1
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Sasmal A, Khan N, Khedri Z, Kellman BP, Srivastava S, Verhagen A, Yu H, Bruntse AB, Diaz S, Varki N, Beddoe T, Paton AW, Paton JC, Chen X, Lewis NE, Varki A. Simple and practical sialoglycan encoding system reveals vast diversity in nature and identifies a universal sialoglycan-recognizing probe derived from AB5 toxin B subunits. Glycobiology 2022; 32:1101-1115. [PMID: 36048714 PMCID: PMC9680115 DOI: 10.1093/glycob/cwac057] [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: 04/04/2022] [Revised: 08/20/2022] [Accepted: 08/23/2022] [Indexed: 01/07/2023] Open
Abstract
Vertebrate sialic acids (Sias) display much diversity in modifications, linkages, and underlying glycans. Slide microarrays allow high-throughput explorations of sialoglycan-protein interactions. A microarray presenting ~150 structurally defined sialyltrisaccharides with various Sias linkages and modifications still poses challenges in planning, data sorting, visualization, and analysis. To address these issues, we devised a simple 9-digit code for sialyltrisaccharides with terminal Sias and underlying two monosaccharides assigned from the nonreducing end, with 3 digits assigning a monosaccharide, its modifications, and linkage. Calculations based on the encoding system reveal >113,000 likely linear sialyltrisaccharides in nature. Notably, a biantennary N-glycan with 2 terminal sialyltrisaccharides could thus have >1010 potential combinations and a triantennary N-glycan with 3 terminal sequences, >1015 potential combinations. While all possibilities likely do not exist in nature, sialoglycans encode enormous diversity. While glycomic approaches are used to probe such diverse sialomes, naturally occurring bacterial AB5 toxin B subunits are simpler tools to track the dynamic sialome in biological systems. Sialoglycan microarray was utilized to compare sialoglycan-recognizing bacterial toxin B subunits. Unlike the poor correlation between B subunits and species phylogeny, there is stronger correlation with Sia-epitope preferences. Further supporting this pattern, we report a B subunit (YenB) from Yersinia enterocolitica (broad host range) recognizing almost all sialoglycans in the microarray, including 4-O-acetylated-Sias not recognized by a Yersinia pestis orthologue (YpeB). Differential Sia-binding patterns were also observed with phylogenetically related B subunits from Escherichia coli (SubB), Salmonella Typhi (PltB), Salmonella Typhimurium (ArtB), extra-intestinal E.coli (EcPltB), Vibrio cholera (CtxB), and cholera family homologue of E. coli (EcxB).
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Affiliation(s)
- Aniruddha Sasmal
- Glycobiology Research and Training Center, University of California San Diego, La Jolla, CA 92093, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Naazneen Khan
- Glycobiology Research and Training Center, University of California San Diego, La Jolla, CA 92093, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Zahra Khedri
- Glycobiology Research and Training Center, University of California San Diego, La Jolla, CA 92093, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Benjamin P Kellman
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Saurabh Srivastava
- Glycobiology Research and Training Center, University of California San Diego, La Jolla, CA 92093, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Andrea Verhagen
- Glycobiology Research and Training Center, University of California San Diego, La Jolla, CA 92093, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Hai Yu
- Department of Chemistry, University of California Davis, CA 95616, USA
| | - Anders Bech Bruntse
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Sandra Diaz
- Glycobiology Research and Training Center, University of California San Diego, La Jolla, CA 92093, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Nissi Varki
- Glycobiology Research and Training Center, University of California San Diego, La Jolla, CA 92093, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Travis Beddoe
- Department of Animal, Plant and Soil Science and Centre for AgriBioscience, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Adrienne W Paton
- Research Centre for Infectious Diseases, Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA 5005, Australia
| | - James C Paton
- Research Centre for Infectious Diseases, Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA 5005, Australia
| | - Xi Chen
- Department of Chemistry, University of California Davis, CA 95616, USA
| | - Nathan E Lewis
- Glycobiology Research and Training Center, University of California San Diego, La Jolla, CA 92093, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Ajit Varki
- Glycobiology Research and Training Center, University of California San Diego, La Jolla, CA 92093, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Research Centre for Infectious Diseases, Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA 5005, Australia
- Department of Medicine, University of California at San Diego, La Jolla, CA 92093, USA
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2
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Influenza A Virus Agnostic Receptor Tropism Revealed Using a Novel Biological System with Terminal Sialic Acid Knockout Cells. J Virol 2022; 96:e0041622. [PMID: 35862707 PMCID: PMC9364805 DOI: 10.1128/jvi.00416-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Avian or human influenza A viruses bind preferentially to avian- or human-type sialic acid receptors, respectively, indicating that receptor tropism is an important factor for determining the viral host range. However, there are currently no reliable methods for analyzing receptor tropism biologically under physiological conditions. In this study, we established a novel system using MDCK cells with avian- or human-type sialic acid receptors and with both sialic acid receptors knocked out (KO). When we examined the replication of human and avian influenza viruses in these KO cells, we observed unique viral receptor tropism that could not be detected using a conventional solid-phase sialylglycan binding assay, which directly assesses physical binding between the virus and sialic acids. Furthermore, we serially passaged an engineered avian-derived H4N5 influenza virus, whose PB2 gene was deleted, in avian-type receptor KO cells stably expressing PB2 to select a mutant with enhanced replication in KO cells; however, its binding to human-type sialylglycan was undetectable using the solid-phase binding assay. These data indicate that a panel of sialic acid receptor KO cells could be a useful tool for determining the biological receptor tropism of influenza A viruses. Moreover, the PB2KO virus experimental system could help to safely and efficiently identify the mutations required for avian influenza viruses to adapt to human cells that could trigger a new influenza pandemic. IMPORTANCE The acquisition of mutations that allow avian influenza A virus hemagglutinins to recognize human-type receptors is mandatory for the transmission of avian viruses to humans, which could lead to a pandemic. In this study, we established a novel system using a set of genetically engineered MDCK cells with knocked out sialic acid receptors to biologically evaluate the receptor tropism for influenza A viruses. Using this system, we observed unique receptor tropism in several virus strains that was undetectable using conventional solid-phase binding assays that measure physical binding between the virus and artificially synthesized sialylglycans. This study contributes to elucidation of the relationship between the physical binding of virus and receptor and viral infectivity. Furthermore, the system using sialic acid knockout cells could provide a useful tool to explore the sialic acid-independent entry mechanism. In addition, our system could be safely used to identify mutations that could acquire human-type receptor tropism.
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3
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Identification of lamprey variable lymphocyte receptors that target the brain vasculature. Sci Rep 2022; 12:6044. [PMID: 35411012 PMCID: PMC9001667 DOI: 10.1038/s41598-022-09962-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 03/28/2022] [Indexed: 12/21/2022] Open
Abstract
AbstractThe blood–brain barrier (BBB) represents a significant bottleneck for the delivery of therapeutics to the central nervous system. In recent years, the promise of coopting BBB receptor-mediated transport systems for brain drug delivery has increased in large part due to the discovery and engineering of BBB-targeting antibodies. Here we describe an innovative screening platform for identification of new BBB targeting molecules from a class of lamprey antigen recognition proteins known as variable lymphocyte receptors (VLRs). Lamprey were immunized with murine brain microvessel plasma membranes, and the resultant repertoire cloned into the yeast surface display system. The library was screened via a unique workflow that identified 16 VLR clones that target extracellular epitopes of in vivo-relevant BBB membrane proteins. Of these, three lead VLR candidates, VLR-Fc-11, VLR-Fc-30, and VLR-Fc-46 selectively target the brain vasculature and traffic within brain microvascular endothelial cells after intravenous administration in mice, with VLR-Fc-30 being confirmed as trafficking into the brain parenchyma. Epitope characterization indicates that the VLRs, in part, recognize sialylated glycostructures. These promising new targeting molecules have the potential for brain targeting and drug delivery with improved brain vascular specificity.
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Systemic Lectin-Glycan Interaction of Pathogenic Enteric Bacteria in the Gastrointestinal Tract. Int J Mol Sci 2022; 23:ijms23031451. [PMID: 35163392 PMCID: PMC8835900 DOI: 10.3390/ijms23031451] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/20/2022] [Accepted: 01/25/2022] [Indexed: 01/27/2023] Open
Abstract
Microorganisms, such as bacteria, viruses, and fungi, and host cells, such as plants and animals, have carbohydrate chains and lectins that reciprocally recognize one another. In hosts, the defense system is activated upon non-self-pattern recognition of microbial pathogen-associated molecular patterns. These are present in Gram-negative and Gram-positive bacteria and fungi. Glycan-based PAMPs are bound to a class of lectins that are widely distributed among eukaryotes. The first step of bacterial infection in humans is the adhesion of the pathogen's lectin-like proteins to the outer membrane surfaces of host cells, which are composed of glycans. Microbes and hosts binding to each other specifically is of critical importance. The adhesion factors used between pathogens and hosts remain unknown; therefore, research is needed to identify these factors to prevent intestinal infection or treat it in its early stages. This review aims to present a vision for the prevention and treatment of infectious diseases by identifying the role of the host glycans in the immune response against pathogenic intestinal bacteria through studies on the lectin-glycan interaction.
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Veličković D, Bečejac T, Mamedov S, Sharma K, Ambalavanan N, Alexandrov T, Anderton CR. Rapid Automated Annotation and Analysis of N-Glycan Mass Spectrometry Imaging Data Sets Using NGlycDB in METASPACE. Anal Chem 2021; 93:13421-13425. [PMID: 34581565 DOI: 10.1021/acs.analchem.1c02347] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Imaging N-glycan spatial distribution in tissues using mass spectrometry imaging (MSI) is emerging as a promising tool in biological and clinical applications. However, there is currently no high-throughput tool for visualization and molecular annotation of N-glycans in MSI data, which significantly slows down data processing and hampers the applicability of this approach. Here, we present how METASPACE, an open-source cloud engine for molecular annotation of MSI data, can be used to automatically annotate, visualize, analyze, and interpret high-resolution mass spectrometry-based spatial N-glycomics data. METASPACE is an emerging tool in spatial metabolomics, but the lack of compatible glycan databases has limited its application for comprehensive N-glycan annotations from MSI data sets. We created NGlycDB, a public database of N-glycans, by adapting available glycan databases. We demonstrate the applicability of NGlycDB in METASPACE by analyzing MALDI-MSI data from formalin-fixed paraffin-embedded (FFPE) human kidney and mouse lung tissue sections. We added NGlycDB to METASPACE for public use, thus, facilitating applications of MSI in glycobiology.
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Affiliation(s)
- Dušan Veličković
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Tamara Bečejac
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Sergii Mamedov
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany
| | - Kumar Sharma
- Center for Renal Precision Medicine, Division of Nephrology, Department of Medicine, The University of Texas Health, San Antonio, Texas 78229, United States
| | - Namasivayam Ambalavanan
- Department of Pediatrics, School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama 35294, United States
| | - Theodore Alexandrov
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California 92093, United States
| | - Christopher R Anderton
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States.,Center for Renal Precision Medicine, Division of Nephrology, Department of Medicine, The University of Texas Health, San Antonio, Texas 78229, United States
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6
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Li Y, Li Y, Xia J, Yang Q, Chen Y, Sun H. 3'-Sulfo-TF Antigen Determined by GAL3ST2/ST3GAL1 Is Essential for Antitumor Activity of Fungal Galectin AAL/AAGL. ACS OMEGA 2021; 6:17379-17390. [PMID: 34278124 PMCID: PMC8280635 DOI: 10.1021/acsomega.1c01544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/04/2021] [Indexed: 06/13/2023]
Abstract
Many lectins have been reported to have antitumor activities; identifying the glycan ligands in tumor cells of lectins is crucial for lectin clinical application. An edible mushroom galectin, Agrocybe aegerita lectin (AAL/AAGL), that has a high antitumor activity has been reported. In this paper, based on the glycan array data, it is showed that the Thomsen-Friedenreich antigen (TF antigen)-related O-glycans were found to be highly correlated with the antitumor activity of AAL/AAGL. Further glycosyltransferase quantification suggested that the ratio between GAL3ST2 and ST3GAL1 (GAL3ST2/ST3GAL1), which determined the 3'-sulfo-TF expression level, was highly correlated with the antitumor activity of AAL/AAGL. Overexpressing the enzyme of GAL3ST2 in HL60 and HeLa cell lines could increase the growth inhibition ratio of AAL/AAGL from 22.7 to 43.9% and 27.8 to 39.1%, respectively. However, ST3GAL1 in Jurkat cells could decrease the growth inhibition ratio from 44.7 to 35.6%. All the data suggested that the 3'-sulfo-TF antigen is one of the main glycan ligands that AAL/AAGL recognizes in tumor cells. AAL/AAGL may potentially serve as a reagent for cancer diagnosis and a targeted therapy for the 3'-sulfo-TF antigen.
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Affiliation(s)
- Yang Li
- College of Life Sciences, Wuhan
University, Wuhan, Hubei Province 430072, P. R. China
| | - Yan Li
- College of Life Sciences, Wuhan
University, Wuhan, Hubei Province 430072, P. R. China
| | - Jing Xia
- College of Life Sciences, Wuhan
University, Wuhan, Hubei Province 430072, P. R. China
| | - Qing Yang
- College
of Food Science and Engineering, Wuhan Polytechnic
University, Wuhan, Hubei Province 430023, P. R. China
| | - Yijie Chen
- College
of Food Science and Technology, Huazhong
Agricultural University, Wuhan, Hubei Province 430070, P. R. China
| | - Hui Sun
- College of Life Sciences, Wuhan
University, Wuhan, Hubei Province 430072, P. R. China
- Hubei
Province key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei Province 430072, P. R. China
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7
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Kellman BP, Lewis NE. Big-Data Glycomics: Tools to Connect Glycan Biosynthesis to Extracellular Communication. Trends Biochem Sci 2021; 46:284-300. [PMID: 33349503 PMCID: PMC7954846 DOI: 10.1016/j.tibs.2020.10.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Revised: 10/05/2020] [Accepted: 10/22/2020] [Indexed: 12/12/2022]
Abstract
Characteristically, cells must sense and respond to environmental cues. Despite the importance of cell-cell communication, our understanding remains limited and often lacks glycans. Glycans decorate proteins and cell membranes at the cell-environment interface, and modulate intercellular communication, from development to pathogenesis. Providing further challenges, glycan biosynthesis and cellular behavior are co-regulating systems. Here, we discuss how glycosylation contributes to extracellular responses and signaling. We further organize approaches for disentangling the roles of glycans in multicellular interactions using newly available datasets and tools, including glycan biosynthesis models, omics datasets, and systems-level analyses. Thus, emerging tools in big data analytics and systems biology are facilitating novel insights on glycans and their relationship with multicellular behavior.
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Affiliation(s)
- Benjamin P Kellman
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA; Department of Bioengineering, University of California San Diego School of Medicine, La Jolla, CA, USA; Bioinformatics and Systems Biology Program, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Nathan E Lewis
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA; Department of Bioengineering, University of California San Diego School of Medicine, La Jolla, CA, USA; Bioinformatics and Systems Biology Program, University of California San Diego School of Medicine, La Jolla, CA, USA; Novo Nordisk Foundation Center for Biosustainability at the University of California San Diego School of Medicine, La Jolla, CA, USA.
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8
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Scherbinina SI, Toukach PV. Three-Dimensional Structures of Carbohydrates and Where to Find Them. Int J Mol Sci 2020; 21:E7702. [PMID: 33081008 PMCID: PMC7593929 DOI: 10.3390/ijms21207702] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 02/06/2023] Open
Abstract
Analysis and systematization of accumulated data on carbohydrate structural diversity is a subject of great interest for structural glycobiology. Despite being a challenging task, development of computational methods for efficient treatment and management of spatial (3D) structural features of carbohydrates breaks new ground in modern glycoscience. This review is dedicated to approaches of chemo- and glyco-informatics towards 3D structural data generation, deposition and processing in regard to carbohydrates and their derivatives. Databases, molecular modeling and experimental data validation services, and structure visualization facilities developed for last five years are reviewed.
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Affiliation(s)
- Sofya I. Scherbinina
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninsky prospect 47, 119991 Moscow, Russia
- Higher Chemical College, D. Mendeleev University of Chemical Technology of Russia, Miusskaya Square 9, 125047 Moscow, Russia
| | - Philip V. Toukach
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninsky prospect 47, 119991 Moscow, Russia
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9
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Cerullo AR, Lai TY, Allam B, Baer A, Barnes WJP, Barrientos Z, Deheyn DD, Fudge DS, Gould J, Harrington MJ, Holford M, Hung CS, Jain G, Mayer G, Medina M, Monge-Nájera J, Napolitano T, Espinosa EP, Schmidt S, Thompson EM, Braunschweig AB. Comparative Animal Mucomics: Inspiration for Functional Materials from Ubiquitous and Understudied Biopolymers. ACS Biomater Sci Eng 2020; 6:5377-5398. [DOI: 10.1021/acsbiomaterials.0c00713] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Antonio R. Cerullo
- The PhD Program in Biochemistry, Graduate Center of the City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
- The Advanced Science Research Center, Graduate Center of the City University of New York, 85 St. Nicholas Terrace, New York, New York 10031, United States
- Department of Chemistry and Biochemistry, Hunter College, 695 Park Avenue, New York, New York 10065, United States
| | - Tsoi Ying Lai
- The Advanced Science Research Center, Graduate Center of the City University of New York, 85 St. Nicholas Terrace, New York, New York 10031, United States
| | - Bassem Allam
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York 11794-5000, United States
| | - Alexander Baer
- Department of Zoology, Institute of Biology, University of Kassel, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany
| | - W. Jon P. Barnes
- Centre for Cell Engineering, Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, Scotland, U.K
| | - Zaidett Barrientos
- Laboratorio de Ecología Urbana, Universidad Estatal a Distancia, Mercedes de Montes de Oca, San José 474-2050, Costa Rica
| | - Dimitri D. Deheyn
- Marine Biology Research Division-0202, Scripps Institute of Oceanography, UCSD, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Douglas S. Fudge
- Schmid College of Science and Technology, Chapman University, 1 University Drive, Orange, California 92866, United States
| | - John Gould
- School of Environmental and Life Sciences, University of Newcastle, University Drive, Callaghan, New South Wales 2308, Australia
| | - Matthew J. Harrington
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Mandë Holford
- The PhD Program in Biochemistry, Graduate Center of the City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
- Department of Chemistry and Biochemistry, Hunter College, 695 Park Avenue, New York, New York 10065, United States
- Department of Invertebrate Zoology, The American Museum of Natural History, New York, New York 10024, United States
- The PhD Program in Chemistry, Graduate Center of the City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
- The PhD Program in Biology, Graduate Center of the City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
| | - Chia-Suei Hung
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, Ohio 45433, United States
| | - Gaurav Jain
- Schmid College of Science and Technology, Chapman University, 1 University Drive, Orange, California 92866, United States
| | - Georg Mayer
- Department of Zoology, Institute of Biology, University of Kassel, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany
| | - Mónica Medina
- Department of Biology, Pennsylvania State University, 208 Mueller Lab, University Park, Pennsylvania 16802, United States
| | - Julian Monge-Nájera
- Laboratorio de Ecología Urbana, Universidad Estatal a Distancia, Mercedes de Montes de Oca, San José 474-2050, Costa Rica
| | - Tanya Napolitano
- The PhD Program in Biochemistry, Graduate Center of the City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
- Department of Chemistry and Biochemistry, Hunter College, 695 Park Avenue, New York, New York 10065, United States
| | - Emmanuelle Pales Espinosa
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York 11794-5000, United States
| | - Stephan Schmidt
- Institute of Organic and Macromolecular Chemistry, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Eric M. Thompson
- Sars Centre for Marine Molecular Biology, Thormøhlensgt. 55, 5020 Bergen, Norway
- Department of Biological Sciences, University of Bergen, N-5006 Bergen, Norway
| | - Adam B. Braunschweig
- The PhD Program in Biochemistry, Graduate Center of the City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
- The Advanced Science Research Center, Graduate Center of the City University of New York, 85 St. Nicholas Terrace, New York, New York 10031, United States
- Department of Chemistry and Biochemistry, Hunter College, 695 Park Avenue, New York, New York 10065, United States
- The PhD Program in Chemistry, Graduate Center of the City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
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10
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Cipollo JF, Parsons LM. Glycomics and glycoproteomics of viruses: Mass spectrometry applications and insights toward structure-function relationships. MASS SPECTROMETRY REVIEWS 2020; 39:371-409. [PMID: 32350911 PMCID: PMC7318305 DOI: 10.1002/mas.21629] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 04/01/2020] [Accepted: 04/05/2020] [Indexed: 05/21/2023]
Abstract
The advancement of viral glycomics has paralleled that of the mass spectrometry glycomics toolbox. In some regard the glycoproteins studied have provided the impetus for this advancement. Viral proteins are often highly glycosylated, especially those targeted by the host immune system. Glycosylation tends to be dynamic over time as viruses propagate in host populations leading to increased number of and/or "movement" of glycosylation sites in response to the immune system and other pressures. This relationship can lead to highly glycosylated, difficult to analyze glycoproteins that challenge the capabilities of modern mass spectrometry. In this review, we briefly discuss five general areas where glycosylation is important in the viral niche and how mass spectrometry has been used to reveal key information regarding structure-function relationships between viral glycoproteins and host cells. We describe the recent past and current glycomics toolbox used in these analyses and give examples of how the requirement to analyze these complex glycoproteins has provided the incentive for some advances seen in glycomics mass spectrometry. A general overview of viral glycomics, special cases, mass spectrometry methods and work-flows, informatics and complementary chemical techniques currently used are discussed. © 2020 The Authors. Mass Spectrometry Reviews published by John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- John F. Cipollo
- Center for Biologics Evaluation and Research, Food and Drug AdministrationSilver SpringMaryland
| | - Lisa M. Parsons
- Center for Biologics Evaluation and Research, Food and Drug AdministrationSilver SpringMaryland
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11
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Choi HK, Lee D, Singla A, Kwon JSI, Wu HJ. The influence of heteromultivalency on lectin-glycan binding behavior. Glycobiology 2019; 29:397-408. [PMID: 30824941 DOI: 10.1093/glycob/cwz010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 02/14/2019] [Accepted: 02/19/2019] [Indexed: 02/06/2023] Open
Abstract
We recently discovered that the nature of lectin multivalency and glycolipid diffusion on cell membranes could lead to the heteromultivalent binding (i.e., a single lectin simultaneously binding to different types of glycolipid ligands). This heteromultivalent binding may even govern the lectin-glycan recognition process. To investigate this, we developed a kinetic Monte Carlo simulation, which only considers the fundamental physics/chemistry principles, to model the process of lectin binding to glycans on cell surfaces. We found that the high-affinity glycan ligands could facilitate lectin binding to other low-affinity glycan ligands, even though these low-affinity ligands are barely detectable in microarrays with immobilized glycan ligands. Such heteromultivalent binding processes significantly change lectin binding behaviors. We hypothesize that living organisms probably utilize this mechanism to regulate the downstream lectin functions. Our finding not only offers a mechanism to describe the concept that lectins are pattern recognition molecules, but also suggests that the two overlooked parameters, surface diffusion of glycan ligand and lectin binding kinetics, can play important roles in glycobiology processes. In this paper, we identified the critical parameters that influence the heteromultivalent binding process. We also discussed how our discovery can impact the current lectin-glycan analysis.
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Affiliation(s)
- Hyun-Kyu Choi
- Department of Chemical Engineering, Texas A&M University, 3122 TAMU, College Station, TX USA
| | - Dongheon Lee
- Department of Chemical Engineering, Texas A&M University, 3122 TAMU, College Station, TX USA
| | - Akshi Singla
- Department of Chemical Engineering, Texas A&M University, 3122 TAMU, College Station, TX USA
| | - Joseph Sang-Il Kwon
- Department of Chemical Engineering, Texas A&M University, 3122 TAMU, College Station, TX USA
| | - Hung-Jen Wu
- Department of Chemical Engineering, Texas A&M University, 3122 TAMU, College Station, TX USA
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Mehta AY, Cummings RD. GLAD: GLycan Array Dashboard, a visual analytics tool for glycan microarrays. Bioinformatics 2019; 35:3536-3537. [PMID: 30715201 PMCID: PMC6748710 DOI: 10.1093/bioinformatics/btz075] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 01/18/2019] [Accepted: 01/30/2019] [Indexed: 01/25/2023] Open
Abstract
MOTIVATION Traditional glycan microarray data is typically presented as excel files with limited visualization and interactivity. Thus, comparisons and analysis of glycan array data have been difficult, and there is need for a tool to facilitate data mining of glycan array data. RESULTS GLAD (GLycan Array Dashboard) is a web-based tool to visualize, analyze, present and mine glycan microarray data. GLAD allows users to input multiple data files to create comparisons. GLAD extends the capability of the microarray data to produce more comparative visualizations in the form of grouped bar charts, heatmaps, calendar heatmaps, force graphs and correlation maps in order to analyze broad sets of samples. Additionally, it allows users to filter, sort and normalize the data and view glycan structures in an interactive manner, to facilitate faster visual data mining. AVAILABILITY AND IMPLEMENTATION GLAD is freely available for use on the Web at https://glycotoolkit.com/Tools/GLAD/ with all major modern browsers (Edge, Firefox, Chrome, Safari). SUPPLEMENTARY INFORMATION Full documentation and video tutorials for GLAD can be found on https://glycotoolkit.com/GLAD.
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Affiliation(s)
- Akul Y Mehta
- National Center for Functional Glycomics, Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Richard D Cummings
- National Center for Functional Glycomics, Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
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Schaefer K, Webb NE, Pang M, Hernandez-Davies JE, Lee KP, Gonzalez P, Douglass MV, Lee B, Baum LG. Galectin-9 binds to O-glycans on protein disulfide isomerase. Glycobiology 2018; 27:878-887. [PMID: 28810662 DOI: 10.1093/glycob/cwx065] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 07/03/2017] [Indexed: 02/07/2023] Open
Abstract
Changes in the T cell surface redox environment regulate critical cell functions, such as cell migration, viral entry and cytokine production. Cell surface protein disulfide isomerase (PDI) contributes to the regulation of T cell surface redox status. Cell surface PDI can be released into the extracellular milieu or can be internalized by T cells. We have found that galectin-9, a soluble lectin expressed by T cells, endothelial cells and dendritic cells, binds to and retains PDI on the cell surface. While endogenous galectin-9 is not required for basal cell surface PDI expression, exogenous galectin-9 mediated retention of cell surface PDI shifted the disulfide/thiol equilibrium on the T cell surface. O-glycans on PDI are required for galectin-9 binding, and PDI recognition appears to be specific for galectin-9, as galectin-1 and galectin-3 do not bind PDI. Galectin-9 is widely expressed by immune and endothelial cells in inflamed tissues, suggesting that T cells would be exposed to abundant galectin-9, in cis and in trans, in infectious or autoimmune conditions.
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Affiliation(s)
| | - Nicholas E Webb
- Department of Pediatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
| | - Mabel Pang
- Department of Pathology and Laboratory Medicine
| | | | | | | | | | - Benhur Lee
- Department of Microbiology, Icahn School of Medicine, Mount Sinai, New York, USA
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Emerging glycobiology tools: A renaissance in accessibility. Cell Immunol 2018; 333:2-8. [PMID: 29759530 DOI: 10.1016/j.cellimm.2018.04.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 04/23/2018] [Accepted: 04/24/2018] [Indexed: 01/01/2023]
Abstract
The glycobiology of the immune response is a topic that has garnered increased attention due to a number of key discoveries surrounding IgG function, the specificity of some broadly neutralizing anti-HIV antibodies, cancer immunoregulation by galectin molecules and others. This review is the opening article in a Special Edition of Cellular Immunology focused on glycoimmunology, and has the goal of setting the context for these articles by providing a mini-review of how glycans impact immunity. We also focus on some of the technological and methodological advances in the field of glycobiology that are being deployed to lower the barrier of entry into the glycosciences, and to more fully interrogate the glycome and its function.
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