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Pongracz T, Mayboroda OA, Wuhrer M. The Human Blood N-Glycome: Unraveling Disease Glycosylation Patterns. JACS AU 2024; 4:1696-1708. [PMID: 38818049 PMCID: PMC11134357 DOI: 10.1021/jacsau.4c00043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/28/2024] [Accepted: 04/01/2024] [Indexed: 06/01/2024]
Abstract
Most of the proteins in the circulation are N-glycosylated, shaping together the total blood N-glycome (TBNG). Glycosylation is known to affect protein function, stability, and clearance. The TBNG is influenced by genetic, environmental, and metabolic factors, in part epigenetically imprinted, and responds to a variety of bioactive signals including cytokines and hormones. Accordingly, physiological and pathological events are reflected in distinct TBNG signatures. Here, we assess the specificity of the emerging disease-associated TBNG signatures with respect to a number of key glycosylation motifs including antennarity, linkage-specific sialylation, fucosylation, as well as expression of complex, hybrid-type and oligomannosidic N-glycans, and show perplexing complexity of the glycomic dimension of the studied diseases. Perspectives are given regarding the protein- and site-specific analysis of N-glycosylation, and the dissection of underlying regulatory layers and functional roles of blood protein N-glycosylation.
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Affiliation(s)
- Tamas Pongracz
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333ZA Leiden, The Netherlands
| | - Oleg A. Mayboroda
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333ZA Leiden, The Netherlands
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333ZA Leiden, The Netherlands
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2
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Garapati K, Budhraja R, Saraswat M, Kim J, Joshi N, Sachdeva GS, Jain A, Ligezka AN, Radenkovic S, Ramarajan MG, Udainiya S, Raymond K, He M, Lam C, Larson A, Edmondson AC, Sarafoglou K, Larson NB, Freeze HH, Schultz MJ, Kozicz T, Morava E, Pandey A. A complement C4-derived glycopeptide is a biomarker for PMM2-CDG. JCI Insight 2024; 9:e172509. [PMID: 38587076 PMCID: PMC7615924 DOI: 10.1172/jci.insight.172509] [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: 05/24/2023] [Accepted: 02/15/2024] [Indexed: 04/09/2024] Open
Abstract
BACKGROUNDDiagnosis of PMM2-CDG, the most common congenital disorder of glycosylation (CDG), relies on measuring carbohydrate-deficient transferrin (CDT) and genetic testing. CDT tests have false negatives and may normalize with age. Site-specific changes in protein N-glycosylation have not been reported in sera in PMM2-CDG.METHODSUsing multistep mass spectrometry-based N-glycoproteomics, we analyzed sera from 72 individuals to discover and validate glycopeptide alterations. We performed comprehensive tandem mass tag-based discovery experiments in well-characterized patients and controls. Next, we developed a method for rapid profiling of additional samples. Finally, targeted mass spectrometry was used for validation in an independent set of samples in a blinded fashion.RESULTSOf the 3,342 N-glycopeptides identified, patients exhibited decrease in complex-type N-glycans and increase in truncated, mannose-rich, and hybrid species. We identified a glycopeptide from complement C4 carrying the glycan Man5GlcNAc2, which was not detected in controls, in 5 patients with normal CDT results, including 1 after liver transplant and 2 with a known genetic variant associated with mild disease, indicating greater sensitivity than CDT. It was detected by targeted analysis in 2 individuals with variants of uncertain significance in PMM2.CONCLUSIONComplement C4-derived Man5GlcNAc2 glycopeptide could be a biomarker for accurate diagnosis and therapeutic monitoring of patients with PMM2-CDG and other CDGs.FUNDINGU54NS115198 (Frontiers in Congenital Disorders of Glycosylation: NINDS; NCATS; Eunice Kennedy Shriver NICHD; Rare Disorders Consortium Disease Network); K08NS118119 (NINDS); Minnesota Partnership for Biotechnology and Medical Genomics; Rocket Fund; R01DK099551 (NIDDK); Mayo Clinic DERIVE Office; Mayo Clinic Center for Biomedical Discovery; IA/CRC/20/1/600002 (Center for Rare Disease Diagnosis, Research and Training; DBT/Wellcome Trust India Alliance).
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Affiliation(s)
- Kishore Garapati
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Rohit Budhraja
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Mayank Saraswat
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Jinyong Kim
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Neha Joshi
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Gunveen S. Sachdeva
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Anu Jain
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | | | | | - Madan Gopal Ramarajan
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Savita Udainiya
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Kimiyo Raymond
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Miao He
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Christina Lam
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, Washington, USA
- Division of Genetic Medicine, Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
| | | | - Andrew C. Edmondson
- Division of Human Genetics, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Kyriakie Sarafoglou
- Division of Pediatric Endocrinology, Department of Pediatrics, University of Minnesota Medical School, Minneapolis, Minnesota, USA
- Department of Experimental and Clinical Pharmacology, University of Minnesota School of Pharmacy, Minneapolis, Minnesota, USA
| | - Nicholas B. Larson
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota, USA
| | - Hudson H. Freeze
- Sanford Children’s Health Research Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Matthew J. Schultz
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Tamas Kozicz
- Department of Clinical Genomics and
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Department of Anatomy, University of Pécs Medical School, Pécs, Hungary
- Department of Genomics and Genetic Sciences, Icahn School of Medicine at Mount Sinai Hospital, New York, New York, USA
| | - Eva Morava
- Department of Clinical Genomics and
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Department of Anatomy, University of Pécs Medical School, Pécs, Hungary
- Department of Genomics and Genetic Sciences, Icahn School of Medicine at Mount Sinai Hospital, New York, New York, USA
| | - Akhilesh Pandey
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
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3
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Li H, Peralta AG, Schoffelen S, Hansen AH, Arnsdorf J, Schinn SM, Skidmore J, Choudhury B, Paulchakrabarti M, Voldborg BG, Chiang AW, Lewis NE. LeGenD: determining N-glycoprofiles using an explainable AI-leveraged model with lectin profiling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.27.587044. [PMID: 38585977 PMCID: PMC10996628 DOI: 10.1101/2024.03.27.587044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Glycosylation affects many vital functions of organisms. Therefore, its surveillance is critical from basic science to biotechnology, including biopharmaceutical development and clinical diagnostics. However, conventional glycan structure analysis faces challenges with throughput and cost. Lectins offer an alternative approach for analyzing glycans, but they only provide glycan epitopes and not full glycan structure information. To overcome these limitations, we developed LeGenD, a lectin and AI-based approach to predict N-glycan structures and determine their relative abundance in purified proteins based on lectin-binding patterns. We trained the LeGenD model using 309 glycoprofiles from 10 recombinant proteins, produced in 30 glycoengineered CHO cell lines. Our approach accurately reconstructed experimentally-measured N-glycoprofiles of bovine Fetuin B and IgG from human sera. Explanatory AI analysis with SHapley Additive exPlanations (SHAP) helped identify the critical lectins for glycoprofile predictions. Our LeGenD approach thus presents an alternative approach for N-glycan analysis.
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Affiliation(s)
- Haining Li
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Angelo G. Peralta
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sanne Schoffelen
- National Biologics Facility Department of Biotechnology and Biomedicine, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby Denmark
| | - Anders Holmgaard Hansen
- National Biologics Facility Department of Biotechnology and Biomedicine, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby Denmark
| | - Johnny Arnsdorf
- National Biologics Facility Department of Biotechnology and Biomedicine, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby Denmark
| | - Song-Min Schinn
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jonathan Skidmore
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
| | - Biswa Choudhury
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mousumi Paulchakrabarti
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Bjorn G. Voldborg
- National Biologics Facility Department of Biotechnology and Biomedicine, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby Denmark
| | - Austin W.T. Chiang
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nathan E. Lewis
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
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4
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Lageveen‐Kammeijer GSM, Kuster B, Reusch D, Wuhrer M. High sensitivity glycomics in biomedicine. MASS SPECTROMETRY REVIEWS 2022; 41:1014-1039. [PMID: 34494287 PMCID: PMC9788051 DOI: 10.1002/mas.21730] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/23/2021] [Accepted: 08/26/2021] [Indexed: 05/15/2023]
Abstract
Many analytical challenges in biomedicine arise from the generally high heterogeneity and complexity of glycan- and glycoconjugate-containing samples, which are often only available in minute amounts. Therefore, highly sensitive workflows and detection methods are required. In this review mass spectrometric workflows and detection methods are evaluated for glycans and glycoproteins. Furthermore, glycomic methodologies and innovations that are tailored for enzymatic treatments, chemical derivatization, purification, separation, and detection at high sensitivity are highlighted. The discussion is focused on the analysis of mammalian N-linked and GalNAc-type O-linked glycans.
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Affiliation(s)
| | - Bernhard Kuster
- Chair for Proteomics and BioanalyticsTechnical University of MunichFreisingGermany
| | - Dietmar Reusch
- Pharma Technical Development EuropeRoche Diagnostics GmbHPenzbergGermany
| | - Manfred Wuhrer
- Leiden University Medical CenterCenter for Proteomics and MetabolomicsLeidenThe Netherlands
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5
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Dhawan V, Cui XT. Carbohydrate based biomaterials for neural interface applications. J Mater Chem B 2022; 10:4714-4740. [PMID: 35702979 DOI: 10.1039/d2tb00584k] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Neuroprosthetic devices that record and modulate neural activities have demonstrated immense potential for bypassing or restoring lost neurological functions due to neural injuries and disorders. However, implantable electrical devices interfacing with brain tissue are susceptible to a series of inflammatory tissue responses along with mechanical or electrical failures which can affect the device performance over time. Several biomaterial strategies have been implemented to improve device-tissue integration for high quality and stable performance. Ranging from developing smaller, softer, and more flexible electrode designs to introducing bioactive coatings and drug-eluting layers on the electrode surface, such strategies have shown different degrees of success but with limitations. With their hydrophilic properties and specific bioactivities, carbohydrates offer a potential solution for addressing some of the limitations of the existing biomolecular approaches. In this review, we summarize the role of polysaccharides in the central nervous system, with a primary focus on glycoproteins and proteoglycans, to shed light on their untapped potential as biomaterials for neural implants. Utilization of glycosaminoglycans for neural interface and tissue regeneration applications is comprehensively reviewed to provide the current state of carbohydrate-based biomaterials for neural implants. Finally, we will discuss the challenges and opportunities of applying carbohydrate-based biomaterials for neural tissue interfaces.
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Affiliation(s)
- Vaishnavi Dhawan
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA. .,Center for Neural Basis of Cognition, Pittsburgh, PA, USA
| | - Xinyan Tracy Cui
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA. .,Center for Neural Basis of Cognition, Pittsburgh, PA, USA.,McGowan Institute for Regenerative Medicine, Pittsburgh, PA, USA
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6
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Pan S, Chen R. Pathological implication of protein post-translational modifications in cancer. Mol Aspects Med 2022; 86:101097. [PMID: 35400524 PMCID: PMC9378605 DOI: 10.1016/j.mam.2022.101097] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 02/07/2023]
Abstract
Protein post-translational modifications (PTMs) profoundly influence protein functions and play crucial roles in essentially all cell biological processes. The diverse realm of PTMs and their crosstalk is linked to many critical signaling events involved in neoplastic transformation, carcinogenesis and metastasis. The pathological roles of various PTMs are implicated in all aspects of cancer hallmark functions, cancer metabolism and regulation of tumor microenvironment. Study of PTMs has become an important area in cancer research to understand cancer biology and discover novel biomarkers and therapeutic targets. With a limited scope, this review attempts to discuss some PTMs of high frequency with recognized importance in cancer biology, including phosphorylation, acetylation, glycosylation, palmitoylation and ubiquitination, as well as their implications in clinical applications. These protein modifications are among the most abundant PTMs and profoundly implicated in carcinogenesis.
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7
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Wang T, Liu L, Voglmeir J. mAbs N-glycosylation: Implications for biotechnology and analytics. Carbohydr Res 2022; 514:108541. [DOI: 10.1016/j.carres.2022.108541] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 03/03/2022] [Accepted: 03/07/2022] [Indexed: 12/29/2022]
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8
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Yu A, Zhao J, Yadav SPS, Molitoris BA, Wagner MC, Mechref Y. Changes in the Expression of Renal Brush Border Membrane N-Glycome in Model Rats with Chronic Kidney Diseases. Biomolecules 2021; 11:1677. [PMID: 34827675 PMCID: PMC8616023 DOI: 10.3390/biom11111677] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 12/15/2022] Open
Abstract
Chronic kidney disease (CKD) is defined by a reduced renal function i.e., glomerular filtration rate (GFR), and the presence of kidney damage is determined by measurement of proteinuria or albuminuria. Albuminuria increases with age and can result from glomerular and/or proximal tubule (PT) alterations. Brush-border membranes (BBMs) on PT cells play an important role in maintaining the stability of PT functions. The PT BBM, a highly dynamic, organized, specialized membrane, contains a variety of glycoproteins required for the functions of PT. Since protein glycosylation regulates many protein functions, the alteration of glycosylation due to the glycan changes has attracted more interests for a variety of disease studies recently. In this work, liquid chromatography-tandem mass spectrometry was utilized to analyze the abundances of permethylated glycans from rats under control to mild CKD, severe CKD, and diabetic conditions. The most significant differences were observed in sialylation level with the highest present in the severe CKD and diabetic groups. Moreover, high mannose N-glycans was enriched in the CKD BBMs. Characterization of all the BBM N-glycan changes supports that these changes are likely to impact the functional properties of the dynamic PT BBM. Further, these changes may lead to the potential discovery of glycan biomarkers for improved CKD diagnosis and new avenues for therapeutic treatments.
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Affiliation(s)
- Aiying Yu
- Department of Chemistry and Biochemistry, Texas Tech University, Texas City, TX 79409, USA; (A.Y.); (J.Z.)
| | - Jingfu Zhao
- Department of Chemistry and Biochemistry, Texas Tech University, Texas City, TX 79409, USA; (A.Y.); (J.Z.)
| | - Shiv Pratap S. Yadav
- Nephrology Division, Department of Medicine, Indiana University, Indianapolis, IN 46202, USA; (S.P.S.Y.); (B.A.M.); (M.C.W.)
| | - Bruce A. Molitoris
- Nephrology Division, Department of Medicine, Indiana University, Indianapolis, IN 46202, USA; (S.P.S.Y.); (B.A.M.); (M.C.W.)
| | - Mark C. Wagner
- Nephrology Division, Department of Medicine, Indiana University, Indianapolis, IN 46202, USA; (S.P.S.Y.); (B.A.M.); (M.C.W.)
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Texas City, TX 79409, USA; (A.Y.); (J.Z.)
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9
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Zhong L, Zhu L, Cai ZW. Mass Spectrometry-based Proteomics and Glycoproteomics in COVID-19 Biomarkers Identification: A Mini-review. JOURNAL OF ANALYSIS AND TESTING 2021; 5:298-313. [PMID: 34513131 PMCID: PMC8423835 DOI: 10.1007/s41664-021-00197-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 07/27/2021] [Indexed: 12/11/2022]
Abstract
The first corona-pandemic, coronavirus disease 2019 (COVID-19) caused a huge health crisis and incalculable damage worldwide. Knowledge of how to cure the disease is urgently needed. Emerging immune escaping mutants of the virus suggested that it may be potentially persistent in human society as a regular health threat as the flu virus. Therefore, it is imperative to identify appropriate biomarkers to indicate pathological and physiological states, and more importantly, clinic outcomes. Proteins are the performers of life functions, and their abundance and modification status can directly reflect the immune status. Protein glycosylation serves a great impact in modulating protein function. The use of both unmodified and glycosylated proteins as biomarkers has also been proved feasible in the studies of SARS, Zika virus, influenza, etc. In recent years, mass spectrometry-based glycoproteomics, as well as proteomics approaches, advanced significantly due to the evolution of mass spectrometry. We focus on the current development of the mass spectrometry-based strategy for COVID-19 biomarkers' investigation. Potential application of glycoproteomics approaches and challenges in biomarkers identification are also discussed.
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Affiliation(s)
- Li Zhong
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, 224 Waterloo Road, Kowloon Tong, Hong Kong SAR, China
| | - Lin Zhu
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, 224 Waterloo Road, Kowloon Tong, Hong Kong SAR, China
| | - Zong-Wei Cai
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, 224 Waterloo Road, Kowloon Tong, Hong Kong SAR, China
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10
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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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11
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Huang J, Jiang B, Liu M, Yang P, Cao W. gQuant, an Automated Tool for Quantitative Glycomic Data Analysis. Front Chem 2021; 9:707738. [PMID: 34395380 PMCID: PMC8355585 DOI: 10.3389/fchem.2021.707738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 07/15/2021] [Indexed: 11/25/2022] Open
Abstract
MALDI-MS-based glycan isotope labeling methods have been effectively and widely used for quantitative glycomics. However, interpretation of the data produced by MALDI-MS is inaccurate and tedious because the bioinformatic tools are inadequate. In this work, we present gQuant, an automated tool for MALDI-MS-based glycan isotope labeling data processing. gQuant was designed with a set of dedicated algorithms to improve the efficiency, accuracy and convenience of quantitation data processing. When tested on the reference data set, gQuant showed a fast processing speed, as it was able to search the glycan data of model glycoproteins in a few minutes and reported more results than the manual analysis did. The reported quantitation ratios matched well with the experimental glycan mixture ratios ranging from 1:10 to 10:1. In addition, gQuant is fully open-source and is coded in Python, which is supported by most operating systems, and it has a user-friendly interface. gQuant can be easily adapted by users for specific experimental designs, such as specific glycan databases, different derivatization types and relative quantitation designs and can thus facilitate fast glycomic quantitation for clinical sample analysis using MALDI-MS-based stable isotope labeling.
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Affiliation(s)
- Jiangming Huang
- The Fifth People's Hospital, Fudan University, and the Shanghai Key Laboratory of Medical Epigenetics, The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Department of Chemistry, Fudan University, Shanghai, China
| | - Biyun Jiang
- The Fifth People's Hospital, Fudan University, and the Shanghai Key Laboratory of Medical Epigenetics, The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Mingqi Liu
- The Fifth People's Hospital, Fudan University, and the Shanghai Key Laboratory of Medical Epigenetics, The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Pengyuan Yang
- The Fifth People's Hospital, Fudan University, and the Shanghai Key Laboratory of Medical Epigenetics, The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Department of Chemistry, Fudan University, Shanghai, China
| | - Weiqian Cao
- The Fifth People's Hospital, Fudan University, and the Shanghai Key Laboratory of Medical Epigenetics, The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, China
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12
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Ho JS, Gharbi A, Schindler B, Yeni O, Brédy R, Legentil L, Ferrières V, Kiessling LL, Compagnon I. Distinguishing Galactoside Isomers with Mass Spectrometry and Gas-Phase Infrared Spectroscopy. J Am Chem Soc 2021; 143:10509-10513. [PMID: 34236183 PMCID: PMC9867933 DOI: 10.1021/jacs.0c11919] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Sequencing glycans is demanding due to their structural diversity. Compared to mammalian glycans, bacterial glycans pose a steeper challenge because they are constructed from a larger pool of monosaccharide building blocks, including pyranose and furanose isomers. Though mammalian glycans incorporate only the pyranose form of galactose (Galp), many pathogens, including Mycobacterium tuberculosis and Klebsiella pneumoniae, contain galactofuranose (Galf) residues in their cell envelope. Thus, glycan sequencing would benefit from methods to distinguish between pyranose and furanose isomers of different anomeric configurations. We used infrared multiple photon dissociation (IRMPD) spectroscopy with mass spectrometry (MS-IR) to differentiate between pyranose- and furanose-linked galactose residues. These targets pose a challenge for MS-IR because the saccharides lack basic groups, and galactofuranose residues are highly flexible. We postulated cationic groups that could complex through hydrogen bonding would offer a solution. Here, we present the first MS-IR analysis of hexose ammonium adducts. We compared their IR fingerprints with those of lithium adducts. We determined the diagnostic MS-IR signatures of the α- and β-anomers of galactose in furanose and pyranose forms. We also showed these signatures could be applied to disaccharides to assign galactose ring size. Our findings highlight the utility of MS-IR for analyzing the unique substructures that occur in bacterial glycans.
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Affiliation(s)
| | | | - Baptiste Schindler
- Univ. Lyon, Université Claude Bernard Lyon 1, F-69622 Villeurbanne, France
| | - Oznur Yeni
- Univ. Lyon, Université Claude Bernard Lyon 1, F-69622 Villeurbanne, France
| | - Richard Brédy
- Univ. Lyon, Université Claude Bernard Lyon 1, F-69622 Villeurbanne, France
| | - Laurent Legentil
- Univ. Rennes, Ecole Nationale Supérieure de Chimie de Rennes, F-35000 Rennes, France
| | - Vincent Ferrières
- Univ. Rennes, Ecole Nationale Supérieure de Chimie de Rennes, F-35000 Rennes, France
| | - Laura L. Kiessling
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Isabelle Compagnon
- Univ. Lyon, Université Claude Bernard Lyon 1, F-69622 Villeurbanne, France
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13
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Jeong S, Kim U, Oh M, Nam J, Park S, Choi Y, Lee D, Kim J, An H. Detection of Aberrant Glycosylation of Serum Haptoglobin for Gastric Cancer Diagnosis Using a Middle-Up-Down Glycoproteome Platform. J Pers Med 2021; 11:jpm11060575. [PMID: 34207451 PMCID: PMC8235735 DOI: 10.3390/jpm11060575] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 06/14/2021] [Accepted: 06/16/2021] [Indexed: 12/20/2022] Open
Abstract
Gastric cancer is a frequently occurring cancer and is the leading cause of cancer-related deaths. Recent studies have shown that aberrant glycosylation of serum haptoglobin is closely related to gastric cancer and has enormous potential for use in diagnosis. However, there is no platform with high reliability and high reproducibility to comprehensively analyze haptoglobin glycosylation covering microheterogeneity to macroheterogeneity for clinical applications. In this study, we developed a middle-up-down glycoproteome platform for fast and accurate monitoring of haptoglobin glycosylation. This platform utilizes an online purification of LC for sample desalting, and an in silico haptoglobin glycopeptide library constructed by combining peptides and N-glycans to readily identify glycopeptides. In addition, site-specific glycosylation with glycan heterogeneity can be obtained through only a single MS analysis. Haptoglobin glycosylation in clinical samples consisting of healthy controls (n = 47) and gastric cancer patients (n = 43) was extensively investigated using three groups of tryptic glycopeptides: GP1 (including Asn184), GP2 (including Asn207 and Asn211), and GP3 (including Asn241). A total of 23 individual glycopeptides were determined as potential biomarkers (p < 0.00001). In addition, to improve diagnostic efficacy, we derived representative group biomarkers with high AUC values (0.929 to 0.977) through logistic regression analysis for each GP group. It has been found that glycosylation of haptoglobin is highly associated with gastric cancer, especially the glycosite Asn241. Our assay not only allows to quickly and easily obtain information on glycosylation heterogeneity of a target glycoprotein but also makes it an efficient tool for biomarker discovery and clinical diagnosis.
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Affiliation(s)
- Seunghyup Jeong
- Asia-Pacific Glycomics Reference Site, Chungnam National University, Daejeon 34134, Korea; (S.J.); (M.O.); (J.N.)
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon 34134, Korea
| | | | - Myungjin Oh
- Asia-Pacific Glycomics Reference Site, Chungnam National University, Daejeon 34134, Korea; (S.J.); (M.O.); (J.N.)
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon 34134, Korea
| | - Jihyeon Nam
- Asia-Pacific Glycomics Reference Site, Chungnam National University, Daejeon 34134, Korea; (S.J.); (M.O.); (J.N.)
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon 34134, Korea
| | - Sehoon Park
- Division of Hematology/Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea;
| | - Yoonjin Choi
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Korea;
| | - Dongho Lee
- Department of Internal Medicine for Gastroenterology, Seoul National University Bundang Hospital, Seongnam 13620, Korea;
| | - Jaehan Kim
- Department of Food and Nutrition, Chungnam National University, Daejeon 34134, Korea;
| | - Hyunjoo An
- Asia-Pacific Glycomics Reference Site, Chungnam National University, Daejeon 34134, Korea; (S.J.); (M.O.); (J.N.)
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon 34134, Korea
- Correspondence:
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14
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Bombyx mori β1,4-N-acetylgalactosaminyltransferase possesses relaxed donor substrate specificity in N-glycan synthesis. Sci Rep 2021; 11:5505. [PMID: 33750826 PMCID: PMC7943597 DOI: 10.1038/s41598-021-84771-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 02/08/2021] [Indexed: 12/15/2022] Open
Abstract
N-Glycosylation is one of the most important post-translational protein modifications in eukaryotic cells. Although more than 200 N-glycogenes contributing to N-glycan biosynthesis have been identified and characterized, the information on insect N-glycosylation is still limited. Here, focusing on insect N-glycosylation, we characterized Bombyx mori N-acetylgalactosaminyltransferase (BmGalNAcT) participating in complex N-glycan biosynthesis in mammals. BmGalNAcT localized at the Golgi and was ubiquitously expressed in every organ and in the developmental stage of the middle silk gland of fifth instar larvae. Analysis of recombinant BmGalNAcT expressed in Sf9 cells showed that BmGalNAcT transferred GalNAc to non-reducing terminals of GlcNAcβ1,2-R with β1,4-linkage. In addition, BmGalNAcT mediated transfer of galactose and N-acetylglucosamine residues but not transfer of either glucose or glucuronic acid from the UDP-sugar donor substrate to the N-glycan. Despite this tri-functional sugar transfer activity, however, most of the endogenous glycoproteins of insect cells were present without GalNAc, Gal, or GlcNAc residues at the non-reducing terminal of β1,2-GlcNAc residue(s). Moreover, overexpression of BmGalNAcT in insect cells had no effect on N-acetylgalactosaminylation, galactosylation, or N-acetylglucosaminylation of the major N-glycan during biosynthesis. These results suggested that B. mori has a novel multifunctional glycosyltransferase, but the N-glycosylation is highly and strictly regulated by the endogenous N-glycosylation machineries.
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15
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Pont L, Kuzyk V, Benavente F, Sanz-Nebot V, Mayboroda OA, Wuhrer M, Lageveen-Kammeijer GSM. Site-Specific N-Linked Glycosylation Analysis of Human Carcinoembryonic Antigen by Sheathless Capillary Electrophoresis-Tandem Mass Spectrometry. J Proteome Res 2021; 20:1666-1675. [PMID: 33560857 PMCID: PMC8023805 DOI: 10.1021/acs.jproteome.0c00875] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
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With 28 potential N-glycosylation sites, human
carcinoembryonic antigen (CEA) bears an extreme amount of N-linked glycosylation, and approximately 60% of its molecular
mass can be attributed to its carbohydrates. CEA is often overexpressed
and released by many solid tumors, including colorectal carcinomas.
CEA displays an impressive heterogeneity and variability in sugar
content; however, site-specific distribution of carbohydrate structures
has not been reported so far. The present study investigated CEA samples
purified from human colon carcinoma and human liver metastases and
enabled the characterization of 21 out of 28 potential N-glycosylation sites with respect to their occupancy. The coverage
was achieved by a multienzymatic digestion approach with specific
enzymes, such as trypsin, endoproteinase Glu-C, and the nonspecific enzyme, Pronase, followed by analysis using
sheathless CE-MS/MS. In total, 893 different N-glycopeptides
and 128 unique N-glycan compositions were identified.
Overall, a great heterogeneity was found both within (micro) and in
between (macro) individual N-glycosylation sites.
Moreover, notable differences were found on certain N-glycosylation sites between primary adenocarcinoma and metastatic
tumor in regard to branching, bisection, sialylation, and fucosylation.
Those features, if further investigated in a targeted manner, may
pave the way toward improved diagnostics and monitoring of colorectal
cancer progression and recurrence. Raw mass spectrometric data and
Skyline processed data files that support the findings of this study
are available in the MassIVE repository with the identifier MSV000086774
[DOI: 10.25345/C5Z50X].
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Affiliation(s)
- Laura Pont
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, 08007 Barcelona, Spain
| | - Valeriia Kuzyk
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands.,Division of Bioanalytical Chemistry, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Fernando Benavente
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, 08007 Barcelona, Spain
| | - Victoria Sanz-Nebot
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, 08007 Barcelona, Spain
| | - Oleg A Mayboroda
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
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16
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Martins ÁM, Ramos CC, Freitas D, Reis CA. Glycosylation of Cancer Extracellular Vesicles: Capture Strategies, Functional Roles and Potential Clinical Applications. Cells 2021; 10:cells10010109. [PMID: 33430152 PMCID: PMC7827205 DOI: 10.3390/cells10010109] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 12/29/2020] [Accepted: 01/04/2021] [Indexed: 12/12/2022] Open
Abstract
Glycans are major constituents of extracellular vesicles (EVs). Alterations in the glycosylation pathway are a common feature of cancer cells, which gives rise to de novo or increased synthesis of particular glycans. Therefore, glycans and glycoproteins have been widely used in the clinic as both stratification and prognosis cancer biomarkers. Interestingly, several of the known tumor-associated glycans have already been identified in cancer EVs, highlighting EV glycosylation as a potential source of circulating cancer biomarkers. These particles are crucial vehicles of cell–cell communication, being able to transfer molecular information and to modulate the recipient cell behavior. The presence of particular glycoconjugates has been described to be important for EV protein sorting, uptake and organ-tropism. Furthermore, specific EV glycans or glycoproteins have been described to be able to distinguish tumor EVs from benign EVs. In this review, the application of EV glycosylation in the development of novel EV detection and capture methodologies is discussed. In addition, we highlight the potential of EV glycosylation in the clinical setting for both cancer biomarker discovery and EV therapeutic delivery strategies.
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Affiliation(s)
- Álvaro M. Martins
- Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugal; (Á.M.M.); (C.C.R.)
- Institute of Molecular Pathology and Immunology (IPATIMUP), University of Porto, 4200-135 Porto, Portugal
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS), University of Porto, 4050-313 Porto, Portugal
| | - Cátia C. Ramos
- Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugal; (Á.M.M.); (C.C.R.)
- Institute of Molecular Pathology and Immunology (IPATIMUP), University of Porto, 4200-135 Porto, Portugal
- Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Daniela Freitas
- Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugal; (Á.M.M.); (C.C.R.)
- Institute of Molecular Pathology and Immunology (IPATIMUP), University of Porto, 4200-135 Porto, Portugal
- Correspondence: (D.F.); (C.A.R.); Tel.:+351-225-570-786 (C.A.R.)
| | - Celso A. Reis
- Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugal; (Á.M.M.); (C.C.R.)
- Institute of Molecular Pathology and Immunology (IPATIMUP), University of Porto, 4200-135 Porto, Portugal
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS), University of Porto, 4050-313 Porto, Portugal
- Faculty of Medicine of the University of Porto (FMUP), 4200-319 Porto, Portugal
- Correspondence: (D.F.); (C.A.R.); Tel.:+351-225-570-786 (C.A.R.)
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17
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L-Fucose treatment of FUT8-CDG. Mol Genet Metab Rep 2020; 25:100680. [PMID: 33312876 PMCID: PMC7719959 DOI: 10.1016/j.ymgmr.2020.100680] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 11/12/2020] [Accepted: 11/12/2020] [Indexed: 11/22/2022] Open
Abstract
FUT8-CDG is a severe multisystem disorder caused by mutations in FUT8, encoding the α-1,6-fucosyltransferase. We report on dizygotic twins with FUT8-CDG presenting with dysmorphisms, failure to thrive, and respiratory abnormalities. Due to the severe phenotype, oral L-fucose supplementation was started. Glycosylation analysis using mass spectrometry indicated a limited response to fucose therapy while the clinical presentation stabilized. Further research is needed to assess the concept of substrate supplementation in FUT8-CDG.
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18
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Barrientos RC, Zhang Q. Recent advances in the mass spectrometric analysis of glycosphingolipidome - A review. Anal Chim Acta 2020; 1132:134-155. [PMID: 32980104 PMCID: PMC7525043 DOI: 10.1016/j.aca.2020.05.051] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 05/17/2020] [Accepted: 05/21/2020] [Indexed: 12/30/2022]
Abstract
Aberrant expression of glycosphingolipids has been implicated in a myriad of diseases, but our understanding of the strucural diversity, spatial distribution, and biological function of this class of biomolecules remains limited. These challenges partly stem from a lack of sensitive tools that can detect, identify, and quantify glycosphingolipids at the molecular level. Mass spectrometry has emerged as a powerful tool poised to address most of these challenges. Here, we review the recent developments in analytical glycosphingolipidomics with an emphasis on sample preparation, mass spectrometry and tandem mass spectrometry-based structural characterization, label-free and labeling-based quantification. We also discuss the nomenclature of glycosphingolipids, and emerging technologies like ion mobility spectrometry in differentiation of glycosphingolipid isomers. The intrinsic advantages and shortcomings of each method are carefully critiqued in line with an individual's research goals. Finally, future perspectives on analytical sphingolipidomics are stated, including a need for novel and more sensive methods in isomer separation, low abundance species detection, and profiling the spatial distribution of glycosphingolipid molecular species in cells and tissues using imaging mass spectrometry.
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Affiliation(s)
- Rodell C Barrientos
- Department of Chemistry and Biochemistry, The University of North Carolina at Greensboro, Greensboro, NC, 27412, United States; UNCG Center for Translational Biomedical Research, NC Research Campus, Kannapolis, NC, 28081, United States
| | - Qibin Zhang
- Department of Chemistry and Biochemistry, The University of North Carolina at Greensboro, Greensboro, NC, 27412, United States; UNCG Center for Translational Biomedical Research, NC Research Campus, Kannapolis, NC, 28081, United States.
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19
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Protein Glycosylation Investigated by Mass Spectrometry: An Overview. Cells 2020; 9:cells9091986. [PMID: 32872358 PMCID: PMC7564411 DOI: 10.3390/cells9091986] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/14/2020] [Accepted: 08/24/2020] [Indexed: 12/16/2022] Open
Abstract
The protein glycosylation is a post-translational modification of crucial importance for its involvement in molecular recognition, protein trafficking, regulation, and inflammation. Indeed, abnormalities in protein glycosylation are correlated with several disease states such as cancer, inflammatory diseases, and congenial disorders. The understanding of cellular mechanisms through the elucidation of glycan composition encourages researchers to find analytical solutions for their detection. Actually, the multiplicity and diversity of glycan structures bond to the proteins, the variations in polarity of the individual saccharide residues, and the poor ionization efficiencies make their detection much trickier than other kinds of biopolymers. An overview of the most prominent techniques based on mass spectrometry (MS) for protein glycosylation (glycoproteomics) studies is here presented. The tricks and pre-treatments of samples are discussed as a crucial step prodromal to the MS analysis to improve the glycan ionization efficiency. Therefore, the different instrumental MS mode is also explored for the qualitative and quantitative analysis of glycopeptides and the glycans structural composition, thus contributing to the elucidation of biological mechanisms.
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20
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Bansal P, Yatsyna V, AbiKhodr AH, Warnke S, Ben Faleh A, Yalovenko N, Wysocki VH, Rizzo TR. Using SLIM-Based IMS-IMS Together with Cryogenic Infrared Spectroscopy for Glycan Analysis. Anal Chem 2020; 92:9079-9085. [PMID: 32456419 PMCID: PMC7349563 DOI: 10.1021/acs.analchem.0c01265] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 05/27/2020] [Indexed: 12/18/2022]
Abstract
The isomeric heterogeneity of glycans poses a great challenge for their analysis. While combining ion mobility spectrometry (IMS) with tandem mass spectrometry is a powerful means for identifying and characterizing glycans, it has difficulty distinguishing the subtlest differences between isomers. Cryogenic infrared spectroscopy provides an additional dimension for glycan identification that is extremely sensitive to their structure. Our approach to glycan analysis combines ultrahigh-resolution IMS-IMS using structures for lossless ion manipulation (SLIM) with cryogenic infrared spectroscopy. We present here the design of a SLIM board containing a series of on-board traps in which we perform collision-induced dissociation (CID) at pressures in the millibar range. We characterize the on-board CID process by comparing the fragments generated from a pentapeptide to those obtained on a commercial tandem mass spectrometer. We then apply our new technique to study the mobility and vibrational spectra of CID fragments from two human milk oligosaccharides. Comparison of both the fragment drift times and IR spectra with those of suitable reference compounds allows us to identify their specific isomeric form, including the anomericity of the glycosidic linkage, demonstrating the power of this tool for glycan analysis.
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Affiliation(s)
- Priyanka Bansal
- Laboratoire
de Chimie Physique Moléculaire, École
Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Vasyl Yatsyna
- Laboratoire
de Chimie Physique Moléculaire, École
Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
- Department
of Physics, University of Gothenburg, 412 96 Gotheburg, Sweden
| | - Ali H. AbiKhodr
- Laboratoire
de Chimie Physique Moléculaire, École
Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Stephan Warnke
- Laboratoire
de Chimie Physique Moléculaire, École
Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Ahmed Ben Faleh
- Laboratoire
de Chimie Physique Moléculaire, École
Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Natalia Yalovenko
- Laboratoire
de Chimie Physique Moléculaire, École
Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Vicki H. Wysocki
- Department
of Chemistry and Biochemistry, The Ohio
State University, Columbus, Ohio 43210, United States
| | - Thomas R. Rizzo
- Laboratoire
de Chimie Physique Moléculaire, École
Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
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21
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Kuo CW, Khoo KH. Strategic Applications of Negative-Mode LC-MS/MS Analyses to Expedite Confident Mass Spectrometry-Based Identification of Multiple Glycosylated Peptides. Anal Chem 2020; 92:7612-7620. [PMID: 32384234 DOI: 10.1021/acs.analchem.0c00236] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Although recent advances in mass spectrometry (MS) have enabled meaningful glycoproteomic undertakings, many technical limitations remain unsolved. Among these, the ability to efficiently sequence the peptide backbone for de novo identification, delineating multiple N- and O-glycosylation sites on single glycopeptides, and deriving more glycan structure information to discriminate isomeric glycoforms are well acknowledged practical problems to be tackled. To address these issues, we explored the use of negative-mode MS2/MS3 fragmentation to supplement current nanoLC-MS2-based sequencing and identification of intact glycopeptides largely performed in positive mode. Consistent with previous reports by others, we found that sulfation and sialylation drastically alter the MS2 fragmentation pattern of glycopeptides in negative mode and the characteristic features identified can be utilized to program the most informative MS3 on the glycan moiety itself. Importantly, direct elimination of one or more O-glycans under negative-mode MS2 affords an easy way to discover additional O-glycosylations on a multiply glycosylated peptide by virtue of enumerating the dehydration scars imprinted on the O-glycosylated sites. Moreover, the characteristic peptide core ion carrying a ring cleavage remnant of the innermost amino sugar residue of an N-glycan can be relied upon to filter out all related N-glycopeptides carrying additional O-glycans defined by specific mass increments. Such enhanced ability to advance from definitive identification of single to multiple site-specific glycosylation on the same peptide backbones is anticipated to have a significant impact on the level of structural and biological insights one can gain in glycoproteomic applications.
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Affiliation(s)
- Chu-Wei Kuo
- Institute of Biological Chemistry, Academia Sinica, Nankang, Taipei 115, Taiwan
| | - Kay-Hooi Khoo
- Institute of Biological Chemistry, Academia Sinica, Nankang, Taipei 115, Taiwan
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22
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Glycomics studies using sialic acid derivatization and mass spectrometry. Nat Rev Chem 2020; 4:229-242. [PMID: 37127981 DOI: 10.1038/s41570-020-0174-3] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/20/2020] [Indexed: 12/13/2022]
Abstract
Proteins can undergo glycosylation during and/or after translation to afford glycoconjugates, which are often secreted by a cell or populate cell surfaces. Changes in the glycan portion can have a strong influence on a glycoconjugate and are associated with a multitude of human pathologies. Of particular interest are sialylated glycoconjugates, which exist as constitutional isomers that differ in their linkages (α2,3, α2,6, α2,8 or α2,9) between sialic acids and their neighbouring monosaccharides. In general, mass spectrometry enables the rapid and sensitive characterization of glycosylation, but there are challenges specific to identifying and (relatively) quantifying sialic acid isomers. These challenges can be addressed using linkage-specific methodologies for sialic acid derivatization, after which mass spectrometry can enable product identification. This Review is concerned with the new and important derivatization approaches reported in the past decade, which have been implemented in various mass-spectrometry-glycomics workflows and have found clinical glycomics applications. The convenience and wide applicability of the approaches make them attractive for studies of sialylation in different types of glycoconjugate.
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23
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Mule SN, Saad JS, Fernandes LR, Stolf BS, Cortez M, Palmisano G. Protein glycosylation inLeishmaniaspp. Mol Omics 2020; 16:407-424. [DOI: 10.1039/d0mo00043d] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Protein glycosylation is a co- and post-translational modification that, inLeishmaniaparasites, plays key roles in vector–parasite–vertebrate host interaction.
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Affiliation(s)
- Simon Ngao Mule
- GlycoProteomics Laboratory
- Department of Parasitology
- Institute of Biomedical Sciences
- University of Sao Paulo
- Sao Paulo - 05508-000
| | - Joyce Silva Saad
- GlycoProteomics Laboratory
- Department of Parasitology
- Institute of Biomedical Sciences
- University of Sao Paulo
- Sao Paulo - 05508-000
| | - Livia Rosa Fernandes
- GlycoProteomics Laboratory
- Department of Parasitology
- Institute of Biomedical Sciences
- University of Sao Paulo
- Sao Paulo - 05508-000
| | - Beatriz S. Stolf
- Department of Parasitology
- Institute of Biomedical Sciences
- University of Sao Paulo
- Sao Paulo
- Brazil
| | - Mauro Cortez
- Department of Parasitology
- Institute of Biomedical Sciences
- University of Sao Paulo
- Sao Paulo
- Brazil
| | - Giuseppe Palmisano
- GlycoProteomics Laboratory
- Department of Parasitology
- Institute of Biomedical Sciences
- University of Sao Paulo
- Sao Paulo - 05508-000
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24
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den Ridder M, Daran-Lapujade P, Pabst M. Shot-gun proteomics: why thousands of unidentified signals matter. FEMS Yeast Res 2019; 20:5682490. [DOI: 10.1093/femsyr/foz088] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 12/19/2019] [Indexed: 12/14/2022] Open
Abstract
ABSTRACT
Mass spectrometry-based proteomics has become a constitutional part of the multi-omics toolbox in yeast research, advancing fundamental knowledge of molecular processes and guiding decisions in strain and product developmental pipelines. Nevertheless, post-translational protein modifications (PTMs) continue to challenge the field of proteomics. PTMs are not directly encoded in the genome; therefore, they require a sensitive analysis of the proteome itself. In yeast, the relevance of post-translational regulators has already been established, such as for phosphorylation, which can directly affect the reaction rates of metabolic enzymes. Whereas, the selective analysis of single modifications has become a broadly employed technique, the sensitive analysis of a comprehensive set of modifications still remains a challenge. At the same time, a large number of fragmentation spectra in a typical shot-gun proteomics experiment remain unidentified. It has been estimated that a good proportion of those unidentified spectra originates from unexpected modifications or natural peptide variants. In this review, recent advancements in microbial proteomics for unrestricted protein modification discovery are reviewed, and recent research integrating this additional layer of information to elucidate protein interaction and regulation in yeast is briefly discussed.
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Affiliation(s)
- Maxime den Ridder
- Delft University of Technology, Department of Biotechnology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Pascale Daran-Lapujade
- Delft University of Technology, Department of Biotechnology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Martin Pabst
- Delft University of Technology, Department of Biotechnology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
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25
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Szigeti M, Guttman A. Sample Preparation Scale-Up for Deep N-glycomic Analysis of Human Serum by Capillary Electrophoresis and CE-ESI-MS. Mol Cell Proteomics 2019; 18:2524-2531. [PMID: 31628258 PMCID: PMC6885710 DOI: 10.1074/mcp.tir119.001669] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 10/15/2019] [Indexed: 12/21/2022] Open
Abstract
We introduce an efficient sample preparation workflow to facilitate deep N-glycomics analysis of the human serum by capillary electrophoresis with laser induced fluorescence (CE-LIF) detection and to accommodate the higher sample concentration requirement of electrospray ionization mass spectrometry connected to capillary electrophoresis (CE-ESI-MS). A novel, temperature gradient denaturing protocol was applied on amine functionalized magnetic bead partitioned glycoproteins to circumvent the otherwise prevalent precipitation issue. During this process, the free sugar content of the serum was significantly decreased as well, accommodating enhanced PNGase F mediated release of the N-linked carbohydrates. The liberated oligosaccharides were tagged with aminopyrene-trisulfonate, utilizing a modified evaporative labeling protocol. Processing the samples with this new workflow enabled deep CE-LIF analysis of the human serum N-glycome and provided the appropriate amount of material for CE-ESI-MS analysis in negative ionization mode.
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Affiliation(s)
- Marton Szigeti
- MTA-PE Translational Glycomics Research Group, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, 10 Egyetem Street, Veszprem, 8200, Hungary; Horváth Csaba Memorial Laboratory of Bioseparation Sciences, Research Center for Molecular Medicine, Doctoral School of Molecular Medicine, Faculty of Medicine, University of Debrecen, 98 Nagyerdei krt., Debrecen, 4032, Hungary
| | - Andras Guttman
- MTA-PE Translational Glycomics Research Group, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, 10 Egyetem Street, Veszprem, 8200, Hungary; Horváth Csaba Memorial Laboratory of Bioseparation Sciences, Research Center for Molecular Medicine, Doctoral School of Molecular Medicine, Faculty of Medicine, University of Debrecen, 98 Nagyerdei krt., Debrecen, 4032, Hungary.
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Robajac D, Masnikosa R, Nemčovič M, Križáková M, Belická Kluková Ľ, Baráth P, Katrlík J, Nedić O. Glycoanalysis of the placental membrane glycoproteins throughout placental development. Mech Ageing Dev 2019; 183:111151. [PMID: 31589880 DOI: 10.1016/j.mad.2019.111151] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 08/20/2019] [Accepted: 10/02/2019] [Indexed: 01/22/2023]
Abstract
Structural changes of glycans are observed in different (patho)physiological conditions. Human placental membrane (glyco)proteins were isolated from the first and third trimester placentas of mothers at different ages. By using lectin microarray, we demonstrated that the placental membrane N-glycome contains several N-glycan groups: high mannose, asialylated and sialylated biantennary moieties, bisected, core fucosylated, fucosylated at other positions (bearing terminal and/or antennary Fuc), α2-6 and α2-3 sialylated structures. Employing MALDI-TOF MS enabled identification of over sixty different N-glycan structures in all samples, with 17 moieties exceeding the relative abundance of 2%. The major MS peaks originated from: 1) biantennary complex type N-glycan with a bisecting GlcNAc residue and 2) a core Fuc paucimannosidic and high mannose type structures M3-M9. Age of mothers and the stage of placental development affected N-glycome. The work presented in this article is the first comprehensive mass spectrometric study of the N-glycome of human placental membrane proteins. Our results may be seen as the baseline which can serve for future MALDI MS profiling of the placental membrane N-glycome in different pathophysiological conditions.
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Affiliation(s)
- Dragana Robajac
- Institute for the Application of Nuclear Energy (INEP), University of Belgrade, Belgrade, 381, Serbia.
| | - Romana Masnikosa
- Institute for the Application of Nuclear Energy (INEP), University of Belgrade, Belgrade, 381, Serbia
| | - Marek Nemčovič
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, 421, Slovakia
| | - Martina Križáková
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, 421, Slovakia
| | | | - Peter Baráth
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, 421, Slovakia
| | - Jaroslav Katrlík
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, 421, Slovakia
| | - Olgica Nedić
- Institute for the Application of Nuclear Energy (INEP), University of Belgrade, Belgrade, 381, Serbia
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27
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Cho BG, Veillon L, Mechref Y. N-Glycan Profile of Cerebrospinal Fluids from Alzheimer's Disease Patients Using Liquid Chromatography with Mass Spectrometry. J Proteome Res 2019; 18:3770-3779. [PMID: 31437391 PMCID: PMC7027932 DOI: 10.1021/acs.jproteome.9b00504] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Glycosylation, an essential post-translational protein modification, is known to be altered in a variety of diseases, including neurodegenerative diseases such as Alzheimer's disease (AD), which is one of the most common neurodegenerative disorders that results in cognitive and memory impairments. To investigate the progression of such a condition, cerebrospinal fluid (CSF), a unique biofluid that may possess significant biochemical and neurochemical changes due to the disease, is utilized. However, due to the low concentration of proteins in CSF, a large volume of the biofluid is often required to comprehensively characterize the glycome in CSF. In this work, a glycomic study of CSF was performed using as little as 10 μL of CSF. This approach was executed with permethylation of released N-glycans with minimal sample cleanup, in conjunction with an online purification system attached to liquid chromatography and a high-resolution mass spectrometer. This technique was then applied to clinical samples. Preliminary data suggest that fucosylated and bisecting GlcNAc structures were higher in abundances in females with AD, while both females and males exhibited lower abundances of high-mannose structures. Although there seems to be statistically significant differences between disease state and disease-free CSF, due to the lack of number of samples, further validation study should be conducted.
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Affiliation(s)
- Byeong Gwan Cho
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061
| | - Lucas Veillon
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061
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28
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Kayili HM, Ertürk AS, Elmacı G, Salih B. Poly(amidoamine) dendrimer-coated magnetic nanoparticles for the fast purification and selective enrichment of glycopeptides and glycans. J Sep Sci 2019; 42:3209-3216. [PMID: 31389124 DOI: 10.1002/jssc.201900492] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 07/29/2019] [Accepted: 08/01/2019] [Indexed: 01/24/2023]
Abstract
Glycosylated proteins modulate various important functions of organisms. To reveal the functions of glycoproteins, in-depth characterization studies are necessary. Although mass spectrometry is a very efficient tool for glycoproteomic and glycomic studies, efficient sample preparation methods are required prior to analyses. In the study, poly(amidoamine) dendrimer-coated magnetic nanoparticles were presented for the specific enrichment and fast purification of glycopeptides and glycans. The enrichment and purification performance of the developed method was evaluated both at the glycopeptide, and the glycan level using several standard glycoprotein digests and released glycan samples. The poly(amidoamine) dendrimer-coated magnetic nanoparticles not only showed selective affinity (Immunoglobulin G/Bovine Serum Albumin, 1/10 by weight) to glycopeptides and released glycans but also good sensitivity (0.4 ng/µL for Immunoglobulin G) for glycoproteomic and glycomic applications. Thirty-five glycopeptides of Immunoglobulin G were detected after enrichment with poly(amidoamine) dendrimer-coated magnetic nanoparticles. In addition, 55 18 O tagged deamidated glycopeptides belonging to human plasma glycoproteome were confirmed. Finally, fifty 2-aminobenzoic acid, and 30 procainamide-labelled human plasma N-glycans released from human plasma glycoproteins were determined after purifications. The results indicate that the proposed enrichment and purification method using poly(amidoamine) dendrimer-coated magnetic nanoparticles could be simply adjusted to sample preparation methods.
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Affiliation(s)
- Hacı Mehmet Kayili
- Department of Biomedical Engineering, Karabük University, Karabük, Turkey
| | - Ali Serol Ertürk
- Department of Analytical Chemistry, Faculty of Pharmacy, Adıyaman University, Adıyaman, Turkey
| | - Gökhan Elmacı
- Department of Chemistry, Adıyaman University, Adıyaman, Turkey
| | - Bekir Salih
- Department of Chemistry, Hacettepe University, Ankara, Turkey
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29
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Abstract
Many important interactions between bacterial pathogens and their hosts are highly specific binding events that involve host or pathogen carbohydrate structures (glycans). Glycan interactions can mediate adhesion, invasion and immune evasion and can act as receptors for toxins. Several bacterial pathogens can also enzymatically alter host glycans to reveal binding targets, degrade the host cell glycans or alter the function of host glycoproteins. In recent years, high-throughput screening technologies, such as lectin, glycan and mucin microarrays, have transformed the field by identifying new bacterial-host glycointeractions, which are crucial for colonization, persistence and disease. In this Review, we discuss interactions involving both host and bacterial glycans that have a role in bacterial pathogenesis. We also highlight recent technological advances that have illuminated the glycoscience of microbial pathogenesis.
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30
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Rojas-Macias MA, Mariethoz J, Andersson P, Jin C, Venkatakrishnan V, Aoki NP, Shinmachi D, Ashwood C, Madunic K, Zhang T, Miller RL, Horlacher O, Struwe WB, Watanabe Y, Okuda S, Levander F, Kolarich D, Rudd PM, Wuhrer M, Kettner C, Packer NH, Aoki-Kinoshita KF, Lisacek F, Karlsson NG. Towards a standardized bioinformatics infrastructure for N- and O-glycomics. Nat Commun 2019; 10:3275. [PMID: 31332201 PMCID: PMC6796180 DOI: 10.1038/s41467-019-11131-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 06/24/2019] [Indexed: 12/21/2022] Open
Abstract
The mass spectrometry (MS)-based analysis of free polysaccharides and glycans released from proteins, lipids and proteoglycans increasingly relies on databases and software. Here, we review progress in the bioinformatics analysis of protein-released N- and O-linked glycans (N- and O-glycomics) and propose an e-infrastructure to overcome current deficits in data and experimental transparency. This workflow enables the standardized submission of MS-based glycomics information into the public repository UniCarb-DR. It implements the MIRAGE (Minimum Requirement for A Glycomics Experiment) reporting guidelines, storage of unprocessed MS data in the GlycoPOST repository and glycan structure registration using the GlyTouCan registry, thereby supporting the development and extension of a glycan structure knowledgebase.
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Affiliation(s)
- Miguel A Rojas-Macias
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 40530, Sweden
| | - Julien Mariethoz
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva, 1211, Switzerland
- Computer Science Department, University of Geneva, Geneva, 1227, Switzerland
| | - Peter Andersson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 40530, Sweden
| | - Chunsheng Jin
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 40530, Sweden
| | - Vignesh Venkatakrishnan
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 40530, Sweden
| | - Nobuyuki P Aoki
- Soka University, Hachioji, 192-8577, Tokyo, Japan
- SparqLite LLC., Hachioji, 192-0032, Tokyo, Japan
| | - Daisuke Shinmachi
- Soka University, Hachioji, 192-8577, Tokyo, Japan
- SparqLite LLC., Hachioji, 192-0032, Tokyo, Japan
| | - Christopher Ashwood
- Department of Molecular Sciences, Macquarie University, Sydney, 2109, Australia
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | | | - Tao Zhang
- Leiden University Medical Center, Leiden, 2333ZA, Netherlands
| | - Rebecca L Miller
- Copenhagen Centre for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, København, DK-2200, Denmark
| | - Oliver Horlacher
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva, 1211, Switzerland
| | - Weston B Struwe
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK
| | - Yu Watanabe
- Graduate School of Medical and Dental Sciences, Niigata University, 950-2181, Niigata, Japan
| | - Shujiro Okuda
- Graduate School of Medical and Dental Sciences, Niigata University, 950-2181, Niigata, Japan
| | - Fredrik Levander
- National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Department of Immunotechnology, Lund University, Lund, 22387, Sweden
| | - Daniel Kolarich
- Institute for Glycomics, Gold Coast Campus, Griffith University, Gold Coast, QLD, QLD 4222, Australia
- ARC Centre for Nanoscale BioPhotonics, Macquarie University and Griffith University, North Ryde and Gold Coast, NSW and QLD, NSW 2109 and QLD 4222, Australia
| | - Pauline M Rudd
- Bioprocessing Technology Institute, AStar, Singapore, 138668, Singapore
| | - Manfred Wuhrer
- Leiden University Medical Center, Leiden, 2333ZA, Netherlands
| | | | - Nicolle H Packer
- Department of Molecular Sciences, Macquarie University, Sydney, 2109, Australia
- Institute for Glycomics, Gold Coast Campus, Griffith University, Gold Coast, QLD, QLD 4222, Australia
- ARC Centre for Nanoscale BioPhotonics, Macquarie University and Griffith University, North Ryde and Gold Coast, NSW and QLD, NSW 2109 and QLD 4222, Australia
| | | | - Frédérique Lisacek
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva, 1211, Switzerland
- Computer Science Department, University of Geneva, Geneva, 1227, Switzerland
- Section of Biology, University of Geneva, Geneva, 1211, Switzerland
| | - Niclas G Karlsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 40530, Sweden.
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31
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Kotsias M, Kozak RP, Gardner RA, Wuhrer M, Spencer DIR. Improved and semi-automated reductive β-elimination workflow for higher throughput protein O-glycosylation analysis. PLoS One 2019; 14:e0210759. [PMID: 30653606 PMCID: PMC6336230 DOI: 10.1371/journal.pone.0210759] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 01/01/2019] [Indexed: 11/19/2022] Open
Abstract
Protein O-glycosylation has shown to be critical for a wide range of biological processes, resulting in an increased interest in studying the alterations in O-glycosylation patterns of biological samples as disease biomarkers as well as for patient stratification and personalized medicine. Given the complexity of O-glycans, often a large number of samples have to be analysed in order to obtain conclusive results. However, most of the O-glycan analysis work done so far has been performed using glycoanalytical technologies that would not be suitable for the analysis of large sample sets, mainly due to limitations in sample throughput and affordability of the methods. Here we report a largely automated system for O-glycan analysis. We adapted reductive β-elimination release of O-glycans to a 96-well plate system and transferred the protocol onto a liquid handling robot. The workflow includes O-glycan release, purification and derivatization through permethylation followed by MALDI-TOF-MS. The method has been validated according to the ICH Q2 (R1) guidelines for the validation of analytical procedures. The semi-automated reductive β-elimination system enabled for the characterization and relative quantitation of O-glycans from commercially available standards. Results of the semi-automated method were in good agreement with the conventional manual in-solution method while even outperforming it in terms of repeatability. Release of O-glycans for 96 samples was achieved within 2.5 hours, and the automated data acquisition on MALDI-TOF-MS took less than 1 minute per sample. This largely automated workflow for O-glycosylation analysis showed to produce rapid, accurate and reliable data, and has the potential to be applied for O-glycan characterization of biological samples, biopharmaceuticals as well as for biomarker discovery.
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Affiliation(s)
| | - Radoslaw P. Kozak
- Ludger Ltd, Culham Science Centre, Abingdon, Oxfordshire, United Kingdom
| | - Richard A. Gardner
- Ludger Ltd, Culham Science Centre, Abingdon, Oxfordshire, United Kingdom
| | - Manfred Wuhrer
- Leiden University Medical Centre, Centre for Proteomics and Metabolomics, Leiden, Netherlands
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32
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Mucha E, Stuckmann A, Marianski M, Struwe WB, Meijer G, Pagel K. In-depth structural analysis of glycans in the gas phase. Chem Sci 2019; 10:1272-1284. [PMID: 30809341 PMCID: PMC6357860 DOI: 10.1039/c8sc05426f] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 01/04/2019] [Indexed: 12/26/2022] Open
Abstract
Although there have been substantial improvements in glycan analysis over the past decade, the lack of both high-resolution and high-throughput methods hampers progress in glycomics. This perspective article highlights the current developments of liquid chromatography, mass spectrometry, ion-mobility spectrometry and cryogenic IR spectroscopy for glycan analysis and gives a critical insight to their individual strengths and limitations. Moreover, we discuss a novel concept in which ion mobility-mass spectrometry and cryogenic IR spectroscopy is combined in a single instrument such that datasets consisting of m/z, collision cross sections and IR fingerprints can be obtained. This multidimensional data will then be compared to a comprehensive reference library of intact glycans and their fragments to accurately identify unknown glycans on a high-throughput scale with minimal sample requirements. Due to the complementarity of the obtained information, this novel approach is highly diagnostic and also suitable for the identification of larger glycans; however, the workflow and instrumentation is straightforward enough to be implemented into a user-friendly setup.
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Affiliation(s)
- Eike Mucha
- Fritz Haber Institute of the Max Planck Society , Department of Molecular Physics , Faradayweg 4-6 , 14195 Berlin , Germany . .,Institute of Chemistry and Biochemistry , Freie Universität Berlin , Takustraße 3 , 14195 Berlin , Germany
| | - Alexandra Stuckmann
- Fritz Haber Institute of the Max Planck Society , Department of Molecular Physics , Faradayweg 4-6 , 14195 Berlin , Germany . .,Institute of Chemistry and Biochemistry , Freie Universität Berlin , Takustraße 3 , 14195 Berlin , Germany
| | - Mateusz Marianski
- Fritz Haber Institute of the Max Planck Society , Department of Molecular Physics , Faradayweg 4-6 , 14195 Berlin , Germany .
| | - Weston B Struwe
- Oxford Glycobiology Institute , Department of Biochemistry , University of Oxford , OX1 3QU Oxford , UK
| | - Gerard Meijer
- Fritz Haber Institute of the Max Planck Society , Department of Molecular Physics , Faradayweg 4-6 , 14195 Berlin , Germany .
| | - Kevin Pagel
- Fritz Haber Institute of the Max Planck Society , Department of Molecular Physics , Faradayweg 4-6 , 14195 Berlin , Germany . .,Institute of Chemistry and Biochemistry , Freie Universität Berlin , Takustraße 3 , 14195 Berlin , Germany
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33
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Adua E, Memarian E, Russell A, Trbojević-Akmačić I, Gudelj I, Jurić J, Roberts P, Lauc G, Wang W. High throughput profiling of whole plasma N-glycans in type II diabetes mellitus patients and healthy individuals: A perspective from a Ghanaian population. Arch Biochem Biophys 2019; 661:10-21. [DOI: 10.1016/j.abb.2018.10.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 10/19/2018] [Accepted: 10/22/2018] [Indexed: 12/25/2022]
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Abstract
Even if a consensus sequence has been identified for a posttranslational modification, the presence of such a sequence motif only indicates the possibility, not the certainty that the modification actually occurs. Proteins can be glycosylated on certain amino acid side chains, and these modifications are designated as C-, N-, and O-glycosylation. C-mannosylation occurs on Trp residues within a relatively loosely defined consensus motif. N-glycosylated species are modified at Asn residues of Asn-Xxx-Ser/Thr/Cys sequons (where Xxx can be any amino acid except proline). N-linked oligosaccharides share a common core structure of GlcNAc2Man3. In addition, an enzyme, peptide N-glycosidase F (PNGase F), removes most of the common N-linked carbohydrates unaltered from proteins while hydrolyzing the originally glycosylated Asn residue to Asp. O-glycosylation occurs at Ser, Thr, and Tyr residues, usually in sequence stretches rich in hydroxy-amino acids. O-glycosylation lacks a common core structure. Mammalian proteins have been reported bearing O-linked N-acetylgalactosamine, fucose, glucose, xylose, mannose, and corresponding elongated structures, as well as N-acetylglucosamine. Chemical methods are used to liberate these oligosaccharides because no enzyme would remove all the different O-linked carbohydrates. Characterization of both N- and O-glycosylation is complicated by the fact that the same positions within a population of protein molecules may feature an array of different carbohydrate structures, or remain unmodified. This site-specific heterogeneity may vary by species and tissue, and may also be affected by physiological changes. For addressing site-specific carbohydrate heterogeneity mass spectrometry has become the method of choice. Reversed-phase HPLC directly coupled with electrospray ionization mass spectrometry (LC/ESI-MS/MS) offers the best solution. Using a mass spectrometer as online detector not only assures the analysis of every component eluting (mass mapping), but also at the same time diagnostic carbohydrate ions can be generated by collisional activation that permits the selective and specific detection of glycopeptides. In addition, ESI-compatible alternative MS/MS techniques, electron-capture and electron-transfer dissociation, aid glycopeptide identification as well as modification site assignments.
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35
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Understanding cellular glycan surfaces in the central nervous system. Biochem Soc Trans 2018; 47:89-100. [PMID: 30559272 DOI: 10.1042/bst20180330] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 10/21/2018] [Accepted: 11/06/2018] [Indexed: 02/06/2023]
Abstract
Glycosylation, the enzymatic process by which glycans are attached to proteins and lipids, is the most abundant and functionally important type of post-translational modification associated with brain development, neurodegenerative disorders, psychopathologies and brain cancers. Glycan structures are diverse and complex; however, they have been detected and targeted in the central nervous system (CNS) by various immunohistochemical detection methods using glycan-binding proteins such as anti-glycan antibodies or lectins and/or characterized with analytical techniques such as chromatography and mass spectrometry. The glycan structures on glycoproteins and glycolipids expressed in neural stem cells play key roles in neural development, biological processes and CNS maintenance, such as cell adhesion, signal transduction, molecular trafficking and differentiation. This brief review will highlight some of the important findings on differential glycan expression across stages of CNS cell differentiation and in pathological disorders and diseases such as Alzheimer's disease, Parkinson's disease, Huntington's disease, multiple sclerosis, amyotrophic lateral sclerosis, schizophrenia and brain cancer.
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36
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Russo D, Capolupo L, Loomba JS, Sticco L, D'Angelo G. Glycosphingolipid metabolism in cell fate specification. J Cell Sci 2018; 131:131/24/jcs219204. [PMID: 30559216 DOI: 10.1242/jcs.219204] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Glycosphingolipids (GSLs) are ubiquitous components of eukaryotic plasma membranes that consist of a ceramide backbone linked to a glycan moiety. Both the ceramide and the glycan parts of GSLs display structural variations that result in a remarkable repertoire of diverse compounds. This diversity of GSLs is exploited during embryogenesis, when different GSLs are produced at specific developmental stages and along several differentiation trajectories. Importantly, plasma membrane receptors interact with GSLs to modify their activities. Consequently, two otherwise identical cells can respond differently to the same stimulus owing to their different GSL composition. The metabolic reprograming of GSLs is in fact a necessary part of developmental programs, as its impairment results in developmental failure or tissue-specific defects. Moreover, single-cell variability is emerging as a fundamental player in development: GSL composition displays cell-to-cell variability in syngeneic cell populations owing to the regulatory gene expression circuits involved in microenvironment adaptation and in differentiation. Here, we discuss how GSLs are synthesized and classified and review the role of GSLs in the establishment and maintenance of cell identity. We further highlight the existence of the regulatory circuits that modify GSL pathways and speculate how GSL heterogeneity might contribute to developmental patterning.
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Affiliation(s)
- Domenico Russo
- Institute of Protein Biochemistry, National Research Council, Via P. Castellino 111, Napoli, Italy
| | - Laura Capolupo
- Institute of Protein Biochemistry, National Research Council, Via P. Castellino 111, Napoli, Italy.,Institute of Bioengineering, Laboratory of Lipid Cell Biology, École polytechnique fédérale de Lausanne (EPFL) CH-1015 Lausanne, Switzerland
| | - Jaipreet Singh Loomba
- Institute of Protein Biochemistry, National Research Council, Via P. Castellino 111, Napoli, Italy.,Institute of Bioengineering, Laboratory of Lipid Cell Biology, École polytechnique fédérale de Lausanne (EPFL) CH-1015 Lausanne, Switzerland
| | - Lucia Sticco
- Institute of Protein Biochemistry, National Research Council, Via P. Castellino 111, Napoli, Italy
| | - Giovanni D'Angelo
- Institute of Protein Biochemistry, National Research Council, Via P. Castellino 111, Napoli, Italy .,Institute of Bioengineering, Laboratory of Lipid Cell Biology, École polytechnique fédérale de Lausanne (EPFL) CH-1015 Lausanne, Switzerland
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37
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Abstract
Sialic acids are cytoprotectors, mainly localized on the surface of cell membranes with multiple and outstanding cell biological functions. The history of their structural analysis, occurrence, and functions is fascinating and described in this review. Reports from different researchers on apparently similar substances from a variety of biological materials led to the identification of a 9-carbon monosaccharide, which in 1957 was designated "sialic acid." The most frequently occurring member of the sialic acid family is N-acetylneuraminic acid, followed by N-glycolylneuraminic acid and O-acetylated derivatives, and up to now over about 80 neuraminic acid derivatives have been described. They appeared first in the animal kingdom, ranging from echinoderms up to higher animals, in many microorganisms, and are also expressed in insects, but are absent in higher plants. Sialic acids are masks and ligands and play as such dual roles in biology. Their involvement in immunology and tumor biology, as well as in hereditary diseases, cannot be underestimated. N-Glycolylneuraminic acid is very special, as this sugar cannot be expressed by humans, but is a xenoantigen with pathogenetic potential. Sialidases (neuraminidases), which liberate sialic acids from cellular compounds, had been known from very early on from studies with influenza viruses. Sialyltransferases, which are responsible for the sialylation of glycans and elongation of polysialic acids, are studied because of their significance in development and, for instance, in cancer. As more information about the functions in health and disease is acquired, the use of sialic acids in the treatment of diseases is also envisaged.
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Affiliation(s)
- Roland Schauer
- Biochemisches Institut, Christian-Albrechts-Universität zu Kiel, Kiel, Germany.
| | - Johannis P Kamerling
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands.
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38
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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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39
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Schindler B, Laloy-Borgna G, Barnes L, Allouche AR, Bouju E, Dugas V, Demesmay C, Compagnon I. Online Separation and Identification of Isomers Using Infrared Multiple Photon Dissociation Ion Spectroscopy Coupled to Liquid Chromatography: Application to the Analysis of Disaccharides Regio-Isomers and Monosaccharide Anomers. Anal Chem 2018; 90:11741-11745. [DOI: 10.1021/acs.analchem.8b02801] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Baptiste Schindler
- Univ Lyon, Université
Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622 Villeurbanne, France
| | - Gabrielle Laloy-Borgna
- Univ Lyon, Université
Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622 Villeurbanne, France
| | - Loïc Barnes
- Univ Lyon, Université
Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622 Villeurbanne, France
| | - Abdul-Rahman Allouche
- Univ Lyon, Université
Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622 Villeurbanne, France
| | - Elodie Bouju
- Univ Lyon, CNRS,
Université Claude Bernard Lyon 1, Ens de Lyon, Institut des
Sciences Analytiques, UMR 5280, 5 Rue de la Doua, F-69100 Villeurbanne, France
| | - Vincent Dugas
- Univ Lyon, CNRS,
Université Claude Bernard Lyon 1, Ens de Lyon, Institut des
Sciences Analytiques, UMR 5280, 5 Rue de la Doua, F-69100 Villeurbanne, France
| | - Claire Demesmay
- Univ Lyon, CNRS,
Université Claude Bernard Lyon 1, Ens de Lyon, Institut des
Sciences Analytiques, UMR 5280, 5 Rue de la Doua, F-69100 Villeurbanne, France
| | - Isabelle Compagnon
- Univ Lyon, Université
Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622 Villeurbanne, France
- Institut Universitaire de France IUF, 103 Boulevard St. Michel, Paris F-75005, France
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40
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Bayat P, Lesage D, Cole RB. Low-energy collision-induced dissociation (low-energy CID), collision-induced dissociation (CID), and higher energy collision dissociation (HCD) mass spectrometry for structural elucidation of saccharides and clarification of their dissolution mechanism in DMAc/LiCl. JOURNAL OF MASS SPECTROMETRY : JMS 2018; 53:705-716. [PMID: 29813177 DOI: 10.1002/jms.4205] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 05/11/2018] [Accepted: 05/18/2018] [Indexed: 06/08/2023]
Abstract
The dissolution mechanism of oligosaccharides in N,N-dimethylacetamide/lithium chloride (DMAc/LiCl), a solvent used for cellulose dissolution, and the capabilities of low-energy collision-induced dissociation (low-energy CID), collision-induced dissociation (CID), and higher energy collision dissociation (HCD) for structural analysis of carbohydrates were investigated. Comparing the spectra obtained using 3 techniques shows that, generally, when working with monolithiated sugars, CID spectra provide more structurally informative fragments, and glycosidic bond cleavage is the main pathway. However, when working with dilithiated sugars, HCD spectra can be more informative providing predominately cross-ring cleavage fragments. This is because HCD is a nonresonant activation technique, and it allows a higher amount of energy to be deposited in a short time, giving access to more endothermic decomposition pathways as well as consecutive fragmentations. The difference in preferred dissociation pathways of monolithiated and dilithiated sugars indicates that the presence of the second lithium strongly influences the relative rate constants for cross-ring cleavages vs glycosidic bond cleavages, and disfavors the latter. Regarding the dissolution mechanism of sugars in DMAc/LiCl, CID and HCD experiments on dilithiated and trilithiated sugars reveal that intensities of product ions containing 2 Li+ or 3 Li+ , respectively, are higher than those bearing only 1 Li+ . In addition, comparing the fragmentation spectra (both HCD and CID) of LiCl-adducted lithiated sugar and NaCl-adducted sodiated sugar shows that while, in the latter case, loss of NaCl is dominant, in the former case, loss of HCl occurs preferentially. The compiled evidence implies that there is a strong and direct interaction between lithium and the saccharide during the dissolution process in the DMAc/LiCl solvent system.
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Affiliation(s)
- Parisa Bayat
- CNRS, Institut Parisien de Chimie Moléculaire (IPCM), Sorbonne Université, 75005, Paris, France
| | - Denis Lesage
- CNRS, Institut Parisien de Chimie Moléculaire (IPCM), Sorbonne Université, 75005, Paris, France
| | - Richard B Cole
- CNRS, Institut Parisien de Chimie Moléculaire (IPCM), Sorbonne Université, 75005, Paris, France
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41
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2013-2014. MASS SPECTROMETRY REVIEWS 2018; 37:353-491. [PMID: 29687922 DOI: 10.1002/mas.21530] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 11/29/2016] [Indexed: 06/08/2023]
Abstract
This review is the eighth update of the original article published in 1999 on the application of Matrix-assisted laser desorption/ionization mass spectrometry (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2014. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, and arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly- saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Much of this material is presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. © 2018 Wiley Periodicals, Inc. Mass Spec Rev 37:353-491, 2018.
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Affiliation(s)
- David J Harvey
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom
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42
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Frost DC, Li L. Recent advances in mass spectrometry-based glycoproteomics. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2018; 95:71-123. [PMID: 24985770 DOI: 10.1016/b978-0-12-800453-1.00003-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Protein glycosylation plays fundamental roles in many biological processes as one of the most common, and the most complex, posttranslational modification. Alterations in glycosylation profile are now known to be associated with many diseases. As a result, the discovery and detailed characterization of glycoprotein disease biomarkers is a primary interest of biomedical research. Advances in mass spectrometry (MS)-based glycoproteomics and glycomics are increasingly enabling qualitative and quantitative approaches for site-specific structural analysis of protein glycosylation. While the complexity presented by glycan heterogeneity and the wide dynamic range of clinically relevant samples like plasma, serum, cerebrospinal fluid, and tissue make comprehensive analyses of the glycoproteome a challenging task, the ongoing efforts into the development of glycoprotein enrichment, enzymatic digestion, and separation strategies combined with novel quantitative MS methodologies have greatly improved analytical sensitivity, specificity, and throughput. This review summarizes current MS-based glycoproteomics approaches and highlights recent advances in its application to cancer biomarker and neurodegenerative disease research.
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Affiliation(s)
- Dustin C Frost
- School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA; Department of Chemistry, University of Wisconsin, Madison, Wisconsin, USA.
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43
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Yazawa S, Yokobori T, Kaira K, Kuwano H, Asao T. A new enzyme immunoassay for the determination of highly sialylated and fucosylated human α 1 -acid glycoprotein as a biomarker of tumorigenesis. Clin Chim Acta 2018; 478:120-128. [DOI: 10.1016/j.cca.2017.12.030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Revised: 12/06/2017] [Accepted: 12/20/2017] [Indexed: 01/02/2023]
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44
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Szabo Z, Thayer JR, Reusch D, Agroskin Y, Viner R, Rohrer J, Patil SP, Krawitzky M, Huhmer A, Avdalovic N, Khan SH, Liu Y, Pohl C. High Performance Anion Exchange and Hydrophilic Interaction Liquid Chromatography Approaches for Comprehensive Mass Spectrometry-Based Characterization of the N-Glycome of a Recombinant Human Erythropoietin. J Proteome Res 2018; 17:1559-1574. [DOI: 10.1021/acs.jproteome.7b00862] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Zoltan Szabo
- ThermoFisher Scientific, 1228 Titan Way, Sunnyvale, California 94088, United States
| | - James R. Thayer
- ThermoFisher Scientific, 1228 Titan Way, Sunnyvale, California 94088, United States
| | - Dietmar Reusch
- Roche Diagnostics GmbH, 2 Nonnenwald, Penzberg 82377, Germany
| | - Yury Agroskin
- ThermoFisher Scientific, 1228 Titan Way, Sunnyvale, California 94088, United States
| | - Rosa Viner
- ThermoFisher Scientific, 355 River Oaks Parkway, San Jose, California 95134, United States
| | - Jeff Rohrer
- ThermoFisher Scientific, 1214 Oakmead Parkway, Sunnyvale, California 94085, United States
| | - Sachin P. Patil
- ThermoFisher Scientific, 1214 Oakmead Parkway, Sunnyvale, California 94085, United States
| | - Michael Krawitzky
- ThermoFisher Scientific, 355 River Oaks Parkway, San Jose, California 95134, United States
| | - Andreas Huhmer
- ThermoFisher Scientific, 355 River Oaks Parkway, San Jose, California 95134, United States
| | - Nebojsa Avdalovic
- ThermoFisher Scientific, 1228 Titan Way, Sunnyvale, California 94088, United States
| | - Shaheer H. Khan
- ThermoFisher Scientific, 180 Oyster Point Blvd, South San Francisco, California 94080, United States
| | - Yan Liu
- ThermoFisher Scientific, 1228 Titan Way, Sunnyvale, California 94088, United States
| | - Christopher Pohl
- ThermoFisher Scientific, 1228 Titan Way, Sunnyvale, California 94088, United States
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45
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Barroso A, Giménez E, Konijnenberg A, Sancho J, Sanz-Nebot V, Sobott F. Evaluation of ion mobility for the separation of glycoconjugate isomers due to different types of sialic acid linkage, at the intact glycoprotein, glycopeptide and glycan level. J Proteomics 2017; 173:22-31. [PMID: 29197583 DOI: 10.1016/j.jprot.2017.11.020] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 11/23/2017] [Accepted: 11/24/2017] [Indexed: 02/07/2023]
Abstract
The study of protein glycosylation can be regarded as an intricate but very important task, making glycomics one of the most challenging and interesting, albeit under-researched, type of "omics" science. Complexity escalates remarkably when considering that carbohydrates can form severely branched structures with many different constituents, which often leads to the formation of multiple isomers. In this regard, ion mobility (IM) spectrometry has recently demonstrated its power for the separation of isomeric compounds. In the present work, the potential of traveling wave IM (TWIMS) for the separation of isomeric glycoconjugates was evaluated, using mouse transferrin (mTf) as model glycoprotein. Particularly, we aim to assess the performance of this platform for the separation of isomeric glycoconjugates due to the type of sialic acid linkage, at the intact glycoprotein, glycopeptide and glycan level. Straightforward separation of isomers was achieved with the analysis of released glycans, as opposed to the glycopeptides which showed a more complex pattern. Finally, the developed methodology was applied to serum samples of mice, to investigate its robustness when analyzing real complex samples. BIOLOGICAL SIGNIFICANCE Ion mobility mass spectrometry is a promising analytical technique for the separation of glycoconjugate isomers due to type of sialic acid linkage. The impact of such a small modification in the glycan structure is more evident in smaller analytes, reason why the analysis of free glycans was easier compared to the intact protein or the glycopeptides. The established methodology could be regarded as starting point in the separation of highly decorated glycoconjugates. This is an important topic nowadays, as differences in the abundance of some glycan isomers could be the key for the early diagnosis, control or differentiation of certain diseases, such as inflammation or cancer.
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Affiliation(s)
- Albert Barroso
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Diagonal 645, 08028 Barcelona, Spain
| | - Estela Giménez
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Diagonal 645, 08028 Barcelona, Spain.
| | - Albert Konijnenberg
- Biomolecular & Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, Antwerp, Belgium
| | - Jaime Sancho
- Instituto de Parasitología y Biomedicina "López-Neyra" (IPBLN), CSIC, Armilla, Granada, Spain
| | - Victoria Sanz-Nebot
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Diagonal 645, 08028 Barcelona, Spain
| | - Frank Sobott
- Biomolecular & Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, Antwerp, Belgium; Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom; School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, United Kingdom.
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46
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Lee H, Lai YH, Ou YM, Tsao CW, Jheng YJ, Kuo SY, Chang HT, Wang YS. Enhancing carbohydrate ion yield by controlling crystalline structures in matrix-assisted laser desorption/ionization mass spectrometry. Anal Chim Acta 2017; 994:49-55. [PMID: 29126468 DOI: 10.1016/j.aca.2017.09.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 09/12/2017] [Accepted: 09/13/2017] [Indexed: 10/18/2022]
Abstract
Carbohydrate analysis is challenging due to lack of sensitive detection and efficient separation methods. Although matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) is a sensitive tool, the low ionization efficiency of carbohydrates makes mass analyses inefficient. This work systematically examines the correlation between MALDI-MS sensitivity and carbohydrate sample morphology. Depending on the properties of the matrix used, the morphology changes through sample recrystallization after drying or imposition of hydrodynamic flows during droplet drying. Observation shows that amorphous solids and finer crystals offer higher carbohydrate sensitivity and spatial homogeneity than larger crystals. Clear evidences of an inverse correlation between sensitivity and crystal size are obtained when various kinds of carbohydrates are mixed with different matrixes. Similar experiments on proteins and peptides showed a negative or negligible effect. The result serves as a general guideline for improving efficiency in routine carbohydrate analysis.
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Affiliation(s)
- Hsun Lee
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan, ROC
| | - Yin-Hung Lai
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan, ROC
| | - Yu-Meng Ou
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan, ROC; Chemistry Department, National Taiwan University, Taipei 106, Taiwan, ROC
| | - Chien-Wei Tsao
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan, ROC; Department of Chemical Engineering and Biotechnology, National Taipei University of Technology, Taipei 106, Taiwan, ROC
| | - Ya-Jin Jheng
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan, ROC
| | - Shu-Yun Kuo
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan, ROC
| | - Huan-Tsung Chang
- Chemistry Department, National Taiwan University, Taipei 106, Taiwan, ROC
| | - Yi-Sheng Wang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan, ROC.
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47
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Hsiao CT, Wang PW, Chang HC, Chen YY, Wang SH, Chern Y, Khoo KH. Advancing a High Throughput Glycotope-centric Glycomics Workflow Based on nanoLC-MS 2-product Dependent-MS 3 Analysis of Permethylated Glycans. Mol Cell Proteomics 2017; 16:2268-2280. [PMID: 29066631 DOI: 10.1074/mcp.tir117.000156] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 10/21/2017] [Indexed: 01/08/2023] Open
Abstract
The intrinsic nature of glycosylation, namely nontemplate encoded, stepwise elongation and termination with a diverse range of isomeric glyco-epitopes (glycotopes), translates into ambiguity in most cases of mass spectrometry (MS)-based glycomic mapping. It is arguable that whether one needs to delineate every single glycomic entity, which may be counterproductive. Instead, one should focus on identifying as many structural features as possible that would collectively define the glycomic characteristics of a cell or tissue, and how these may change in response to self-programmed development, immuno-activation, and malignant transformation. We have been pursuing this line of analytical strategy that homes in on identifying the terminal sulfo-, sialyl, and/or fucosylated glycotopes by comprehensive nanoLC-MS2-product dependent MS3 analysis of permethylated glycans, in conjunction with development of a data mining computational tool, GlyPick, to enable an automated, high throughput, semi-quantitative glycotope-centric glycomic mapping amenable to even nonexperts. We demonstrate in this work that diagnostic MS2 ions can be relied on to inform the presence of specific glycotopes, whereas their possible isomeric identities can be resolved at MS3 level. Both MS2 and associated MS3 data can be acquired exhaustively and processed automatically by GlyPick. The high acquisition speed, resolution, and mass accuracy afforded by top-notch Orbitrap Fusion MS system now allow a sensible spectral count and/or summed ion intensity-based glycome-wide glycotope quantification. We report here the technical aspects, reproducibility and optimization of such an analytical approach that uses the same acidic reverse phase C18 nanoLC conditions fully compatible with proteomic analysis to allow rapid hassle-free switching. We further show how this workflow is particularly effective when applied to larger, multiply sialylated and fucosylated N-glycans derived from mouse brain. The complexity of their terminal glycotopes including variants of fucosylated and disialylated type 1 and 2 chains would otherwise not be adequately delineated by any conventional LC-MS/MS analysis.
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Affiliation(s)
- Cheng-Te Hsiao
- From the ‡Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan.,§Institute of Biological Chemistry and
| | | | | | - Yen-Ying Chen
- From the ‡Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan
| | | | - Yijuang Chern
- ¶Institute of Biomedical Sciences, Academia Sinica, Nankang, Taipei 115, Taiwan
| | - Kay-Hooi Khoo
- From the ‡Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan; .,§Institute of Biological Chemistry and
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48
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Giorgetti J, D'Atri V, Canonge J, Lechner A, Guillarme D, Colas O, Wagner-Rousset E, Beck A, Leize-Wagner E, François YN. Monoclonal antibody N-glycosylation profiling using capillary electrophoresis - Mass spectrometry: Assessment and method validation. Talanta 2017; 178:530-537. [PMID: 29136858 DOI: 10.1016/j.talanta.2017.09.083] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 09/20/2017] [Accepted: 09/28/2017] [Indexed: 01/08/2023]
Abstract
Characterization of therapeutic proteins represents a major challenge for analytical sciences due to their heterogeneity caused by post-translational modifications (PTM). Among these PTM, glycosylation which is possibly the most prominent, require comprehensive identification because of their major influence on protein structure and effector functions of monoclonal antibodies (mAbs). As a consequence, glycosylation profiling must be deeply characterized. For this application, several analytical methods such as separation-based or MS-based methods, were evaluated. However, no CE-ESI-MS approach has been assessed and validated. Here, we illustrate how the use of CE-ESI-MS method permits the comprehensive characterization of mAbs N-glycosylation at the glycopeptide level to perform relative quantitation of N-glycan species. Validation of the CE-ESI-MS method in terms of robustness and reproducibility was demonstrated through the relative quantitation of glycosylation profiles for ten different mAbs produced in different cell lines. Glycosylation patterns obtained for each mAbs were compared to Hydrophilic Interaction Chromatography of 2-aminobenzamide labelled glycans with fluorescence detector (HILIC-FD) analysis considered as a reference method. Very similar glycoprofiling were obtained with the CE-ESI-MS and HILIC-FD demonstrating the attractiveness of CE-ESI-MS method to characterize and quantify the glycosylation heterogeneity of a wide range of therapeutic mAbs with high accuracy and precision.
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Affiliation(s)
- Jérémie Giorgetti
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS), UMR 7140 (Unistra-CNRS), Université de Strasbourg, France
| | - Valentina D'Atri
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Centre Médical Universitaire (CMU), Rue Michel-Servet 1, 1206 Geneva, Switzerland
| | - Julie Canonge
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS), UMR 7140 (Unistra-CNRS), Université de Strasbourg, France
| | - Antony Lechner
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS), UMR 7140 (Unistra-CNRS), Université de Strasbourg, France
| | - Davy Guillarme
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Centre Médical Universitaire (CMU), Rue Michel-Servet 1, 1206 Geneva, Switzerland
| | - Olivier Colas
- Centre d'immunologie Pierre Fabre, Saint-Julien-en-Genevois, France
| | | | - Alain Beck
- Centre d'immunologie Pierre Fabre, Saint-Julien-en-Genevois, France
| | - Emmanuelle Leize-Wagner
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS), UMR 7140 (Unistra-CNRS), Université de Strasbourg, France
| | - Yannis-Nicolas François
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS), UMR 7140 (Unistra-CNRS), Université de Strasbourg, France.
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49
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Campbell MT, Chen D, Wallbillich NJ, Glish GL. Distinguishing Biologically Relevant Hexoses by Water Adduction to the Lithium-Cationized Molecule. Anal Chem 2017; 89:10504-10510. [DOI: 10.1021/acs.analchem.7b02647] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Matthew T. Campbell
- Department of Chemistry,
Caudill Laboratories, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
| | - Dazhe Chen
- Department of Chemistry,
Caudill Laboratories, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
| | - Nicholas J. Wallbillich
- Department of Chemistry,
Caudill Laboratories, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
| | - Gary L. Glish
- Department of Chemistry,
Caudill Laboratories, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
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50
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Abrahams JL, Campbell MP, Packer NH. Building a PGC-LC-MS N-glycan retention library and elution mapping resource. Glycoconj J 2017; 35:15-29. [PMID: 28905148 DOI: 10.1007/s10719-017-9793-4] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 08/10/2017] [Accepted: 08/18/2017] [Indexed: 11/27/2022]
Abstract
Porous graphitised carbon-liquid chromatography (PGC-LC) has been proven to be a powerful technique for the analysis and characterisation of complex mixtures of isomeric and isobaric glycan structures. Here we evaluate the elution behaviour of N-glycans on PGC-LC and thereby provide the potential of using chromatographic separation properties, together with mass spectrometry (MS) fragmentation, to determine glycan structure assignments more easily. We used previously reported N-glycan structures released from the purified glycoproteins Immunoglobulin G (IgG), Immunoglobulin A (IgA), lactoferrin, α1-acid glycoprotein, Ribonuclease B (RNase B), fetuin and ovalbumin to profile their behaviour on capillary PGC-LC-MS. Over 100 glycan structures were determined by MS/MS, and together with targeted exoglycosidase digestions, created a N-glycan PGC retention library covering a full spectrum of biologically significant N-glycans from pauci mannose to sialylated tetra-antennary classes. The resultant PGC retention library ( http://www.glycostore.org/showPgc ) incorporates retention times and supporting fragmentation spectra including exoglycosidase digestion products, and provides detailed knowledge on the elution properties of N-glycans by PGC-LC. Consequently, this platform should serve as a valuable resource for facilitating the detailed analysis of the glycosylation of both purified recombinant, and complex mixtures of, glycoproteins using established workflows.
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Affiliation(s)
- Jodie L Abrahams
- Department of Chemistry and Biomolecular Sciences, Faculty of Science & Engineering, Macquarie University, North Ryde, Sydney, NSW, 2109, Australia
- Institute for Glycomics, Griffith University, QLD, Gold Coast, 4222, Australia
| | - Matthew P Campbell
- Department of Chemistry and Biomolecular Sciences, Faculty of Science & Engineering, Macquarie University, North Ryde, Sydney, NSW, 2109, Australia
- Institute for Glycomics, Griffith University, QLD, Gold Coast, 4222, Australia
| | - Nicolle H Packer
- Department of Chemistry and Biomolecular Sciences, Faculty of Science & Engineering, Macquarie University, North Ryde, Sydney, NSW, 2109, Australia.
- Institute for Glycomics, Griffith University, QLD, Gold Coast, 4222, Australia.
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