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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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Yin H, Zhu J. Methods for quantification of glycopeptides by liquid separation and mass spectrometry. MASS SPECTROMETRY REVIEWS 2023; 42:887-917. [PMID: 35099083 PMCID: PMC9339036 DOI: 10.1002/mas.21771] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 11/14/2021] [Accepted: 01/13/2022] [Indexed: 05/05/2023]
Abstract
Recent advances in analytical techniques provide the opportunity to quantify even low-abundance glycopeptides derived from complex biological mixtures, allowing for the identification of glycosylation differences between healthy samples and those derived from disease states. Herein, we discuss the sample preparation procedures and the mass spectrometry (MS) strategies that have facilitated glycopeptide quantification, as well as the standards used for glycopeptide quantification. For sample preparation, various glycopeptide enrichment methods are summarized including the columns used for glycopeptide separation in liquid chromatography separation. For MS analysis strategies, MS1 level-based quantification and MS2 level-based quantification are described, either with or without labeling, where we have covered isotope labeling, TMT/iTRAQ labeling, data dependent acquisition, data independent acquisition, multiple reaction monitoring, and parallel reaction monitoring. The strengths and weaknesses of these methods are compared, particularly those associated with the figures of merit that are important for clinical biomarker studies and the pathological and functional studies of glycoproteins in various diseases. Possible future developments for glycopeptide quantification are discussed.
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Affiliation(s)
- Haidi Yin
- Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518132, China
- Correspondence to: Haidi Yin, Shenzhen Bay Laboratory, A1201, Shenzhen, Guangdong, 518132, China. Phone: 0755-26849276. , Jianhui Zhu, Department of Surgery, University of Michigan, 1150 West Medical Center Drive, Building MSRB1, Rm A500, Ann Arbor, MI 48109-0656, USA. Tel: 734-615-2567. Fax: 734-615-2088.
| | - Jianhui Zhu
- Department of Surgery, University of Michigan, Ann Arbor, MI 48109, USA
- Correspondence to: Haidi Yin, Shenzhen Bay Laboratory, A1201, Shenzhen, Guangdong, 518132, China. Phone: 0755-26849276. , Jianhui Zhu, Department of Surgery, University of Michigan, 1150 West Medical Center Drive, Building MSRB1, Rm A500, Ann Arbor, MI 48109-0656, USA. Tel: 734-615-2567. Fax: 734-615-2088.
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3
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Wong TL, Mooney BP, Cavallero GJ, Guan M, Li L, Zaia J, Wan XF. Glycoproteomic Analyses of Influenza A Viruses Using timsTOF Pro MS. J Proteome Res 2023; 22:62-77. [PMID: 36480915 DOI: 10.1021/acs.jproteome.2c00469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
N-Linked glycosylation in hemagglutinin and neuraminidase glycoproteins of influenza viruses affects antigenic and receptor binding properties, and precise analyses of site-specific glycoforms in these proteins are critical in understanding the antigenic and immunogenic properties of influenza viruses. In this study, we developed a glycoproteomic approach by using a timsTOF Pro mass spectrometer (MS) to determine the abundance and heterogeneity of site-specific glycosylation for influenza glycoproteins. Compared with a Q Exactive HF MS, the timsTOF Pro MS method without the hydrophilic interaction liquid chromatography column enrichment achieved similar glycopeptide coverage and quantities but was more effective in identifying low-abundance glycopeptides. We quantified the distributions of intact site-specific glycopeptides in hemagglutinin of A/chicken/Wuxi/0405005/2013 (H7N9) and A/mute swan/Rhode Island/A00325125/2008 (H7N3). Results showed that hemagglutinin for both viruses had complex N-glycans at N22, N38, N240, and N483 but only high-mannose glycans at N411 and, however, that the type and quantities of glycans were distinct between these viruses. Collisional cross section (CCS) provided by the ion mobility spectrometry from the timsTOF Pro MS data differentiated sialylation linkages of the glycopeptides. In summary, timsTOF Pro MS method can quantify intact site-specific glycans for influenza glycoproteins without enrichment and thus facilitate influenza vaccine development and production.
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Affiliation(s)
- Tin Long Wong
- Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, Missouri65211, United States.,Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, Missouri65211, United States.,Bond Life Sciences Center, University of Missouri, Columbia, Missouri65211, United States
| | - Brian P Mooney
- Department of Biochemistry and Charles W. Gehrke Proteomics Center, University of Missouri, Columbia, Missouri65211, United States
| | - Gustavo J Cavallero
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts02118, United States
| | - Minhui Guan
- Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, Missouri65211, United States.,Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, Missouri65211, United States.,Bond Life Sciences Center, University of Missouri, Columbia, Missouri65211, United States
| | - Lei Li
- Department of Chemistry, Georgia State University, Atlanta, Georgia30302, United States
| | - Joseph Zaia
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts02118, United States
| | - Xiu-Feng Wan
- Center for Influenza and Emerging Infectious Diseases, University of Missouri, Columbia, Missouri65211, United States.,Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, Missouri65211, United States.,Bond Life Sciences Center, University of Missouri, Columbia, Missouri65211, United States.,Department of Electrical Engineering & Computer Science, College of Engineering, University of Missouri, Columbia, Missouri65211, United States
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2019-2020. MASS SPECTROMETRY REVIEWS 2022:e21806. [PMID: 36468275 DOI: 10.1002/mas.21806] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
This review is the tenth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2020. Also included are papers that describe methods appropriate to analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. The review is basically divided into three sections: (1) general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, quantification and the use of arrays. (2) Applications to various structural types such as oligo- and polysaccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals, and (3) other areas such as medicine, industrial processes and glycan synthesis where MALDI is extensively used. Much of the material relating to applications is presented in tabular form. The reported work shows increasing use of incorporation of new techniques such as ion mobility and the enormous impact that MALDI imaging is having. MALDI, although invented nearly 40 years ago is still an ideal technique for carbohydrate analysis and advancements in the technique and range of applications show little sign of diminishing.
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Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
- Department of Chemistry, University of Oxford, Oxford, Oxfordshire, United Kingdom
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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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White MR, Nikolaidis NM, McCormack F, Crouch EC, Hartshorn KL. Viral Evasion of Innate Immune Defense: The Case of Resistance of Pandemic H1N1 Influenza A Virus to Human Mannose-Binding Proteins. Front Microbiol 2021; 12:774711. [PMID: 34956139 PMCID: PMC8692257 DOI: 10.3389/fmicb.2021.774711] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 11/03/2021] [Indexed: 12/14/2022] Open
Abstract
Mannose-binding lectins effectively inhibit most seasonal strains of influenza A virus and contribute to the innate host defense vs. these viruses. In contrast, pandemic IAV strains are largely resistant to these lectins, likely contributing to increased spread and worse outcomes. In this paper, we evaluated the inhibition of IAV by mannose-binding lectins of human, bacterial, and fungal origin to understand and possibly increase activity vs. the pandemic IAV. A modified version of the human surfactant protein D (SP-D) neck and carbohydrate recognition domain (NCRD) with combinatorial substitutions at the 325 and 343 positions, previously shown to inhibit pandemic H3N2 IAV in vitro and in vivo, and to inhibit pandemic H1N1 in vitro, failed to protect mice from pandemic H1N1 in vivo in the current study. We attempted a variety of maneuvers to improve the activity of the mutant NCRDs vs. the 2009 pandemic H1N1, including the formation of full-length SP-D molecules containing the mutant NCRD, cross-linking of NCRDs through the use of antibodies, combining SP-D or NCRDs with alpha-2-macroglobulin, and introducing an additional mutation to the double mutant NCRD. None of these substantially increased the antiviral activity for the pandemic H1N1. We also tested the activity of bacterial and algal mannose-binding lectins, cyanovirin, and griffithsin, against IAV. These had strong activity against seasonal IAV, which was largely retained against pandemic H1N1. We propose mechanisms to account for differences in activity of SP-D constructs against pandemic H3N2 and H1N1, and for differences in activity of cyanovirin vs. SP-D constructs.
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Affiliation(s)
- Mitchell R. White
- Department of Medicine, Section of Hematology and Oncology, School of Medicine, Boston University, Boston, MA, United States
| | - Nikolaos M. Nikolaidis
- Division of Pulmonary and Critical Care Medicine, University of Cincinnati, Cincinnati, OH, United States,Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
| | - Francis McCormack
- Division of Pulmonary and Critical Care Medicine, University of Cincinnati, Cincinnati, OH, United States,Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
| | - Erika C. Crouch
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, United States
| | - Kevan L. Hartshorn
- Department of Medicine, Section of Hematology and Oncology, School of Medicine, Boston University, Boston, MA, United States,*Correspondence: Kevan L. Hartshorn,
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Hartshorn KL. Innate Immunity and Influenza A Virus Pathogenesis: Lessons for COVID-19. Front Cell Infect Microbiol 2020; 10:563850. [PMID: 33194802 PMCID: PMC7642997 DOI: 10.3389/fcimb.2020.563850] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 09/11/2020] [Indexed: 12/15/2022] Open
Abstract
There is abundant evidence that the innate immune response to influenza A virus (IAV) is highly complex and plays a key role in protection against IAV induced infection and illness. Unfortunately it also clear that aspects of innate immunity can lead to severe morbidity or mortality from IAV, including inflammatory lung injury, bacterial superinfection, and exacerbation of reactive airways disease. We review broadly the virus and host factors that result in adverse outcomes from IAV and show evidence that inflammatory responses can become damaging even apart from changes in viral replication per se, with special focus on the positive and adverse effects of neutrophils and monocytes. We then evaluate in detail the role of soluble innate inhibitors including surfactant protein D and antimicrobial peptides that have a potential dual capacity for down-regulating viral replication and also inhibiting excessive inflammatory responses and how these innate host factors could possibly be harnessed to treat IAV infection. Where appropriate we draw comparisons and contrasts the SARS-CoV viruses and IAV in an effort to point out where the extensive knowledge existing regarding severe IAV infection could help guide research into severe COVID 19 illness or vice versa.
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Affiliation(s)
- Kevan L Hartshorn
- Section of Hematology Oncology, Boston University School of Medicine, Boston, MA, United States
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Cornish EF, Filipovic I, Åsenius F, Williams DJ, McDonnell T. Innate Immune Responses to Acute Viral Infection During Pregnancy. Front Immunol 2020; 11:572567. [PMID: 33101294 PMCID: PMC7556209 DOI: 10.3389/fimmu.2020.572567] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 08/31/2020] [Indexed: 02/06/2023] Open
Abstract
Immunological adaptations in pregnancy allow maternal tolerance of the semi-allogeneic fetus but also increase maternal susceptibility to infection. At implantation, the endometrial stroma, glands, arteries and immune cells undergo anatomical and functional transformation to create the decidua, the specialized secretory endometrium of pregnancy. The maternal decidua and the invading fetal trophoblast constitute a dynamic junction that facilitates a complex immunological dialogue between the two. The decidual and peripheral immune systems together assume a pivotal role in regulating the critical balance between tolerance and defense against infection. Throughout pregnancy, this equilibrium is repeatedly subjected to microbial challenge. Acute viral infection in pregnancy is associated with a wide spectrum of adverse consequences for both mother and fetus. Vertical transmission from mother to fetus can cause developmental anomalies, growth restriction, preterm birth and stillbirth, while the mother is predisposed to heightened morbidity and maternal death. A rapid, effective response to invasive pathogens is therefore essential in order to avoid overwhelming maternal infection and consequent fetal compromise. This sentinel response is mediated by the innate immune system: a heritable, highly evolutionarily conserved system comprising physical barriers, antimicrobial peptides (AMP) and a variety of immune cells—principally neutrophils, macrophages, dendritic cells, and natural killer cells—which express pattern-receptors that detect invariant molecular signatures unique to pathogenic micro-organisms. Recognition of these signatures during acute infection triggers signaling cascades that enhance antimicrobial properties such as phagocytosis, secretion of pro-inflammatory cytokines and activation of the complement system. As well as coordinating the initial immune response, macrophages and dendritic cells present microbial antigens to lymphocytes, initiating and influencing the development of specific, long-lasting adaptive immunity. Despite extensive progress in unraveling the immunological adaptations of pregnancy, pregnant women remain particularly susceptible to certain acute viral infections and continue to experience mortality rates equivalent to those observed in pandemics several decades ago. Here, we focus specifically on the pregnancy-induced vulnerabilities in innate immunity that contribute to the disproportionately high maternal mortality observed in the following acute viral infections: Lassa fever, Ebola virus disease (EVD), dengue fever, hepatitis E, influenza, and novel coronavirus infections.
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Affiliation(s)
- Emily F Cornish
- Elizabeth Garrett Anderson Institute for Women's Health, University College London, London, United Kingdom
| | - Iva Filipovic
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institute, Stockholm, Sweden
| | - Fredrika Åsenius
- Elizabeth Garrett Anderson Institute for Women's Health, University College London, London, United Kingdom
| | - David J Williams
- Elizabeth Garrett Anderson Institute for Women's Health, University College London, London, United Kingdom
| | - Thomas McDonnell
- Department of Biochemical Engineering, University College London, London, United Kingdom
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