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Fang J, Zhou ZJ, Yuan S, Qiu Y, Ge XY. Lineage classification and selective site identification of Orthoebolavirus zairense. Microbes Infect 2024:105304. [PMID: 38278475 DOI: 10.1016/j.micinf.2024.105304] [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: 11/23/2023] [Revised: 01/19/2024] [Accepted: 01/21/2024] [Indexed: 01/28/2024]
Abstract
As the high pathogenic species of Filoviridae virus family, Orthoebolavirus zairense (EBOV) shows frequent outbreaks in human in recently years since its first emerging in 1976 in Democratic Republic of the Congo (COD), bringing ongoing risks and burden on public health safety. Here, the phylogenetic relationship among major outbreaks was analyzed. The results showed that EBOV isolates could be divided into four lineages according to spatial and temporal epidemics. Then, the positive selection sites (PSSs) were detected on all proteins of the EBOV, exhibiting lineage characteristic. Particularly, sites in GP and VP24 were identified to be significantly under positive selection, and partial of which were maintained in the latest isolates in 2021. GP and L were found to have high variability between lineages. Substitutions including F443L and F443S in GP, as well as F1610L and I1951V in L could be characteristic of the two large outbreaks in COD (2018) and West Africa (2014), respectively. Further, substitutions of significant PSSs in VP24 and L proteins were visualized for analysis of structural changes, which may affect EBOV pathogenesis. In summary, our results gains insights in genetic characteristic and adaptive evolution of EBOV, which could facilitate gene functional research against EBOV.
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Affiliation(s)
- Jie Fang
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, 27 Tianma Rd., Changsha, Hunan, 410012, China
| | - Zhi-Jian Zhou
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, 27 Tianma Rd., Changsha, Hunan, 410012, China
| | - Shuofeng Yuan
- Department of Microbiology, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Ye Qiu
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, 27 Tianma Rd., Changsha, Hunan, 410012, China
| | - Xing-Yi Ge
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, 27 Tianma Rd., Changsha, Hunan, 410012, China.
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2
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Lennemann NJ, Corliss L, Maury W. Modification of N-Linked Glycan Sites in Viral Glycoproteins. Methods Mol Biol 2024; 2762:27-41. [PMID: 38315358 DOI: 10.1007/978-1-0716-3666-4_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Post-translational modification of proteins by the addition of sugar chains, or glycans, is a functionally important hallmark of proteins trafficked through the secretory system. These proteins are termed glycoproteins. Glycans are known to be important for initiating signaling through binding of cell surface receptors, facilitating protein folding, and maintaining protein stability. For pathogens, glycans can also mask vulnerable protein regions from neutralizing antibodies. Thus, there is a need to develop methods to decipher the role of specific glycans attached to proteins in order to understand their biological role. Here, we describe established methods for identifying glycosylated residues and understanding their role in protein synthesis and function using viral glycoproteins as a model.
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Affiliation(s)
- Nicholas J Lennemann
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Lochlain Corliss
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Wendy Maury
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, USA
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3
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Wuo M, Dugan AE, Halim M, Hauser BM, Feldman J, Caradonna TM, Zhang S, Pepi LE, Atyeo C, Fischinger S, Alter G, Garcia-Beltran WF, Azadi P, Hung D, Schmidt AG, Kiessling LL. Lectin Fingerprinting Distinguishes Antibody Neutralization in SARS-CoV-2. ACS CENTRAL SCIENCE 2023; 9:947-956. [PMID: 37252360 PMCID: PMC10214521 DOI: 10.1021/acscentsci.2c01471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Indexed: 05/31/2023]
Abstract
Enveloped viruses co-opt host glycosylation pathways to decorate their surface proteins. As viruses evolve, emerging strains can modify their glycosylation patterns to influence host interactions and subvert immune recognition. Still, changes in viral glycosylation or their impact on antibody protection cannot be predicted from genomic sequences alone. Using the highly glycosylated SARS-CoV-2 Spike protein as a model system, we present a lectin fingerprinting method that rapidly reports on changes in variant glycosylation state, which are linked to antibody neutralization. In the presence of antibodies or convalescent and vaccinated patient sera, unique lectin fingerprints emerge that distinguish neutralizing versus non-neutralizing antibodies. This information could not be inferred from direct binding interactions between antibodies and the Spike receptor-binding domain (RBD) binding data alone. Comparative glycoproteomics of the Spike RBD of wild-type (Wuhan-Hu-1) and Delta (B.1.617.2) variants reveal O-glycosylation differences as a key determinant of immune recognition differences. These data underscore the interplay between viral glycosylation and immune recognition and reveal lectin fingerprinting to be a rapid, sensitive, and high-throughput assay to distinguish the neutralization potential of antibodies that target critical viral glycoproteins.
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Affiliation(s)
- Michael
G. Wuo
- Department
of Chemistry, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States
| | - Amanda E. Dugan
- Department
of Chemistry, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States
| | - Melanie Halim
- Department
of Chemistry, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States
| | - Blake M. Hauser
- Ragon
Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts 02139, United States
| | - Jared Feldman
- Ragon
Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts 02139, United States
| | - Timothy M. Caradonna
- Ragon
Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts 02139, United States
| | - Shuting Zhang
- The
Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Department
of Molecular Biology and Center for Computational and Integrative
Biology, Massachusetts General Hospital, Boston, Massachusetts 02139, United States
- Department
of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Lauren E. Pepi
- Complex
Carbohydrate Research Center, University
of Georgia, Athens, Georgia 30602, United States
| | - Caroline Atyeo
- Ragon
Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts 02139, United States
| | - Stephanie Fischinger
- Ragon
Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts 02139, United States
| | - Galit Alter
- Ragon
Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts 02139, United States
| | | | - Parastoo Azadi
- Complex
Carbohydrate Research Center, University
of Georgia, Athens, Georgia 30602, United States
| | - Deb Hung
- The
Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Department
of Molecular Biology and Center for Computational and Integrative
Biology, Massachusetts General Hospital, Boston, Massachusetts 02139, United States
- Department
of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Aaron G. Schmidt
- Ragon
Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts 02139, United States
- Department
of Microbiology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Laura L. Kiessling
- Department
of Chemistry, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States
- The
Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Koch
Institute for Integrative Cancer Research, MIT, Cambridge, Massachusetts 02139, United States
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4
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Andrés C, González-Sánchez A, Jiménez M, Márquez-Algaba E, Piñana M, Fernández-Naval C, Esperalba J, Saubi N, Quer J, Rando-Segura A, Miarons M, Codina MG, Ruiz-Camps I, Pumarola T, Abrisqueta P, Antón A. Emergence of Delta and Omicron variants carrying resistance-associated mutations in immunocompromised patients undergoing sotrovimab treatment with long-term viral excretion. Clin Microbiol Infect 2023; 29:240-246. [PMID: 36067943 DOI: 10.1016/j.cmi.2022.08.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 08/19/2022] [Accepted: 08/25/2022] [Indexed: 02/07/2023]
Abstract
OBJECTIVES To monitor the early emergence of genetic mutations related to reduced susceptibility to monoclonal anti-body (mAb)-based treatment in immunocompromised patients with long-term viral excretion using whole-genome sequencing at a tertiary university hospital in Barcelona, Spain. METHODS Serial severe acute respiratory syndrome coronavirus 2-positive samples (mid-December 2021-mid-March 2022) from eight immunosuppressed, fully vaccinated patients (for solid-organ transplantation or haematologic malignancies) with long-term viral excretion despite undergoing mAb therapy (sotrovimab) for coronavirus disease 2019 were selected. Whole-genome sequencing was performed following the ARTIC, version 4.1, protocol on the MiSeq platform. Mutations in the coding sequence of the spike protein with a frequency of ≥5% were studied. RESULTS A total of 37 samples from the studied cases were analysed. All the cases, except one, were confirmed to have the Omicron variant BA.1; one had Delta (AY.100). Thirty-four different mutations were detected within the receptor-binding domain of the spike protein in 62.5% of patients, eight of which were not lineage related and located in the sotrovimab target epitope (P337L, E340D, E340R, E340K, E340V, E340Q, R346T and K356T). Except for P337L, all changes showed a significant increase in frequency or fixation after the administration of sotrovimab. Some of them have been associated with either reduced susceptibility to mAb therapy, such as those at position 340, or the acquisition of a new glycosylation site (346 and 356 positions). CONCLUSIONS This study highlights the importance of monitoring for early in vivo selection of mutations associated with reduced susceptibility to mAb therapy, especially in immunocompromised patients receiving anti-viral drugs, whose immune response is not able to control viral replication, resulting in long-term viral shedding, and those receiving selective evolution pressure. Virologic surveillance of genetically resistant viruses to available anti-viral therapies is considered a priority for both patients and the community.
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Affiliation(s)
- Cristina Andrés
- Respiratory Viruses Unit, Virology Section, Microbiology Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Institut de Recerca, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron, Barcelona, Spain; Centro de Instigación Biomédica en red de Enfermedades Infecciosas CIBERINFEC, Instituto Carlos III, Madrid, Spain
| | - Alejandra González-Sánchez
- Respiratory Viruses Unit, Virology Section, Microbiology Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Institut de Recerca, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron, Barcelona, Spain; Centro de Instigación Biomédica en red de Enfermedades Infecciosas CIBERINFEC, Instituto Carlos III, Madrid, Spain
| | - Moraima Jiménez
- Department of Hematology, Vall d'Hebron Hospital Universitari, Experimental Hematology, Vall d'Hebron Institute of Oncology, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron, Barcelona, Spain
| | - Ester Márquez-Algaba
- Department of Infectious Diseases. Vall d'Hebron University Hospital, Department of Medicine, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Maria Piñana
- Respiratory Viruses Unit, Virology Section, Microbiology Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Institut de Recerca, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron, Barcelona, Spain; Centro de Instigación Biomédica en red de Enfermedades Infecciosas CIBERINFEC, Instituto Carlos III, Madrid, Spain
| | - Candela Fernández-Naval
- Centro de Instigación Biomédica en red de Enfermedades Infecciosas CIBERINFEC, Instituto Carlos III, Madrid, Spain; Department of Microbiology, Vall d'Hebron Hospital Universitari, Vall d'Hebron Institut de Recerca, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Passeig Vall d'Hebron, Barcelona, Spain
| | - Juliana Esperalba
- Centro de Instigación Biomédica en red de Enfermedades Infecciosas CIBERINFEC, Instituto Carlos III, Madrid, Spain; Department of Microbiology, Vall d'Hebron Hospital Universitari, Vall d'Hebron Institut de Recerca, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Passeig Vall d'Hebron, Barcelona, Spain
| | - Narcís Saubi
- Respiratory Viruses Unit, Virology Section, Microbiology Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Institut de Recerca, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron, Barcelona, Spain; Centro de Instigación Biomédica en red de Enfermedades Infecciosas CIBERINFEC, Instituto Carlos III, Madrid, Spain
| | - Josep Quer
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d'Hebron Institut of Research, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, Av. Monforte de Lemos, Madrid, Spain; Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona (UAB), UAB Campus, Plaça Cívica, Bellaterra, Spain
| | - Ariadna Rando-Segura
- Centro de Instigación Biomédica en red de Enfermedades Infecciosas CIBERINFEC, Instituto Carlos III, Madrid, Spain; Department of Microbiology, Vall d'Hebron Hospital Universitari, Vall d'Hebron Institut de Recerca, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Passeig Vall d'Hebron, Barcelona, Spain
| | - Marta Miarons
- Pharmacy Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron, Barcelona, Spain
| | - Maria Gema Codina
- Centro de Instigación Biomédica en red de Enfermedades Infecciosas CIBERINFEC, Instituto Carlos III, Madrid, Spain; Department of Microbiology, Vall d'Hebron Hospital Universitari, Vall d'Hebron Institut de Recerca, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Passeig Vall d'Hebron, Barcelona, Spain
| | - Isabel Ruiz-Camps
- Centro de Instigación Biomédica en red de Enfermedades Infecciosas CIBERINFEC, Instituto Carlos III, Madrid, Spain; Department of Infectious Diseases. Vall d'Hebron University Hospital, Department of Medicine, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Tomàs Pumarola
- Centro de Instigación Biomédica en red de Enfermedades Infecciosas CIBERINFEC, Instituto Carlos III, Madrid, Spain; Department of Microbiology, Vall d'Hebron Hospital Universitari, Vall d'Hebron Institut de Recerca, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Passeig Vall d'Hebron, Barcelona, Spain.
| | - Pau Abrisqueta
- Department of Hematology, Vall d'Hebron Hospital Universitari, Experimental Hematology, Vall d'Hebron Institute of Oncology, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron, Barcelona, Spain
| | - Andrés Antón
- Respiratory Viruses Unit, Virology Section, Microbiology Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Institut de Recerca, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron, Barcelona, Spain; Centro de Instigación Biomédica en red de Enfermedades Infecciosas CIBERINFEC, Instituto Carlos III, Madrid, Spain
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5
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Junk mail: Viral envelopes promote zoonoses. Proc Natl Acad Sci U S A 2023; 120:e2219962120. [PMID: 36623201 PMCID: PMC9933117 DOI: 10.1073/pnas.2219962120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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6
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Escudero-Pérez B, Lawrence P, Castillo-Olivares J. Immune correlates of protection for SARS-CoV-2, Ebola and Nipah virus infection. Front Immunol 2023; 14:1156758. [PMID: 37153606 PMCID: PMC10158532 DOI: 10.3389/fimmu.2023.1156758] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 03/20/2023] [Indexed: 05/09/2023] Open
Abstract
Correlates of protection (CoP) are biological parameters that predict a certain level of protection against an infectious disease. Well-established correlates of protection facilitate the development and licensing of vaccines by assessing protective efficacy without the need to expose clinical trial participants to the infectious agent against which the vaccine aims to protect. Despite the fact that viruses have many features in common, correlates of protection can vary considerably amongst the same virus family and even amongst a same virus depending on the infection phase that is under consideration. Moreover, the complex interplay between the various immune cell populations that interact during infection and the high degree of genetic variation of certain pathogens, renders the identification of immune correlates of protection difficult. Some emerging and re-emerging viruses of high consequence for public health such as SARS-CoV-2, Nipah virus (NiV) and Ebola virus (EBOV) are especially challenging with regards to the identification of CoP since these pathogens have been shown to dysregulate the immune response during infection. Whereas, virus neutralising antibodies and polyfunctional T-cell responses have been shown to correlate with certain levels of protection against SARS-CoV-2, EBOV and NiV, other effector mechanisms of immunity play important roles in shaping the immune response against these pathogens, which in turn might serve as alternative correlates of protection. This review describes the different components of the adaptive and innate immune system that are activated during SARS-CoV-2, EBOV and NiV infections and that may contribute to protection and virus clearance. Overall, we highlight the immune signatures that are associated with protection against these pathogens in humans and could be used as CoP.
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Affiliation(s)
- Beatriz Escudero-Pérez
- WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Luebeck-Borstel-Reims, Braunschweig, Germany
- *Correspondence: Beatriz Escudero-Pérez, ; Javier Castillo-Olivares,
| | - Philip Lawrence
- CONFLUENCE: Sciences et Humanités (EA 1598), Université Catholique de Lyon (UCLy), Lyon, France
| | - Javier Castillo-Olivares
- Laboratory of Viral Zoonotics, University of Cambridge, Cambridge, United Kingdom
- *Correspondence: Beatriz Escudero-Pérez, ; Javier Castillo-Olivares,
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7
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Crook OM, Davies CTR, Breckels LM, Christopher JA, Gatto L, Kirk PDW, Lilley KS. Inferring differential subcellular localisation in comparative spatial proteomics using BANDLE. Nat Commun 2022; 13:5948. [PMID: 36216816 PMCID: PMC9550814 DOI: 10.1038/s41467-022-33570-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 09/20/2022] [Indexed: 11/08/2022] Open
Abstract
The steady-state localisation of proteins provides vital insight into their function. These localisations are context specific with proteins translocating between different subcellular niches upon perturbation of the subcellular environment. Differential localisation, that is a change in the steady-state subcellular location of a protein, provides a step towards mechanistic insight of subcellular protein dynamics. High-accuracy high-throughput mass spectrometry-based methods now exist to map the steady-state localisation and re-localisation of proteins. Here, we describe a principled Bayesian approach, BANDLE, that uses these data to compute the probability that a protein differentially localises upon cellular perturbation. Extensive simulation studies demonstrate that BANDLE reduces the number of both type I and type II errors compared to existing approaches. Application of BANDLE to several datasets recovers well-studied translocations. In an application to cytomegalovirus infection, we obtain insights into the rewiring of the host proteome. Integration of other high-throughput datasets allows us to provide the functional context of these data.
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Affiliation(s)
- Oliver M Crook
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, CB2 1GA, Cambridge, UK.
- MRC Biostatistics Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK.
- Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, CB2 0AW, UK.
| | - Colin T R Davies
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, CB2 1GA, Cambridge, UK
- Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, CB2 0AW, UK
- Mechanistic Biology and Profiling, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Lisa M Breckels
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, CB2 1GA, Cambridge, UK
- Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Josie A Christopher
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, CB2 1GA, Cambridge, UK
- Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Laurent Gatto
- de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200, Brussels, Belgium
| | - Paul D W Kirk
- MRC Biostatistics Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, CB2 1GA, Cambridge, UK.
- Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, CB2 0AW, UK.
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8
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Gemler BT, Mukherjee C, Howland CA, Huk D, Shank Z, Harbo LJ, Tabbaa OP, Bartling CM. Function-based classification of hazardous biological sequences: Demonstration of a new paradigm for biohazard assessments. Front Bioeng Biotechnol 2022; 10:979497. [PMID: 36277394 PMCID: PMC9585941 DOI: 10.3389/fbioe.2022.979497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 08/31/2022] [Indexed: 12/04/2022] Open
Abstract
Bioengineering applies analytical and engineering principles to identify functional biological building blocks for biotechnology applications. While these building blocks are leveraged to improve the human condition, the lack of simplistic, machine-readable definition of biohazards at the function level is creating a gap for biosafety practices. More specifically, traditional safety practices focus on the biohazards of known pathogens at the organism-level and may not accurately consider novel biodesigns with engineered functionalities at the genetic component-level. This gap is motivating the need for a paradigm shift from organism-centric procedures to function-centric biohazard identification and classification practices. To address this challenge, we present a novel methodology for classifying biohazards at the individual sequence level, which we then compiled to distinguish the biohazardous property of pathogenicity at the whole genome level. Our methodology is rooted in compilation of hazardous functions, defined as a set of sequences and associated metadata that describe coarse-level functions associated with pathogens (e.g., adherence, immune subversion). We demonstrate that the resulting database can be used to develop hazardous “fingerprints” based on the functional metadata categories. We verified that these hazardous functions are found at higher levels in pathogens compared to non-pathogens, and hierarchical clustering of the fingerprints can distinguish between these two groups. The methodology presented here defines the hazardous functions associated with bioengineering functional building blocks at the sequence level, which provide a foundational framework for classifying biological hazards at the organism level, thus leading to the improvement and standardization of current biosecurity and biosafety practices.
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9
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Halajian EA, LeBlanc EV, Gee K, Colpitts CC. Activation of TLR4 by viral glycoproteins: A double-edged sword? Front Microbiol 2022; 13:1007081. [PMID: 36246240 PMCID: PMC9557975 DOI: 10.3389/fmicb.2022.1007081] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 09/15/2022] [Indexed: 11/25/2022] Open
Abstract
Recognition of viral infection by pattern recognition receptors is paramount for a successful immune response to viral infection. However, an unbalanced proinflammatory response can be detrimental to the host. Recently, multiple studies have identified that the SARS-CoV-2 spike protein activates Toll-like receptor 4 (TLR4), resulting in the induction of proinflammatory cytokine expression. Activation of TLR4 by viral glycoproteins has also been observed in the context of other viral infection models, including respiratory syncytial virus (RSV), dengue virus (DENV) and Ebola virus (EBOV). However, the mechanisms involved in virus-TLR4 interactions have remained unclear. Here, we review viral glycoproteins that act as pathogen-associated molecular patterns to induce an immune response via TLR4. We explore the current understanding of the mechanisms underlying how viral glycoproteins are recognized by TLR4 and discuss the contribution of TLR4 activation to viral pathogenesis. We identify contentious findings and research gaps that highlight the importance of understanding viral glycoprotein-mediated TLR4 activation for potential therapeutic approaches.
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Affiliation(s)
| | | | - Katrina Gee
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, ON, Canada
| | - Che C. Colpitts
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, ON, Canada
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10
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de Oliveira Ribeiro G, Gill DE, do Socorro Foro Ramos E, Villanova F, Soares D’Athaide Ribeiro E, Monteiro FJC, Morais VS, Rego MODS, Araújo ELL, Pandey RP, Raj VS, Deng X, Delwart E, da Costa AC, Leal É. Chikungunya Virus Asian Lineage Infection in the Amazon Region Is Maintained by Asiatic and Caribbean-Introduced Variants. Viruses 2022; 14:v14071445. [PMID: 35891427 PMCID: PMC9319912 DOI: 10.3390/v14071445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/22/2022] [Accepted: 06/25/2022] [Indexed: 02/04/2023] Open
Abstract
The simultaneous transmission of two lineages of the chikungunya virus (CHIKV) was discovered after the pathogen’s initial arrival in Brazil. In Oiapoque (Amapá state, north Brazil), the Asian lineage (CHIKV-Asian) was discovered, while in Bahia state, the East-Central-South-African lineage (CHIKV-ECSA) was discovered (northeast Brazil). Since then, the CHIKV-Asian lineage has been restricted to the Amazon region (mostly in the state of Amapá), whereas the ECSA lineage has expanded across the country. Despite the fact that the Asian lineage was already present in the Amazon region, the ECSA lineage brought from the northeast caused a large outbreak in the Amazonian state of Roraima (north Brazil) in 2017. Here, CHIKV spread in the Amazon region was studied by a Zika–Dengue–Chikungunya PCR assay in 824 serum samples collected between 2013 and 2016 from individuals with symptoms of viral infection in the Amapá state. We found 11 samples positive for CHIKV-Asian, and, from these samples, we were able to retrieve 10 full-length viral genomes. A comprehensive phylogenetic study revealed that nine CHIKV sequences came from a local transmission cluster related to Caribbean strains, whereas one sequence was related to sequences from the Philippines. These findings imply that CHIKV spread in different ways in Roraima and Amapá, despite the fact that both states had similar climatic circumstances and mosquito vector frequencies.
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Affiliation(s)
- Geovani de Oliveira Ribeiro
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, Brazil; (G.d.O.R.); (E.d.S.F.R.); (F.V.)
| | - Danielle Elise Gill
- Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, Brazil; (D.E.G.); (V.S.M.); (A.C.d.C.)
| | - Endrya do Socorro Foro Ramos
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, Brazil; (G.d.O.R.); (E.d.S.F.R.); (F.V.)
| | - Fabiola Villanova
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, Brazil; (G.d.O.R.); (E.d.S.F.R.); (F.V.)
| | - Edcelha Soares D’Athaide Ribeiro
- Public Health Laboratory of Amapa-LACEN/AP, Health Surveillance Superintendence of Amapa, Macapa 68905-230, Brazil; (E.S.D.R.); (F.J.C.M.); (M.O.d.S.R.)
| | - Fred Julio Costa Monteiro
- Public Health Laboratory of Amapa-LACEN/AP, Health Surveillance Superintendence of Amapa, Macapa 68905-230, Brazil; (E.S.D.R.); (F.J.C.M.); (M.O.d.S.R.)
| | - Vanessa S. Morais
- Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, Brazil; (D.E.G.); (V.S.M.); (A.C.d.C.)
| | - Marlisson Octavio da S. Rego
- Public Health Laboratory of Amapa-LACEN/AP, Health Surveillance Superintendence of Amapa, Macapa 68905-230, Brazil; (E.S.D.R.); (F.J.C.M.); (M.O.d.S.R.)
| | - Emerson Luiz Lima Araújo
- General Coordination of Public Health, Laboratories of the Strategic Articulation, Department of the Health Surveillance Secretariat of the Ministry of Health (CGLAB/DAEVS/SVS-MS), Brasília 70719-040, Brazil;
| | - Ramendra Pati Pandey
- Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat 131029, Haryana, India; (R.P.P.); (V.S.R.); (E.D.)
| | - V. Samuel Raj
- Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat 131029, Haryana, India; (R.P.P.); (V.S.R.); (E.D.)
| | - Xutao Deng
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA 94118, USA;
- Department Laboratory Medicine, University of California San Francisco, San Francisco, CA 94118, USA
| | - Eric Delwart
- Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat 131029, Haryana, India; (R.P.P.); (V.S.R.); (E.D.)
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA 94118, USA;
| | - Antonio Charlys da Costa
- Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, Brazil; (D.E.G.); (V.S.M.); (A.C.d.C.)
| | - Élcio Leal
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, Brazil; (G.d.O.R.); (E.d.S.F.R.); (F.V.)
- Correspondence:
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11
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Harris JE. The repeated setbacks of HIV vaccine development laid the groundwork for SARS-CoV-2 vaccines. HEALTH POLICY AND TECHNOLOGY 2022; 11:100619. [PMID: 35340773 PMCID: PMC8935961 DOI: 10.1016/j.hlpt.2022.100619] [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] [Indexed: 11/18/2022]
Abstract
The decades-long effort to produce a workable HIV vaccine has hardly been a waste of public and private resources. To the contrary, the scientific know-how acquired along the way has served as the critical foundation for the development of vaccines against the novel, pandemic SARS-CoV-2 virus. We retell the real-world story of HIV vaccine research - with all its false leads and missteps - in a way that sheds light on the current state of the art of antiviral vaccines. We find that HIV-related R&D had more than a general spillover effect. In fact, the repeated failures of phase 2 and 3 clinical trials of HIV vaccine candidates have served as a critical stimulus to the development of successful vaccine technologies today. We rebut the counterargument that HIV vaccine development has been no more than a blind alley, and that recently developed vaccines against COVID-19 are really descendants of successful vaccines against Ebola, MERS, and SARS. These successful vaccines likewise owe much to the vicissitudes of HIV vaccine development. We then discuss how the failures of HIV vaccine development have taught us how adapt SARS-CoV-2 vaccines to immune escape from emerging variants. Finally, we inquire whether recent advances in the development of vaccines against SARS-CoV-2 might in turn further the development of an HIV vaccine - what we describe as a reverse spillover effect.
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Affiliation(s)
- Jeffrey E Harris
- Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- Eisner Health, Los Angeles, CA 90015, USA
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12
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Zhang Q, Yang J, Tillieux S, Guo Z, Natividade RDS, Koehler M, Petitjean S, Cui Z, Alsteens D. Stepwise Enzymatic-Dependent Mechanism of Ebola Virus Binding to Cell Surface Receptors Monitored by AFM. NANO LETTERS 2022; 22:1641-1648. [PMID: 35108019 DOI: 10.1021/acs.nanolett.1c04677] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Ebola virus (EBOV) is responsible for several outbreaks of hemorrhagic fever with high mortality, raising great public concern. Several cell surface receptors have been identified to mediate EBOV binding and internalization, including phosphatidylserine (PS) receptors (TIM-1) and C-type lectin receptors (DC-SIGNR). However, the role of TIM-1 during early cell surface binding remains elusive and in particular whether TIM-1 acts as a specific receptor for EBOV. Here, we used force-distance curve-based atomic force microscopy (FD-based AFM) to quantify the binding between TIM-1/DC-SIGNR and EBOV glycoprotein (GP) and observed that both receptors specifically bind to GP with high-affinity. Since TIM-1 can also directly interact with PS at the single-molecule level, we also confirmed that TIM-1 acts as dual-function receptors of EBOV. These results highlight the direct involvement of multiple high-affinity receptors in the first steps of binding to cell surfaces, thus offering new perspectives for the development of anti-EBOV therapeutic molecules.
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Affiliation(s)
- Qingrong Zhang
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve 1348, Belgium
| | - Jinsung Yang
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve 1348, Belgium
| | - Sueli Tillieux
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve 1348, Belgium
| | - Zhengyuan Guo
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China
| | - Rita Dos Santos Natividade
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve 1348, Belgium
| | - Melanie Koehler
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve 1348, Belgium
| | - Simon Petitjean
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve 1348, Belgium
| | - Zongqiang Cui
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China
| | - David Alsteens
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve 1348, Belgium
- Walloon Excellence in Life sciences and Biotechnology (WELBIO), Wavre 1300, Belgium
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13
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Ebola Virus GP Activates Endothelial Cells via Host Cytoskeletal Signaling Factors. Viruses 2022; 14:v14010142. [PMID: 35062347 PMCID: PMC8781776 DOI: 10.3390/v14010142] [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: 12/28/2021] [Accepted: 01/10/2022] [Indexed: 01/01/2023] Open
Abstract
Ebola virus disease (EVD) is a lethal disease caused by the highly pathogenic Ebola virus (EBOV), and its major symptoms in severe cases include vascular leakage and hemorrhage. These symptoms are caused by abnormal activation and disruption of endothelial cells (ECs) whose mediators include EBOV glycoprotein (GP) without the need for viral replication. However, the detailed molecular mechanisms underlying virus-host interactions remain largely unknown. Here, we show that EBOV-like particles (VLPs) formed by GP, VP40, and NP activate ECs in a GP-dependent manner, as demonstrated by the upregulation of intercellular adhesion molecules-1 (ICAM-1) expression. VLPs-mediated ECs activation showed a different kinetic pattern from that of TNF-α-mediated activation and was associated with apoptotic ECs disruption. In contrast to TNF-α, VLPs induced ICAM-1 overexpression at late time points. Furthermore, screening of host cytoskeletal signaling inhibitors revealed that focal adhesion kinase inhibitors were found to be potent inhibitors of ICAM-1 expression mediated by both TNF-α and VLPs. Our results suggest that EBOV GP stimulates ECs to induce endothelial activation and dysfunction with the involvement of host cytoskeletal signaling factors, which represent potential therapeutic targets for EVD.
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14
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Coutinho JVP, Macedo-da-Silva J, Mule SN, Kronenberger T, Rosa-Fernandes L, Wrenger C, Palmisano G. Glycoprotein molecular dynamics analysis: SARS-CoV-2 spike glycoprotein case study. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 131:277-309. [PMID: 35871894 PMCID: PMC9181370 DOI: 10.1016/bs.apcsb.2022.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Molecular Dynamics (MD) is a method used to calculate the movement of atoms and molecules broadly applied to several aspects of science. It involves computational simulation, which makes it, at first glance, not easily accessible. The rise of several automated tools to perform molecular simulations has allowed researchers to navigate through the various steps of MD. This enables to elucidate structural properties of proteins that could not be analyzed otherwise, such as the impact of glycosylation. Glycosylation dictates the physicochemical and biological properties of a protein modulating its solubility, stability, resistance to proteolysis, interaction partners, enzymatic activity, binding and recognition. Given the high conformational and compositional diversity of the glycan chains, assessing their influence on the protein structure is challenging using conventional analytical techniques. In this manuscript, we present a step-by-step workflow to build and perform MD analysis of glycoproteins focusing on the SPIKE glycoprotein of SARS-CoV-2 to appraise the impact of glycans in structure stabilization and antibody occlusion.
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Affiliation(s)
| | - Janaina Macedo-da-Silva
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Simon Ngao Mule
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Thales Kronenberger
- Department of Internal Medicine VIII, University Hospital Tuebingen, Tuebingen, Germany,Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard-Karls-Universität, Tuebingen, Germany,Cluster of Excellence iFIT (EXC 2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tuebingen, Tuebingen, Germany,Tuebingen Center for Academic Drug Discovery & Development (TüCAD2), Tuebingen, Germany
| | - Livia Rosa-Fernandes
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Carsten Wrenger
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Giuseppe Palmisano
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil,Faculty of Science and engineering, Macquarie University, Sydney, NSW, Australia,Corresponding author:
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15
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Kumari M, Tetala KKR. A review on recent advances in the enrichment of glycopeptides and glycoproteins by liquid chromatographic methods: 2016-Present. Electrophoresis 2021; 43:388-402. [PMID: 34757643 DOI: 10.1002/elps.202100172] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 11/05/2021] [Accepted: 11/06/2021] [Indexed: 01/06/2023]
Abstract
Among various protein post-translational modifications (PTMs), glycosylation has received special attention due to its immense role in molecular interactions, cellular signal transduction, immune response, etc. Aberration in glycan moieties of a glycoprotein is associated with cancer, diabetes, and bacterial and viral infections. In biofluids (plasma, saliva, urine, milk, etc.), glycoproteins are low in abundance and are masked by the presence of high abundant proteins. Hence, prior to their identification using mass spectrometry methods, liquid chromatography (LC)-based approaches were widely used. A general enrichment strategy involves a protein digestion step, followed by LC-based enrichment and desorption of glycopeptides, and enzymatic excision of the glycans. The focus of this review article is to highlight the articles published since 2016 that dealt with different LC-based approaches for glycopeptide and glycoprotein enrichment. The preparation of stationary phases, their surface activation, and ligand immobilization strategies have been discussed in detail. Finally, the major developments and future trends in the field have been summarized.
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Affiliation(s)
- Mona Kumari
- Centre for Bioseparation Technology (CBST), Vellore Institute of Technology (VIT), Vellore, Tamilnadu, India
| | - Kishore K R Tetala
- Centre for Bioseparation Technology (CBST), Vellore Institute of Technology (VIT), Vellore, Tamilnadu, India
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16
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Structural and Functional Aspects of Ebola Virus Proteins. Pathogens 2021; 10:pathogens10101330. [PMID: 34684279 PMCID: PMC8538763 DOI: 10.3390/pathogens10101330] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/11/2021] [Accepted: 10/14/2021] [Indexed: 01/14/2023] Open
Abstract
Ebola virus (EBOV), member of genus Ebolavirus, family Filoviridae, have a non-segmented, single-stranded RNA that contains seven genes: (a) nucleoprotein (NP), (b) viral protein 35 (VP35), (c) VP40, (d) glycoprotein (GP), (e) VP30, (f) VP24, and (g) RNA polymerase (L). All genes encode for one protein each except GP, producing three pre-proteins due to the transcriptional editing. These pre-proteins are translated into four products, namely: (a) soluble secreted glycoprotein (sGP), (b) Δ-peptide, (c) full-length transmembrane spike glycoprotein (GP), and (d) soluble small secreted glycoprotein (ssGP). Further, shed GP is released from infected cells due to cleavage of GP by tumor necrosis factor α-converting enzyme (TACE). This review presents a detailed discussion on various functional aspects of all EBOV proteins and their residues. An introduction to ebolaviruses and their life cycle is also provided for clarity of the available analysis. We believe that this review will help understand the roles played by different EBOV proteins in the pathogenesis of the disease. It will help in targeting significant protein residues for therapeutic and multi-protein/peptide vaccine development.
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17
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Thornlow DN, Macintyre AN, Oguin TH, Karlsson AB, Stover EL, Lynch HE, Sempowski GD, Schmidt AG. Altering the Immunogenicity of Hemagglutinin Immunogens by Hyperglycosylation and Disulfide Stabilization. Front Immunol 2021; 12:737973. [PMID: 34691043 PMCID: PMC8528956 DOI: 10.3389/fimmu.2021.737973] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 09/20/2021] [Indexed: 11/13/2022] Open
Abstract
Influenza virus alters glycosylation patterns on its surface exposed glycoproteins to evade host adaptive immune responses. The viral hemagglutinin (HA), in particular the H3 subtype, has increased its overall surface glycosylation since its introduction in 1968. We previously showed that modulating predicted N-linked glycosylation sites on H3 A/Hong Kong/1/1968 HA identified a conserved epitope at the HA interface. This epitope is occluded on the native HA trimer but is likely exposed during HA "breathing" on the virion surface. Antibodies directed to this site are protective via an ADCC-mediated mechanism. This glycan engineering strategy made an otherwise subdominant epitope dominant in the murine model. Here, we asked whether cysteine stabilization of the hyperglycosylated HA trimer could reverse this immunodominance by preventing access to the interface epitope and focus responses to the HA receptor binding site (RBS). While analysis of serum responses from immunized mice did not show a redirection to the RBS, cysteine stabilization did result in an overall reduction in immunogenicity of the interface epitope. Thus, glycan engineering and cysteine stabilization are two strategies that can be used together to alter immunodominance patterns to HA. These results add to rational immunogen design approaches used to manipulate immune responses for the development of next-generation influenza vaccines.
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Affiliation(s)
- Dana N. Thornlow
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, United States
- Department of Microbiology, Harvard Medical School, Boston, MA, United States
| | - Andrew N. Macintyre
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
| | - Thomas H. Oguin
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
| | - Amelia B. Karlsson
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
| | - Erica L. Stover
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
| | - Heather E. Lynch
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
| | - Gregory D. Sempowski
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
- Departments of Medicine and Pathology, Duke University School of Medicine, Durham, NC, United States
| | - Aaron G. Schmidt
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, United States
- Department of Microbiology, Harvard Medical School, Boston, MA, United States
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18
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Hu Z, Liu X. "Antigen Camouflage and Decoy" Strategy to Overcome Interference From Maternally Derived Antibody With Newcastle Disease Virus-Vectored Vaccines: More Than a Simple Combination. Front Microbiol 2021; 12:735250. [PMID: 34512613 PMCID: PMC8432293 DOI: 10.3389/fmicb.2021.735250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 08/09/2021] [Indexed: 11/29/2022] Open
Affiliation(s)
- Zenglei Hu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Xiufan Liu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China.,Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, China.,Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
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19
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Schön K, Lepenies B, Goyette-Desjardins G. Impact of Protein Glycosylation on the Design of Viral Vaccines. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2021; 175:319-354. [PMID: 32935143 DOI: 10.1007/10_2020_132] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Glycans play crucial roles in various biological processes such as cell proliferation, cell-cell interactions, and immune responses. Since viruses co-opt cellular biosynthetic pathways, viral glycosylation mainly depends on the host cell glycosylation machinery. Consequently, several viruses exploit the cellular glycosylation pathway to their advantage. It was shown that viral glycosylation is strongly dependent on the host system selected for virus propagation and/or protein expression. Therefore, the use of different expression systems results in various glycoforms of viral glycoproteins that may differ in functional properties. These differences clearly illustrate that the choice of the expression system can be important, as the resulting glycosylation may influence immunological properties. In this review, we will first detail protein N- and O-glycosylation pathways and the resulting glycosylation patterns; we will then discuss different aspects of viral glycosylation in pathogenesis and in vaccine development; and finally, we will elaborate on how to harness viral glycosylation in order to optimize the design of viral vaccines. To this end, we will highlight specific examples to demonstrate how glycoengineering approaches and exploitation of different expression systems could pave the way towards better self-adjuvanted glycan-based viral vaccines.
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Affiliation(s)
- Kathleen Schön
- Immunology Unit and Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Hanover, Germany
- Institute for Parasitology, Centre for Infection Medicine, University of Veterinary Medicine Hannover, Hanover, Germany
| | - Bernd Lepenies
- Immunology Unit and Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Hanover, Germany.
| | - Guillaume Goyette-Desjardins
- Immunology Unit and Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Hanover, Germany.
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20
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Li Y, Liu D, Wang Y, Su W, Liu G, Dong W. The Importance of Glycans of Viral and Host Proteins in Enveloped Virus Infection. Front Immunol 2021; 12:638573. [PMID: 33995356 PMCID: PMC8116741 DOI: 10.3389/fimmu.2021.638573] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 04/15/2021] [Indexed: 12/15/2022] Open
Abstract
Animal viruses are parasites of animal cells that have characteristics such as heredity and replication. Viruses can be divided into non-enveloped and enveloped viruses if a lipid bilayer membrane surrounds them or not. All the membrane proteins of enveloped viruses that function in attachment to target cells or membrane fusion are modified by glycosylation. Glycosylation is one of the most common post-translational modifications of proteins and plays an important role in many biological behaviors, such as protein folding and stabilization, virus attachment to target cell receptors and inhibition of antibody neutralization. Glycans of the host receptors can also regulate the attachment of the viruses and then influence the virus entry. With the development of glycosylation research technology, the research and development of novel virus vaccines and antiviral drugs based on glycan have received increasing attention. Here, we review the effects of host glycans and viral proteins on biological behaviors of viruses, and the opportunities for prevention and treatment of viral infectious diseases.
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Affiliation(s)
- Yuqing Li
- Department of Biochemistry and Molecular Biology, Institute of Glycobiology, Dalian Medical University, Dalian, China
| | - Dongqi Liu
- The Queen's University of Belfast Joint College, China Medical University, Shenyang, China
| | - Yating Wang
- Department of Biochemistry and Molecular Biology, Institute of Glycobiology, Dalian Medical University, Dalian, China
| | - Wenquan Su
- Dalian Medical University, Dalian, China
| | - Gang Liu
- Department of Biochemistry and Molecular Biology, Institute of Glycobiology, Dalian Medical University, Dalian, China
| | - Weijie Dong
- Department of Biochemistry and Molecular Biology, Institute of Glycobiology, Dalian Medical University, Dalian, China
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21
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Convergence of a common solution for broad ebolavirus neutralization by glycan cap-directed human antibodies. Cell Rep 2021; 35:108984. [PMID: 33852862 PMCID: PMC8133395 DOI: 10.1016/j.celrep.2021.108984] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 02/19/2021] [Accepted: 03/23/2021] [Indexed: 11/23/2022] Open
Abstract
Antibodies that target the glycan cap epitope on the ebolavirus glycoprotein (GP) are common in the adaptive response of survivors. A subset is known to be broadly neutralizing, but the details of their epitopes and basis for neutralization are not well understood. Here, we present cryoelectron microscopy (cryo-EM) structures of diverse glycan cap antibodies that variably synergize with GP base-binding antibodies. These structures describe a conserved site of vulnerability that anchors the mucin-like domains (MLDs) to the glycan cap, which we call the MLD anchor and cradle. Antibodies that bind to the MLD cradle share common features, including use of IGHV1–69 and IGHJ6 germline genes, which exploit hydrophobic residues and form β-hairpin structures to mimic the MLD anchor, disrupt MLD attachment, destabilize GP quaternary structure, and block cleavage events required for receptor binding. Our results provide a molecular basis for ebolavirus neutralization by broadly reactive glycan cap antibodies. A rare subset of ebolavirus antibodies targeting the glycan cap are broadly neutralizing. Murin et al. report cryo-EM structures and custom in vitro assays identifying a conserved site of vulnerability in the glycan cap and detail mechanisms of action, including structural mimicry, trimer instability, and blocking cleavage.
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22
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Armaly Z, Kinaneh S, Skorecki K. Renal Manifestations of Covid-19: Physiology and Pathophysiology. J Clin Med 2021; 10:1216. [PMID: 33804075 PMCID: PMC8000200 DOI: 10.3390/jcm10061216] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/09/2021] [Accepted: 03/11/2021] [Indexed: 02/07/2023] Open
Abstract
Corona virus disease 2019 (COVID-19) imposes a serious public health pandemic affecting the whole world, as it is spreading exponentially. Besides its high infectivity, SARS-CoV-2 causes multiple serious derangements, where the most prominent is severe acute respiratory syndrome as well as multiple organ dysfunction including heart and kidney injury. While the deleterious impact of SARS-CoV-2 on pulmonary and cardiac systems have attracted remarkable attention, the adverse effects of this virus on the renal system is still underestimated. Kidney susceptibility to SARS-CoV-2 infection is determined by the presence of angiotensin-converting enzyme 2 (ACE2) receptor which is used as port of the viral entry into targeted cells, tissue tropism, pathogenicity and subsequent viral replication. The SARS-CoV-2 cellular entry receptor, ACE2, is widely expressed in proximal epithelial cells, vascular endothelial and smooth muscle cells and podocytes, where it supports kidney integrity and function via the enzymatic production of Angiotensin 1-7 (Ang 1-7), which exerts vasodilatory, anti-inflammatory, antifibrotic and diuretic/natriuretic actions via activation of the Mas receptor axis. Loss of this activity constitutes the potential basis for the renal damage that occurs in COVID-19 patients. Indeed, several studies in a small sample of COVID-19 patients revealed relatively high incidence of acute kidney injury (AKI) among them. Although SARS-CoV-1 -induced AKI was attributed to multiorgan failure and cytokine release syndrome, as the virus was not detectable in the renal tissue of infected patients, SARS-CoV-2 antigens were detected in kidney tubules, suggesting that SARS-CoV-2 infects the human kidney directly, and eventually induces AKI characterized with high morbidity and mortality. The mechanisms underlying this phenomenon are largely unknown. However, the fact that ACE2 plays a crucial role against renal injury, the deprivation of the kidney of this advantageous enzyme, along with local viral replication, probably plays a central role. The current review focuses on the critical role of ACE2 in renal physiology, its involvement in the development of kidney injury during SARS-CoV-2 infection, renal manifestations and therapeutic options. The latter includes exogenous administration of Ang (1-7) as an appealing option, given the high incidence of AKI in this ACE2-depleted disorder, and the benefits of ACE2/Ang1-7 including vasodilation, diuresis, natriuresis, attenuation of inflammation, oxidative stress, cell proliferation, apoptosis and coagulation.
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Affiliation(s)
- Zaher Armaly
- Department of Nephrology, Nazareth Hospital, EMMS, Nazareth 16100, Israel;
- The Bar-Ilan University Azrieli Faculty of Medicine, Safed 1311502, Israel;
| | - Safa Kinaneh
- Department of Nephrology, Nazareth Hospital, EMMS, Nazareth 16100, Israel;
| | - Karl Skorecki
- The Bar-Ilan University Azrieli Faculty of Medicine, Safed 1311502, Israel;
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Pathania AS, Prathipati P, Abdul BAA, Chava S, Katta SS, Gupta SC, Gangula PR, Pandey MK, Durden DL, Byrareddy SN, Challagundla KB. COVID-19 and Cancer Comorbidity: Therapeutic Opportunities and Challenges. Theranostics 2021; 11:731-753. [PMID: 33391502 PMCID: PMC7738845 DOI: 10.7150/thno.51471] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 10/12/2020] [Indexed: 01/07/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) is a viral disease caused by a novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that affects the respiratory system of infected individuals. COVID-19 spreads between humans through respiratory droplets produced when an infected person coughs or sneezes. The COVID-19 outbreak originated in Wuhan, China at the end of 2019. As of 29 Sept 2020, over 235 countries, areas or territories across the globe reported a total of 33,441,919 confirmed cases, and 1,003,497 confirmed deaths due to COVID-19. Individuals of all ages are at risk for infection, but in most cases disease severity is associated with age and pre-existing diseases that compromise immunity, like cancer. Numerous reports suggest that people with cancer can be at higher risk of severe illness and related deaths from COVID-19. Therefore, managing cancer care under this pandemic is challenging and requires a collaborative multidisciplinary approach for optimal care of cancer patients in hospital settings. In this comprehensive review, we discuss the impact of the COVID-19 pandemic on cancer patients, their care, and treatment. Further, this review covers the SARS-CoV-2 pandemic, genome characterization, COVID-19 pathophysiology, and associated signaling pathways in cancer, and the choice of anticancer agents as repurposed drugs for treating COVID-19.
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Affiliation(s)
- Anup S. Pathania
- Department of Biochemistry and Molecular Biology & The Fred and Pamela Buffett Cancer Center; University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Philip Prathipati
- Laboratory of Bioinformatics, National Institutes of Biomedical Innovation, Health and Nutrition, Saito-Asagi Ibaraki City, Osaka 567-0085, Japan
| | - Bakrudeen AA. Abdul
- Department of Biochemistry, Center for Research & Development, PRIST Deemed University, Vallam, Tamil Nadu 613403, India
| | - Srinivas Chava
- Department of Biochemistry and Molecular Biology & The Fred and Pamela Buffett Cancer Center; University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Santharam S. Katta
- Department of Biotechnology, School of Applied Sciences, REVA University, Rukmini Knowledge Park Kattigenahalli, Yelahanka, Bangalore, Karnataka 560064, India
| | - Subash C. Gupta
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Pandu R. Gangula
- Department of Oral Diagnostic Sciences and Research, School of Dentistry, Meharry Medical College, Nashville, TN 37208, USA
| | - Manoj K. Pandey
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, NJ 08103, USA
| | - Donald L. Durden
- Levine Cancer Institute, Atrium Health, Charlotte, NC 28202, USA
- Department of Pediatrics, University of California, San Diego, San Diego, CA 92093, USA
- SignalRx Pharmaceuticals, Omaha, NE 68124, USA
| | - Siddappa N. Byrareddy
- Department of Biochemistry and Molecular Biology & The Fred and Pamela Buffett Cancer Center; University of Nebraska Medical Center, Omaha, NE 68198, USA
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Kishore B. Challagundla
- Department of Biochemistry and Molecular Biology & The Fred and Pamela Buffett Cancer Center; University of Nebraska Medical Center, Omaha, NE 68198, USA
- The Children's Health Research Institute, University of Nebraska Medical Center, Omaha, NE, 68198, USA
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Characterization of rVSVΔG-ZEBOV-GP glycoproteins using automated capillary western blotting. Vaccine 2020; 38:7166-7174. [DOI: 10.1016/j.vaccine.2020.08.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 07/25/2020] [Accepted: 08/01/2020] [Indexed: 12/16/2022]
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MARCH8 Inhibits Ebola Virus Glycoprotein, Human Immunodeficiency Virus Type 1 Envelope Glycoprotein, and Avian Influenza Virus H5N1 Hemagglutinin Maturation. mBio 2020; 11:mBio.01882-20. [PMID: 32934085 PMCID: PMC7492737 DOI: 10.1128/mbio.01882-20] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Enveloped viruses express three classes of fusion proteins that are required for their entry into host cells via mediating virus and cell membrane fusion. Class I fusion proteins are produced from influenza viruses, retroviruses, Ebola viruses, and coronaviruses. They are first synthesized as a type I transmembrane polypeptide precursor that is subsequently glycosylated and oligomerized. Most of these precursors are cleaved en route to the plasma membrane by a cellular protease furin in the late secretory pathway, generating the trimeric N-terminal receptor-binding and C-terminal fusion subunits. Here, we show that a cellular protein, MARCH8, specifically inhibits the furin-mediated cleavage of EBOV GP, HIV-1 Env, and H5N1 HA. Further analyses uncovered that MARCH8 blocked the EBOV GP glycosylation in the Golgi and inhibited its transport from the Golgi to the plasma membrane. Thus, MARCH8 has a very broad antiviral activity by specifically inactivating different viral fusion proteins. Membrane-associated RING-CH-type 8 (MARCH8) strongly blocks human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein (Env) incorporation into virions by downregulating its cell surface expression, but the mechanism is still unclear. We now report that MARCH8 also blocks the Ebola virus (EBOV) glycoprotein (GP) incorporation via surface downregulation. To understand how these viral fusion proteins are downregulated, we investigated the effects of MARCH8 on EBOV GP maturation and externalization via the conventional secretion pathway. MARCH8 interacted with EBOV GP and furin when detected by immunoprecipitation and retained the GP/furin complex in the Golgi when their location was tracked by a bimolecular fluorescence complementation (BiFC) assay. MARCH8 did not reduce the GP expression or affect the GP modification by high-mannose N-glycans in the endoplasmic reticulum (ER), but it inhibited the formation of complex N-glycans on the GP in the Golgi. Additionally, the GP O-glycosylation and furin-mediated proteolytic cleavage were also inhibited. Moreover, we identified a novel furin cleavage site on EBOV GP and found that only those fully glycosylated GPs were processed by furin and incorporated into virions. Furthermore, the GP shedding and secretion were all blocked by MARCH8. MARCH8 also blocked the furin-mediated cleavage of HIV-1 Env (gp160) and the highly pathogenic avian influenza virus H5N1 hemagglutinin (HA). We conclude that MARCH8 has a very broad antiviral activity by prohibiting different viral fusion proteins from glycosylation and proteolytic cleavage in the Golgi, which inhibits their transport from the Golgi to the plasma membrane and incorporation into virions.
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Piñana M, Vila J, Maldonado C, Galano-Frutos JJ, Valls M, Sancho J, Nuvials FX, Andrés C, Martín-Gómez MT, Esperalba J, Codina MG, Pumarola T, Antón A. Insights into immune evasion of human metapneumovirus: novel 180- and 111-nucleotide duplications within viral G gene throughout 2014-2017 seasons in Barcelona, Spain. J Clin Virol 2020; 132:104590. [PMID: 32957052 PMCID: PMC7418790 DOI: 10.1016/j.jcv.2020.104590] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 07/24/2020] [Accepted: 08/10/2020] [Indexed: 11/30/2022]
Abstract
HMPV has a prevalence of 3%, affecting equally children and adults. 180- and 111-nucleotide duplications emerged, increasing in prevalence over seasons. G proteins w/ duplications protruded more from the membrane than w/o duplication. Viruses w/ duplications were more associated to LRTI in adults than w/o duplication. These facts suggest these duplications might enhance an immune evasion mechanism
Background Human metapneumovirus (HMPV) is an important aetiologic agent of respiratory tract infection (RTI). This study aimed to describe its genetic diversity and clinical impact in patients attended at a tertiary university hospital in Barcelona from the 2014-2015 to the 2016-2017 seasons, focusing on the emerging duplications in G gene and their structural properties. Methods Laboratory-confirmed HMPV were characterised based on partial-coding F and G gene sequences with MEGA.v6.0. Computational analysis of disorder propensity, aggregation propensity and glycosylation sites in viral G predicted protein sequence were carried out. Clinical data was retrospectively reviewed and further associated to virological features. Results HMPV prevalence was 3%. The 180- and 111-nucleotide duplications occurred in A2c lineage G protein increased in prevalence throughout the study, in addition to short genetic changes observed in other HMPV lineages. The A2c G protein without duplications was calculated to protrude over F protein in 23% of cases and increased to a 39% and a 46% with the 111- and 180-nucleotide duplications, respectively. Children did not seem to be more affected by these mutant viruses, but there was a strong association of these variants to LRTI in adults. Discussion HMPV presents a high genetic diversity in all lineages. Novel variants carrying duplications might present an evolutionary advantage due to an improved steric shielding, which would have been responsible for the reported increasing prevalence and the association to LRTI in adults.
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Affiliation(s)
- Maria Piñana
- Respiratory Viruses Unit, Microbiology Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Jorgina Vila
- Paediatric Hospitalization Unit, Paediatrics Department, Hospital Universitari Maternoinfantil Vall d'Hebron, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Carolina Maldonado
- Intensive Care Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Juan José Galano-Frutos
- Biochemistry and Molecular and Cell Biology Department, Sciences Faculty, Universidad de Zaragoza, Zaragoza, Spain; Biocomputation and Complex Systems Physics Institute (BIFI). Joint Units BIFI-IQFR (CSIC) and GBs-CSIC, Universidad de Zaragoza, Zaragoza, Spain
| | - Maria Valls
- Paediatric Hospitalization Unit, Paediatrics Department, Hospital Universitari Maternoinfantil Vall d'Hebron, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Javier Sancho
- Biochemistry and Molecular and Cell Biology Department, Sciences Faculty, Universidad de Zaragoza, Zaragoza, Spain; Biocomputation and Complex Systems Physics Institute (BIFI). Joint Units BIFI-IQFR (CSIC) and GBs-CSIC, Universidad de Zaragoza, Zaragoza, Spain; Aragon Health Research Institute (IIS Aragón), Zaragoza, Spain
| | - Francesc Xavier Nuvials
- Intensive Care Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Cristina Andrés
- Respiratory Viruses Unit, Microbiology Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - María Teresa Martín-Gómez
- Respiratory Viruses Unit, Microbiology Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Juliana Esperalba
- Respiratory Viruses Unit, Microbiology Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Maria Gema Codina
- Respiratory Viruses Unit, Microbiology Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Tomàs Pumarola
- Respiratory Viruses Unit, Microbiology Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain.
| | - Andrés Antón
- Respiratory Viruses Unit, Microbiology Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
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Julia da Silva Pessoa Vieira C, José Ferreira da Silva D, Rigotti Kubiszeski J, Ceschini Machado L, Pena LJ, Vieira de Morais Bronzoni R, da Luz Wallau G. The Emergence of Chikungunya ECSA Lineage in a Mayaro Endemic Region on the Southern Border of the Amazon Forest. Trop Med Infect Dis 2020; 5:E105. [PMID: 32604785 PMCID: PMC7345197 DOI: 10.3390/tropicalmed5020105] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/17/2020] [Accepted: 06/19/2020] [Indexed: 12/13/2022] Open
Abstract
Anthropic changes on the edges of the tropical forests may facilitate the emergence of new viruses from the sylvatic environment and the simultaneous circulation of sylvatic and urban viruses in the human population. In this study, we investigated the presence of arboviruses (arthropod-borne viruses) in the sera of 354 patients, sampled from February 2014 to October 2018 in Sinop city. We sequenced the complete genomes of one chikungunya virus (CHIKV)-positive and one out of the 33 Mayaro virus (MAYV)-positive samples. The CHIKV genome obtained here belongs to the East/Central/South African (ECSA) genotype and the MAYV genome belongs to the L genotype. These genomes clustered with other viral strains from different Brazilian states, but the CHIKV strain circulating in Sinop did not cluster with other genomes from the Mato Grosso state, suggesting that at least two independent introductions of this virus occurred in Mato Grosso. Interestingly, the arrival of CHIKV in Sinop seems to not have caused a surge in human cases in the following years, as observed in the rest of the state, suggesting that cross immunity from MAYV infection might be protecting the population from CHIKV infection. These findings reinforce the need for continued genomic surveillance in order to evaluate how simultaneously circulating alphaviruses infecting the human population will unfold.
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Affiliation(s)
- Carla Julia da Silva Pessoa Vieira
- Health Sciences Institute, Federal University of Mato Grosso, Sinop 78550-728, MT, Brazil; (C.J.d.S.P.V.); (D.J.F.d.S.); (J.R.K.); (R.V.d.M.B.)
| | - David José Ferreira da Silva
- Health Sciences Institute, Federal University of Mato Grosso, Sinop 78550-728, MT, Brazil; (C.J.d.S.P.V.); (D.J.F.d.S.); (J.R.K.); (R.V.d.M.B.)
| | - Janaína Rigotti Kubiszeski
- Health Sciences Institute, Federal University of Mato Grosso, Sinop 78550-728, MT, Brazil; (C.J.d.S.P.V.); (D.J.F.d.S.); (J.R.K.); (R.V.d.M.B.)
| | - Laís Ceschini Machado
- Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife 50670-420, PE, Brazil; (L.C.M.); (L.J.P.)
| | - Lindomar José Pena
- Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife 50670-420, PE, Brazil; (L.C.M.); (L.J.P.)
| | - Roberta Vieira de Morais Bronzoni
- Health Sciences Institute, Federal University of Mato Grosso, Sinop 78550-728, MT, Brazil; (C.J.d.S.P.V.); (D.J.F.d.S.); (J.R.K.); (R.V.d.M.B.)
| | - Gabriel da Luz Wallau
- Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife 50670-420, PE, Brazil; (L.C.M.); (L.J.P.)
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Hariharan V, Kane RS. Glycosylation as a tool for rational vaccine design. Biotechnol Bioeng 2020; 117:2556-2570. [PMID: 32330286 DOI: 10.1002/bit.27361] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 04/01/2020] [Accepted: 04/22/2020] [Indexed: 12/31/2022]
Abstract
The discovery of broadly neutralizing antibodies that can neutralize multiple strains or subtypes of a pathogen has renewed interest in the development of broadly protective vaccines. To that end, there has been an interest in designing immunofocusing strategies to direct the immune response to specific, conserved regions on antigenic proteins. Modulation of glycosylation is one such immunofocusing strategy; extensive glycosylation is often exploited by pathogens for immune evasion. Masking epitopes on protein immunogens with "self" glycans can also shield the underlying protein surface from humoral immune surveillance. We review recent advances in applying glycosylation as an immunofocusing tool. We also highlight recent interesting work in the HIV-1 field involving the identification and elicitation of broadly neutralizing antibodies that incorporate glycans into their binding epitopes.
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Affiliation(s)
- Vivek Hariharan
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia
| | - Ravi S Kane
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia
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van Bilsen JHM, Dulos R, van Stee MF, Meima MY, Rouhani Rankouhi T, Neergaard Jacobsen L, Staudt Kvistgaard A, Garthoff JA, Knippels LMJ, Knipping K, Houben GF, Verschuren L, Meijerink M, Krishnan S. Seeking Windows of Opportunity to Shape Lifelong Immune Health: A Network-Based Strategy to Predict and Prioritize Markers of Early Life Immune Modulation. Front Immunol 2020; 11:644. [PMID: 32362896 PMCID: PMC7182036 DOI: 10.3389/fimmu.2020.00644] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 03/20/2020] [Indexed: 01/01/2023] Open
Abstract
A healthy immune status is strongly conditioned during early life stages. Insights into the molecular drivers of early life immune development and function are prerequisite to identify strategies to enhance immune health. Even though several starting points for targeted immune modulation have been identified and are being developed into prophylactic or therapeutic approaches, there is no regulatory guidance on how to assess the risk and benefit balance of such interventions. Six early life immune causal networks, each compromising a different time period in early life (the 1st, 2nd, 3rd trimester of gestations, birth, newborn, and infant period), were generated. Thereto information was extracted and structured from early life literature using the automated text mining and machine learning tool: Integrated Network and Dynamical Reasoning Assembler (INDRA). The tool identified relevant entities (e.g., genes/proteins/metabolites/processes/diseases), extracted causal relationships among these entities, and assembled them into early life-immune causal networks. These causal early life immune networks were denoised using GeneMania, enriched with data from the gene-disease association database DisGeNET and Gene Ontology resource tools (GO/GO-SLIM), inferred missing relationships and added expert knowledge to generate information-dense early life immune networks. Analysis of the six early life immune networks by PageRank, not only confirmed the central role of the "commonly used immune markers" (e.g., chemokines, interleukins, IFN, TNF, TGFB, and other immune activation regulators (e.g., CD55, FOXP3, GATA3, CD79A, C4BPA), but also identified less obvious candidates (e.g., CYP1A2, FOXK2, NELFCD, RENBP). Comparison of the different early life periods resulted in the prediction of 11 key early life genes overlapping all early life periods (TNF, IL6, IL10, CD4, FOXP3, IL4, NELFCD, CD79A, IL5, RENBP, and IFNG), and also genes that were only described in certain early life period(s). Concluding, here we describe a network-based approach that provides a science-based and systematical method to explore the functional development of the early life immune system through time. This systems approach aids the generation of a testing strategy for the safety and efficacy of early life immune modulation by predicting the key candidate markers during different phases of early life immune development.
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Affiliation(s)
| | - Remon Dulos
- Netherlands Organisation for Applied Scientific Research (TNO), Zeist, Netherlands
| | - Mariël F van Stee
- Netherlands Organisation for Applied Scientific Research (TNO), Zeist, Netherlands
| | - Marie Y Meima
- Netherlands Organisation for Applied Scientific Research (TNO), Zeist, Netherlands
| | | | | | | | | | - Léon M J Knippels
- Danone Nutricia Research, Utrecht, Netherlands.,Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands
| | - Karen Knipping
- Danone Nutricia Research, Utrecht, Netherlands.,Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands
| | - Geert F Houben
- Netherlands Organisation for Applied Scientific Research (TNO), Zeist, Netherlands
| | - Lars Verschuren
- Netherlands Organisation for Applied Scientific Research (TNO), Zeist, Netherlands
| | - Marjolein Meijerink
- Netherlands Organisation for Applied Scientific Research (TNO), Zeist, Netherlands
| | - Shaji Krishnan
- Netherlands Organisation for Applied Scientific Research (TNO), Zeist, Netherlands
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X-ray Structures of the Post-fusion 6-Helix Bundle of the Human Syncytins and their Functional Implications. J Mol Biol 2019; 431:4922-4940. [PMID: 31711961 PMCID: PMC7094397 DOI: 10.1016/j.jmb.2019.10.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 10/22/2019] [Accepted: 10/23/2019] [Indexed: 12/27/2022]
Abstract
The retroviral envelope-derived proteins syncytin-1 and syncytin-2 (syn1 and syn2) drive placentation in humans by forming a syncytiotophoblast, a structure allowing for an exchange interface between maternal and fetal blood during pregnancy. Despite their essential role, little is known about the molecular mechanism underlying the syncytins' function. We report here the X-ray structures of the syn1 and syn2 transmembrane subunit ectodomains, featuring a 6-helix bundle (6HB) typical of the post-fusion state of gamma-retrovirus and filovirus fusion proteins. Contrary to the filoviruses, for which the fusion glycoprotein was crystallized both in the post-fusion and in the spring-loaded pre-fusion form, the highly unstable nature of the syncytins' prefusion form has precluded structural studies. We undertook a proline-scanning approach searching for regions in the syn1 6HB central helix that tolerate the introduction of helix-breaker residues and still fold correctly in the pre-fusion form. We found that there is indeed such a region, located two α-helical turns downstream a stutter in the central coiled-coil helix - precisely where the breaks of the spring-loaded helix of the filoviruses map. These mutants were fusion-inactive as they cannot form the 6HB, similar to the “SOSIP” mutant of HIV Env that allowed the high-resolution structural characterization of its labile pre-fusion form. These results now open a new window of opportunity to engineer more stable variants of the elusive pre-fusion trimer of the syncytins and other gamma-retroviruses envelope proteins for structural characterization. A typical retroviral γ-type Env protein 6-helix bundle in post-fusion syncytins. An extensive ionic interactions network correlates with higher stability of syn1. Spring-loaded pre-fusion form hinted by structural homology with filoviruses. Helix-breaking residues in the central coiled-coil allow folding in pre-fusion form.
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Zhu W, Banadyga L, Emeterio K, Wong G, Qiu X. The Roles of Ebola Virus Soluble Glycoprotein in Replication, Pathogenesis, and Countermeasure Development. Viruses 2019; 11:v11110999. [PMID: 31683550 PMCID: PMC6893644 DOI: 10.3390/v11110999] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 10/28/2019] [Accepted: 10/29/2019] [Indexed: 12/30/2022] Open
Abstract
Ebola virus (EBOV) is a highly lethal pathogen that has caused several outbreaks of severe hemorrhagic fever in humans since its emergence in 1976. The EBOV glycoprotein (GP1,2) is the sole viral envelope protein and a major component of immunogenicity; it is encoded by the GP gene along with two truncated versions: soluble GP (sGP) and small soluble GP (ssGP). sGP is, in fact, the primary product of the GP gene, and it is secreted in abundance during EBOV infection. Since sGP shares large portions of its sequence with GP1,2, it has been hypothesized that sGP may subvert the host immune response by inducing antibodies against sGP rather than GP1,2. Several reports have shown that sGP plays multiple roles that contribute to the complex pathogenesis of EBOV. In this review, we focus on sGP and discuss its possible roles with regards to the pathogenesis of EBOV and the development of specific antiviral drugs.
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Affiliation(s)
- Wenjun Zhu
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada.
| | - Logan Banadyga
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada.
| | - Karla Emeterio
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada.
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada.
| | - Gary Wong
- Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China.
- Département de microbiologie-infectiologie et d'immunologie, Université Laval, Québec, QC G1V 0A6, Canada.
| | - Xiangguo Qiu
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada.
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32
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Watanabe Y, Bowden TA, Wilson IA, Crispin M. Exploitation of glycosylation in enveloped virus pathobiology. Biochim Biophys Acta Gen Subj 2019; 1863:1480-1497. [PMID: 31121217 PMCID: PMC6686077 DOI: 10.1016/j.bbagen.2019.05.012] [Citation(s) in RCA: 318] [Impact Index Per Article: 63.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 05/13/2019] [Accepted: 05/17/2019] [Indexed: 12/12/2022]
Abstract
Glycosylation is a ubiquitous post-translational modification responsible for a multitude of crucial biological roles. As obligate parasites, viruses exploit host-cell machinery to glycosylate their own proteins during replication. Viral envelope proteins from a variety of human pathogens including HIV-1, influenza virus, Lassa virus, SARS, Zika virus, dengue virus, and Ebola virus have evolved to be extensively glycosylated. These host-cell derived glycans facilitate diverse structural and functional roles during the viral life-cycle, ranging from immune evasion by glycan shielding to enhancement of immune cell infection. In this review, we highlight the imperative and auxiliary roles glycans play, and how specific oligosaccharide structures facilitate these functions during viral pathogenesis. We discuss the growing efforts to exploit viral glycobiology in the development of anti-viral vaccines and therapies.
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Affiliation(s)
- Yasunori Watanabe
- School of Biological Sciences and Institute of Life Sciences, University of Southampton, Southampton SO17 1BJ, UK; Division of Structural Biology, University of Oxford, Wellcome Centre for Human Genetics, Oxford OX3 7BN, UK; Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Thomas A Bowden
- Division of Structural Biology, University of Oxford, Wellcome Centre for Human Genetics, Oxford OX3 7BN, UK
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Max Crispin
- School of Biological Sciences and Institute of Life Sciences, University of Southampton, Southampton SO17 1BJ, UK.
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Understudied Factors Influencing Fc-Mediated Immune Responses against Viral Infections. Vaccines (Basel) 2019; 7:vaccines7030103. [PMID: 31480293 PMCID: PMC6789852 DOI: 10.3390/vaccines7030103] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 08/27/2019] [Accepted: 08/28/2019] [Indexed: 12/26/2022] Open
Abstract
Antibodies play a crucial role in host defense against viruses, both by preventing infection and by controlling viral replication. Besides their capacity to neutralize viruses, antibodies also exert their antiviral effects by crystallizable fragment (Fc)-mediated effector mechanisms. This involves a bridge between innate and adaptive immune systems, wherein antibodies form immune complexes that drive numerous innate immune effector functions, including antibody-dependent cellular cytotoxicity, antibody-dependent complement-mediated lysis, and antibody-dependent phagocytosis. Here, we review certain mechanisms that modulate these antibody-mediated effector functions against virally infected cells, such as viral glycoprotein shedding, viral glycoprotein internalization, antibody cooperativity, and antibody glycosylation. These mechanisms can either protect viral replication or enhance infected cell clearance. Here we discuss the importance of these understudied factors in modulating Fc-mediated effector functions.
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Perez-Zsolt D, Erkizia I, Pino M, García-Gallo M, Martin MT, Benet S, Chojnacki J, Fernández-Figueras MT, Guerrero D, Urrea V, Muñiz-Trabudua X, Kremer L, Martinez-Picado J, Izquierdo-Useros N. Anti-Siglec-1 antibodies block Ebola viral uptake and decrease cytoplasmic viral entry. Nat Microbiol 2019; 4:1558-1570. [PMID: 31160823 DOI: 10.1038/s41564-019-0453-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 04/11/2019] [Indexed: 12/14/2022]
Abstract
Several Ebola viruses cause outbreaks of lethal haemorrhagic fever in humans, but developing therapies tackle only Zaire Ebola virus. Dendritic cells (DCs) are targets of this infection in vivo. Here, we found that Ebola virus entry into activated DCs requires the sialic acid-binding Ig-like lectin 1 (Siglec-1/CD169), which recognizes sialylated gangliosides anchored to viral membranes. Blockage of the Siglec-1 receptor by anti-Siglec-1 monoclonal antibodies halted Ebola viral uptake and cytoplasmic entry, offering cross-protection against other ganglioside-containing viruses such as human immunodeficiency virus type 1.
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Affiliation(s)
- Daniel Perez-Zsolt
- IrsiCaixa AIDS Research Institute, Badalona, Spain.,Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | - Maria Pino
- IrsiCaixa AIDS Research Institute, Badalona, Spain
| | - Mónica García-Gallo
- Protein Tools Unit and Department of Immunology and Oncology, Spanish National Center for Biotechnology, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Maria Teresa Martin
- Protein Tools Unit and Department of Immunology and Oncology, Spanish National Center for Biotechnology, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Susana Benet
- IrsiCaixa AIDS Research Institute, Badalona, Spain.,Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | - María Teresa Fernández-Figueras
- Department of Pathology, Hospital Universitari General de Catalunya-Grupo Quirón Salud, Barcelona, Spain.,Universitat Internacional de Catalunya, Barcelona, Spain.,Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Badalona, Spain
| | - Dolores Guerrero
- Otorhinolaryngology Department, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Victor Urrea
- IrsiCaixa AIDS Research Institute, Badalona, Spain
| | - Xabier Muñiz-Trabudua
- IrsiCaixa AIDS Research Institute, Badalona, Spain.,Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Leonor Kremer
- Protein Tools Unit and Department of Immunology and Oncology, Spanish National Center for Biotechnology, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Javier Martinez-Picado
- IrsiCaixa AIDS Research Institute, Badalona, Spain. .,University of Vic-Central University of Catalonia, Vic, Spain. .,Catalan Institution for Research and Advanced Studies, Barcelona, Spain.
| | - Nuria Izquierdo-Useros
- IrsiCaixa AIDS Research Institute, Badalona, Spain. .,Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Badalona, Spain.
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35
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Pleet ML, DeMarino C, Stonier SW, Dye JM, Jacobson S, Aman MJ, Kashanchi F. Extracellular Vesicles and Ebola Virus: A New Mechanism of Immune Evasion. Viruses 2019; 11:v11050410. [PMID: 31052499 PMCID: PMC6563240 DOI: 10.3390/v11050410] [Citation(s) in RCA: 25] [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: 03/29/2019] [Revised: 04/29/2019] [Accepted: 05/01/2019] [Indexed: 02/06/2023] Open
Abstract
Ebola virus (EBOV) disease can result in a range of symptoms anywhere from virtually asymptomatic to severe hemorrhagic fever during acute infection. Additionally, spans of asymptomatic persistence in recovering survivors is possible, during which transmission of the virus may occur. In acute infection, substantial cytokine storm and bystander lymphocyte apoptosis take place, resulting in uncontrolled, systemic inflammation in affected individuals. Recently, studies have demonstrated the presence of EBOV proteins VP40, glycoprotein (GP), and nucleoprotein (NP) packaged into extracellular vesicles (EVs) during infection. EVs containing EBOV proteins have been shown to induce apoptosis in recipient immune cells, as well as contain pro-inflammatory cytokines. In this manuscript, we review the current field of knowledge on EBOV EVs including the mechanisms of their biogenesis, their cargo and their effects in recipient cells. Furthermore, we discuss some of the effects that may be induced by EBOV EVs that have not yet been characterized and highlight the remaining questions and future directions.
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Affiliation(s)
- Michelle L Pleet
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA 20110, USA.
| | - Catherine DeMarino
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA 20110, USA.
| | - Spencer W Stonier
- Department, Emergent BioSolutions, Gaithersburg, MD 20879, USA.
- Virology Division, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA.
| | - John M Dye
- Virology Division, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA.
| | - Steven Jacobson
- Viral Immunology Section, Neuroimmunology Branch, National Institute for Neurological Disease and Stroke, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - M Javad Aman
- Department. Integrated BioTherapeutics, Inc., Gaithersburg, MD 20850, USA.
| | - Fatah Kashanchi
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA 20110, USA.
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36
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Dolzhikova IV, Tukhvatulin AI, Gromova AS, Grousova DM, Tukhvatulina NM, Tokarskaya EA, Logunov DY, Naroditskiy BS, Gintsburg AL. Glycoprotein GP as a basis for the universal vaccine against Ebola virus disease. BULLETIN OF RUSSIAN STATE MEDICAL UNIVERSITY 2019. [DOI: 10.24075/brsmu.2019.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Ebola virus disease (EVD) is one of the deadliest viral infections affecting humans and nonhuman primates. Of 6 known representatives of the Ebolavirus genus responsible for the disease, 3 can infect humans, causing acute highly contagious fever characterized by up to 90% fatality. These include Bundibugyo ebolavirus (BDBV), Zaire ebolavirus (ZEBOV) and Sudan ebolavirus (SUDV). The majority of the reported EVD cases are caused by ZEBOV. Vaccine development against the virus started in 1976, immediately after the causative agent of the infection was identified. So far, 4 vaccines have been approved. All of them are based on the protective epitope of the ZEBOV glycoprotein GP. Because SUDV and BDBV can also cause outbreaks and epidemics, it is vital to design a vaccine capable of conferring protection against all known ebolaviruses posing a threat to the human population. This article presents systematized data on the structure, immunogenicity and protective properties of ebolavirus glycoprotein GP, looks closely at the immunodominant epitopes of ZEBOV, SUDV and BDBV glycoprotein GP required to elicit a protective immune response, and offers a rational perspective on the development of a universal vaccine against EVD that relies on the use of vectors expressing two variants of GP represented by ZEBOV and SUDV.
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Affiliation(s)
- IV Dolzhikova
- N.F. Gamaleya Research Institute of Epidemiology and Microbiology, Moscow, Russia
| | - AI Tukhvatulin
- N.F. Gamaleya Research Institute of Epidemiology and Microbiology, Moscow, Russia
| | - AS Gromova
- N.F. Gamaleya Research Institute of Epidemiology and Microbiology, Moscow, Russia
| | - DM Grousova
- N.F. Gamaleya Research Institute of Epidemiology and Microbiology, Moscow, Russia
| | - NM Tukhvatulina
- N.F. Gamaleya Research Institute of Epidemiology and Microbiology, Moscow, Russia
| | - EA Tokarskaya
- N.F. Gamaleya Research Institute of Epidemiology and Microbiology, Moscow, Russia
| | - DYu Logunov
- N.F. Gamaleya Research Institute of Epidemiology and Microbiology, Moscow, Russia
| | - BS Naroditskiy
- N.F. Gamaleya Research Institute of Epidemiology and Microbiology, Moscow, Russia
| | - AL Gintsburg
- N.F. Gamaleya Research Institute of Epidemiology and Microbiology, Moscow, Russia
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Antibody responses to viral infections: a structural perspective across three different enveloped viruses. Nat Microbiol 2019; 4:734-747. [PMID: 30886356 PMCID: PMC6818971 DOI: 10.1038/s41564-019-0392-y] [Citation(s) in RCA: 125] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 01/29/2019] [Indexed: 02/07/2023]
Abstract
Antibodies serve as critical barriers to viral infection. Humoral immunity to a virus is achieved through the dual role of antibodies in communicating the presence of invading pathogens in infected cells to effector cells and interfering with processes essential to the viral lifecycle, chiefly entry into the host cell. For individuals that successfully control infection, virus-elicited antibodies can provide lifelong surveillance and protection from future insults. One approach to understand the nature of a successful immune response has been to utilize structural biology to uncover the molecular details of the antibodies derived from vaccines or natural infection and how they interact with their cognate microbial antigens. The ability to isolate antigen specific B-cells and rapidly solve structures of functional, monoclonal antibodies in complex with viral glycoprotein surface antigens has greatly expanded our knowledge of the sites of vulnerability on viruses. In this review, we compare the adaptive humoral immune responses to HIV, influenza, and filoviruses, with a particular focus on neutralizing antibodies. The pathogenesis of each of these viruses is quite different, providing an opportunity for comparison of immune responses: HIV causes a persistent, chronic infection; influenza an acute infection with multiple exposures during a lifetime and annual vaccination; and filoviruses, a virulent, acute infection. Neutralizing antibodies that develop under these different constraints are therefore sentinels that can provide insight into the underlying humoral immune responses and important lessons to guide future development of vaccines and immunotherapeutics.
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38
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Gordon TB, Hayward JA, Marsh GA, Baker ML, Tachedjian G. Host and Viral Proteins Modulating Ebola and Marburg Virus Egress. Viruses 2019; 11:v11010025. [PMID: 30609802 PMCID: PMC6357148 DOI: 10.3390/v11010025] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 12/21/2018] [Accepted: 01/01/2019] [Indexed: 12/11/2022] Open
Abstract
The filoviruses Ebolavirus and Marburgvirus are among the deadliest viral pathogens known to infect humans, causing emerging diseases with fatality rates of up to 90% during some outbreaks. The replication cycles of these viruses are comprised of numerous complex molecular processes and interactions with their human host, with one key feature being the means by which nascent virions exit host cells to spread to new cells and ultimately to a new host. This review focuses on our current knowledge of filovirus egress and the viral and host factors and processes that are involved. Within the virus, these factors consist of the major matrix protein, viral protein 40 (VP40), which is necessary and sufficient for viral particle release, and nucleocapsid and glycoprotein that interact with VP40 to promote egress. In the host cell, some proteins are hijacked by filoviruses in order to enhance virion budding capacity that include members of the family of E3 ubiquitin ligase and the endosomal sorting complexes required for transport (ESCRT) pathway, while others such as tetherin inhibit viral egress. An understanding of these molecular interactions that modulate viral particle egress provides an important opportunity to identify new targets for the development of antivirals to prevent and treat filovirus infections.
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Affiliation(s)
- Tamsin B Gordon
- Health Security Program, Life Sciences Discipline, Burnet Institute, Melbourne, VIC 3004, Australia.
- Department of Microbiology, Monash University, Clayton, VIC 3168, Australia.
| | - Joshua A Hayward
- Health Security Program, Life Sciences Discipline, Burnet Institute, Melbourne, VIC 3004, Australia.
- Department of Microbiology, Monash University, Clayton, VIC 3168, Australia.
| | - Glenn A Marsh
- Department of Microbiology, Monash University, Clayton, VIC 3168, Australia.
- CSIRO Australian Animal Health Laboratory, Health and Biosecurity Business Unit, Geelong, VIC 3220, Australia.
| | - Michelle L Baker
- CSIRO Australian Animal Health Laboratory, Health and Biosecurity Business Unit, Geelong, VIC 3220, Australia.
| | - Gilda Tachedjian
- Health Security Program, Life Sciences Discipline, Burnet Institute, Melbourne, VIC 3004, Australia.
- Department of Microbiology, Monash University, Clayton, VIC 3168, Australia.
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne VIC 3010, Australia.
- School of Science, College of Science, Engineering and Health, RMIT University, Melbourne, VIC 3000, Australia.
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39
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Cross RW, Fenton KA, Geisbert TW. Small animal models of filovirus disease: recent advances and future directions. Expert Opin Drug Discov 2018; 13:1027-1040. [DOI: 10.1080/17460441.2018.1527827] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Robert W. Cross
- Galveston National Laboratory, The University of Texas Medical Branch, Galveston, TX, USA
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Karla A. Fenton
- Galveston National Laboratory, The University of Texas Medical Branch, Galveston, TX, USA
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Thomas W. Geisbert
- Galveston National Laboratory, The University of Texas Medical Branch, Galveston, TX, USA
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX, USA
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40
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Dhama K, Karthik K, Khandia R, Chakraborty S, Munjal A, Latheef SK, Kumar D, Ramakrishnan MA, Malik YS, Singh R, Malik SVS, Singh RK, Chaicumpa W. Advances in Designing and Developing Vaccines, Drugs, and Therapies to Counter Ebola Virus. Front Immunol 2018; 9:1803. [PMID: 30147687 PMCID: PMC6095993 DOI: 10.3389/fimmu.2018.01803] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Accepted: 07/23/2018] [Indexed: 01/10/2023] Open
Abstract
Ebola virus (EBOV), a member of the family Filoviridae, is responsible for causing Ebola virus disease (EVD) (formerly named Ebola hemorrhagic fever). This is a severe, often fatal illness with mortality rates varying from 50 to 90% in humans. Although the virus and associated disease has been recognized since 1976, it was only when the recent outbreak of EBOV in 2014-2016 highlighted the danger and global impact of this virus, necessitating the need for coming up with the effective vaccines and drugs to counter its pandemic threat. Albeit no commercial vaccine is available so far against EBOV, a few vaccine candidates are under evaluation and clinical trials to assess their prophylactic efficacy. These include recombinant viral vector (recombinant vesicular stomatitis virus vector, chimpanzee adenovirus type 3-vector, and modified vaccinia Ankara virus), Ebola virus-like particles, virus-like replicon particles, DNA, and plant-based vaccines. Due to improvement in the field of genomics and proteomics, epitope-targeted vaccines have gained top priority. Correspondingly, several therapies have also been developed, including immunoglobulins against specific viral structures small cell-penetrating antibody fragments that target intracellular EBOV proteins. Small interfering RNAs and oligomer-mediated inhibition have also been verified for EVD treatment. Other treatment options include viral entry inhibitors, transfusion of convalescent blood/serum, neutralizing antibodies, and gene expression inhibitors. Repurposed drugs, which have proven safety profiles, can be adapted after high-throughput screening for efficacy and potency for EVD treatment. Herbal and other natural products are also being explored for EVD treatment. Further studies to better understand the pathogenesis and antigenic structures of the virus can help in developing an effective vaccine and identifying appropriate antiviral targets. This review presents the recent advances in designing and developing vaccines, drugs, and therapies to counter the EBOV threat.
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Affiliation(s)
- Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Kumaragurubaran Karthik
- Central University Laboratory, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India
| | - Rekha Khandia
- Department of Biochemistry and Genetics, Barkatullah University, Bhopal, India
| | - Sandip Chakraborty
- Department of Veterinary Microbiology, College of Veterinary Sciences and Animal Husbandry, Agartala, India
| | - Ashok Munjal
- Department of Biochemistry and Genetics, Barkatullah University, Bhopal, India
| | - Shyma K. Latheef
- Immunology Section, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Deepak Kumar
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | | | - Yashpal Singh Malik
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Rajendra Singh
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Satya Veer Singh Malik
- Division of Veterinary Public Health, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Raj Kumar Singh
- ICAR-Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, India
| | - Wanpen Chaicumpa
- Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine SIriraj Hospital, Mahidol University, Bangkok, Thailand
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41
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Clark LE, Mahmutovic S, Raymond DD, Dilanyan T, Koma T, Manning JT, Shankar S, Levis SC, Briggiler AM, Enria DA, Wucherpfennig KW, Paessler S, Abraham J. Vaccine-elicited receptor-binding site antibodies neutralize two New World hemorrhagic fever arenaviruses. Nat Commun 2018; 9:1884. [PMID: 29760382 PMCID: PMC5951886 DOI: 10.1038/s41467-018-04271-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 04/16/2018] [Indexed: 01/26/2023] Open
Abstract
While five arenaviruses cause human hemorrhagic fevers in the Western Hemisphere, only Junin virus (JUNV) has a vaccine. The GP1 subunit of their envelope glycoprotein binds transferrin receptor 1 (TfR1) using a surface that substantially varies in sequence among the viruses. As such, receptor-mimicking antibodies described to date are type-specific and lack the usual breadth associated with this mode of neutralization. Here we isolate, from the blood of a recipient of the live attenuated JUNV vaccine, two antibodies that cross-neutralize Machupo virus with varying efficiency. Structures of GP1-Fab complexes explain the basis for efficient cross-neutralization, which involves avoiding receptor mimicry and targeting a conserved epitope within the receptor-binding site (RBS). The viral RBS, despite its extensive sequence diversity, is therefore a target for cross-reactive antibodies with activity against New World arenaviruses of public health concern.
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MESH Headings
- Amino Acid Sequence
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/isolation & purification
- Antibodies, Viral/chemistry
- Antibodies, Viral/isolation & purification
- Antigens, CD/chemistry
- Antigens, CD/genetics
- Antigens, CD/immunology
- Antigens, Viral/chemistry
- Antigens, Viral/genetics
- Antigens, Viral/immunology
- Arenaviruses, New World/genetics
- Arenaviruses, New World/immunology
- Binding Sites, Antibody
- Cross Reactions
- Epitopes/chemistry
- Epitopes/genetics
- Epitopes/immunology
- HEK293 Cells
- Hemorrhagic Fever, American/immunology
- Hemorrhagic Fever, American/prevention & control
- Hemorrhagic Fever, American/virology
- Humans
- Immune Sera/chemistry
- Immunoglobulin Fab Fragments/chemistry
- Immunoglobulin Fab Fragments/isolation & purification
- Junin virus/genetics
- Junin virus/immunology
- Models, Molecular
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Protein Structure, Tertiary
- Protein Subunits/chemistry
- Protein Subunits/genetics
- Protein Subunits/immunology
- Receptors, Transferrin/chemistry
- Receptors, Transferrin/genetics
- Receptors, Transferrin/immunology
- Receptors, Virus/chemistry
- Receptors, Virus/genetics
- Receptors, Virus/immunology
- Sequence Alignment
- Sequence Homology, Amino Acid
- Viral Envelope Proteins/chemistry
- Viral Envelope Proteins/genetics
- Viral Envelope Proteins/immunology
- Viral Vaccines/administration & dosage
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Affiliation(s)
- Lars E Clark
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA
| | - Selma Mahmutovic
- Laboratory of Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Donald D Raymond
- Laboratory of Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Taleen Dilanyan
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA
| | - Takaaki Koma
- Department of Pathology, University of Texas Medical Branch at Galveston, Galveston, TX, 77555, USA
| | - John T Manning
- Department of Pathology, University of Texas Medical Branch at Galveston, Galveston, TX, 77555, USA
| | - Sundaresh Shankar
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA
| | - Silvana C Levis
- Instituto Nacional de Enfermedades Virales Humanas "Dr. Julio I. Maiztegui", Monteagudo 251 Pergamino, Buenos Aires, 2700, Argentina
| | - Ana M Briggiler
- Instituto Nacional de Enfermedades Virales Humanas "Dr. Julio I. Maiztegui", Monteagudo 251 Pergamino, Buenos Aires, 2700, Argentina
| | - Delia A Enria
- Instituto Nacional de Enfermedades Virales Humanas "Dr. Julio I. Maiztegui", Monteagudo 251 Pergamino, Buenos Aires, 2700, Argentina
| | - Kai W Wucherpfennig
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
- Program in Immunology, Harvard Medical School, Boston, MA, 02115, USA
| | - Slobodan Paessler
- Department of Pathology, University of Texas Medical Branch at Galveston, Galveston, TX, 77555, USA
| | - Jonathan Abraham
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA.
- Laboratory of Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
- Department of Medicine, Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, 02115, USA.
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42
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Rotem E, Faingold O, Charni M, Klug YA, Harari D, Shmuel-Galia L, Nudelman A, Rotter V, Shai Y. The HTLV-1 gp21 fusion peptide inhibits antigen specific T-cell activation in-vitro and in mice. PLoS Pathog 2018; 14:e1007044. [PMID: 29727445 PMCID: PMC5955599 DOI: 10.1371/journal.ppat.1007044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 05/16/2018] [Accepted: 04/18/2018] [Indexed: 11/17/2022] Open
Abstract
The ability of the Lentivirus HIV-1 to inhibit T-cell activation by its gp41 fusion protein is well documented, yet limited data exists regarding other viral fusion proteins. HIV-1 utilizes membrane binding region of gp41 to inhibit T-cell receptor (TCR) complex activation. Here we examined whether this T-cell suppression strategy is unique to the HIV-1 gp41. We focused on T-cell modulation by the gp21 fusion peptide (FP) of the Human T-lymphotropic Virus 1 (HTLV-1), a Deltaretrovirus that like HIV infects CD4+ T-cells. Using mouse and human in-vitro T-cell models together with in-vivo T-cell hyper activation mouse model, we reveal that HTLV-1's FP inhibits T-cell activation and unlike the HIV FP, bypasses the TCR complex. HTLV FP inhibition induces a decrease in Th1 and an elevation in Th2 responses observed in mRNA, cytokine and transcription factor profiles. Administration of the HTLV FP in a T-cell hyper activation mouse model of multiple sclerosis alleviated symptoms and delayed disease onset. We further pinpointed the modulatory region within HTLV-1's FP to the same region previously identified as the HIV-1 FP active region, suggesting that through convergent evolution both viruses have obtained the ability to modulate T-cells using the same region of their fusion protein. Overall, our findings suggest that fusion protein based T-cell modulation may be a common viral trait.
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Affiliation(s)
- Etai Rotem
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Omri Faingold
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Meital Charni
- Department of molecular cell biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Yoel A Klug
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Daniel Harari
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Liraz Shmuel-Galia
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Alon Nudelman
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Varda Rotter
- Department of molecular cell biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Yechiel Shai
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
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43
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Abstract
The Filoviridae are a family of negative-strand RNA viruses that include several important human pathogens. Ebola virus (EBOV) and Marburg virus are well-known filoviruses which cause life-threatening viral hemorrhagic fever in human and nonhuman primates. In addition to severe pathogenesis, filoviruses also exhibit a propensity for human-to-human transmission by close contact, posing challenges to containment and crisis management. Past outbreaks, in particular the recent West African EBOV epidemic, have been responsible for thousands of deaths and vaulted the filoviruses into public consciousness. Both national and international health agencies continue to regard potential filovirus outbreaks as critical threats to global public health. To develop effective countermeasures, a basic understanding of filovirus biology is needed. This review encompasses the epidemiology, ecology, molecular biology, and evolution of the filoviruses.
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Affiliation(s)
- Jackson Emanuel
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States
| | - Andrea Marzi
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States
| | - Heinz Feldmann
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States.
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Wang B, Wang Y, Frabutt DA, Zhang X, Yao X, Hu D, Zhang Z, Liu C, Zheng S, Xiang SH, Zheng YH. Mechanistic understanding of N-glycosylation in Ebola virus glycoprotein maturation and function. J Biol Chem 2017; 292:5860-5870. [PMID: 28196864 DOI: 10.1074/jbc.m116.768168] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 02/12/2017] [Indexed: 01/04/2023] Open
Abstract
The Ebola virus (EBOV) trimeric envelope glycoprotein (GP) precursors are cleaved into the receptor-binding GP1 and the fusion-mediating GP2 subunits and incorporated into virions to initiate infection. GP1 and GP2 form heterodimers that have 15 or two N-glycosylation sites (NGSs), respectively. Here we investigated the mechanism of how N-glycosylation contributes to GP expression, maturation, and function. As reported before, we found that, although GP1 NGSs are not critical, the two GP2 NGSs, Asn563 and Asn618, are essential for GP function. Further analysis uncovered that Asn563 and Asn618 regulate GP processing, demannosylation, oligomerization, and conformation. Consequently, these two NGSs are required for GP incorporation into EBOV-like particles and HIV type 1 (HIV-1) pseudovirions and determine viral transduction efficiency. Using CRISPR/Cas9 technology, we knocked out the two classical endoplasmic reticulum chaperones calnexin (CNX) and/or calreticulin (CRT) and found that both CNX and CRT increase GP expression. Nevertheless, NGSs are not required for the GP interaction with CNX or CRT. Together, we conclude that, although Asn563 and Asn618 are not required for EBOV GP expression, they synergistically regulate its maturation, which determines its functionality.
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Affiliation(s)
- Bin Wang
- From the Harbin Veterinary Research Institute, CAAS-Michigan State University Joint Laboratory of Innate Immunity, State Key Laboratory of Veterinary Biotechnology, Chinese Academy of Agricultural Sciences, Harbin 150059, China
| | - Yujie Wang
- From the Harbin Veterinary Research Institute, CAAS-Michigan State University Joint Laboratory of Innate Immunity, State Key Laboratory of Veterinary Biotechnology, Chinese Academy of Agricultural Sciences, Harbin 150059, China
| | - Dylan A Frabutt
- the Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824
| | - Xihe Zhang
- the Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824
| | - Xiaoyu Yao
- From the Harbin Veterinary Research Institute, CAAS-Michigan State University Joint Laboratory of Innate Immunity, State Key Laboratory of Veterinary Biotechnology, Chinese Academy of Agricultural Sciences, Harbin 150059, China
| | - Dan Hu
- From the Harbin Veterinary Research Institute, CAAS-Michigan State University Joint Laboratory of Innate Immunity, State Key Laboratory of Veterinary Biotechnology, Chinese Academy of Agricultural Sciences, Harbin 150059, China
| | - Zhuo Zhang
- From the Harbin Veterinary Research Institute, CAAS-Michigan State University Joint Laboratory of Innate Immunity, State Key Laboratory of Veterinary Biotechnology, Chinese Academy of Agricultural Sciences, Harbin 150059, China
| | - Chaonan Liu
- the College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Shimin Zheng
- the College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Shi-Hua Xiang
- the Nebraska Center for Virology and School of Veterinary Medicine and Biomedical Sciences, University of Nebraska, Lincoln, Nebraska 68583, and
| | - Yong-Hui Zheng
- From the Harbin Veterinary Research Institute, CAAS-Michigan State University Joint Laboratory of Innate Immunity, State Key Laboratory of Veterinary Biotechnology, Chinese Academy of Agricultural Sciences, Harbin 150059, China, .,the Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824
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45
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Ning YJ, Deng F, Hu Z, Wang H. The roles of ebolavirus glycoproteins in viral pathogenesis. Virol Sin 2016; 32:3-15. [PMID: 27853993 PMCID: PMC6791933 DOI: 10.1007/s12250-016-3850-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 10/09/2016] [Indexed: 12/20/2022] Open
Abstract
Ebolaviruses are highly dangerous pathogens exhibiting extreme virulence in humans and nonhuman primates. The majority of ebolavirus species, most notably Zaire ebolavirus, can cause Ebola virus disease (EVD), formerly known as Ebola hemorrhagic fever, in humans. EVD is associated with case-fatality rates as high as 90%, and there is currently no specific treatment or licensed vaccine available against EVD. Understanding the molecular biology and pathogenesis of ebolaviruses is important for the development of antiviral therapeutics. Ebolavirus encodes several forms of glycoproteins (GPs), which have some interesting characteristics, including the transcriptional editing coding strategy and extensive O-glycosylation modification, clustered in the mucin-like domain of GP1, full-length GP (GP1,2), and shed GP. In addition to the canonical role of the spike protein, GP1,2, in viral entry, ebolavirus GPs appear to have multiple additional functions, likely contributing to the complex pathogenesis of the virus. Here, we review the roles of ebolavirus GPs in viral pathogenesis.
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Affiliation(s)
- Yun-Jia Ning
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Fei Deng
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Zhihong Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Hualin Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.
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46
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Zhang Q, Gui M, Niu X, He S, Wang R, Feng Y, Kroeker A, Zuo Y, Wang H, Wang Y, Li J, Li C, Shi Y, Shi X, Gao GF, Xiang Y, Qiu X, Chen L, Zhang L. Potent neutralizing monoclonal antibodies against Ebola virus infection. Sci Rep 2016; 6:25856. [PMID: 27181584 PMCID: PMC4867612 DOI: 10.1038/srep25856] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 04/18/2016] [Indexed: 01/11/2023] Open
Abstract
Ebola virus infections cause a deadly hemorrhagic disease for which no vaccines or therapeutics has received regulatory approval. Here we show isolation of three (Q206, Q314 and Q411) neutralizing monoclonal antibodies (mAbs) against the surface glycoprotein (GP) of Ebola virus identified in West Africa in 2014 through sequential immunization of Chinese rhesus macaques and antigen-specific single B cell sorting. These mAbs demonstrated potent neutralizing activities against both pseudo and live Ebola virus independent of complement. Biochemical, single particle EM, and mutagenesis analysis suggested Q206 and Q411 recognized novel epitopes in the head while Q314 targeted the glycan cap in the GP1 subunit. Q206 and Q411 appeared to influence GP binding to its receptor NPC1. Treatment with these mAbs provided partial but significant protection against disease in a mouse model of Ebola virus infection. These novel mAbs could serve as promising candidates for prophylactic and therapeutic interventions against Ebola virus infection.
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Affiliation(s)
- Qi Zhang
- Comprehensive AIDS Research Center, and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Miao Gui
- Beijing Advanced Innovation Center for Structure Biology, and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xuefeng Niu
- State Key Laboratory of Respiratory Disease, First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510230, China
| | - Shihua He
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, R3E 3R2 Canada.,Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, R3E 0J9 Canada
| | - Ruoke Wang
- Comprehensive AIDS Research Center, and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yupeng Feng
- Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Andrea Kroeker
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, R3E 3R2 Canada.,Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, R3E 0J9 Canada
| | - Yanan Zuo
- Comprehensive AIDS Research Center, and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Hua Wang
- Comprehensive AIDS Research Center, and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Ying Wang
- Comprehensive AIDS Research Center, and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Jiade Li
- Comprehensive AIDS Research Center, and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Chufang Li
- State Key Laboratory of Respiratory Disease, First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510230, China
| | - Yi Shi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology and Research Network of Immunity and Health, and Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Xuanling Shi
- Comprehensive AIDS Research Center, and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Medicine, Tsinghua University, Beijing 100084, China
| | - George F Gao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology and Research Network of Immunity and Health, and Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Ye Xiang
- Beijing Advanced Innovation Center for Structure Biology, and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xiangguo Qiu
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, R3E 3R2 Canada.,Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, R3E 0J9 Canada
| | - Ling Chen
- State Key Laboratory of Respiratory Disease, First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510230, China.,Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Linqi Zhang
- Comprehensive AIDS Research Center, and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Medicine, Tsinghua University, Beijing 100084, China
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47
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Gram AM, Oosenbrug T, Lindenbergh MFS, Büll C, Comvalius A, Dickson KJI, Wiegant J, Vrolijk H, Lebbink RJ, Wolterbeek R, Adema GJ, Griffioen M, Heemskerk MHM, Tscharke DC, Hutt-Fletcher LM, Wiertz EJHJ, Hoeben RC, Ressing ME. The Epstein-Barr Virus Glycoprotein gp150 Forms an Immune-Evasive Glycan Shield at the Surface of Infected Cells. PLoS Pathog 2016; 12:e1005550. [PMID: 27077376 PMCID: PMC4831753 DOI: 10.1371/journal.ppat.1005550] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 03/14/2016] [Indexed: 12/15/2022] Open
Abstract
Cell-mediated immunity plays a key role in host control of viral infection. This is exemplified by life-threatening reactivations of e.g. herpesviruses in individuals with impaired T-cell and/or iNKT cell responses. To allow lifelong persistence and virus production in the face of primed immunity, herpesviruses exploit immune evasion strategies. These include a reduction in viral antigen expression during latency and a number of escape mechanisms that target antigen presentation pathways. Given the plethora of foreign antigens expressed in virus-producing cells, herpesviruses are conceivably most vulnerable to elimination by cell-mediated immunity during the replicative phase of infection. Here, we show that a prototypic herpesvirus, Epstein-Barr virus (EBV), encodes a novel, broadly acting immunoevasin, gp150, that is expressed during the late phase of viral replication. In particular, EBV gp150 inhibits antigen presentation by HLA class I, HLA class II, and the non-classical, lipid-presenting CD1d molecules. The mechanism of gp150-mediated T-cell escape does not depend on degradation of the antigen-presenting molecules nor does it require gp150’s cytoplasmic tail. Through its abundant glycosylation, gp150 creates a shield that impedes surface presentation of antigen. This is an unprecedented immune evasion mechanism for herpesviruses. In view of its likely broader target range, gp150 could additionally have an impact beyond escape of T cell activation. Importantly, B cells infected with a gp150-null mutant EBV displayed rescued levels of surface antigen presentation by HLA class I, HLA class II, and CD1d, supporting an important role for iNKT cells next to classical T cells in fighting EBV infection. At the same time, our results indicate that EBV gp150 prolongs the timespan for producing viral offspring at the most vulnerable stage of the viral life cycle. The human herpesvirus Epstein-Barr virus (EBV) is an important human pathogen involved in infectious mononucleosis and several malignant tumors, including lymphomas in the immunosuppressed. Upon primary infection, a balance between virus and host is established, to which EBV’s capacity to dodge T cell-mediated attack contributes. Here we identify the late protein EBV gp150 as a novel immunoevasin, frustrating antigen presentation by HLA class I, class II, and CD1d molecules. EBV gp150’s many sialoglycans create a shield impeding surface detection of presented antigen. Interestingly, exploiting glycan shielding as a mechanism to mask surface exposed proteins on infected cells could permit EBV to additionally modulate other aspects of host antiviral defense. B cells producing wild-type EBV escaped immune recognition more efficiently than those infected with a gp150-null virus, pointing towards a role for gp150 in natural infection. Our results reveal a novel, broadly active strategy by which a herpesvirus glycoprotein, EBV gp150, blocks antigen presentation to T cells through glycan shielding, a new paradigm in herpesvirus immune evasion.
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Affiliation(s)
- Anna M. Gram
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Timo Oosenbrug
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Christian Büll
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Anouskha Comvalius
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Kathryn J. I. Dickson
- John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Joop Wiegant
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Hans Vrolijk
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Robert Jan Lebbink
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ron Wolterbeek
- Department of Medical Statistics & Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands
| | - Gosse J. Adema
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Marieke Griffioen
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - David C. Tscharke
- John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Lindsey M. Hutt-Fletcher
- Department of Microbiology and Immunology, Louisiana State University Health Sciences Center, Shreveport, Louisiana, United States of America
| | | | - Rob C. Hoeben
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Maaike E. Ressing
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
- * E-mail:
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48
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Rotem E, Reuven EM, Klug YA, Shai Y. The Transmembrane Domain of HIV-1 gp41 Inhibits T-Cell Activation by Targeting Multiple T-Cell Receptor Complex Components through Its GxxxG Motif. Biochemistry 2016; 55:1049-57. [PMID: 26828096 DOI: 10.1021/acs.biochem.5b01307] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
To successfully infect and persist within its host, HIV-1 utilizes several immunosuppressive motifs within its gp41 envelope glycoprotein to manipulate and evade the immune system. The transmembrane domain (TMD) of gp41 downregulates T-cell receptor (TCR) signaling through a hitherto unknown mechanism. Interactions between TMDs within the membrane milieu have been shown to be typically mediated by particular amino acids, such as interactions between basic and acidic residues and dimerization motifs as GxxxG. The HIV-1 TMD exhibits both a polar arginine (Arg(696)) residue and a GxxxG motif, making them ideal candidates for mediators of TMD-TCR interaction. Using a primary T-cell activation assay and biochemical and biophysical methods, we demonstrate that the gp41 TMD directly interacts with TMDs of the TCR and the CD3 coreceptors (δ, γ, and ε) within the membrane, presumably leading to impairment of complex assembly. Additionally, we reveal that although Arg(696) does not affect TMD immunosuppression, the GxxxG motif is crucial in mediating gp41's TMD interaction with the CD3 coreceptors of the TCR. These findings suggest that compared with other gp41 immunosuppressive motifs, the gp41 TMD has multiple targets within the TCR complex, suggesting less susceptibility to evolutionary pressure and consequently being advantageous for the virus over the host immune response. Furthermore, as the GxxxG motif mediates interactions of the gp41 TMD with multiple receptors, it emerges as an attractive drug target. This multitarget inhibitory mechanism might be a strategy utilized by HIV to interfere with the function of additional host receptors.
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Affiliation(s)
- Etai Rotem
- Department of Biological Chemistry, The Weizmann Institute of Science , Rehovot 76100, Israel
| | - Eliran Moshe Reuven
- Department of Biological Chemistry, The Weizmann Institute of Science , Rehovot 76100, Israel
| | - Yoel A Klug
- Department of Biological Chemistry, The Weizmann Institute of Science , Rehovot 76100, Israel
| | - Yechiel Shai
- Department of Biological Chemistry, The Weizmann Institute of Science , Rehovot 76100, Israel
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49
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Egorov VV, Gorshkov AN, Murugova TN, Vasin AV, Lebedev DV, Isaev-Ivanov VV, Kiselev OI. Characterization of oligomerization of a peptide from the ebola virus glycoprotein by small-angle neutron scattering. CRYSTALLOGR REP+ 2016. [DOI: 10.1134/s1063774516010065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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50
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Springer SA, Gagneux P. Glycomics: revealing the dynamic ecology and evolution of sugar molecules. J Proteomics 2015; 135:90-100. [PMID: 26626628 DOI: 10.1016/j.jprot.2015.11.022] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Revised: 11/11/2015] [Accepted: 11/23/2015] [Indexed: 01/11/2023]
Abstract
Sugars are the most functionally and structurally diverse molecules in the biological world. Glycan structures range from tiny single monosaccharide units to giant chains thousands of units long. Some glycans are branched, their monosaccharides linked together in many different combinations and orientations. Some exist as solitary molecules; others are conjugated to proteins and lipids and alter their collective functional properties. In addition to structural and storage roles, glycan molecules participate in and actively regulate physiological and developmental processes. Glycans also mediate cellular interactions within and between individuals. Their roles in ecology and evolution are pivotal, but not well studied because glycan biochemistry requires different methods than standard molecular biology practice. The properties of glycans are in some ways convenient, and in others challenging. Glycans vary on organismal timescales, and in direct response to physiological and ecological conditions. Their mature structures are physical records of both genetic and environmental influences during maturation. We describe the scope of natural glycan variation and discuss how studying glycans will allow researchers to further integrate the fields of ecology and evolution.
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Affiliation(s)
- Stevan A Springer
- Glycobiology Research and Training Center, University of California San Diego, La Jolla, CA 92039, USA; Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92039, USA.
| | - Pascal Gagneux
- Glycobiology Research and Training Center, University of California San Diego, La Jolla, CA 92039, USA; Department of Pathology, University of California San Diego, La Jolla, CA 92039, USA.
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