbell
- Biomolecular Frontiers Research Centre, Macquarie University, North Ryde, NSW, Australia
| | - Nicolle H Packer
- Biomolecular Frontiers Research Centre, Macquarie University, North Ryde, NSW, Australia
| | - Jonas Ståhle
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
| | | | - Barbara Adamczyk
- NIBRT GlycoScience Group, NIBRT-The National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Co., Dublin, Ireland
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Box 440, 405 30, Gothenburg, Sweden
| | - Miguel A Rojas-Macias
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Box 440, 405 30, Gothenburg, Sweden
| | - Chunsheng Jin
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Box 440, 405 30, Gothenburg, Sweden
| | - Niclas G Karlsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Box 440, 405 30, Gothenburg, Sweden.
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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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