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Parsons LM, Zoueva O, Grubbs G, Plant E, Jankowska E, Xie Y, Song H, Gao GF, Ye Z, Khurana S, Cipollo JF. Glycosylation of H4 influenza strains with pandemic potential and susceptibilities to lung surfactant SP-D. Front Mol Biosci 2023; 10:1207670. [PMID: 37383151 PMCID: PMC10296771 DOI: 10.3389/fmolb.2023.1207670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 05/23/2023] [Indexed: 06/30/2023] Open
Abstract
We recently reported that members of group 1 influenza A virus (IAV) containing H2, H5, H6, and H11 hemagglutinins (HAs) are resistant to lung surfactant protein D (SP-D). H3 viruses, members of group 2 IAV, have high affinity for SP-D, which depends on the presence of high-mannose glycans at glycosite N165 on the head of HA. The low affinity of SP-D for the group 1 viruses is due to the presence of complex glycans at an analogous glycosite on the head of HA, and replacement with high-mannose glycan at this site evoked strong interaction with SP-D. Thus, if members of group 1 IAV were to make the zoonotic leap to humans, the pathogenicity of such strains could be problematic since SP-D, as a first-line innate immunity factor in respiratory tissues, could be ineffective as demonstrated in vitro. Here, we extend these studies to group 2 H4 viruses that are representative of those with specificity for avian or swine sialyl receptors, i.e., those with receptor-binding sites with either Q226 and G228 for avian or recent Q226L and G228S mutations that facilitate swine receptor specificity. The latter have increased pathogenicity potential in humans due to a switch from avian sialylα2,3 to sialylα2,6 glycan receptor preference. A better understanding of the potential action of SP-D against these strains will provide important information regarding the pandemic risk of such strains. Our glycomics and in vitro analyses of four H4 HAs reveal SP-D-favorable glycosylation patterns. Therefore, susceptibilities to this first-line innate immunity defense respiratory surfactant against such H4 viruses are high and align with H3 HA glycosylation.
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Affiliation(s)
- Lisa M. Parsons
- Food and Drug Administration, Center for Biologics Evaluation and Research, Division of Bacterial, Parasitic and Allergenic Products, Silver Spring, MD, United States
| | - Olga Zoueva
- Food and Drug Administration, Center for Biologics Evaluation and Research, Division of Viral Products, Silver Spring, MD, United States
| | - Gabrielle Grubbs
- Food and Drug Administration, Center for Biologics Evaluation and Research, Division of Viral Products, Silver Spring, MD, United States
| | - Ewan Plant
- Food and Drug Administration, Center for Biologics Evaluation and Research, Division of Viral Products, Silver Spring, MD, United States
| | - Ewa Jankowska
- Food and Drug Administration, Center for Biologics Evaluation and Research, Division of Bacterial, Parasitic and Allergenic Products, Silver Spring, MD, United States
| | - Yijia Xie
- Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Hao Song
- Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - George F. Gao
- Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Zhiping Ye
- Food and Drug Administration, Center for Biologics Evaluation and Research, Division of Viral Products, Silver Spring, MD, United States
| | - Surender Khurana
- Food and Drug Administration, Center for Biologics Evaluation and Research, Division of Viral Products, Silver Spring, MD, United States
| | - John F. Cipollo
- Food and Drug Administration, Center for Biologics Evaluation and Research, Division of Bacterial, Parasitic and Allergenic Products, Silver Spring, MD, United States
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Parsons LM, Cipollo JF. Assign-MALDI - A free software for assignment of MALDI-TOF MS spectra of glycans derivatized using common and novel labeling strategies. Proteomics 2023; 23:e2200320. [PMID: 36427241 DOI: 10.1002/pmic.202200320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 11/26/2022]
Abstract
Matrix Assisted Laser Desorption/Ionization Time-of-flight (MALDI-ToF) MS is a popular method to analyze glycans released from proteins, cell lines, and tissue samples. Chemical modification of glycans (derivatization) can enhance ionization, enable semi-quantitation, and assist in linkage identification. However, the mass changes incurred by novel and more recently developed derivatizations are not accommodated by most spectral assignment programs, necessitating manual assignment which increases both the difficultly and the likelihood of error. AssignMALDI is a software tool designed to create glycan databases with customized derivatizations (labels) and automatically assign glycan masses in MALDI-TOF spectra using the new database. It can also average peak intensities across multiple spectra and prepare publication-ready assignment tables. To make it easy to use with different platforms, all input files and most output files are in text format. An interactive display enables users to inspect and edit peak assignments prior to producing charts and tables for publication. The program is freely available through GitHUB and Python-savvy users can add or adjust features as needed.
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Affiliation(s)
- Lisa M Parsons
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, USA
| | - John F Cipollo
- United States Pharmacopeia Science-Global Biologics Department, Rockville, Maryland, USA
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3
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2017-2018. MASS SPECTROMETRY REVIEWS 2023; 42:227-431. [PMID: 34719822 DOI: 10.1002/mas.21721] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 07/26/2021] [Accepted: 07/26/2021] [Indexed: 06/13/2023]
Abstract
This review is the tenth 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 2018. Also included are papers that describe methods appropriate to glycan and glycoprotein analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, new methods, matrices, derivatization, MALDI imaging, fragmentation and the use of 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. Most of the applications are 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. The reported work shows increasing use of combined new techniques such as ion mobility and highlights the impact that MALDI imaging is having across a range of diciplines. MALDI is still an ideal technique for carbohydrate analysis and advancements in the technique and the range of applications continue steady progress.
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Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
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4
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Chang D, Zaia J. Methods to improve quantitative glycoprotein coverage from bottom-up LC-MS data. MASS SPECTROMETRY REVIEWS 2022; 41:922-937. [PMID: 33764573 DOI: 10.1002/mas.21692] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 12/24/2020] [Accepted: 03/11/2021] [Indexed: 05/18/2023]
Abstract
Advances in mass spectrometry instrumentation, methods development, and bioinformatics have greatly improved the ease and accuracy of site-specific, quantitative glycoproteomics analysis. Data-dependent acquisition is the most popular method for identification and quantification of glycopeptides; however, complete coverage of glycosylation site glycoforms remains elusive with this method. Targeted acquisition methods improve the precision and accuracy of quantification, but at the cost of throughput and discoverability. Data-independent acquisition (DIA) holds great promise for more complete and highly quantitative site-specific glycoproteomics analysis, while maintaining the ability to discover novel glycopeptides without prior knowledge. We review additional features that can be used to increase selectivity and coverage to the DIA workflow: retention time modeling, which would simplify the interpretation of complex tandem mass spectra, and ion mobility separation, which would maximize the sampling of all precursors at a giving chromatographic retention time. The instrumentation and bioinformatics to incorporate these features into glycoproteomics analysis exist. These improvements in quantitative, site-specific analysis will enable researchers to assess glycosylation similarity in related biological systems, answering new questions about the interplay between glycosylation state and biological function.
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Affiliation(s)
- Deborah Chang
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Joseph Zaia
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
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Pralow A, Hoffmann M, Nguyen-Khuong T, Pioch M, Hennig R, Genzel Y, Rapp E, Reichl U. Comprehensive N-glycosylation analysis of the influenza A virus proteins HA and NA from adherent and suspension MDCK cells. FEBS J 2021; 288:4869-4891. [PMID: 33629527 DOI: 10.1111/febs.15787] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 02/04/2021] [Accepted: 02/22/2021] [Indexed: 12/25/2022]
Abstract
Glycosylation is considered as a critical quality attribute for the production of recombinant biopharmaceuticals such as hormones, blood clotting factors, or monoclonal antibodies. In contrast, glycan patterns of immunogenic viral proteins, which differ significantly between the various expression systems, are hardly analyzed yet. The influenza A virus (IAV) proteins hemagglutinin (HA) and neuraminidase (NA) have multiple N-glycosylation sites, and alteration of N-glycan micro- and macroheterogeneity can have strong effects on virulence and immunogenicity. Here, we present a versatile and powerful glycoanalytical workflow that enables a comprehensive N-glycosylation analysis of IAV glycoproteins. We challenged our workflow with IAV (A/PR/8/34 H1N1) propagated in two closely related Madin-Darby canine kidney (MDCK) cell lines, namely an adherent MDCK cell line and its corresponding suspension cell line. As expected, N-glycan patterns of HA and NA from virus particles produced in both MDCK cell lines were similar. Detailed analysis of the HA N-glycan microheterogeneity showed an increasing variability and a higher complexity for N-glycosylation sites located closer to the head region of the molecule. In contrast, NA was found to be exclusively N-glycosylated at site N73. Almost all N-glycan structures were fucosylated. Furthermore, HA and NA N-glycan structures were exclusively hybrid- and complex-type structures, to some extent terminated with alpha-linked galactose(s) but also with blood group H type 2 and blood group A epitopes. In contrast to the similarity of the overall glycan pattern, differences in the relative abundance of individual structures were identified. This concerned, in particular, oligomannose-type, alpha-linked galactose, and multiantennary complex-type N-glycans.
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Affiliation(s)
- Alexander Pralow
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Marcus Hoffmann
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Terry Nguyen-Khuong
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Markus Pioch
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - René Hennig
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany.,glyXera GmbH, Magdeburg, Germany
| | - Yvonne Genzel
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Erdmann Rapp
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany.,glyXera GmbH, Magdeburg, Germany
| | - Udo Reichl
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany.,Chair of Bioprocess Engineering, Otto von Guericke University, Magdeburg, Germany
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6
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Multiscale Simulations Examining Glycan Shield Effects on Drug Binding to Influenza Neuraminidase. Biophys J 2020; 119:2275-2289. [PMID: 33130120 DOI: 10.1016/j.bpj.2020.10.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 10/08/2020] [Accepted: 10/21/2020] [Indexed: 12/18/2022] Open
Abstract
Influenza neuraminidase is an important drug target. Glycans are present on neuraminidase and are generally considered to inhibit antibody binding via their glycan shield. In this work, we studied the effect of glycans on the binding kinetics of antiviral drugs to the influenza neuraminidase. We created all-atom in silico systems of influenza neuraminidase with experimentally derived glycoprofiles consisting of four systems with different glycan conformations and one system without glycans. Using Brownian dynamics simulations, we observe a two- to eightfold decrease in the rate of ligand binding to the primary binding site of neuraminidase due to the presence of glycans. These glycans are capable of covering much of the surface area of neuraminidase, and the ligand binding inhibition is derived from glycans sterically occluding the primary binding site on a neighboring monomer. Our work also indicates that drugs preferentially bind to the primary binding site (i.e., the active site) over the secondary binding site, and we propose a binding mechanism illustrating this. These results help illuminate the complex interplay between glycans and ligand binding on the influenza membrane protein neuraminidase.
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Chang D, Hackett WE, Zhong L, Wan XF, Zaia J. Measuring Site-specific Glycosylation Similarity between Influenza a Virus Variants with Statistical Certainty. Mol Cell Proteomics 2020; 19:1533-1545. [PMID: 32601173 PMCID: PMC8143645 DOI: 10.1074/mcp.ra120.002031] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 06/26/2020] [Indexed: 12/30/2022] Open
Abstract
Influenza A virus (IAV) mutates rapidly, resulting in antigenic drift and poor year-to-year vaccine effectiveness. One challenge in designing effective vaccines is that genetic mutations frequently cause amino acid variations in IAV envelope protein hemagglutinin (HA) that create new N-glycosylation sequons; resulting N-glycans cause antigenic shielding, allowing viral escape from adaptive immune responses. Vaccine candidate strain selection currently involves correlating antigenicity with HA protein sequence among circulating strains, but quantitative comparison of site-specific glycosylation information may likely improve the ability to design vaccines with broader effectiveness against evolving strains. However, there is poor understanding of the influence of glycosylation on immunodominance, antigenicity, and immunogenicity of HA, and there are no well-tested methods for comparing glycosylation similarity among virus samples. Here, we present a method for statistically rigorous quantification of similarity between two related virus strains that considers the presence and abundance of glycopeptide glycoforms. We demonstrate the strength of our approach by determining that there was a quantifiable difference in glycosylation at the protein level between WT IAV HA from A/Switzerland/9715293/2013 (SWZ13) and a mutant strain of SWZ13, even though no N-glycosylation sequons were changed. We determined site-specifically that WT and mutant HA have varying similarity at the glycosylation sites of the head domain, reflecting competing pressures to evade host immune response while retaining viral fitness. To our knowledge, our results are the first to quantify changes in glycosylation state that occur in related proteins of considerable glycan heterogeneity. Our results provide a method for understanding how changes in glycosylation state are correlated with variations in protein sequence, which is necessary for improving IAV vaccine strain selection. Understanding glycosylation will be especially important as we find new expression vectors for vaccine production, as glycosylation state depends greatly on the host species.
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Affiliation(s)
- Deborah Chang
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts, USA
| | - William E Hackett
- Boston University Bioinformatics Program, Boston University, Boston, Massachusetts, USA
| | - Lei Zhong
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi, USA
| | - Xiu-Feng Wan
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi, USA; MU Center for Research on Influenza Systems Biology (CRISB), University of Missouri, Columbia, Missouri, USA; Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, Missouri, USA; Department of Electrical Engineering & Computer Science, College of Engineering, University of Missouri, Columbia, Missouri, USA; Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA; MU Institute for Data Science & Informatics, University of Missouri, Columbia, Missouri, USA
| | - Joseph Zaia
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts, USA; Boston University Bioinformatics Program, Boston University, Boston, Massachusetts, USA.
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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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Thompson AJ, Cao L, Ma Y, Wang X, Diedrich JK, Kikuchi C, Willis S, Worth C, McBride R, Yates JR, Paulson JC. Human Influenza Virus Hemagglutinins Contain Conserved Oligomannose N-Linked Glycans Allowing Potent Neutralization by Lectins. Cell Host Microbe 2020; 27:725-735.e5. [PMID: 32298658 PMCID: PMC7158820 DOI: 10.1016/j.chom.2020.03.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 02/13/2020] [Accepted: 03/17/2020] [Indexed: 12/12/2022]
Abstract
Hemagglutinins (HAs) from human influenza viruses adapt to bind α2-6-linked sialosides, overcoming a receptor-defined species barrier distinct from the α2-3 specificity of avian virus progenitors. Additionally, human-adapted HAs gain glycosylation sites over time, although their biological function is poorly defined. Using quantitative glycomic analysis, we show that HAs from human pandemic viruses exhibit significant proportions of high-mannose type N-linked glycans throughout the head domain. By contrast, poorly adapted avian-origin HAs contain predominately complex-type glycans, which have greater structural diversity. Although oligomannose levels vary, they are present in all tested recombinant HAs and whole viruses and can be specifically targeted for universal detection. The positions of high-mannose glycosites on the HA of human H1N1 and H3N2 strains are conserved. Additionally, high-mannose-binding lectins possess a broad capacity to neutralize and prevent infection with contemporary H3N2 strains. These findings reveal the biological significance of HA glycosylation and therapeutic potential of targeting these structures.
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Affiliation(s)
- Andrew J Thompson
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Liwei Cao
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Yuanhui Ma
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Xiaoning Wang
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Jolene K Diedrich
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Chika Kikuchi
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Shelby Willis
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Charli Worth
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - Ryan McBride
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - John R Yates
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA
| | - James C Paulson
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA; Department of Immunology & Microbiology, Scripps Research, La Jolla, CA 92037, USA.
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Sharma VK, Sharma I, Glick J. The expanding role of mass spectrometry in the field of vaccine development. MASS SPECTROMETRY REVIEWS 2020; 39:83-104. [PMID: 29852530 PMCID: PMC7027533 DOI: 10.1002/mas.21571] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 04/30/2018] [Indexed: 05/09/2023]
Abstract
Biological mass spectrometry has evolved as a core analytical technology in the last decade mainly because of its unparalleled ability to perform qualitative as well as quantitative profiling of enormously complex biological samples with high mass accuracy, sensitivity, selectivity and specificity. Mass spectrometry-based techniques are also routinely used to assess glycosylation and other post-translational modifications, disulfide bond linkage, and scrambling as well as for the detection of host cell protein contaminants in the field of biopharmaceuticals. The role of mass spectrometry in vaccine development has been very limited but is now expanding as the landscape of global vaccine development is shifting towards the development of recombinant vaccines. In this review, the role of mass spectrometry in vaccine development is presented, some of the ongoing efforts to develop vaccines for diseases with global unmet medical need are discussed and the regulatory challenges of implementing mass spectrometry techniques in a quality control laboratory setting are highlighted.
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Affiliation(s)
| | - Ity Sharma
- Independent CMC ConsultantParamusNew Jersey
| | - James Glick
- Novartis Institutes for BioMedical ResearchEast HanoverNew Jersey
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11
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Influenza Virus Hemagglutinins H2, H5, H6, and H11 Are Not Targets of Pulmonary Surfactant Protein D: N-Glycan Subtypes in Host-Pathogen Interactions. J Virol 2020; 94:JVI.01951-19. [PMID: 31826991 DOI: 10.1128/jvi.01951-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 12/01/2019] [Indexed: 11/20/2022] Open
Abstract
Seasonal influenza carrying key hemagglutinin (HA) head region glycosylation sites can be removed from the lung by pulmonary surfactant protein D (SP-D). Little is known about HA head glycosylation of low-pathogenicity avian influenza virus (LPAIV) subtypes. These can pose a pandemic threat through reassortment and emergence in human populations. Since the presence of head region high-mannose glycosites dictates SP-D activity, the ability to predict these glycosite glycan subtypes may be of value. Here, we investigate the activities of two recombinant human SP-D forms against representative LPAIV strains, including H2N1, H5N1, H6N1, H11N9, an avian H3N8, and a human seasonal H3N2 subtype. Using mass spectrometry, we determined the glycan subclasses and heterogeneities at each head glycosylation site. Sequence alignment and molecular structure analysis of the HAs were performed for LPAIV strains in comparison to seasonal H3N2 and avian H3N8. Intramolecular contacts were determined between the protein backbone and glycosite glycan based on available three-dimensional structure data. We found that glycosite "N165" (H3 numbering) is occupied by high-mannose glycans in H3 HA but by complex glycans in all LPAIV HAs. SP-D was not active on LPAIV but was on H3 HAs. Since SP-D affinity for influenza HA depends on the presence of high-mannose glycan on the head region, our data demonstrate that SP-D may not protect against virus containing these HA subtypes. Our results also demonstrate that glycan subtype can be predicted at some glycosites based on sequence comparisons and three-dimensional structural analysis.IMPORTANCE Low-pathogenicity avian influenza virus (LPAIV) subtypes can reassort with circulating human strains and pandemic viruses can emerge in human populations, as was seen in the 1957 pandemic, in which an H2 virus reassorted with the circulating H1N1 to create a novel H2N2 genotype. Lung surfactant protein D (SP-D), a key factor in first-line innate immunity defense, removes influenza type A virus (IAV) through interaction with hemagglutinin (HA) head region high-mannose glycan(s). While it is known that both H1 and H3 HAs have one or more key high-mannose glycosites in the head region, little is known about similar glycosylation of LPAIV strains H2N1, H5N1, H6N1, or H11N9, which may pose future health risks. Here, we demonstrate that the hemagglutinins of LPAIV strains do not have the required high-mannose glycans and do not interact with SP-D, and that sequence analysis can predict glycan subtype, thus predicting the presence or absence of this virulence marker.
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12
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Chang D, Zaia J. Why Glycosylation Matters in Building a Better Flu Vaccine. Mol Cell Proteomics 2019; 18:2348-2358. [PMID: 31604803 PMCID: PMC6885707 DOI: 10.1074/mcp.r119.001491] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 08/18/2019] [Indexed: 12/20/2022] Open
Abstract
Low vaccine efficacy against seasonal influenza A virus (IAV) stems from the ability of the virus to evade existing immunity while maintaining fitness. Although most potent neutralizing antibodies bind antigenic sites on the globular head domain of the IAV envelope glycoprotein hemagglutinin (HA), the error-prone IAV polymerase enables rapid evolution of key antigenic sites, resulting in immune escape. Significantly, the appearance of new N-glycosylation consensus sequences (sequons, NXT/NXS, rarely NXC) on the HA globular domain occurs among the more prevalent mutations as an IAV strain undergoes antigenic drift. The appearance of new glycosylation shields underlying amino acid residues from antibody contact, tunes receptor specificity, and balances receptor avidity with virion escape, all of which help maintain viral propagation through seasonal mutations. The World Health Organization selects seasonal vaccine strains based on information from surveillance, laboratory, and clinical observations. Although the genetic sequences are known, mature glycosylated structures of circulating strains are not defined. In this review, we summarize mass spectrometric methods for quantifying site-specific glycosylation in IAV strains and compare the evolution of IAV glycosylation to that of human immunodeficiency virus. We argue that the determination of site-specific glycosylation of IAV glycoproteins would enable development of vaccines that take advantage of glycosylation-dependent mechanisms whereby virus glycoproteins are processed by antigen presenting cells.
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Affiliation(s)
- Deborah Chang
- Dept. of Biochemistry, Boston University School of Medicine, Boston, MA 02118
| | - Joseph Zaia
- Dept. of Biochemistry, Boston University School of Medicine, Boston, MA 02118.
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13
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Hargett AA, Renfrow MB. Glycosylation of viral surface proteins probed by mass spectrometry. Curr Opin Virol 2019; 36:56-66. [PMID: 31202133 PMCID: PMC7102858 DOI: 10.1016/j.coviro.2019.05.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 05/02/2019] [Accepted: 05/03/2019] [Indexed: 12/17/2022]
Abstract
Glycosylation is a common and biologically significant post-translational modification that is found on numerous virus surface proteins (VSPs). Many of these glycans affect virulence through modulating virus receptor binding, masking antigenic sites, or by stimulating the host immune response. Mass spectrometry (MS) has arisen as a pivotal technique for the characterization of VSP glycosylation. This review will cover how MS-based analyses, such as released glycan profiles, glycan site localization, site-occupancy, and site-specific heterogeneity, are being utilized to map VSP glycosylation. Furthermore, this review will provide information on how MS glycoprofiling data are being used in conjunction with molecular and structural experiments to provide a better understanding of the role of specific glycans in VSP function.
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Affiliation(s)
- Audra A Hargett
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Matthew B Renfrow
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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Parsons LM, Bouwman KM, Azurmendi H, de Vries RP, Cipollo JF, Verheije MH. Glycosylation of the viral attachment protein of avian coronavirus is essential for host cell and receptor binding. J Biol Chem 2019; 294:7797-7809. [PMID: 30902814 PMCID: PMC6514631 DOI: 10.1074/jbc.ra119.007532] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 03/01/2019] [Indexed: 12/16/2022] Open
Abstract
Avian coronaviruses, including infectious bronchitis virus (IBV), are important
respiratory pathogens of poultry. The heavily glycosylated IBV spike protein is
responsible for binding to host tissues. Glycosylation sites in the spike
protein are highly conserved across viral genotypes, suggesting an important
role for this modification in the virus life cycle. Here, we analyzed the
N-glycosylation of the receptor-binding domain (RBD) of IBV
strain M41 spike protein and assessed the role of this modification in host
receptor binding. Ten single Asn–to–Ala substitutions at the
predicted N-glycosylation sites of the M41–RBD were
evaluated along with two control Val–to–Ala substitutions. CD
analysis revealed that the secondary structure of all variants was retained
compared with the unmodified M41–RBD construct. Six of the 10
glycosylation variants lost binding to chicken trachea tissue and an
ELISA-presented α2,3-linked sialic acid oligosaccharide ligand.
LC/MSE glycomics analysis revealed that glycosylation sites have
specific proportions of N-glycan subtypes. Overall, the
glycosylation patterns of most variant RBDs were highly similar to those of the
unmodified M41–RBD construct. In silico docking
experiments with the recently published cryo-EM structure of the M41 IBV spike
protein and our glycosylation results revealed a potential ligand receptor site
that is ringed by four glycosylation sites that dramatically impact ligand
binding. Combined with the results of previous array studies, the glycosylation
and mutational analyses presented here suggest a unique glycosylation-dependent
binding modality for the M41 spike protein.
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Affiliation(s)
- Lisa M Parsons
- From the Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland 20993
| | - Kim M Bouwman
- the Division of Pathology, Department of Pathobiology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands, and
| | - Hugo Azurmendi
- From the Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland 20993
| | - Robert P de Vries
- the Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3512 JE Utrecht, The Netherlands
| | - John F Cipollo
- From the Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland 20993,
| | - Monique H Verheije
- the Division of Pathology, Department of Pathobiology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands, and
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15
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Streltsov VA, Schmidt PM, McKimm-Breschkin JL. Structure of an Influenza A virus N9 neuraminidase with a tetrabrachion-domain stalk. Acta Crystallogr F Struct Biol Commun 2019; 75:89-97. [PMID: 30713159 PMCID: PMC6360442 DOI: 10.1107/s2053230x18017892] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 12/18/2018] [Indexed: 12/26/2022] Open
Abstract
The influenza neuraminidase (NA) is a homotetramer with head, stalk, transmembrane and cytoplasmic regions. The structure of the NA head with a stalk has never been determined. The NA head from an N9 subtype influenza A virus, A/tern/Australia/G70C/1975 (H1N9), was expressed with an artificial stalk derived from the tetrabrachion (TB) tetramerization domain from Staphylothermus marinus. The NA was successfully crystallized both with and without the TB stalk, and the structures were determined to 2.6 and 2.3 Å resolution, respectively. Comparisons of the two NAs with the native N9 NA structure from egg-grown virus showed that the artificial TB stalk maintained the native NA head structure, supporting previous biological observations.
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Affiliation(s)
- Victor A. Streltsov
- CSIRO Manufacturing, 343 Royal Parade, Parkville, Victoria 3052, Australia
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, 30 Royal Parade, Parkville, Victoria 3052, Australia
| | - Peter M. Schmidt
- CSIRO Manufacturing, 343 Royal Parade, Parkville, Victoria 3052, Australia
- R&D, CSL Behring GmbH, Emil-von-Behring Strasse 76, 35041 Marburg, Germany
| | - Jennifer L. McKimm-Breschkin
- CSIRO Manufacturing, 343 Royal Parade, Parkville, Victoria 3052, Australia
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Melbourne, Victoria 3000, Australia
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16
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Cao L, Diedrich JK, Ma Y, Wang N, Pauthner M, Park SKR, Delahunty CM, McLellan JS, Burton DR, Yates JR, Paulson JC. Global site-specific analysis of glycoprotein N-glycan processing. Nat Protoc 2018; 13:1196-1212. [PMID: 29725121 PMCID: PMC5941933 DOI: 10.1038/nprot.2018.024] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
N-glycans contribute to the folding, stability and functions of the proteins they decorate. They are produced by transfer of the glycan precursor to the sequon Asn-X-Thr/Ser, followed by enzymatic trimming to a high-mannose-type core and sequential addition of monosaccharides to generate complex-type and hybrid glycans. This process, mediated by the concerted action of multiple enzymes, produces a mixture of related glycoforms at each glycosite, making analysis of glycosylation difficult. To address this analytical challenge, we developed a robust semiquantitative mass spectrometry (MS)-based method that determines the degree of glycan occupancy at each glycosite and the proportion of N-glycans processed from high-mannose type to complex type. It is applicable to virtually any glycoprotein, and a complete analysis can be conducted with 30 μg of protein. Here, we provide a detailed description of the method that includes procedures for (i) proteolytic digestion of glycoprotein(s) with specific and nonspecific proteases; (ii) denaturation of proteases by heating; (iii) sequential treatment of the glycopeptide mixture with two endoglycosidases, Endo H and PNGase F, to create unique mass signatures for the three glycosylation states; (iv) LC-MS/MS analysis; and (v) data analysis for identification and quantitation of peptides for the three glycosylation states. Full coverage of site-specific glycosylation of glycoproteins is achieved, with up to thousands of high-confidence spectra hits for each glycosite. The protocol can be performed by an experienced technician or student/postdoc with basic skills for proteomics experiments and takes ∼7 d to complete.
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Affiliation(s)
- Liwei Cao
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, USA.,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery and IAVI Neutralizing Antibody Center, Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, USA
| | - Jolene K Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, USA
| | - Yuanhui Ma
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, USA
| | - Nianshuang Wang
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Matthias Pauthner
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery and IAVI Neutralizing Antibody Center, Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, USA
| | - Sung-Kyu Robin Park
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, USA
| | - Claire M Delahunty
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, USA
| | - Jason S McLellan
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Dennis R Burton
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery and IAVI Neutralizing Antibody Center, Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, USA.,Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, USA
| | - James C Paulson
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, USA.,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery and IAVI Neutralizing Antibody Center, Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, USA
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17
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Zheng J, Perlman S. Immune responses in influenza A virus and human coronavirus infections: an ongoing battle between the virus and host. Curr Opin Virol 2018; 28:43-52. [PMID: 29172107 PMCID: PMC5835172 DOI: 10.1016/j.coviro.2017.11.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 11/02/2017] [Indexed: 12/25/2022]
Abstract
Respiratory viruses, especially influenza A viruses and coronaviruses such as MERS-CoV, represent continuing global threats to human health. Despite significant advances, much needs to be learned. Recent studies in virology and immunology have improved our understanding of the role of the immune system in protection and in the pathogenesis of these infections and of co-evolution of viruses and their hosts. These findings, together with sophisticated molecular structure analyses, omics tools and computer-based models, have helped delineate the interaction between respiratory viruses and the host immune system, which will facilitate the development of novel treatment strategies and vaccines with enhanced efficacy.
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Affiliation(s)
- Jian Zheng
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, IA 52242, United States
| | - Stanley Perlman
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, IA 52242, United States.
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18
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She YM, Farnsworth A, Li X, Cyr TD. Topological N-glycosylation and site-specific N-glycan sulfation of influenza proteins in the highly expressed H1N1 candidate vaccines. Sci Rep 2017; 7:10232. [PMID: 28860626 PMCID: PMC5579265 DOI: 10.1038/s41598-017-10714-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 08/14/2017] [Indexed: 01/20/2023] Open
Abstract
The outbreak of a pandemic influenza H1N1 in 2009 required the rapid generation of high-yielding vaccines against the A/California/7/2009 virus, which were achieved by either addition or deletion of a glycosylation site in the influenza proteins hemagglutinin and neuraminidase. In this report, we have systematically evaluated the glycan composition, structural distribution and topology of glycosylation for two high-yield candidate reassortant vaccines (NIBRG-121xp and NYMC-X181A) by combining various enzymatic digestions with high performance liquid chromatography and multiple-stage mass spectrometry. Proteomic data analyses of the full-length protein sequences determined 9 N-glycosylation sites of hemagglutinin, and defined 6 N-glycosylation sites and the glycan structures of low abundance neuraminidase, which were occupied by high-mannose, hybrid and complex-type N-glycans. A total of ~300 glycopeptides were analyzed and manually validated by tandem mass spectrometry. The specific N-glycan structure and topological location of these N-glycans are highly correlated to the spatial protein structure and the residential ligand binding. Interestingly, sulfation, fucosylation and bisecting N-acetylglucosamine of N-glycans were also reliably identified at the specific glycosylation sites of the two influenza proteins that may serve a crucial role in regulating the protein structure and increasing the protein abundance of the influenza virus reassortants.
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Affiliation(s)
- Yi-Min She
- Centre for Biologics Evaluation, Biologics and Genetic Therapies Directorate, Health Canada, Ottawa, Ontario, K1A 0K9, Canada
| | - Aaron Farnsworth
- Centre for Biologics Evaluation, Biologics and Genetic Therapies Directorate, Health Canada, Ottawa, Ontario, K1A 0K9, Canada
| | - Xuguang Li
- Centre for Biologics Evaluation, Biologics and Genetic Therapies Directorate, Health Canada, Ottawa, Ontario, K1A 0K9, Canada
| | - Terry D Cyr
- Centre for Biologics Evaluation, Biologics and Genetic Therapies Directorate, Health Canada, Ottawa, Ontario, K1A 0K9, Canada.
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