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Chittum JE, Thompson A, Desai UR. Glycosaminoglycan microarrays for studying glycosaminoglycan-protein systems. Carbohydr Polym 2024; 335:122106. [PMID: 38616080 PMCID: PMC11032185 DOI: 10.1016/j.carbpol.2024.122106] [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: 01/31/2024] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/16/2024]
Abstract
More than 3000 proteins are now known to bind to glycosaminoglycans (GAGs). Yet, GAG-protein systems are rather poorly understood in terms of selectivity of recognition, molecular mechanism of action, and translational promise. High-throughput screening (HTS) technologies are critically needed for studying GAG biology and developing GAG-based therapeutics. Microarrays, developed within the past two decades, have now improved to the point of being the preferred tool in the HTS of biomolecules. GAG microarrays, in which GAG sequences are immobilized on slides, while similar to other microarrays, have their own sets of challenges and considerations. GAG microarrays are rapidly becoming the first choice in studying GAG-protein systems. Here, we review different modalities and applications of GAG microarrays presented to date. We discuss advantages and disadvantages of this technology, explain covalent and non-covalent immobilization strategies using different chemically reactive groups, and present various assay formats for qualitative and quantitative interpretations, including selectivity screening, binding affinity studies, competitive binding studies etc. We also highlight recent advances in implementing this technology, cataloging of data, and project its future promise. Overall, the technology of GAG microarray exhibits enormous potential of evolving into more than a mere screening tool for studying GAG - protein systems.
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Affiliation(s)
- John E Chittum
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, United States of America; Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, United States of America
| | - Ally Thompson
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, United States of America; Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, United States of America
| | - Umesh R Desai
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, United States of America; Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, United States of America.
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2
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Palomino TV, Muddiman DC. Mass spectrometry imaging of N-linked glycans: Fundamentals and recent advances. MASS SPECTROMETRY REVIEWS 2024. [PMID: 38934211 DOI: 10.1002/mas.21895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 06/06/2024] [Accepted: 06/09/2024] [Indexed: 06/28/2024]
Abstract
With implications in several medical conditions, N-linked glycosylation is one of the most important posttranslation modifications present in all living organisms. Due to their nontemplate synthesis, glycan structures are extraordinarily complex and require multiple analytical techniques for complete structural elucidation. Mass spectrometry is the most common way to investigate N-linked glycans; however, with techniques such as liquid-chromatography mass spectrometry, there is complete loss of spatial information. Mass spectrometry imaging is a transformative analytical technique that can visualize the spatial distribution of ions within a biological sample and has been shown to be a powerful tool to investigate N-linked glycosylation. This review covers the fundamentals of mass spectrometry imaging and N-linked glycosylation and highlights important findings of recent key studies aimed at expanding and improving the glycomics imaging field.
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Affiliation(s)
- Tana V Palomino
- FTMS Laboratory for Human Health Research, Department of Chemistry, North Carolina State University, Raleigh, North Carolina, USA
| | - David C Muddiman
- FTMS Laboratory for Human Health Research, Department of Chemistry, North Carolina State University, Raleigh, North Carolina, USA
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3
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2021-2022. MASS SPECTROMETRY REVIEWS 2024. [PMID: 38925550 DOI: 10.1002/mas.21873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 02/05/2024] [Accepted: 02/12/2024] [Indexed: 06/28/2024]
Abstract
The use of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry for the analysis of carbohydrates and glycoconjugates is a well-established technique and this review is the 12th update of the original article published in 1999 and brings coverage of the literature to the end of 2022. As with previous review, this review also includes a few papers that describe methods appropriate to analysis by MALDI, such as sample preparation, even though the ionization method is not MALDI. The review follows the same format as previous reviews. It is divided into three sections: (1) general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, quantification and the use of computer software for structural identification. (2) Applications to various structural types such as oligo- and polysaccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals, and (3) other general areas such as medicine, industrial processes, natural products and glycan synthesis where MALDI is extensively used. Much of the material relating to applications is presented in tabular form. MALDI is still an ideal technique for carbohydrate analysis, particularly in its ability to produce single ions from each analyte and advancements in the technique and range of applications show little sign of diminishing.
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Nilsson J, Eriksson P, Naguib MM, Jax E, Sihlbom C, Olsson BM, Lundkvist Å, Olsen B, Järhult JD, Larson G, Ellström P. Expression of influenza A virus glycan receptor candidates in mallard, chicken, and tufted duck. Glycobiology 2024; 34:cwad098. [PMID: 38127648 PMCID: PMC10987293 DOI: 10.1093/glycob/cwad098] [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: 06/14/2023] [Revised: 11/09/2023] [Accepted: 11/28/2023] [Indexed: 12/23/2023] Open
Abstract
Influenza A virus (IAV) pandemics result from interspecies transmission events within the avian reservoir and further into mammals including humans. Receptor incompatibility due to differently expressed glycan structures between species has been suggested to limit zoonotic IAV transmission from the wild bird reservoir as well as between different bird species. Using glycoproteomics, we have studied the repertoires of expressed glycan structures with focus on putative sialic acid-containing glycan receptors for IAV in mallard, chicken and tufted duck; three bird species with different roles in the zoonotic ecology of IAV. The methodology used pinpoints specific glycan structures to specific glycosylation sites of identified glycoproteins and was also used to successfully discriminate α2-3- from α2-6-linked terminal sialic acids by careful analysis of oxonium ions released from glycopeptides in tandem MS/MS (MS2), and MS/MS/MS (MS3). Our analysis clearly demonstrated that all three bird species can produce complex N-glycans including α2-3-linked sialyl Lewis structures, as well as both N- and O- glycans terminated with both α2-3- and α2-6-linked Neu5Ac. We also found the recently identified putative IAV receptor structures, Man-6P N-glycopeptides, in all tissues of the three bird species. Furthermore, we found many similarities in the repertoires of expressed receptors both between the bird species investigated and to previously published data from pigs and humans. Our findings of sialylated glycan structures, previously anticipated to be mammalian specific, in all three bird species may have major implications for our understanding of the role of receptor incompatibility in interspecies transmission of IAV.
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Affiliation(s)
- Jonas Nilsson
- Department of Laboratory Medicine, University of Gothenburg, Sahlgrenska University Hospital, Vita Stråket 12, Gothenburg SE-413 45, Sweden
- Laboratory of Clinical Chemistry, Sahlgrenska University Hospital, Bruna Stråket 16, Gothenburg SE-413 45, Sweden
- Proteomics Core Facility, University of Gothenburg, Sahlgrenska Academy, Medicinaregatan 9E, Gothenburg SE-405 30, Sweden
| | - Per Eriksson
- Zoonosis Science Center, Department of Medical Sciences, Husargatan 3, Uppsala University, Uppsala, SE-75185, Sweden
| | - Mahmoud M Naguib
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Husargatan 3, Uppsala University, Uppsala, SE-75237, Sweden
| | - Elinor Jax
- Department of Migration, Max Planck Institute of Animal Behavior, Am Obstberg 1, Radolfzell, Baden-Württemberg DE-78315, Germany
| | - Carina Sihlbom
- Proteomics Core Facility, University of Gothenburg, Sahlgrenska Academy, Medicinaregatan 9E, Gothenburg SE-405 30, Sweden
| | - Britt-Marie Olsson
- Proteomics Core Facility, University of Gothenburg, Sahlgrenska Academy, Medicinaregatan 9E, Gothenburg SE-405 30, Sweden
| | - Åke Lundkvist
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Husargatan 3, Uppsala University, Uppsala, SE-75237, Sweden
| | - Björn Olsen
- Zoonosis Science Center, Department of Medical Sciences, Husargatan 3, Uppsala University, Uppsala, SE-75185, Sweden
| | - Josef D Järhult
- Zoonosis Science Center, Department of Medical Sciences, Husargatan 3, Uppsala University, Uppsala, SE-75185, Sweden
| | - Göran Larson
- Department of Laboratory Medicine, University of Gothenburg, Sahlgrenska University Hospital, Vita Stråket 12, Gothenburg SE-413 45, Sweden
- Laboratory of Clinical Chemistry, Sahlgrenska University Hospital, Bruna Stråket 16, Gothenburg SE-413 45, Sweden
| | - Patrik Ellström
- Zoonosis Science Center, Department of Medical Sciences, Husargatan 3, Uppsala University, Uppsala, SE-75185, Sweden
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Atanasova D, Mirgorodskaya E, Moparthi L, Koch S, Haarhaus M, Narisawa S, Millán JL, Landberg E, Magnusson P. Glycoproteomic profile of human tissue-nonspecific alkaline phosphatase expressed in osteoblasts. JBMR Plus 2024; 8:ziae006. [PMID: 38505526 PMCID: PMC10945725 DOI: 10.1093/jbmrpl/ziae006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/10/2024] [Accepted: 01/11/2024] [Indexed: 03/21/2024] Open
Abstract
Tissue-nonspecific alkaline phosphatase (TNALP) is a glycoprotein expressed by osteoblasts that promotes bone mineralization. TNALP catalyzes the hydrolysis of the mineralization inhibitor inorganic pyrophosphate and ATP to provide inorganic phosphate, thus controlling the inorganic pyrophosphate/inorganic phosphate ratio to enable the growth of hydroxyapatite crystals. N-linked glycosylation of TNALP is essential for protein stability and enzymatic activity and is responsible for the presence of different bone isoforms of TNALP associated with functional and clinical differences. The site-specific glycosylation profiles of TNALP are, however, elusive. TNALP has 5 potential N-glycosylation sites located at the asparagine (N) residues 140, 230, 271, 303, and 430. The objective of this study was to reveal the presence and structure of site-specific glycosylation in TNALP expressed in osteoblasts. Calvarial osteoblasts derived from Alpl+/- expressing SV40 Large T antigen were transfected with soluble epitope-tagged human TNALP. Purified TNALP was analyzed with a lectin microarray, matrix-assisted laser desorption/ionization-time of flight mass spectrometry, and liquid chromatography with tandem mass spectrometry. The results showed that all sites (n = 5) were fully occupied predominantly with complex-type N-glycans. High abundance of galactosylated biantennary N-glycans with various degrees of sialylation was observed on all sites, as well as glycans with no terminal galactose and sialic acid. Furthermore, all sites had core fucosylation except site N271. Modelling of TNALP, with the protein structure prediction software ColabFold, showed possible steric hindrance by the adjacent side chain of W270, which could explain the absence of core fucosylation at N271. These novel findings provide evidence for N-linked glycosylation on all 5 sites of TNALP, as well as core fucosylation on 4 out of 5 sites. We anticipate that this new knowledge can aid in the development of functional and clinical assays specific for the TNALP bone isoforms.
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Affiliation(s)
- Diana Atanasova
- Department of Clinical Chemistry, and Department of Biomedical and Clinical Sciences, Linköping University, Linköping SE-58185, Sweden
| | - Ekaterina Mirgorodskaya
- Proteomics Core Facility, Sahlgrenska Academy, University of Gothenburg, Gothenburg SE-41346, Sweden
| | - Lavanya Moparthi
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping SE-58185, Sweden
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping SE-58185, Sweden
| | - Stefan Koch
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping SE-58185, Sweden
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping SE-58185, Sweden
| | - Mathias Haarhaus
- Division of Renal Medicine, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Karolinska University Hospital, Stockholm SE-14186, Sweden
| | - Sonoko Narisawa
- Sanford Children’s Health Research Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, United States
| | - José Luis Millán
- Sanford Children’s Health Research Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, United States
| | - Eva Landberg
- Department of Clinical Chemistry, and Department of Biomedical and Clinical Sciences, Linköping University, Linköping SE-58185, Sweden
| | - Per Magnusson
- Department of Clinical Chemistry, and Department of Biomedical and Clinical Sciences, Linköping University, Linköping SE-58185, Sweden
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Takahashi Y, Shiota M, Fujita A, Yamada I, Aoki-Kinoshita KF. GlyComb: A novel glycoconjugate data repository that bridges glycomics and proteomics. J Biol Chem 2024; 300:105624. [PMID: 38176651 PMCID: PMC10850976 DOI: 10.1016/j.jbc.2023.105624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 12/03/2023] [Accepted: 12/26/2023] [Indexed: 01/06/2024] Open
Abstract
The glycosylation of proteins and lipids is known to be closely related to the mechanisms of various diseases such as influenza, cancer, and muscular dystrophy. Therefore, it has become clear that the analysis of post-translational modifications of proteins, including glycosylation, is important to accurately understand the functions of each protein molecule and the interactions among them. In order to conduct large-scale analyses more efficiently, it is essential to promote the accumulation, sharing, and reuse of experimental and analytical data in accordance with the FAIR (Findability, Accessibility, Interoperability, and Re-usability) data principles. However, a FAIR data repository for storing and sharing glycoconjugate information, including glycopeptides and glycoproteins, in a standardized format did not exist. Therefore, we have developed GlyComb (https://glycomb.glycosmos.org) as a new standardized data repository for glycoconjugate data. Currently, GlyComb can assign a unique identifier to a set of glycosylation information associated with a specific peptide sequence or UniProt ID. By standardizing glycoconjugate data via GlyComb identifiers and coordinating with existing web resources such as GlyTouCan and GlycoPOST, a comprehensive system for data submission and data sharing among researchers can be established. Here we introduce how GlyComb is able to integrate the variety of glycoconjugate data already registered in existing data repositories to obtain a better understanding of the available glycopeptides and glycoproteins, and their glycosylation patterns. We also explain how this system can serve as a foundation for a better understanding of glycan function.
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Affiliation(s)
- Yushi Takahashi
- Department of Bioinformatics, Graduate School of Engineering, Soka University, Tokyo, Japan
| | - Masaaki Shiota
- Glycan and Life Systems Integration Center, Faculty of Science and Engineering, Soka University, Tokyo, Japan
| | - Akihiro Fujita
- Glycan and Life Systems Integration Center, Faculty of Science and Engineering, Soka University, Tokyo, Japan
| | - Issaku Yamada
- Laboratory of Glycoinformatics, The Noguchi Institute, Tokyo, Japan
| | - Kiyoko F Aoki-Kinoshita
- Department of Bioinformatics, Graduate School of Engineering, Soka University, Tokyo, Japan; Glycan and Life Systems Integration Center, Faculty of Science and Engineering, Soka University, Tokyo, Japan.
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Chernykh A, Abrahams JL, Grant OC, Kambanis L, Sumer-Bayraktar Z, Ugonotti J, Kawahara R, Corcilius L, Payne RJ, Woods RJ, Thaysen-Andersen M. Position-specific N- and O-glycosylation of the reactive center loop impacts neutrophil elastase-mediated proteolysis of corticosteroid-binding globulin. J Biol Chem 2024; 300:105519. [PMID: 38042488 PMCID: PMC10784704 DOI: 10.1016/j.jbc.2023.105519] [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: 03/21/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/04/2023] Open
Abstract
Corticosteroid-binding globulin (CBG) delivers anti-inflammatory cortisol to inflamed tissues through proteolysis of an exposed reactive center loop (RCL) by neutrophil elastase (NE). We previously demonstrated that RCL-localized Asn347-linked N-glycans impact NE proteolysis, but a comprehensive structure-function characterization of the RCL glycosylation is still required to better understand CBG glycobiology. Herein, we first performed RCL-centric glycoprofiling of serum-derived CBG to elucidate the Asn347-glycans and then used molecular dynamics simulations to study their impact on NE proteolysis. Importantly, we also identified O-glycosylation (di/sialyl T) across four RCL sites (Thr338/Thr342/Thr345/Ser350) of serum CBG close to the NE-targeted Val344-Thr345 cleavage site. A restricted N- and O-glycan co-occurrence pattern on the RCL involving exclusively Asn347 and Thr338 glycosylation was experimentally observed and supported in silico by modeling of a CBG-GalNAc-transferase (GalNAc-T) complex with various RCL glycans. GalNAc-T2 and GalNAc-T3 abundantly expressed by liver and gall bladder, respectively, showed in vitro a capacity to transfer GalNAc (Tn) to multiple RCL sites suggesting their involvement in RCL O-glycosylation. Recombinant CBG was then used to determine roles of RCL O-glycosylation through longitudinal NE-centric proteolysis experiments, which demonstrated that both sialoglycans (disialyl T) and asialoglycans (T) decorating Thr345 inhibit NE proteolysis. Synthetic RCL O-glycopeptides expanded on these findings by showing that Thr345-Tn and Thr342-Tn confer strong and moderate protection against NE cleavage, respectively. Molecular dynamics substantiated that short Thr345-linked O-glycans abrogate NE interactions. In conclusion, we report on biologically relevant CBG RCL glycosylation events, which improve our understanding of mechanisms governing cortisol delivery to inflamed tissues.
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Affiliation(s)
- Anastasia Chernykh
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Jodie L Abrahams
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia; Glycosciences Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
| | - Oliver C Grant
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Lucas Kambanis
- School of Chemistry, The University of Sydney, Sydney, New South Wales, Australia; Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Zeynep Sumer-Bayraktar
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia; Glycometabolic Biochemistry Team, Cluster of Pioneering Research, RIKEN, Wako, Saitama, Japan
| | - Julian Ugonotti
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Rebeca Kawahara
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia; Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, Japan
| | - Leo Corcilius
- School of Chemistry, The University of Sydney, Sydney, New South Wales, Australia; Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Richard J Payne
- School of Chemistry, The University of Sydney, Sydney, New South Wales, Australia; Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Robert J Woods
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Morten Thaysen-Andersen
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia; Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, Japan.
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8
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Jin C, Venkatakrishnan V, Thomsson KA, Aoki NP, Shinmachi D, Aoki-Kinoshita KF, Hayes CA, Lisacek F, Karlsson NG. UniCarb-DB: An MS/MS Experimental Glycomic Fragmentation Database. Methods Mol Biol 2024; 2836:77-96. [PMID: 38995537 DOI: 10.1007/978-1-0716-4007-4_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
Glycosylation is a unique posttranslational modification that dynamically shapes the surface of cells. Glycans attached to proteins or lipids in a cell or tissue are studied as a whole and collectively designated as a glycome. UniCarb-DB is a glycomic spectral library of tandem mass spectrometry (MS/MS) fragment data. The current version of the database consists of over 1500 entries and over 1000 unique structures. Each entry contains parent ion information with associated MS/MS spectra, metadata about the original publication, experimental conditions, and biological origin. Each structure is also associated with the GlyTouCan glycan structure repository allowing easy access to other glycomic resources. The database can be directly utilized by mass spectrometry (MS) experimentalists through the conversion of data generated by MS into structural information. Flexible online search tools along with a downloadable version of the database are easily incorporated in either commercial or open-access MS software. This chapter highlights UniCarb-DB online search tool to browse differences of isomeric structures between spectra, a peak matching search between user-generated MS/MS spectra and spectra stored in UniCarb-DB and more advanced MS tools for combined quantitative and qualitative glycomics.
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Affiliation(s)
- 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
| | - Nobuyuki P Aoki
- Soka University, Hachioji, Tokyo, Japan
- SparqLite.com, Hachioji, Tokyo, Japan
| | | | | | - Catherine A Hayes
- 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
| | - Frédérique Lisacek
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Niclas G Karlsson
- Proteomics Core Facility at Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
- Division of Pharmacy, Department of Life Science and Health, Faculty of Health Science, Oslo Metropolitan University, Oslo, Norway.
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9
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Šimunović J, Gašperšič J, Černigoj U, Vidič J, Štrancar A, Novokmet M, Razdorov G, Pezer M, Lauc G, Trbojević-Akmačić I. High-throughput immunoaffinity enrichment and N-glycan analysis of human plasma haptoglobin. Biotechnol Bioeng 2023; 120:491-502. [PMID: 36324280 DOI: 10.1002/bit.28280] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/24/2022] [Accepted: 10/30/2022] [Indexed: 11/06/2022]
Abstract
Haptoglobin (Hp) is a positive acute phase protein, synthesized in the liver, with four N-glycosylation sites carrying mainly complex type N-glycans. Its glycosylation is altered in different types of diseases but still has not been extensively studied mainly due to analytical challenges, especially the lack of a fast, efficient, and robust high-throughput Hp isolation procedure. Here, we describe the development of a high-throughput method for Hp enrichment from human plasma, based on monolithic chromatographic support in immunoaffinity mode and downstream Hp N-glycome analysis by hydrophilic interaction ultrahigh-performance liquid chromatography with fluorescent detection (HILIC-UHPLC-FLR). Chromatographic monolithic supports in a 96-well format enable fast, efficient, and robust Hp enrichment directly from diluted plasma samples. The N-glycome analysis demonstrated that a degree of Hp deglycosylation differs depending on the conditions used for N-glycan release and on the specific glycosylation site, with Asn 241 being the most resistant to deglycosylation under tested conditions. HILIC-UHPLC-FLR analysis enables robust quantification of 28 individual chromatographic peaks, in which N-glycan compositions were determined by UHPLC coupled to electrospray ionization quadrupole time of flight mass spectrometry. The developed analytical approach enables fast evaluation of total Hp N-glycosylation and is applicable in large-scale studies.
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Affiliation(s)
| | | | - Urh Černigoj
- Sartorius BIA Separations d.o.o., Ajdovščina, Slovenia
| | - Jana Vidič
- Sartorius BIA Separations d.o.o., Ajdovščina, Slovenia
| | - Aleš Štrancar
- Sartorius BIA Separations d.o.o., Ajdovščina, Slovenia
| | | | | | - Marija Pezer
- Genos Glycoscience Research Laboratory, Zagreb, Croatia
| | - Gordan Lauc
- Genos Glycoscience Research Laboratory, Zagreb, Croatia.,Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia
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10
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Beihammer G, Romero-Pérez A, Maresch D, Figl R, Mócsai R, Grünwald-Gruber C, Altmann F, Van Damme EJM, Strasser R. Pseudomonas syringae DC3000 infection increases glucosylated N-glycans in Arabidopsis thaliana. Glycoconj J 2023; 40:97-108. [PMID: 36269466 PMCID: PMC9925501 DOI: 10.1007/s10719-022-10084-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 09/26/2022] [Accepted: 09/29/2022] [Indexed: 11/04/2022]
Abstract
Studying the interaction between the hemibiotrophic bacterium Pseudomonas syringae pv. tomato DC3000 and Arabidopsis thaliana has shed light onto the various forms of mechanisms plants use to defend themselves against pathogen attack. While a lot of emphasis has been put on investigating changes in protein expression in infected plants, only little information is available on the effect infection plays on the plants N-glycan composition. To close this gap in knowledge, total N-glycans were enriched from P. syringae DC3000-infected and mock treated Arabidopsis seedlings and analyzed via MALDI-TOF-MS. Additionally, fluorescently labelled N-glycans were quantified via HPLC-FLD. N-glycans from infected plants were overall less processed and displayed increased amounts of oligomannosidic N-glycans. As multiple peaks for certain oligomannosidic glycoforms were detected upon separation via liquid chromatography, a porous graphitic carbon (PGC)-analysis was conducted to separate individual N-glycan isomers. Indeed, multiple different N-glycan isomers with masses of two N-acetylhexosamine residues plus 8, 9 or 10 hexoses were detected in the infected plants which were absent in the mock controls. Treatment with jack bean α-mannosidase resulted in incomplete removal of hexoses from these N-glycans, indicating the presence of glucose residues. This hints at the accumulation of misfolded glycoproteins in the infected plants, likely because of endoplasmic reticulum (ER) stress. In addition, poly-hexose structures susceptible to α-amylase treatment were found in the DC3000-infected plants, indicating alterations in starch metabolism due to the infection process.
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Affiliation(s)
- Gernot Beihammer
- Institute of Plant Biotechnology and Cell Biology, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Andrea Romero-Pérez
- Laboratory of Biochemistry and Glycobiology, Department of Biotechnology, Ghent University, Ghent, Belgium
| | - Daniel Maresch
- Institute of Biochemistry, Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria
- Core Facility Mass Spectrometry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Rudolf Figl
- Institute of Biochemistry, Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria
- Core Facility Mass Spectrometry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Réka Mócsai
- Institute of Biochemistry, Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Clemens Grünwald-Gruber
- Institute of Biochemistry, Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria
- Core Facility Mass Spectrometry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Friedrich Altmann
- Institute of Biochemistry, Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Els J M Van Damme
- Laboratory of Biochemistry and Glycobiology, Department of Biotechnology, Ghent University, Ghent, Belgium
| | - Richard Strasser
- Institute of Plant Biotechnology and Cell Biology, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria.
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11
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2019-2020. MASS SPECTROMETRY REVIEWS 2022:e21806. [PMID: 36468275 DOI: 10.1002/mas.21806] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
This review is the tenth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2020. Also included are papers that describe methods appropriate to analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. The review is basically divided into three sections: (1) general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, quantification and the use of arrays. (2) Applications to various structural types such as oligo- and polysaccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals, and (3) other areas such as medicine, industrial processes and glycan synthesis where MALDI is extensively used. Much of the material relating to applications is presented in tabular form. The reported work shows increasing use of incorporation of new techniques such as ion mobility and the enormous impact that MALDI imaging is having. MALDI, although invented nearly 40 years ago is still an ideal technique for carbohydrate analysis and advancements in the technique and range of applications show little sign of diminishing.
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Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
- Department of Chemistry, University of Oxford, Oxford, Oxfordshire, United Kingdom
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12
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Rasheduzzaman M, Murugan AVM, Zhang X, Oliveira T, Dolcetti R, Kenny L, Johnson NW, Kolarich D, Punyadeera C. Head and neck cancer N-glycome traits are cell line and HPV status–dependent. Anal Bioanal Chem 2022; 414:8401-8411. [DOI: 10.1007/s00216-022-04376-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 10/05/2022] [Accepted: 10/10/2022] [Indexed: 11/29/2022]
Abstract
Abstract
Glycosylation is the most common post-translational modification of proteins, and glycosylation changes at cell surfaces are frequently associated with malignant epithelia including head and neck squamous cell carcinoma (HNSCC). In HNSCC, 5-year survival remains poor, averaging around 50% globally: this is partly related to late diagnosis. Specific protein glycosylation signatures on malignant keratinocytes have promise as diagnostic and prognostic biomarkers and as therapeutic targets. Nevertheless, HNSCC-specific glycome is to date largely unknown. Herein, we tested six established HNSCC cell lines to capture the qualitative and semi-quantitative N-glycome using porous graphitized carbon liquid chromatography coupled to electrospray ionisation tandem mass spectrometry. Oligomannose-type N-glycans were the predominant features in all HNSCC cell lines analysed (57.5–70%). The levels of sialylated N-glycans showed considerable cell line-dependent differences ranging from 24 to 35%. Importantly, α2-6 linked sialylated N-glycans were dominant across most HNSCC cell lines except in SCC-9 cells where similar levels of α2-6 and α2-3 sialylated N-glycans were observed. Furthermore, we found that HPV-positive cell lines contained higher levels of phosphorylated oligomannose N-glycans, which hint towards an upregulation of lysosomal pathways. Almost all fucose-type N-glycans carried core-fucose residues with just minor levels (< 4%) of Lewis-type fucosylation identified. We also observed paucimannose-type N-glycans (2–5.5%), though in low levels. Finally, we identified oligomannose N-glycans carrying core-fucose residues and confirmed their structure by tandem mass spectrometry. This first systematic mapping of the N-glycome revealed diverse and specific glycosylation features in HNSCC, paving the way for further studies aimed at assessing their possible diagnostic relevance.
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13
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Trbojević-Akmačić I, Lageveen-Kammeijer GSM, Heijs B, Petrović T, Deriš H, Wuhrer M, Lauc G. High-Throughput Glycomic Methods. Chem Rev 2022; 122:15865-15913. [PMID: 35797639 PMCID: PMC9614987 DOI: 10.1021/acs.chemrev.1c01031] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Glycomics aims to identify the structure and function of the glycome, the complete set of oligosaccharides (glycans), produced in a given cell or organism, as well as to identify genes and other factors that govern glycosylation. This challenging endeavor requires highly robust, sensitive, and potentially automatable analytical technologies for the analysis of hundreds or thousands of glycomes in a timely manner (termed high-throughput glycomics). This review provides a historic overview as well as highlights recent developments and challenges of glycomic profiling by the most prominent high-throughput glycomic approaches, with N-glycosylation analysis as the focal point. It describes the current state-of-the-art regarding levels of characterization and most widely used technologies, selected applications of high-throughput glycomics in deciphering glycosylation process in healthy and disease states, as well as future perspectives.
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Affiliation(s)
| | | | - Bram Heijs
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Tea Petrović
- Genos,
Glycoscience Research Laboratory, Borongajska cesta 83H, 10 000 Zagreb, Croatia
| | - Helena Deriš
- Genos,
Glycoscience Research Laboratory, Borongajska cesta 83H, 10 000 Zagreb, Croatia
| | - Manfred Wuhrer
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Gordan Lauc
- Genos,
Glycoscience Research Laboratory, Borongajska cesta 83H, 10 000 Zagreb, Croatia
- Faculty
of Pharmacy and Biochemistry, University
of Zagreb, A. Kovačića 1, 10 000 Zagreb, Croatia
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14
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Marty MT. Fundamentals: How Do We Calculate Mass, Error, and Uncertainty in Native Mass Spectrometry? JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1807-1812. [PMID: 36130030 DOI: 10.1021/jasms.2c00218] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Mass spectrometry (MS) is uniquely powerful for measuring the mass of intact proteins and other biomolecules. New applications have expanded intact protein analysis into biopharmaceuticals, native MS, and top-down proteomics, all of which have driven the need for more automated data-processing pipelines. However, key metrics in the field are often not precisely defined. For example, there are different views on how to calculate uncertainty from spectra. This Critical Insight will explore the different definitions of mass, error, and uncertainty. It will discuss situations where different definitions may be more suitable and provide recommendations for best practices. Targeting both beginners and experts, the goal of the discussion is to provide a common foundation of terminology, enhance statistical rigor, and improve automation of data analysis.
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Affiliation(s)
- Michael T Marty
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, Arizona 85721, United States
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15
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Grabarics M, Lettow M, Kirschbaum C, Greis K, Manz C, Pagel K. Mass Spectrometry-Based Techniques to Elucidate the Sugar Code. Chem Rev 2022; 122:7840-7908. [PMID: 34491038 PMCID: PMC9052437 DOI: 10.1021/acs.chemrev.1c00380] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Indexed: 12/22/2022]
Abstract
Cells encode information in the sequence of biopolymers, such as nucleic acids, proteins, and glycans. Although glycans are essential to all living organisms, surprisingly little is known about the "sugar code" and the biological roles of these molecules. The reason glycobiology lags behind its counterparts dealing with nucleic acids and proteins lies in the complexity of carbohydrate structures, which renders their analysis extremely challenging. Building blocks that may differ only in the configuration of a single stereocenter, combined with the vast possibilities to connect monosaccharide units, lead to an immense variety of isomers, which poses a formidable challenge to conventional mass spectrometry. In recent years, however, a combination of innovative ion activation methods, commercialization of ion mobility-mass spectrometry, progress in gas-phase ion spectroscopy, and advances in computational chemistry have led to a revolution in mass spectrometry-based glycan analysis. The present review focuses on the above techniques that expanded the traditional glycomics toolkit and provided spectacular insight into the structure of these fascinating biomolecules. To emphasize the specific challenges associated with them, major classes of mammalian glycans are discussed in separate sections. By doing so, we aim to put the spotlight on the most important element of glycobiology: the glycans themselves.
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Affiliation(s)
- Márkó Grabarics
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Maike Lettow
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Carla Kirschbaum
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Kim Greis
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Christian Manz
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Kevin Pagel
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
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16
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Lageveen-Kammeijer GSM, Rapp E, Chang D, Rudd PM, Kettner C, Zaia J. The minimum information required for a glycomics experiment (MIRAGE): reporting guidelines for capillary electrophoresis. Glycobiology 2022; 32:580-587. [DOI: 10.1093/glycob/cwac021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
The Minimum Information Required for a Glycomics Experiment (MIRAGE) is an initiative to standardize the reporting of glycoanalytical methods and to assess their reproducibility. To date, the MIRAGE Commission has published several reporting guidelines that describe what information should be provided for sample preparation methods, mass spectrometry methods, liquid chromatography (LC) analysis, exoglycosidase digestions, glycan microarray methods and nuclear magnetic resonance methods. Here we present the first version of reporting guidelines for glyco(proteo)mics analysis by capillary electrophoresis (CE) for standardized and high-quality reporting of experimental conditions in the scientific literature. The guidelines cover all aspects of a glyco(proteo)mics CE experiment including sample preparation, CE operation mode (CZE, CGE, CEC, MEKC, cIEF, cITP), instrument configuration, capillary separation conditions, detection, data analysis, and experimental descriptors. These guidelines are linked to other MIRAGE guidelines and are freely available through the project website https://www.beilstein-institut.de/en/projects/mirage/guidelines/#ce_analysis (doi:10.3762/mirage.7).
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Affiliation(s)
| | - Erdmann Rapp
- Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany
- glyXera GmbH, Brenneckestrasse 20 – ZENIT, 39120, Magdeburg, Germany
| | - Deborah Chang
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University Medical Campus, 715 Albany Street, Boston, MA 02118, USA
| | - Pauline M Rudd
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, Centros, Singapore
| | - Carsten Kettner
- Beilstein-Institut, Trakehner Str. 7-9, 60487 Frankfurt am Main, Germany
| | - Joseph Zaia
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University Medical Campus, 715 Albany Street, Boston, MA 02118, USA
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17
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Barbosa EA, Alves GSC, Coura MDMA, Silva HDLE, Rocha FSD, Nunes JB, Watanabe MDS, Andrade AC, Brand GD. A first look at the N- and O-glycosylation landscape in anuran skin secretions. Biochimie 2022; 197:19-37. [DOI: 10.1016/j.biochi.2022.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 01/08/2022] [Accepted: 01/17/2022] [Indexed: 11/26/2022]
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18
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Oliveira T, Zhang M, Joo EJ, Abdel-Azim H, Chen CW, Yang L, Chou CH, Qin X, Chen J, Alagesan K, Almeida A, Jacob F, Packer NH, von Itzstein M, Heisterkamp N, Kolarich D. Glycoproteome remodeling in MLL-rearranged B-cell precursor acute lymphoblastic leukemia. Am J Cancer Res 2021; 11:9519-9537. [PMID: 34646384 PMCID: PMC8490503 DOI: 10.7150/thno.65398] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/03/2021] [Indexed: 01/13/2023] Open
Abstract
B-cell precursor acute lymphoblastic leukemia (BCP-ALL) with mixed-lineage leukemia gene rearrangement (MLL-r) is a poor-prognosis subtype for which additional therapeutic targets are urgently needed. Currently no multi-omics data set for primary MLL r patient cells exists that integrates transcriptomics, proteomics and glycomics to gain an inclusive picture of theranostic targets. Methods: We have integrated transcriptomics, proteomics and glycomics to i) obtain the first inclusive picture of primary patient BCP-ALL cells and identify molecular signatures that distinguish leukemic from normal precursor B-cells and ii) better understand the benefits and limitations of the applied technologies to deliver deep molecular sequence data across major cellular biopolymers. Results: MLL-r cells feature an extensive remodeling of their glycocalyx, with increased levels of Core 2-type O-glycans and complex N-glycans as well as significant changes in sialylation and fucosylation. Notably, glycosaminoglycan remodeling from chondroitin sulfate to heparan sulfate was observed. A survival screen, to determine if glycan remodeling enzymes are redundant, identified MGAT1 and NGLY1, essential components of the N-glycosylation/degradation pathway, as highly relevant within this in vitro screening. OGT and OGA, unique enzymes that regulate intracellular O-GlcNAcylation, were also indispensable. Transcriptomics and proteomics further identified Fes and GALNT7-mediated glycosylation as possible therapeutic targets. While there is overall good correlation between transcriptomics and proteomics data, we demonstrate that a systematic combined multi-omics approach delivers important diagnostic information that is missed when applying a single omics technology. Conclusions: Apart from confirming well-known MLL-r BCP-ALL glycoprotein markers, our integrated multi-omics workflow discovered previously unidentified diagnostic/therapeutic protein targets.
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Affiliation(s)
- Tiago Oliveira
- Institute for Glycomics, Griffith University, Gold Coast Campus, QLD, Australia
| | - Mingfeng Zhang
- Department of Systems Biology, Beckman Research Institute City of Hope, Monrovia, CA, USA
| | - Eun Ji Joo
- Department of Systems Biology, Beckman Research Institute City of Hope, Monrovia, CA, USA
| | - Hisham Abdel-Azim
- Division of Hematology/Oncology and Bone Marrow Transplant, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Chun-Wei Chen
- Department of Systems Biology, Beckman Research Institute City of Hope, Monrovia, CA, USA
| | - Lu Yang
- Department of Systems Biology, Beckman Research Institute City of Hope, Monrovia, CA, USA
| | - Chih-Hsing Chou
- Division of Hematology/Oncology and Bone Marrow Transplant, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Xi Qin
- Department of Systems Biology, Beckman Research Institute City of Hope, Monrovia, CA, USA
| | - Jianjun Chen
- Department of Systems Biology, Beckman Research Institute City of Hope, Monrovia, CA, USA
| | - Kathirvel Alagesan
- Institute for Glycomics, Griffith University, Gold Coast Campus, QLD, Australia
| | - Andreia Almeida
- Institute for Glycomics, Griffith University, Gold Coast Campus, QLD, Australia
| | - Francis Jacob
- Glyco-Oncology, Ovarian Cancer Research, Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Nicolle H Packer
- Institute for Glycomics, Griffith University, Gold Coast Campus, QLD, Australia.,Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia.,ARC Centre of Excellence for Nanoscale BioPhotonics, Griffith University, QLD and Macquarie University, NSW, Australia
| | - Mark von Itzstein
- Institute for Glycomics, Griffith University, Gold Coast Campus, QLD, Australia
| | - Nora Heisterkamp
- Department of Systems Biology, Beckman Research Institute City of Hope, Monrovia, CA, USA.,✉ Corresponding authors: Equal contributions of Nora Heisterkamp, E-mail: ; and Daniel Kolarich, E-mail:
| | - Daniel Kolarich
- Institute for Glycomics, Griffith University, Gold Coast Campus, QLD, Australia.,ARC Centre of Excellence for Nanoscale BioPhotonics, Griffith University, QLD and Macquarie University, NSW, Australia.,✉ Corresponding authors: Equal contributions of Nora Heisterkamp, E-mail: ; and Daniel Kolarich, E-mail:
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19
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Oliveira T, Thaysen-Andersen M, Packer NH, Kolarich D. The Hitchhiker's guide to glycoproteomics. Biochem Soc Trans 2021; 49:1643-1662. [PMID: 34282822 PMCID: PMC8421054 DOI: 10.1042/bst20200879] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 06/03/2021] [Accepted: 06/23/2021] [Indexed: 02/06/2023]
Abstract
Protein glycosylation is one of the most common post-translational modifications that are essential for cell function across all domains of life. Changes in glycosylation are considered a hallmark of many diseases, thus making glycoproteins important diagnostic and prognostic biomarker candidates and therapeutic targets. Glycoproteomics, the study of glycans and their carrier proteins in a system-wide context, is becoming a powerful tool in glycobiology that enables the functional analysis of protein glycosylation. This 'Hitchhiker's guide to glycoproteomics' is intended as a starting point for anyone who wants to explore the emerging world of glycoproteomics. The review moves from the techniques that have been developed for the characterisation of single glycoproteins to technologies that may be used for a successful complex glycoproteome characterisation. Examples of the variety of approaches, methodologies, and technologies currently used in the field are given. This review introduces the common strategies to capture glycoprotein-specific and system-wide glycoproteome data from tissues, body fluids, or cells, and a perspective on how integration into a multi-omics workflow enables a deep identification and characterisation of glycoproteins - a class of biomolecules essential in regulating cell function.
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Affiliation(s)
- Tiago Oliveira
- Institute for Glycomics, Griffith University, Gold Coast Campus, Gold Coast, Queensland, Australia
| | | | - Nicolle H. Packer
- Institute for Glycomics, Griffith University, Gold Coast Campus, Gold Coast, Queensland, Australia
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales, Australia
- ARC Centre of Excellence for Nanoscale BioPhotonics, Griffith University, QLD and Macquarie University, NSW, Australia
| | - Daniel Kolarich
- Institute for Glycomics, Griffith University, Gold Coast Campus, Gold Coast, Queensland, Australia
- ARC Centre of Excellence for Nanoscale BioPhotonics, Griffith University, QLD and Macquarie University, NSW, Australia
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20
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Coff L, Abrahams JL, Collett S, Power C, Nowak BF, Kolarich D, Bott NJ, Ramsland PA. Profiling the glycome of Cardicola forsteri, a blood fluke parasitic to bluefin tuna. Int J Parasitol 2021; 52:1-12. [PMID: 34391752 DOI: 10.1016/j.ijpara.2021.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 06/16/2021] [Accepted: 06/17/2021] [Indexed: 11/05/2022]
Abstract
Infections by blood flukes (Cardicola spp.) are considered the most significant health issue for ranched bluefin tuna, a major aquaculture industry in Japan and Australia. The host-parasite interfaces of trematodes, namely their teguments, are particularly rich in carbohydrates, which function both in evasion and modulation of the host immune system, while some are primary antigenic targets. In this study, histochemistry and mass spectrometry techniques were used to profile the glycans of Cardicola forsteri. Fluorescent lectin staining of adult flukes indicates the presence of oligomannose (Concanavalin A-reactive) and fucosylated (Pisum sativum agglutinin-reactive) N-glycans. Additionally, reactivity of succinylated wheat germ agglutinin (s-WGA) was localised to several internal organs of the digestive and monoecious reproductive systems. Glycan structures were further investigated with tandem mass spectrometry, which revealed structures indicated by lectin reactivity. While O-glycans from these adult specimens were not detectable by mass spectrometry, several oligomannose, paucimannosidic, and complex-type N-glycans were identified, including some carrying hexuronic acid and many carrying core xylose. This is, to our knowledge, the first glycomic characterisation of a marine platyhelminth, with broader implications for research into other trematodes.
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Affiliation(s)
- Lachlan Coff
- School of Science, STEM College, RMIT University, Bundoora, VIC 3083, Australia
| | - Jodie L Abrahams
- Institute for Glycomics, Griffith University, Southport, QLD 4215, Australia
| | - Simon Collett
- School of Science, STEM College, RMIT University, Bundoora, VIC 3083, Australia
| | - Cecilia Power
- School of Science, STEM College, RMIT University, Bundoora, VIC 3083, Australia
| | - Barbara F Nowak
- School of Science, STEM College, RMIT University, Bundoora, VIC 3083, Australia; Institute for Marine and Antarctic Studies, University of Tasmania, Locked Bag 1370, Launceston, TAS 7250, Australia
| | - Daniel Kolarich
- Institute for Glycomics, Griffith University, Southport, QLD 4215, Australia; ARC Centre of Excellence for Nanoscale BioPhotonics, Griffith University, Southport, QLD 4215, Australia
| | - Nathan J Bott
- School of Science, STEM College, RMIT University, Bundoora, VIC 3083, Australia.
| | - Paul A Ramsland
- School of Science, STEM College, RMIT University, Bundoora, VIC 3083, Australia; Department of Immunology, Monash University, Melbourne, VIC 3004, Australia; Department of Surgery, Austin Health, University of Melbourne, Heidelberg, VIC 3084, Australia.
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21
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Matthies I, Abrahams JL, Jensen P, Oliveira T, Kolarich D, Larsen MR. N-Glycosylation in isolated rat nerve terminals. Mol Omics 2021; 17:517-532. [PMID: 34106099 DOI: 10.1039/d0mo00044b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
N-linked glycosylation is a ubiquitous protein modification that is capable of modulating protein structure, function and interactions. Many proteins in the brain associated with the synapse and important for synaptic transmission are highly glycosylated and their glycosylation could be important for learning and memory related molecular processes and synaptic plasticity. In the present study, we extend the knowledge of the synaptic glycome and glycoproteome by performing glycan- and intact glycopeptide-focused analyses of isolated rat nerve terminals (synaptosomes) by LC-MS/MS. Overall, glycomics identified a total of 41 N-glycans in isolated synaptosomes. Sialylated N-glycans represented only 7% of the total abundance of the rat synaptosome N-glycome with oligomannose, neutral hybrid and complex type N-glycans being the most abundant structures. Using detergent extraction of the active zone proteins from the synaptosomes revealed a change in the active zone glycan abundance in comparison with the rest of the synaptosome glycan content. Characterization of intact sialylated N-linked glycopeptides enriched by titanium dioxide chromatography revealed more than 85% selectivity of sialylated species and the presence of NeuGc on active zone proteins. In addition, both disialic and trisialic acid modified glycans were present on synaptic glycoproteins, although oxonium ion profiling revealed that trisialic units were only present on glycoproteins in the detergent soluble fraction. However, correct identification of intact sialylated N-linked glycopeptides using the Byonic program failed, most likely due to the lack of peptide backbone fragmentation during tandem mass spectrometry.
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Affiliation(s)
- Inga Matthies
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark
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22
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Aoki-Kinoshita KF. Glycome informatics: using systems biology to gain mechanistic insights into glycan biosynthesis. Curr Opin Chem Eng 2021. [DOI: 10.1016/j.coche.2021.100683] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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23
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Characterization and statistical modeling of glycosylation changes in sickle cell disease. Blood Adv 2021; 5:1463-1473. [PMID: 33666655 DOI: 10.1182/bloodadvances.2020003376] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 01/20/2021] [Indexed: 12/20/2022] Open
Abstract
Sickle cell disease is an inherited genetic disorder that causes anemia, pain crises, organ infarction, and infections in 13 million people worldwide. Previous studies have revealed changes in sialic acid levels associated with red blood cell sickling and showed that stressed red blood cells bare surface-exposed clustered terminal mannose structures mediating hemolysis, but detailed glycan structures and anti-glycan antibodies in sickle cell disease remain understudied. Here, we compiled results obtained through lectin arrays, glycan arrays, and mass spectrometry to interrogate red blood cell glycoproteins and glycan-binding proteins found in the plasma of healthy individuals and patients with sickle cell disease and sickle cell trait. Lectin arrays and mass spectrometry revealed an increase in α2,6 sialylation and a decrease in α2,3 sialylation and blood group antigens displayed on red blood cells. Increased binding of proteins to immunogenic asialo and sialyl core 1, Lewis A, and Lewis Y structures was observed in plasma from patients with sickle cell disease, suggesting a heightened anti-glycan immune response. Data modeling affirmed glycan expression and plasma protein binding changes in sickle cell disease but additionally revealed further changes in ABO blood group expression. Our data provide detailed insights into glycan changes associated with sickle cell disease and refer glycans as potential therapeutic targets.
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24
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Abstract
The glycosylation process is extremely heterogeneous, dynamic, and complex compared with any other post-translational modification of protein. In the context of recombinant glycoproteins, glycosylation is a critical attribute as glycans could dramatically alter protein functions and properties including activity, half-life, in vivo localization, stability, and, last but not least, immunogenicity. Liquid chromatography combined to mass spectrometry constitutes the most powerful analytical approach to achieve the comprehensive glycan profile description or comparison of glycoproteins. This chapter details a versatile yet straightforward LC-MS approach for sample preparation, analysis, and data interpretation, enabling the evaluation of site-specific N-glycosylation of recombinant glycoproteins.
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25
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Kellman BP, Lewis NE. Big-Data Glycomics: Tools to Connect Glycan Biosynthesis to Extracellular Communication. Trends Biochem Sci 2021; 46:284-300. [PMID: 33349503 PMCID: PMC7954846 DOI: 10.1016/j.tibs.2020.10.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Revised: 10/05/2020] [Accepted: 10/22/2020] [Indexed: 12/12/2022]
Abstract
Characteristically, cells must sense and respond to environmental cues. Despite the importance of cell-cell communication, our understanding remains limited and often lacks glycans. Glycans decorate proteins and cell membranes at the cell-environment interface, and modulate intercellular communication, from development to pathogenesis. Providing further challenges, glycan biosynthesis and cellular behavior are co-regulating systems. Here, we discuss how glycosylation contributes to extracellular responses and signaling. We further organize approaches for disentangling the roles of glycans in multicellular interactions using newly available datasets and tools, including glycan biosynthesis models, omics datasets, and systems-level analyses. Thus, emerging tools in big data analytics and systems biology are facilitating novel insights on glycans and their relationship with multicellular behavior.
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Affiliation(s)
- Benjamin P Kellman
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA; Department of Bioengineering, University of California San Diego School of Medicine, La Jolla, CA, USA; Bioinformatics and Systems Biology Program, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Nathan E Lewis
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA; Department of Bioengineering, University of California San Diego School of Medicine, La Jolla, CA, USA; Bioinformatics and Systems Biology Program, University of California San Diego School of Medicine, La Jolla, CA, USA; Novo Nordisk Foundation Center for Biosustainability at the University of California San Diego School of Medicine, La Jolla, CA, USA.
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26
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Ferreira JA, Relvas-Santos M, Peixoto A, M N Silva A, Lara Santos L. Glycoproteogenomics: Setting the Course for Next-generation Cancer Neoantigen Discovery for Cancer Vaccines. GENOMICS, PROTEOMICS & BIOINFORMATICS 2021; 19:25-43. [PMID: 34118464 PMCID: PMC8498922 DOI: 10.1016/j.gpb.2021.03.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 01/25/2021] [Accepted: 03/01/2021] [Indexed: 12/24/2022]
Abstract
Molecular-assisted precision oncology gained tremendous ground with high-throughput next-generation sequencing (NGS), supported by robust bioinformatics. The quest for genomics-based cancer medicine set the foundations for improved patient stratification, while unveiling a wide array of neoantigens for immunotherapy. Upfront pre-clinical and clinical studies have successfully used tumor-specific peptides in vaccines with minimal off-target effects. However, the low mutational burden presented by many lesions challenges the generalization of these solutions, requiring the diversification of neoantigen sources. Oncoproteogenomics utilizing customized databases for protein annotation by mass spectrometry (MS) is a powerful tool toward this end. Expanding the concept toward exploring proteoforms originated from post-translational modifications (PTMs) will be decisive to improve molecular subtyping and provide potentially targetable functional nodes with increased cancer specificity. Walking through the path of systems biology, we highlight that alterations in protein glycosylation at the cell surface not only have functional impact on cancer progression and dissemination but also originate unique molecular fingerprints for targeted therapeutics. Moreover, we discuss the outstanding challenges required to accommodate glycoproteomics in oncoproteogenomics platforms. We envisage that such rationale may flag a rather neglected research field, generating novel paradigms for precision oncology and immunotherapy.
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Affiliation(s)
- José Alexandre Ferreira
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto 4200-072, Portugal; Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto 4050-313, Portugal; Porto Comprehensive Cancer Center (P.ccc), Porto 4200-072, Portugal.
| | - Marta Relvas-Santos
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto 4200-072, Portugal; Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto 4050-313, Portugal; REQUIMTE-LAQV, Department of Chemistry and Biochemistry, Faculty of Sciences of the University of Porto, Porto 4169-007, Portugal
| | - Andreia Peixoto
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto 4200-072, Portugal; Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto 4050-313, Portugal
| | - André M N Silva
- REQUIMTE-LAQV, Department of Chemistry and Biochemistry, Faculty of Sciences of the University of Porto, Porto 4169-007, Portugal
| | - Lúcio Lara Santos
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto 4200-072, Portugal; Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto 4050-313, Portugal; Porto Comprehensive Cancer Center (P.ccc), Porto 4200-072, Portugal
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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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Abstract
Glycoproteomics is unquestionably on the rise and its current development benefits from past experience in proteomics, in particular when attending to bioinformatics needs. An extensive range of software solutions is available, but the reproducibility of mass spectrometry data processing remains challenging. One of the key issues in running automated glycopeptide identification software is the selection of a reference glycan composition file. The default choices are often too broad, and a fastidious literature search to properly target this selection can be avoided. This chapter suggests the use of GlyConnect Compozitor to collect relevant information on glycosylation in a given tissue or cell line and shape an appropriate glycan composition set that can be input in the majority of search engines accommodating user-defined compositions.
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Thaysen-Andersen M, Kolarich D, Packer NH. Glycomics & Glycoproteomics: From Analytics to Function. Mol Omics 2020; 17:8-10. [PMID: 33295916 DOI: 10.1039/d0mo90019b] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Morten Thaysen-Andersen, Daniel Kolarich and Nicolle H. Packer introduce the Molecular Omics themed issue on Glycomics & Glycoproteomics: From Analytics to Function.
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30
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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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Cipollo JF, Parsons LM. Glycomics and glycoproteomics of viruses: Mass spectrometry applications and insights toward structure-function relationships. MASS SPECTROMETRY REVIEWS 2020; 39:371-409. [PMID: 32350911 PMCID: PMC7318305 DOI: 10.1002/mas.21629] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 04/01/2020] [Accepted: 04/05/2020] [Indexed: 05/21/2023]
Abstract
The advancement of viral glycomics has paralleled that of the mass spectrometry glycomics toolbox. In some regard the glycoproteins studied have provided the impetus for this advancement. Viral proteins are often highly glycosylated, especially those targeted by the host immune system. Glycosylation tends to be dynamic over time as viruses propagate in host populations leading to increased number of and/or "movement" of glycosylation sites in response to the immune system and other pressures. This relationship can lead to highly glycosylated, difficult to analyze glycoproteins that challenge the capabilities of modern mass spectrometry. In this review, we briefly discuss five general areas where glycosylation is important in the viral niche and how mass spectrometry has been used to reveal key information regarding structure-function relationships between viral glycoproteins and host cells. We describe the recent past and current glycomics toolbox used in these analyses and give examples of how the requirement to analyze these complex glycoproteins has provided the incentive for some advances seen in glycomics mass spectrometry. A general overview of viral glycomics, special cases, mass spectrometry methods and work-flows, informatics and complementary chemical techniques currently used are discussed. © 2020 The Authors. Mass Spectrometry Reviews published by John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- John F. Cipollo
- Center for Biologics Evaluation and Research, Food and Drug AdministrationSilver SpringMaryland
| | - Lisa M. Parsons
- Center for Biologics Evaluation and Research, Food and Drug AdministrationSilver SpringMaryland
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32
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The GlyCosmos Portal: a unified and comprehensive web resource for the glycosciences. Nat Methods 2020; 17:649-650. [DOI: 10.1038/s41592-020-0879-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Thompson AJ, Cao L, Ma Y, Wang X, Diedrich JK, Kikuchi C, Willis S, Worth C, McBride R, Yates JR, Paulson JC. Human Influenza Virus Hemagglutinins Contain Conserved Oligomannose N-Linked Glycans Allowing Potent Neutralization by Lectins. Cell Host Microbe 2020; 27:725-735.e5. [PMID: 32298658 PMCID: PMC7158820 DOI: 10.1016/j.chom.2020.03.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 02/13/2020] [Accepted: 03/17/2020] [Indexed: 12/12/2022]
Abstract
Hemagglutinins (HAs) from human influenza viruses adapt to bind α2-6-linked sialosides, overcoming a receptor-defined species barrier distinct from the α2-3 specificity of avian virus progenitors. Additionally, human-adapted HAs gain glycosylation sites over time, although their biological function is poorly defined. Using quantitative glycomic analysis, we show that HAs from human pandemic viruses exhibit significant proportions of high-mannose type N-linked glycans throughout the head domain. By contrast, poorly adapted avian-origin HAs contain predominately complex-type glycans, which have greater structural diversity. Although oligomannose levels vary, they are present in all tested recombinant HAs and whole viruses and can be specifically targeted for universal detection. The positions of high-mannose glycosites on the HA of human H1N1 and H3N2 strains are conserved. Additionally, high-mannose-binding lectins possess a broad capacity to neutralize and prevent infection with contemporary H3N2 strains. These findings reveal the biological significance of HA glycosylation and therapeutic potential of targeting these structures.
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Affiliation(s)
- Andrew J Thompson
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Liwei Cao
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Yuanhui Ma
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Xiaoning Wang
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Jolene K Diedrich
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Chika Kikuchi
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Shelby Willis
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Charli Worth
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Ryan McBride
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - John R Yates
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - James C Paulson
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA; Department of Immunology & Microbiology, Scripps Research, La Jolla, CA 92037, USA.
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34
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Ricard-Blum S, Miele AE. Omic approaches to decipher the molecular mechanisms of fibrosis, and design new anti-fibrotic strategies. Semin Cell Dev Biol 2020; 101:161-169. [DOI: 10.1016/j.semcdb.2019.12.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 12/16/2019] [Accepted: 12/16/2019] [Indexed: 12/17/2022]
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Abnormal Galactosylated-Glycans recognized by Bandeiraea Simplicifolia Lectin I in saliva of patients with breast Cancer. Glycoconj J 2020; 37:373-394. [PMID: 32103424 DOI: 10.1007/s10719-020-09910-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 01/09/2020] [Accepted: 01/22/2020] [Indexed: 02/07/2023]
Abstract
Currently, the definitive diagnosis in breast cancer requires biopsy and histopathology, such the most effective markers are tissue-based. However, the advantages of saliva in collection and storage make it possible for assessing human pathology and contributing to the development of cancer-related biomarkers for clinical application. The present study validated alteration of salivary protein glycopatterns recognized by Bandeiraea simplicifolia lectin I (BS-I) in the saliva of patients with breast diseases using saliva microarrays, and the N/O-glycan profiles of their salivary glycoproteins isolated by the BS-I-magnetic particle conjugates from 259 female subjects (66 healthy volunteers (HV), 65 benign breast cyst or tumor patients (BB), 66 patients with breast cancer in stage I (BC-I) and 62 patients with breast cancer in stage II (BC-II)) were analyzed by MALDI-TOF/TOF-MS. The results showed that the expression level of galactosylated glycans recognized by BS-I was significantly increased in patients with breast cancer compared with HV (p < 0.05). Totally, there were 11/10, 10/19, 7/24 and 7/9 galactosylated N-/O-linked glycans were identified and annotated from the pooled salivary samples of HV, BB, BC-I and BC-II, respectively. One galactosylated N-glycan peak (m/z 2773.977), and 4 galactosylated O-glycan peaks (m/z 868.295, 882.243, 884.270 and 1030.348) were found only in BC-I. These findings could provide pivotal information on galactosylated N/O-linked glycans related to breast cancer, and promote the study of biomarkers for early-stage breast cancer based on precise alterations of galactosylated N/O-glycans in saliva.
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Weatherly DB, Arpinar FS, Porterfield M, Tiemeyer M, York WS, Ranzinger R. GRITS Toolbox-a freely available software for processing, annotating and archiving glycomics mass spectrometry data. Glycobiology 2020; 29:452-460. [PMID: 30913289 DOI: 10.1093/glycob/cwz023] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 03/13/2019] [Accepted: 03/20/2019] [Indexed: 11/14/2022] Open
Abstract
Mass spectrometry (MS) is one of the most effective techniques for high-throughput, high-resolution characterization of glycan structures. Although many software applications have been developed over the last decades for the interpretation of MS data of glycan structures, only a few are capable of dealing with the large data sets produced by glycomics analysis. Furthermore, these applications utilize databases that can lead to redundant glycan annotations and do not support post-processing of the data within the software or by third party applications. To address the needs, we present GRITS Toolbox, a freely-available, platform-independent software application capable of storing and processing glycomics MS data along with associated metadata. GRITS Toolbox automatically annotates MS data using an integrated glycan identification module that references manually curated databases of mammalian glycans (provided with the software) or any user-defined databases. Extensive display routines are provided to post-process the data and refine the automated annotation using expert knowledge of the user. The software also allows side by side comparison of annotations from different MS runs or samples and exporting of annotations into Excel format.
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Affiliation(s)
- D Brent Weatherly
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - F Sena Arpinar
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Melody Porterfield
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Michael Tiemeyer
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - William S York
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Rene Ranzinger
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
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Coff L, Chan J, Ramsland PA, Guy AJ. Identifying glycan motifs using a novel subtree mining approach. BMC Bioinformatics 2020; 21:42. [PMID: 32019496 PMCID: PMC7001330 DOI: 10.1186/s12859-020-3374-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 01/20/2020] [Indexed: 11/17/2022] Open
Abstract
Background Glycans are complex sugar chains, crucial to many biological processes. By participating in binding interactions with proteins, glycans often play key roles in host–pathogen interactions. The specificities of glycan-binding proteins, such as lectins and antibodies, are governed by motifs within larger glycan structures, and improved characterisations of these determinants would aid research into human diseases. Identification of motifs has previously been approached as a frequent subtree mining problem, and we extend these approaches with a glycan notation that allows recognition of terminal motifs. Results In this work, we customised a frequent subtree mining approach by altering the glycan notation to include information on terminal connections. This allows specific identification of terminal residues as potential motifs, better capturing the complexity of glycan-binding interactions. We achieved this by including additional nodes in a graph representation of the glycan structure to indicate the presence or absence of a linkage at particular backbone carbon positions. Combining this frequent subtree mining approach with a state-of-the-art feature selection algorithm termed minimum-redundancy, maximum-relevance (mRMR), we have generated a classification pipeline that is trained on data from a glycan microarray. When applied to a set of commonly used lectins, the identified motifs were consistent with known binding determinants. Furthermore, logistic regression classifiers trained using these motifs performed well across most lectins examined, with a median AUC value of 0.89. Conclusions We present here a new subtree mining approach for the classification of glycan binding and identification of potential binding motifs. The Carbohydrate Classification Accounting for Restricted Linkages (CCARL) method will assist in the interpretation of glycan microarray experiments and will aid in the discovery of novel binding motifs for further experimental characterisation.
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Affiliation(s)
- Lachlan Coff
- School of Science, College of Science, Engineering and Health, RMIT University, 3000, Melbourne, Australia
| | - Jeffrey Chan
- School of Science, College of Science, Engineering and Health, RMIT University, 3000, Melbourne, Australia
| | - Paul A Ramsland
- School of Science, College of Science, Engineering and Health, RMIT University, 3000, Melbourne, Australia.,Department of Immunology, Monash University, 3004, Melbourne, Australia.,Department of Surgery Austin Health, University of Melbourne, 3084, Heidelberg, Australia
| | - Andrew J Guy
- School of Science, College of Science, Engineering and Health, RMIT University, 3000, Melbourne, Australia.
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Ashwood C, Waas M, Weerasekera R, Gundry RL. Reference glycan structure libraries of primary human cardiomyocytes and pluripotent stem cell-derived cardiomyocytes reveal cell-type and culture stage-specific glycan phenotypes. J Mol Cell Cardiol 2020; 139:33-46. [PMID: 31972267 DOI: 10.1016/j.yjmcc.2019.12.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 12/23/2019] [Accepted: 12/27/2019] [Indexed: 12/16/2022]
Abstract
Cell surface glycoproteins play critical roles in maintaining cardiac structure and function in health and disease and the glycan-moiety attached to the protein is critical for proper protein folding, stability and signaling [1]. However, despite mounting evidence that glycan structures are key modulators of heart function and must be considered when developing cardiac biomarkers, we currently do not have a comprehensive view of the glycans present in the normal human heart. In the current study, we used porous graphitized carbon liquid chromatography interfaced with mass spectrometry (PGC-LC-MS) to generate glycan structure libraries for primary human heart tissue homogenate, cardiomyocytes (CM) enriched from human heart tissue, and human induced pluripotent stem cell derived CM (hiPSC-CM). Altogether, we established the first reference structure libraries of the cardiac glycome containing 265 N- and O-glycans. Comparing the N-glycome of CM enriched from primary heart tissue to that of heart tissue homogenate, the same pool of N-glycan structures was detected in each sample type but the relative signal of 21 structures significantly differed between samples, with the high mannose class increased in enriched CM. Moreover, by comparing primary CM to hiPSC-CM collected during 20-100 days of differentiation, dynamic changes in the glycan profile throughout in vitro differentiation were observed and differences between primary and hiPSC-CM were revealed. Namely, >30% of the N-glycome significantly changed across these time-points of differentiation and only 23% of the N-glycan structures were shared between hiPSC-CM and primary CM. These observations are an important complement to current genomic, transcriptomic, and proteomic profiling and reveal new considerations for the use and interpretation of hiPSC-CM models for studies of human development, disease, and drug testing. Finally, these data are expected to support future regenerative medicine efforts by informing targets for evaluating the immunogenic potential of hiPSC-CM and harnessing differences between immature, proliferative hiPSC-CM and adult primary CM.
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Affiliation(s)
- Christopher Ashwood
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Matthew Waas
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Ranjuna Weerasekera
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Rebekah L Gundry
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Center for Biomedical Mass Spectrometry Research, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
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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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Campbell MP, Abrahams JL, Rapp E, Struwe WB, Costello CE, Novotny M, Ranzinger R, York WS, Kolarich D, Rudd PM, Kettner C. The minimum information required for a glycomics experiment (MIRAGE) project: LC guidelines. Glycobiology 2019; 29:349-354. [PMID: 30778580 DOI: 10.1093/glycob/cwz009] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 02/11/2019] [Accepted: 02/13/2019] [Indexed: 11/13/2022] Open
Abstract
The Minimum Information Required for a Glycomics Experiment (MIRAGE) is an initiative created by experts in the fields of glycobiology, glycoanalytics and glycoinformatics to design guidelines that improve the reporting and reproducibility of glycoanalytical methods. Previously, the MIRAGE Commission has published guidelines for describing sample preparation methods and the reporting of glycan array and mass spectrometry techniques and data collections. Here, we present the first version of guidelines that aim to improve the quality of the reporting of liquid chromatography (LC) glycan data in the scientific literature. These guidelines cover all aspects of instrument setup and modality of data handling and manipulation and is cross-linked with other MIRAGE recommendations. The most recent version of the MIRAGE-LC guidelines is freely available at the MIRAGE project website doi:10.3762/mirage.4.
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Affiliation(s)
- Matthew P Campbell
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
| | - Jodie L Abrahams
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
| | - Erdmann Rapp
- Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, Magdeburg, Germany
| | - Weston B Struwe
- Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, Oxford, UK
| | - Catherine E Costello
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University School of Medicine, 670 Albany Street, Suite 504, Boston, MA, USA
| | - Milos Novotny
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, IN, USA
| | - Rene Ranzinger
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA, USA
| | - William S York
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA, USA
| | - Daniel Kolarich
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia.,ARC Centre for Nanoscale BioPhotonics, Griffith University, Gold Coast, Queensland, Australia
| | - Pauline M Rudd
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, Centros, Singapore
| | - Carsten Kettner
- Beilstein-Institut, Trakehner Str. 7-9, Frankfurt am Main, Germany
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Glycan size and attachment site location affect electron transfer dissociation (ETD) fragmentation and automated glycopeptide identification. Glycoconj J 2019; 36:487-493. [DOI: 10.1007/s10719-019-09888-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 08/09/2019] [Accepted: 08/09/2019] [Indexed: 10/25/2022]
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McQuillan AM, Byrd-Leotis L, Heimburg-Molinaro J, Cummings RD. Natural and Synthetic Sialylated Glycan Microarrays and Their Applications. Front Mol Biosci 2019; 6:88. [PMID: 31572731 PMCID: PMC6753469 DOI: 10.3389/fmolb.2019.00088] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 08/28/2019] [Indexed: 12/28/2022] Open
Abstract
This focused chapter serves as a short survey of glycan microarrays that are available with sialylated glycans, including both defined and shotgun arrays, their generation, and their utility in studying differential binding interactions to sialylated compounds, highlighting N-glycolyl (Gc) modified sialylated compounds. A brief discussion of binding interactions by lectins, antibodies, and viruses, and their relevance that have been observed with sialylated glycan microarrays is presented, as well as a discussion of cross-comparisons of array platforms and efforts to centralize and standardize the glycan microarray data.
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Affiliation(s)
- Alyssa M. McQuillan
- Department of Surgery, Beth Israel Deaconess Medical Center, National Center for Functional Glycomics, Harvard Medical School, Boston, MA, United States
| | - Lauren Byrd-Leotis
- Department of Surgery, Beth Israel Deaconess Medical Center, National Center for Functional Glycomics, Harvard Medical School, Boston, MA, United States
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, United States
| | - Jamie Heimburg-Molinaro
- Department of Surgery, Beth Israel Deaconess Medical Center, National Center for Functional Glycomics, Harvard Medical School, Boston, MA, United States
| | - Richard D. Cummings
- Department of Surgery, Beth Israel Deaconess Medical Center, National Center for Functional Glycomics, Harvard Medical School, Boston, MA, United States
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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: 59] [Impact Index Per Article: 11.8] [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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Zhang J, Zhong Y, Zhang P, Du H, Shu J, Liu X, Zhang H, Guo Y, Jia Z, Niu L, Yang F, Li Z. Identification of abnormal fucosylated-glycans recognized by LTL in saliva of HBV-induced chronic hepatitis, cirrhosis, and hepatocellular carcinoma. Glycobiology 2019; 29:242-259. [PMID: 30535277 DOI: 10.1093/glycob/cwy108] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 04/12/2018] [Accepted: 12/06/2018] [Indexed: 12/26/2022] Open
Abstract
The hepatitis B virus (HBV)-induced chronic liver diseases are serious health threats worldwide. There is evidence to display the alterations of salivary N-linked glycans related to the development of HBV-infected liver diseases. Here, we further investigated the alterations of fucosylated N/O-glycans recognized by LTL in saliva from 120 subjects (30 healthy volunteers (HV), 30 patients with hepatitis B (HB), 30 patients with hepatic cirrhosis (HC), and 30 patients with hepatocellular carcinoma (HCC)) using salivary microarrys and MALDI-TOF/TOF-MS. The results showed that the expression level of fucosylated glycans recognized by LTL was significantly increased in HCC compared with other subjects (P < 0.0001). Besides, the fucosylated glycoproteins were isolated from pooled saliva of HV, HB, HC, and HCC by LTL-magnetic particle conjugates. Then, N/O- glycans were released from the isolated glycoproteins with PNGase F and NaClO, and were identified by MALDI-TOF-MS, respectively. Totally, there were 21/20, 25/18, 29/19, and 28/24 N/O-glycan peaks that were identified and annotated with proposed structures in saliva of HV, HB, HC, and HCC. Among the total, there were 8 N-glycan peaks (e.g., m/z 1905.634, 2158.777 and 2905.036) and 15 O-glycan peaks (e.g., 1177.407, 1308.444 and 1322.444) that only presented in patients with HBV-induced liver diseases. One N-glycan peak (m/z 2205.766) was unique in HC, and 9 O-glycan peaks (e.g., m/z 1157.420, 1163.417 and 1193.402) were unique in HCC. This study could facilitate the discovery of biomarkers for HC and HCC based on precise alterations of fucosylated N/O-glycans in saliva.
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Affiliation(s)
- Jiaxu Zhang
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, China
| | - Yaogang Zhong
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, China
| | - Peixin Zhang
- Center of Infectious Diseases, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Haoqi Du
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, China
| | - Jian Shu
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, China
| | - Xiawei Liu
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, China
| | - Hua Zhang
- Department of Oncology, Shaanxi Provincial People's Hospital, Xi'an, China
| | - Yonghong Guo
- Department of Infectious Diseases, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Zhansheng Jia
- Center of Infectious Diseases, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Lili Niu
- Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institution of Biophysics, Chineses Academy of Sciences, Beijing, China
| | - Fuquan Yang
- Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institution of Biophysics, Chineses Academy of Sciences, Beijing, China
| | - Zheng Li
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, China
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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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Bowser LE, Young M, Wenger OK, Ammous Z, Brigatti KW, Carson VJ, Moser T, Deline J, Aoki K, Morlet T, Scott EM, Puffenberger EG, Robinson DL, Hendrickson C, Salvin J, Gottlieb S, Heaps AD, Tiemeyer M, Strauss KA. Recessive GM3 synthase deficiency: Natural history, biochemistry, and therapeutic frontier. Mol Genet Metab 2019; 126:475-488. [PMID: 30691927 DOI: 10.1016/j.ymgme.2019.01.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/20/2019] [Accepted: 01/20/2019] [Indexed: 11/19/2022]
Abstract
GM3 synthase, encoded by ST3GAL5, initiates synthesis of all downstream cerebral gangliosides. Here, we present biochemical, functional, and natural history data from 50 individuals homozygous for a pathogenic ST3GAL5 c.862C>T founder allele (median age 8.1, range 0.7-30.5 years). GM3 and its derivatives were undetectable in plasma. Weight and head circumference were normal at birth and mean Apgar scores were 7.7 ± 2.0 (1 min) and 8.9 ± 0.5 (5 min). Somatic growth failure, progressive microcephaly, global developmental delay, visual inattentiveness, and dyskinetic movements developed within a few months of life. Infantile-onset epileptic encephalopathy was characterized by a slow, disorganized, high-voltage background, poor state transitions, absent posterior rhythm, and spike trains from multiple independent cortical foci; >90% of electrographic seizures were clinically silent. Hearing loss affected cochlea and central auditory pathways and 76% of children tested failed the newborn hearing screen. Development stagnated early in life; only 13 (26%) patients sat independently (median age 30 months), three (6%) learned to crawl, and none achieved reciprocal communication. Incessant irritability, often accompanied by insomnia, began during infancy and contributed to high parental stress. Despite catastrophic neurological dysfunction, neuroimaging showed only subtle or no destructive changes into late childhood and hospitalizations were surprisingly rare (0.2 per patient per year). Median survival was 23.5 years. Our observations corroborate findings from transgenic mice which indicate that gangliosides might have a limited role in embryonic neurodevelopment but become vital for postnatal brain growth and function. These results have critical implications for the design and implementation of ganglioside restitution therapies.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Kazuhiro Aoki
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Thierry Morlet
- Auditory Physiology and Psychoacoustics Research Laboratory, Nemours Alfred I. duPont Hospital for Children, Wilmington, DE, USA
| | - Ethan M Scott
- Department of Pediatrics, Akron Children's Hospital, Akron, OH, USA
| | | | | | | | - Jonathan Salvin
- Division of Pediatric Ophthalmology, Nemours Alfred I. duPont Hospital for Children, Wilmington, DE, USA
| | - Steven Gottlieb
- Division of Pediatric Neurology, Nemours Alfred I. duPont Hospital for Children, Wilmington, DE, USA
| | | | - Michael Tiemeyer
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
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Nonomura Y, Sawamura S, Hanzawa K, Nishikaze T, Sekiya S, Higuchi T, Nin F, Uetsuka S, Inohara H, Okuda S, Miyoshi E, Horii A, Takahashi S, Natsuka S, Hibino H. Characterisation of N-glycans in the epithelial-like tissue of the rat cochlea. Sci Rep 2019; 9:1551. [PMID: 30733536 PMCID: PMC6367448 DOI: 10.1038/s41598-018-38079-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 12/17/2018] [Indexed: 01/08/2023] Open
Abstract
Membrane proteins (such as ion channels, transporters, and receptors) and secreted proteins are essential for cellular activities. N-linked glycosylation is involved in stability and function of these proteins and occurs at Asn residues. In several organs, profiles of N-glycans have been determined by comprehensive analyses. Nevertheless, the cochlea of the mammalian inner ear, a tiny organ mediating hearing, has yet to be examined. Here, we focused on the stria vascularis, an epithelial-like tissue in the cochlea, and characterised N-glycans by liquid chromatography with mass spectrometry. This hypervascular tissue not only expresses several ion transporters and channels to control the electrochemical balance in the cochlea but also harbours different transporters and receptors that maintain structure and activity of the organ. Seventy-nine N-linked glycans were identified in the rat stria vascularis. Among these, in 55 glycans, the complete structures were determined; in the other 24 species, partial glycosidic linkage patterns and full profiles of the monosaccharide composition were identified. In the process of characterisation, several sialylated glycans were subjected sequentially to two different alkylamidation reactions; this derivatisation helped to distinguish α2,3-linkage and α2,6-linkage sialyl isomers with mass spectrometry. These data should accelerate elucidation of the molecular architecture of the cochlea.
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Affiliation(s)
- Yoriko Nonomura
- Department of Molecular Physiology, Niigata University School of Medicine, Niigata, Japan
- Department of Otorhinolaryngology-Head and Neck Surgery, Niigata University School of Medicine, Niigata, Japan
| | - Seishiro Sawamura
- Department of Molecular Physiology, Niigata University School of Medicine, Niigata, Japan
| | - Ken Hanzawa
- Department of Biology, Faculty of Science, Niigata University, Niigata, Japan
| | - Takashi Nishikaze
- Koichi Tanaka Mass Spectrometry Research Laboratory, Shimadzu Corporation, Kyoto, Japan
| | - Sadanori Sekiya
- Koichi Tanaka Mass Spectrometry Research Laboratory, Shimadzu Corporation, Kyoto, Japan
| | - Taiga Higuchi
- Department of Molecular Physiology, Niigata University School of Medicine, Niigata, Japan
| | - Fumiaki Nin
- Department of Molecular Physiology, Niigata University School of Medicine, Niigata, Japan
- Center for Transdisciplinary Research, Niigata University, Niigata, Japan
| | - Satoru Uetsuka
- Department of Otorhinolaryngology-Head and Neck Surgery, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Hidenori Inohara
- Department of Otorhinolaryngology-Head and Neck Surgery, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Shujiro Okuda
- Bioinformatics Laboratory, Niigata University School of Medicine, Niigata, Japan
| | - Eiji Miyoshi
- Division of Health Sciences, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Arata Horii
- Department of Otorhinolaryngology-Head and Neck Surgery, Niigata University School of Medicine, Niigata, Japan
| | - Sugata Takahashi
- Department of Otorhinolaryngology-Head and Neck Surgery, Niigata University School of Medicine, Niigata, Japan
| | - Shunji Natsuka
- Department of Biology, Faculty of Science, Niigata University, Niigata, Japan
| | - Hiroshi Hibino
- Department of Molecular Physiology, Niigata University School of Medicine, Niigata, Japan.
- Center for Transdisciplinary Research, Niigata University, Niigata, Japan.
- AMED-CREST, AMED, Niigata, Japan.
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48
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Alocci D, Mariethoz J, Gastaldello A, Gasteiger E, Karlsson NG, Kolarich D, Packer NH, Lisacek F. GlyConnect: Glycoproteomics Goes Visual, Interactive, and Analytical. J Proteome Res 2018; 18:664-677. [DOI: 10.1021/acs.jproteome.8b00766] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Davide Alocci
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Rue Michel-Servet 1, CH-1211 Geneva, Switzerland
- Computer Science Department, University of Geneva, CH-1227 Geneva, Switzerland
| | - Julien Mariethoz
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Rue Michel-Servet 1, CH-1211 Geneva, Switzerland
- Computer Science Department, University of Geneva, CH-1227 Geneva, Switzerland
| | - Alessandra Gastaldello
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Rue Michel-Servet 1, CH-1211 Geneva, Switzerland
- Computer Science Department, University of Geneva, CH-1227 Geneva, Switzerland
| | - Elisabeth Gasteiger
- Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CH-1211 Geneva, Switzerland
| | - Niclas G. Karlsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Daniel Kolarich
- Institute for Glycomics, Griffith University, Southport, Queensland 4215, Australia
- ARC Centre for Nanoscale BioPhotonics, Macquarie University and Griffith University, Sydney, New South Wales 2109, Australia
| | - Nicolle H. Packer
- Institute for Glycomics, Griffith University, Southport, Queensland 4215, Australia
- ARC Centre for Nanoscale BioPhotonics, Macquarie University and Griffith University, Sydney, New South Wales 2109, Australia
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Frédérique Lisacek
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Rue Michel-Servet 1, CH-1211 Geneva, Switzerland
- Computer Science Department, University of Geneva, CH-1227 Geneva, Switzerland
- Section of Biology, University of Geneva, CH-1211 Geneva, Switzerland
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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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Gustafsson OJR, Winderbaum LJ, Condina MR, Boughton BA, Hamilton BR, Undheim EAB, Becker M, Hoffmann P. Balancing sufficiency and impact in reporting standards for mass spectrometry imaging experiments. Gigascience 2018; 7:5074354. [PMID: 30124809 PMCID: PMC6203951 DOI: 10.1093/gigascience/giy102] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 07/24/2018] [Accepted: 08/07/2018] [Indexed: 02/06/2023] Open
Abstract
Reproducibility, or a lack thereof, is an increasingly important topic across many research fields. A key aspect of reproducibility is accurate reporting of both experiments and the resulting data. Herein, we propose a reporting guideline for mass spectrometry imaging (MSI). Previous standards have laid out guidelines sufficient to guarantee a certain quality of reporting; however, they set a high bar and as a consequence can be exhaustive and broad, thus limiting uptake.To help address this lack of uptake, we propose a reporting supplement-Minimum Information About a Mass Spectrometry Imaging Experiment (MIAMSIE)-and its abbreviated reporting standard version, MSIcheck. MIAMSIE is intended to improve author-driven reporting. It is intentionally not exhaustive, but is rather designed for extensibility and could therefore eventually become analogous to existing standards that aim to guarantee reporting quality. Conversely, its abbreviated form MSIcheck is intended as a diagnostic tool focused on key aspects in MSI reporting.We discuss how existing standards influenced MIAMSIE/MSIcheck and how these new approaches could positively impact reporting quality, followed by test implementation of both standards to demonstrate their use. For MIAMSIE, we report on author reviews of four articles and a dataset. For MSIcheck, we show a snapshot review of a one-month subset of the MSI literature that indicated issues with data provision and the reporting of both data analysis steps and calibration settings for MS systems. Although our contribution is MSI specific, we believe the underlying approach could be considered as a general strategy for improving scientific reporting.
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Affiliation(s)
- Ove J R Gustafsson
- ARC Centre of Excellence in Convergent Bio-Nano Science & Technology (CBNS), University of South Australia, Mawson Lakes, South Australia 5095, Australia
- Future Industries Institute, University of South Australia, Mawson Lakes, South Australia 5095, Australia
| | - Lyron J Winderbaum
- Future Industries Institute, University of South Australia, Mawson Lakes, South Australia 5095, Australia
| | - Mark R Condina
- Future Industries Institute, University of South Australia, Mawson Lakes, South Australia 5095, Australia
| | - Berin A Boughton
- Metabolomics Australia, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Brett R Hamilton
- Centre for Microscopy and Microanalysis, University of Queensland, St. Lucia, Queensland 4072, Australia
- Centre for Advanced Imaging, University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Eivind A B Undheim
- Centre for Advanced Imaging, University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Michael Becker
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach a.d. Riss 88397, Germany
| | - Peter Hoffmann
- Future Industries Institute, University of South Australia, Mawson Lakes, South Australia 5095, Australia
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