1
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Lubow J, Levoir LM, Ralph DK, Belmont L, Contreras M, Cartwright-Acar CH, Kikawa C, Kannan S, Davidson E, Duran V, Rebellon-Sanchez DE, Sanz AM, Rosso F, Doranz BJ, Einav S, Matsen IV FA, Goo L. Single B cell transcriptomics identifies multiple isotypes of broadly neutralizing antibodies against flaviviruses. PLoS Pathog 2023; 19:e1011722. [PMID: 37812640 PMCID: PMC10586629 DOI: 10.1371/journal.ppat.1011722] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 10/19/2023] [Accepted: 09/28/2023] [Indexed: 10/11/2023] Open
Abstract
Sequential dengue virus (DENV) infections often generate neutralizing antibodies against all four DENV serotypes and sometimes, Zika virus. Characterizing cross-flavivirus broadly neutralizing antibody (bnAb) responses can inform countermeasures that avoid enhancement of infection associated with non-neutralizing antibodies. Here, we used single cell transcriptomics to mine the bnAb repertoire following repeated DENV infections. We identified several new bnAbs with comparable or superior breadth and potency to known bnAbs, and with distinct recognition determinants. Unlike all known flavivirus bnAbs, which are IgG1, one newly identified cross-flavivirus bnAb (F25.S02) was derived from IgA1. Both IgG1 and IgA1 versions of F25.S02 and known bnAbs displayed neutralizing activity, but only IgG1 enhanced infection in monocytes expressing IgG and IgA Fc receptors. Moreover, IgG-mediated enhancement of infection was inhibited by IgA1 versions of bnAbs. We demonstrate a role for IgA in flavivirus infection and immunity with implications for vaccine and therapeutic strategies.
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Affiliation(s)
- Jay Lubow
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Lisa M. Levoir
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Duncan K. Ralph
- Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Laura Belmont
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington, United States of America
| | - Maya Contreras
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Catiana H. Cartwright-Acar
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Caroline Kikawa
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Medical Scientist Training Program, University of Washington, Seattle, Washington, United States of America
| | - Shruthi Kannan
- Integral Molecular, Inc., Philadelphia, Pennsylvania, United States of America
| | - Edgar Davidson
- Integral Molecular, Inc., Philadelphia, Pennsylvania, United States of America
| | - Veronica Duran
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, United States of America
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | | | - Ana M. Sanz
- Clinical Research Center, Fundación Valle del Lili, Cali, Colombia
| | - Fernando Rosso
- Clinical Research Center, Fundación Valle del Lili, Cali, Colombia
- Department of Internal Medicine, Division of Infectious Diseases, Fundación Valle del Lili, Cali, Colombia
| | - Benjamin J. Doranz
- Integral Molecular, Inc., Philadelphia, Pennsylvania, United States of America
| | - Shirit Einav
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, United States of America
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Frederick A. Matsen IV
- Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Department of Statistics, University of Washington, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Seattle, Washington, United States of America
| | - Leslie Goo
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
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2
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Ooi EE, Kalimuddin S. Insights into dengue immunity from vaccine trials. Sci Transl Med 2023; 15:eadh3067. [PMID: 37437017 DOI: 10.1126/scitranslmed.adh3067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 06/08/2023] [Indexed: 07/14/2023]
Abstract
The quest for an effective dengue vaccine has culminated in two approved vaccines and another that has completed phase 3 clinical trials. However, shortcomings exist in each, suggesting that the knowledge on dengue immunity used to develop these vaccines was incomplete. Vaccine trial findings could refine our understanding of dengue immunity, because these are experimentally derived, placebo-controlled data. Results from these trials suggest that neutralizing antibody titers alone are insufficient to inform protection against symptomatic infection, implicating a role for cellular immunity in protection. These findings have relevance for both future dengue vaccine development and application of current vaccines for maximal public health benefit.
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Affiliation(s)
- Eng Eong Ooi
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
- Viral Research and Experimental Medicine Centre, SingHealth Duke-NUS Academic Medical Centre, Singapore 169857, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore 117549, Singapore
| | - Shirin Kalimuddin
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
- Department of Infectious Diseases, Singapore General Hospital, Singapore 169856, Singapore
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3
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Lubow J, Levoir LM, Ralph DK, Belmont L, Contreras M, Cartwright-Acar CH, Kikawa C, Kannan S, Davidson E, Doranz BJ, Duran V, Sanchez DE, Sanz AM, Rosso F, Einav S, Matsen FA, Goo L. Single B cell transcriptomics identifies multiple isotypes of broadly neutralizing antibodies against flaviviruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.09.536175. [PMID: 37090561 PMCID: PMC10120628 DOI: 10.1101/2023.04.09.536175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Sequential dengue virus (DENV) infections often generate neutralizing antibodies against all four DENV serotypes and sometimes, Zika virus. Characterizing cross-flavivirus broadly neutralizing antibody (bnAb) responses can inform countermeasure strategies that avoid infection enhancement associated with non-neutralizing antibodies. Here, we used single cell transcriptomics to mine the bnAb repertoire following secondary DENV infection. We identified several new bnAbs with comparable or superior breadth and potency to known bnAbs, and with distinct recognition determinants. Unlike all known flavivirus bnAbs, which are IgG1, one newly identified cross-flavivirus bnAb (F25.S02) was derived from IgA1. Both IgG1 and IgA1 versions of F25.S02 and known bnAbs displayed neutralizing activity, but only IgG1 enhanced infection in monocytes expressing IgG and IgA Fc receptors. Moreover, IgG-mediated enhancement of infection was inhibited by IgA1 versions of bnAbs. We demonstrate a role for IgA in flavivirus infection and immunity with implications for vaccine and therapeutic strategies.
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4
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A. Dowd K, Sirohi D, D. Speer S, VanBlargan LA, Chen RE, Mukherjee S, Whitener BM, Govero J, Aleshnick M, Larman B, Sukupolvi-Petty S, Sevvana M, Miller AS, Klose T, Zheng A, Koenig S, Kielian M, Kuhn RJ, Diamond MS, Pierson TC. prM-reactive antibodies reveal a role for partially mature virions in dengue virus pathogenesis. Proc Natl Acad Sci U S A 2023; 120:e2218899120. [PMID: 36638211 PMCID: PMC9933121 DOI: 10.1073/pnas.2218899120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 11/28/2022] [Indexed: 01/15/2023] Open
Abstract
Cleavage of the flavivirus premembrane (prM) structural protein during maturation can be inefficient. The contribution of partially mature flavivirus virions that retain uncleaved prM to pathogenesis during primary infection is unknown. To investigate this question, we characterized the functional properties of newly-generated dengue virus (DENV) prM-reactive monoclonal antibodies (mAbs) in vitro and using a mouse model of DENV disease. Anti-prM mAbs neutralized DENV infection in a virion maturation state-dependent manner. Alanine scanning mutagenesis and cryoelectron microscopy of anti-prM mAbs in complex with immature DENV defined two modes of attachment to a single antigenic site. In vivo, passive transfer of intact anti-prM mAbs resulted in an antibody-dependent enhancement of disease. However, protection against DENV-induced lethality was observed when the transferred mAbs were genetically modified to inhibit their ability to interact with Fcγ receptors. These data establish that in addition to mature forms of the virus, partially mature infectious prM+ virions can also contribute to pathogenesis during primary DENV infections.
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Affiliation(s)
- Kimberly A. Dowd
- Viral Pathogenesis Section, Laboratory of Viral Diseases, National Institutes of Health, Bethesda, MD20892
| | - Devika Sirohi
- Department of Biological Sciences, Purdue University, West Lafayette, IN47907
- Purdue Institute of Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, IN47907
| | - Scott D. Speer
- Viral Pathogenesis Section, Laboratory of Viral Diseases, National Institutes of Health, Bethesda, MD20892
| | - Laura A. VanBlargan
- Department of Medicine, Washington University School of Medicine, St. Louis, MO63110
| | - Rita E. Chen
- Department of Medicine, Washington University School of Medicine, St. Louis, MO63110
| | - Swati Mukherjee
- Viral Pathogenesis Section, Laboratory of Viral Diseases, National Institutes of Health, Bethesda, MD20892
| | - Bradley M. Whitener
- Department of Medicine, Washington University School of Medicine, St. Louis, MO63110
| | - Jennifer Govero
- Department of Medicine, Washington University School of Medicine, St. Louis, MO63110
| | - Maya Aleshnick
- Viral Pathogenesis Section, Laboratory of Viral Diseases, National Institutes of Health, Bethesda, MD20892
| | - Bridget Larman
- Viral Pathogenesis Section, Laboratory of Viral Diseases, National Institutes of Health, Bethesda, MD20892
| | - Soila Sukupolvi-Petty
- Department of Medicine, Washington University School of Medicine, St. Louis, MO63110
| | - Madhumati Sevvana
- Department of Biological Sciences, Purdue University, West Lafayette, IN47907
- Purdue Institute of Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, IN47907
| | - Andrew S. Miller
- Department of Biological Sciences, Purdue University, West Lafayette, IN47907
- Purdue Institute of Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, IN47907
| | - Thomas Klose
- Department of Biological Sciences, Purdue University, West Lafayette, IN47907
- Purdue Institute of Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, IN47907
| | - Aihua Zheng
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY10461
| | | | - Margaret Kielian
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY10461
| | - Richard J. Kuhn
- Department of Biological Sciences, Purdue University, West Lafayette, IN47907
- Purdue Institute of Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, IN47907
| | - Michael S. Diamond
- Department of Medicine, Washington University School of Medicine, St. Louis, MO63110
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO63110
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO63110
| | - Theodore C. Pierson
- Viral Pathogenesis Section, Laboratory of Viral Diseases, National Institutes of Health, Bethesda, MD20892
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5
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Keelapang P, Supasa P, Sriburi R, Puttikhunt C, Cardosa J, Kasinrerk W, Malasit P, Sittisombut N. A group of infection-enhancing and focus size-reducing monoclonal antibodies recognized an 'a and c' strands epitope in the pr domain of Dengue Virus prM. Virus Res 2023; 323:199015. [PMID: 36455752 PMCID: PMC9742851 DOI: 10.1016/j.virusres.2022.199015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/31/2022] [Accepted: 11/28/2022] [Indexed: 11/30/2022]
Abstract
Partial cleavage of a dengue virus envelope protein, prM, by furin results in a mixture of extracellular particles with variable levels of maturation and infectivity. Partially mature particles can infect leukocytes via interaction between the prM-anti-prM antibody complex with Fcγ receptors. Known prM epitopes involved in antibody-mediated infection are localized to the pr domain. In this study, a group of murine anti-prM monoclonal antibodies with strong infection-enhancing activity was found to reduce the focus size of subsets of multiple dengue serotypes that they could enhance. By employing sets of overlapping peptides, four antibodies recognizing 2-mercaptoethanol-insensitive epitopes were mapped to a common tetrapeptide located distantly in the b-c loop and furin binding site. Substitution mutations of each, or both, of the tetrapeptides in virus-like particles, however, failed to reduce binding. Further mapping experiments were performed using immature virus-like particles with abolished furin binding site to minimize the differential influence of various pr substitutions on pr-M cleavage. Reduction of antibody binding was detected when single alanine substitutions were introduced into the 'a' strand and 'c' strand of pr domain. These findings suggest that the pr 'a and c' strands region is the major binding site of these unusual focus size-reducing anti-prM antibodies.
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Affiliation(s)
- Poonsook Keelapang
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand; Medical Biotechnology Research Unit. National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Bangkok, Thailand
| | - Piyada Supasa
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Rungtawan Sriburi
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Chunya Puttikhunt
- Medical Biotechnology Research Unit. National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Bangkok, Thailand; Molecular Biology of Dengue and Flaviviruses Research Team, Medical Molecular Biotechnology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumthani, Thailand; Division of Dengue Hemorrhagic Fever Research and Siriraj Center of Research Excellence in Dengue and Emerging Pathogens, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Jane Cardosa
- Institute of Health and Community Medicine, Universiti Malaysia Sarawak, Kuching, Sarawak, Malaysia
| | - Watchara Kasinrerk
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand; Biomedical Technology Research Center, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency at the Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Prida Malasit
- Medical Biotechnology Research Unit. National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Bangkok, Thailand; Division of Dengue Hemorrhagic Fever Research and Siriraj Center of Research Excellence in Dengue and Emerging Pathogens, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Nopporn Sittisombut
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand; Medical Biotechnology Research Unit. National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Bangkok, Thailand
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6
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Smith SA, Chruszcz M, Chapman MD, Pomés A. Human Monoclonal IgE Antibodies-a Major Milestone in Allergy. Curr Allergy Asthma Rep 2023; 23:53-65. [PMID: 36459330 PMCID: PMC9831959 DOI: 10.1007/s11882-022-01055-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/14/2022] [Indexed: 12/04/2022]
Abstract
PURPOSE OF REVIEW Bound to its high affinity receptor on mast cells and basophils, the IgE antibody molecule plays an integral role in the allergic reaction. Through interactions with the allergen, it provides the sensitivity and specificity parameters for cell activation and mediator release that produce allergic symptoms. Advancements in human hybridoma technologies allow for the generation and molecular definition of naturally occurring allergen-specific human IgE monoclonal antibodies. RECENT FINDINGS A high-resolution structure of dust mite allergen Der p 2 in complex with Fab of the human IgE mAb 2F10 was recently determined using X-ray crystallography. The structure reveals the fine molecular details of IgE 2F10 binding its 750 Å2 conformational epitope on Der p 2. This review provides an overview of this major milestone in allergy, the first atomic resolution structure of an authentic human IgE epitope. The molecular insights that IgE epitopes provide will allow for structure-based design approaches to the development of novel diagnostics, antibody therapeutics, and immunotherapies.
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Affiliation(s)
- Scott A Smith
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.
| | - Maksymilian Chruszcz
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, 29208, USA
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7
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Phanomchoeng G, Kukiattikoon C, Plengkham S, Boonyasuppayakorn S, Salakij S, Poomrittigul S, Wuttisittikulkij L. Machine-learning-based automated quantification machine for virus plaque assay counting. PeerJ Comput Sci 2022; 8:e878. [PMID: 35494866 PMCID: PMC9044226 DOI: 10.7717/peerj-cs.878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
The plaque assay is a standard quantification system in virology for verifying infectious particles. One of the complex steps of plaque assay is the counting of the number of viral plaques in multiwell plates to study and evaluate viruses. Manual counting plaques are time-consuming and subjective. There is a need to reduce the workload in plaque counting and for a machine to read virus plaque assay; thus, herein, we developed a machine-learning (ML)-based automated quantification machine for viral plaque counting. The machine consists of two major systems: hardware for image acquisition and ML-based software for image viral plaque counting. The hardware is relatively simple to set up, affordable, portable, and automatically acquires a single image or multiple images from a multiwell plate for users. For a 96-well plate, the machine could capture and display all images in less than 1 min. The software is implemented by K-mean clustering using ML and unsupervised learning algorithms to help users and reduce the number of setup parameters for counting and is evaluated using 96-well plates of dengue virus. Bland-Altman analysis indicates that more than 95% of the measurement error is in the upper and lower boundaries [±2 standard deviation]. Also, gage repeatability and reproducibility analysis showed that the machine is capable of applications. Moreover, the average correct measurements by the machine are 85.8%. The ML-based automated quantification machine effectively quantifies the number of viral plaques.
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Affiliation(s)
- Gridsada Phanomchoeng
- Department of Mechanical Engineering, Faculty of Engineering, Chulalongkorn University, Chulalongkorn University, Bangkok, Thailand
- Applied Medical Virology Research Unit, Chulalongkorn University, Chulalongkorn University, Bangkok, Thailand
| | - Chayatorn Kukiattikoon
- Department of Mechanical Engineering, Faculty of Engineering, Chulalongkorn University, Chulalongkorn University, Bangkok, Thailand
| | - Suphanut Plengkham
- Department of Mechanical Engineering, Faculty of Engineering, Chulalongkorn University, Chulalongkorn University, Bangkok, Thailand
| | - Siwaporn Boonyasuppayakorn
- Applied Medical Virology Research Unit, Chulalongkorn University, Chulalongkorn University, Bangkok, Thailand
- Department of Microbiology, Chulalongkorn University, Chulalongkorn University, Bangkok, Thailand
| | - Saran Salakij
- Department of Mechanical Engineering, Faculty of Engineering, Chulalongkorn University, Chulalongkorn University, Bangkok, Thailand
- Applied Medical Virology Research Unit, Chulalongkorn University, Chulalongkorn University, Bangkok, Thailand
| | - Suvit Poomrittigul
- Department of Software Engineering and Information System, Pathumwan Institute of Technology, Pathumwan Institute of Technology, Bangkok, Thailand
| | - Lunchakorn Wuttisittikulkij
- Department of Electrical Engineering, Faculty of Engineering, Chulalongkorn University, Chulalongkorn University, Bangkok, Thailand
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8
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Dengue Virus Serotype 1 Conformational Dynamics Confers Virus Strain-Dependent Patterns of Neutralization by Polyclonal Sera. J Virol 2021; 95:e0095621. [PMID: 34549976 DOI: 10.1128/jvi.00956-21] [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] [Indexed: 12/17/2022] Open
Abstract
Dengue virus cocirculates globally as four serotypes (DENV1 to -4) that vary up to 40% at the amino acid level. Viral strains within a serotype further cluster into multiple genotypes. Eliciting a protective tetravalent neutralizing antibody response is a major goal of vaccine design, and efforts to characterize epitopes targeted by polyclonal mixtures of antibodies are ongoing. Previously, we identified two E protein residues (126 and 157) that defined the serotype-specific antibody response to DENV1 genotype 4 strain West Pac-74. DENV1 and DENV2 human vaccine sera neutralized DENV1 viruses incorporating these substitutions equivalently. In this study, we explored the contribution of these residues to the neutralization of DENV1 strains representing distinct genotypes. While neutralization of the genotype 1 strain TVP2130 was similarly impacted by mutation at E residues 126 and 157, mutation of these residues in the genotype 2 strain 16007 did not markedly change neutralization sensitivity, indicating the existence of additional DENV1 type-specific antibody targets. The accessibility of antibody epitopes can be strongly influenced by the conformational dynamics of virions and modified allosterically by amino acid variation. We found that changes at E domain II residue 204, shown previously to impact access to a poorly accessible E domain III epitope, impacted sensitivity of DENV1 16007 to neutralization by vaccine immune sera. Our data identify a role for minor sequence variation in changes to the antigenic structure that impacts antibody recognition by polyclonal immune sera. Understanding how the many structures sampled by flaviviruses influence antibody recognition will inform the design and evaluation of DENV immunogens. IMPORTANCE Dengue virus (DENV) is an important human pathogen that cocirculates globally as four serotypes. Because sequential infection by different DENV serotypes is associated with more severe disease, eliciting a protective neutralizing antibody response against all four serotypes is a major goal of vaccine efforts. Here, we report that neutralization of DENV serotype 1 by polyclonal antibody is impacted by minor sequence variation among virus strains. Our data suggest that mechanisms that control neutralization sensitivity extend beyond variation within antibody epitopes but also include the influence of single amino acids on the ensemble of structural states sampled by structurally dynamic virions. A more detailed understanding of the antibody targets of DENV-specific polyclonal sera and factors that govern their access to antibody has important implications for flavivirus antigen design and evaluation.
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9
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Natali EN, Babrak LM, Miho E. Prospective Artificial Intelligence to Dissect the Dengue Immune Response and Discover Therapeutics. Front Immunol 2021; 12:574411. [PMID: 34211454 PMCID: PMC8239437 DOI: 10.3389/fimmu.2021.574411] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 05/17/2021] [Indexed: 01/02/2023] Open
Abstract
Dengue virus (DENV) poses a serious threat to global health as the causative agent of dengue fever. The virus is endemic in more than 128 countries resulting in approximately 390 million infection cases each year. Currently, there is no approved therapeutic for treatment nor a fully efficacious vaccine. The development of therapeutics is confounded and hampered by the complexity of the immune response to DENV, in particular to sequential infection with different DENV serotypes (DENV1-5). Researchers have shown that the DENV envelope (E) antigen is primarily responsible for the interaction and subsequent invasion of host cells for all serotypes and can elicit neutralizing antibodies in humans. The advent of high-throughput sequencing and the rapid advancements in computational analysis of complex data, has provided tools for the deconvolution of the DENV immune response. Several types of complex statistical analyses, machine learning models and complex visualizations can be applied to begin answering questions about the B- and T-cell immune responses to multiple infections, antibody-dependent enhancement, identification of novel therapeutics and advance vaccine research.
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Affiliation(s)
- Eriberto N. Natali
- Institute of Medical Engineering and Medical Informatics, School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland FHNW, Muttenz, Switzerland
| | - Lmar M. Babrak
- Institute of Medical Engineering and Medical Informatics, School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland FHNW, Muttenz, Switzerland
| | - Enkelejda Miho
- Institute of Medical Engineering and Medical Informatics, School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland FHNW, Muttenz, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- aiNET GmbH, Basel, Switzerland
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10
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Cross RW, Bornholdt ZA, Prasad AN, Borisevich V, Agans KN, Deer DJ, Abelson DM, Kim DH, Shestowsky WS, Campbell LA, Bunyan E, Geisbert JB, Fenton KA, Zeitlin L, Porter DP, Geisbert TW. Combination therapy protects macaques against advanced Marburg virus disease. Nat Commun 2021; 12:1891. [PMID: 33767178 PMCID: PMC7994808 DOI: 10.1038/s41467-021-22132-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 03/03/2021] [Indexed: 11/08/2022] Open
Abstract
Monoclonal antibodies (mAbs) and remdesivir, a small-molecule antiviral, are promising monotherapies for many viruses, including members of the genera Marburgvirus and Ebolavirus (family Filoviridae), and more recently, SARS-CoV-2. One of the major challenges of acute viral infections is the treatment of advanced disease. Thus, extending the window of therapeutic intervention is critical. Here, we explore the benefit of combination therapy with a mAb and remdesivir in a non-human primate model of Marburg virus (MARV) disease. While rhesus monkeys are protected against lethal infection when treatment with either a human mAb (MR186-YTE; 100%), or remdesivir (80%), is initiated 5 days post-inoculation (dpi) with MARV, no animals survive when either treatment is initiated alone beginning 6 dpi. However, by combining MR186-YTE with remdesivir beginning 6 dpi, significant protection (80%) is achieved, thereby extending the therapeutic window. These results suggest value in exploring combination therapy in patients presenting with advanced filovirus disease.
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Affiliation(s)
- Robert W Cross
- Galveston National Laboratory, University of Texas Medical Branch, 301 University Blvd, Galveston, TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX, USA
| | | | - Abhishek N Prasad
- Galveston National Laboratory, University of Texas Medical Branch, 301 University Blvd, Galveston, TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX, USA
| | - Viktoriya Borisevich
- Galveston National Laboratory, University of Texas Medical Branch, 301 University Blvd, Galveston, TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX, USA
| | - Krystle N Agans
- Galveston National Laboratory, University of Texas Medical Branch, 301 University Blvd, Galveston, TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX, USA
| | - Daniel J Deer
- Galveston National Laboratory, University of Texas Medical Branch, 301 University Blvd, Galveston, TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX, USA
| | - Dafna M Abelson
- Mapp Biopharmaceutical, Inc., 6160 Lusk Blvd Ste C200, San Diego, CA, USA
| | - Do H Kim
- Mapp Biopharmaceutical, Inc., 6160 Lusk Blvd Ste C200, San Diego, CA, USA
| | | | | | - Elaine Bunyan
- Gilead Sciences, Inc., 333 Lakeside Dr, Foster City, CA, USA
| | - Joan B Geisbert
- Galveston National Laboratory, University of Texas Medical Branch, 301 University Blvd, Galveston, TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX, USA
| | - Karla A Fenton
- Galveston National Laboratory, University of Texas Medical Branch, 301 University Blvd, Galveston, TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX, USA
| | - Larry Zeitlin
- Mapp Biopharmaceutical, Inc., 6160 Lusk Blvd Ste C200, San Diego, CA, USA.
| | | | - Thomas W Geisbert
- Galveston National Laboratory, University of Texas Medical Branch, 301 University Blvd, Galveston, TX, USA.
- Department of Microbiology and Immunology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX, USA.
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11
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Young E, Carnahan RH, Andrade DV, Kose N, Nargi RS, Fritch EJ, Munt JE, Doyle MP, White L, Baric TJ, Stoops M, DeSilva A, Tse LV, Martinez DR, Zhu D, Metz S, Wong MP, Espinosa DA, Montoya M, Biering SB, Sukulpolvi-Petty S, Kuan G, Balmaseda A, Diamond MS, Harris E, Crowe JE, Baric RS. Identification of Dengue Virus Serotype 3 Specific Antigenic Sites Targeted by Neutralizing Human Antibodies. Cell Host Microbe 2021; 27:710-724.e7. [PMID: 32407709 PMCID: PMC7309352 DOI: 10.1016/j.chom.2020.04.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/18/2020] [Accepted: 04/06/2020] [Indexed: 12/31/2022]
Abstract
The rational design of dengue virus (DENV) vaccines requires a detailed understanding of the molecular basis for antibody-mediated immunity. The durably protective antibody response to DENV after primary infection is serotype specific. However, there is an incomplete understanding of the antigenic determinants for DENV type-specific (TS) antibodies, especially for DENV serotype 3, which has only one well-studied, strongly neutralizing human monoclonal antibody (mAb). Here, we investigated the human B cell response in children after natural DENV infection in the endemic area of Nicaragua and isolated 15 DENV3 TS mAbs recognizing the envelope (E) glycoprotein. Functional epitope mapping of these mAbs and small animal prophylaxis studies revealed a complex landscape with protective epitopes clustering in at least 6-7 antigenic sites. Potently neutralizing TS mAbs recognized sites principally in E glycoprotein domains I and II, and patterns suggest frequent recognition of quaternary structures on the surface of viral particles.
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Affiliation(s)
- Ellen Young
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Robert H Carnahan
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Daniela V Andrade
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California Berkeley, Berkeley, CA, USA
| | - Nurgun Kose
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Rachel S Nargi
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ethan J Fritch
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Jennifer E Munt
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Michael P Doyle
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Laura White
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Thomas J Baric
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Mark Stoops
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Aravinda DeSilva
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Longping V Tse
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - David R Martinez
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Deanna Zhu
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Stefan Metz
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Marcus P Wong
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California Berkeley, Berkeley, CA, USA
| | - Diego A Espinosa
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California Berkeley, Berkeley, CA, USA
| | - Magelda Montoya
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California Berkeley, Berkeley, CA, USA
| | - Scott B Biering
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California Berkeley, Berkeley, CA, USA
| | - Soila Sukulpolvi-Petty
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Guillermina Kuan
- Health Center Sócrates Flores Vivas, Ministry of Health, Managua, Nicaragua
| | - Angel Balmaseda
- National Virology Laboratory, National Center for Diagnosis and Reference, Ministry of Health, Managua, Nicaragua
| | - Michael S Diamond
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA; Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63110, USA; Pathology & Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California Berkeley, Berkeley, CA, USA.
| | - James E Crowe
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Ralph S Baric
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina, Chapel Hill, NC, USA; Department of Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill, NC, USA.
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12
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Tu HA, Nivarthi UK, Graham NR, Eisenhauer P, Delacruz MJ, Pierce KK, Whitehead SS, Boyson JE, Botten JW, Kirkpatrick BD, Durbin AP, deSilva AM, Diehl SA. Stimulation of B Cell Immunity in Flavivirus-Naive Individuals by the Tetravalent Live Attenuated Dengue Vaccine TV003. Cell Rep Med 2020; 1:100155. [PMID: 33377126 PMCID: PMC7762770 DOI: 10.1016/j.xcrm.2020.100155] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 09/09/2020] [Accepted: 11/18/2020] [Indexed: 02/05/2023]
Abstract
The tetravalent live attenuated dengue vaccine candidate TV003 induces neutralizing antibodies against all four dengue virus serotypes (DENV1-DENV4) and protects against experimental challenge with DENV2 in humans. Here, we track vaccine viremia and B and T cell responses to this vaccination/challenge model to understand how vaccine viremia links adaptive immunity and development of protective antibody responses. TV003 viremia triggers an acute plasmablast response that, in combination with DENV-specific CD4+ T cells, correlates with serum neutralizing antibodies. TV003 vaccinees develop DENV2-reactive memory B cells, including serotype-specific and multivalent specificities in line with the composition of serum antibodies. There is no post-challenge plasmablast response in vaccinees, although stronger and earlier post-TV003 plasmablast responses associate with sterile humoral protection from DENV2 challenge. TV003 vaccine triggers plasmablasts and memory B cells, which, with support from CD4+ T cells, functionally link early vaccine viremia and the serum antibody responses.
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Affiliation(s)
- Huy A. Tu
- Department of Microbiology and Molecular Genetics, Vaccine Testing Center, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
- Cellular, Molecular, and Biomedical Sciences Graduate Program, University of Vermont, Burlington, VT 05405, USA
| | - Usha K. Nivarthi
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Nancy R. Graham
- Department of Microbiology and Molecular Genetics, Vaccine Testing Center, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Philip Eisenhauer
- Department of Medicine, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Matthew J. Delacruz
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Kristen K. Pierce
- Department of Microbiology and Molecular Genetics, Vaccine Testing Center, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
- Department of Medicine, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Stephen S. Whitehead
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jonathan E. Boyson
- Cellular, Molecular, and Biomedical Sciences Graduate Program, University of Vermont, Burlington, VT 05405, USA
- Department of Surgery, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Jason W. Botten
- Department of Microbiology and Molecular Genetics, Vaccine Testing Center, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
- Cellular, Molecular, and Biomedical Sciences Graduate Program, University of Vermont, Burlington, VT 05405, USA
- Department of Medicine, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Beth D. Kirkpatrick
- Department of Microbiology and Molecular Genetics, Vaccine Testing Center, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
- Department of Medicine, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Anna P. Durbin
- Department of International Health, Center for Immunization Research, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Aravinda M. deSilva
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Sean A. Diehl
- Department of Microbiology and Molecular Genetics, Vaccine Testing Center, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
- Cellular, Molecular, and Biomedical Sciences Graduate Program, University of Vermont, Burlington, VT 05405, USA
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13
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Subdominance in Antibody Responses: Implications for Vaccine Development. Microbiol Mol Biol Rev 2020; 85:85/1/e00078-20. [PMID: 33239435 DOI: 10.1128/mmbr.00078-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Vaccines work primarily by eliciting antibodies, even when recovery from natural infection depends on cellular immunity. Large efforts have therefore been made to identify microbial antigens that elicit protective antibodies, but these endeavors have encountered major difficulties, as witnessed by the lack of vaccines against many pathogens. This review summarizes accumulating evidence that subdominant protein regions, i.e., surface-exposed regions that elicit relatively weak antibody responses, are of particular interest for vaccine development. This concept may seem counterintuitive, but subdominance may represent an immune evasion mechanism, implying that the corresponding region potentially is a key target for protective immunity. Following a presentation of the concepts of immunodominance and subdominance, the review will present work on subdominant regions in several major human pathogens: the protozoan Plasmodium falciparum, two species of pathogenic streptococci, and the dengue and influenza viruses. Later sections are devoted to the molecular basis of subdominance, its potential role in immune evasion, and general implications for vaccine development. Special emphasis will be placed on the fact that a whole surface-exposed protein domain can be subdominant, as demonstrated for all of the pathogens described here. Overall, the available data indicate that subdominant protein regions are of much interest for vaccine development, not least in bacterial and protozoal systems, for which antibody subdominance remains largely unexplored.
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14
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Wilken L, Rimmelzwaan GF. Adaptive Immunity to Dengue Virus: Slippery Slope or Solid Ground for Rational Vaccine Design? Pathogens 2020; 9:pathogens9060470. [PMID: 32549226 PMCID: PMC7350362 DOI: 10.3390/pathogens9060470] [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: 05/22/2020] [Revised: 06/11/2020] [Accepted: 06/12/2020] [Indexed: 12/15/2022] Open
Abstract
The four serotypes of dengue virus are the most widespread causes of arboviral disease, currently placing half of the human population at risk of infection. Pre-existing immunity to one dengue virus serotype can predispose to severe disease following secondary infection with a different serotype. The phenomenon of immune enhancement has complicated vaccine development and likely explains the poor long-term safety profile of a recently licenced dengue vaccine. Therefore, alternative vaccine strategies should be considered. This review summarises studies dissecting the adaptive immune responses to dengue virus infection and (experimental) vaccination. In particular, we discuss the roles of (i) neutralising antibodies, (ii) antibodies to non-structural protein 1, and (iii) T cells in protection and pathogenesis. We also address how these findings could translate into next-generation vaccine approaches that mitigate the risk of enhanced dengue disease. Finally, we argue that the development of a safe and efficacious dengue vaccine is an attainable goal.
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15
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Swanstrom JA, Nivarthi UK, Patel B, Delacruz MJ, Yount B, Widman DG, Durbin AP, Whitehead SS, De Silva AM, Baric RS. Beyond Neutralizing Antibody Levels: The Epitope Specificity of Antibodies Induced by National Institutes of Health Monovalent Dengue Virus Vaccines. J Infect Dis 2020; 220:219-227. [PMID: 30895307 PMCID: PMC6581895 DOI: 10.1093/infdis/jiz109] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 03/19/2019] [Indexed: 11/24/2022] Open
Abstract
Background Dengue virus is an emerging mosquito-borne flavivirus responsible for considerable morbidity and mortality worldwide. The Division of Intramural Research, National Institute of Allergy and Infectious Diseases of the US National Institutes of Health (NIH) has developed live attenuated vaccines to each of the 4 serotypes of dengue virus (DENV1–4). While overall levels of DENV neutralizing antibodies (nAbs) in humans have been correlated with protection, these correlations vary depending on DENV serotype, prevaccination immunostatus, age, and study site. By combining both the level and molecular specificity of nAbs to each serotype, it may be possible to develop more robust correlates that predict long-term outcome. Methods Using depletions and recombinant chimeric epitope transplant DENVs, we evaluate the molecular specificity and mapped specific epitopes and antigenic regions targeted by vaccine-induced nAbs in volunteers who received the NIH monovalent vaccines against each DENV serotype. Results After monovalent vaccination, subjects developed high levels of nAbs that mainly targeted epitopes that are unique (type-specific) to each DENV serotype. The DENV1, 2, and 4 monovalent vaccines induced type-specific nAbs directed to quaternary structure envelope epitopes known to be targets of strongly neutralizing antibodies induced by wild-type DENV infections. Conclusions Our results reported here on the molecular specificity of NIH vaccine–induced antibodies enable new strategies, beyond the absolute levels of nAbs, for determining correlates and mechanisms of protective immunity.
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Affiliation(s)
- Jesica A Swanstrom
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill
| | - Usha K Nivarthi
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill
| | - Bhumi Patel
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill
| | - Matthew J Delacruz
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill
| | - Boyd Yount
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill
| | - Douglas G Widman
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill
| | - Anna P Durbin
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore.,Center for Immunization Research, Johns Hopkins Bloomberg School of Public Health, Baltimore
| | - Stephen S Whitehead
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Aravinda M De Silva
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill
| | - Ralph S Baric
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill
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16
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Shaw JB, Liu W, Vasil′ev YV, Bracken CC, Malhan N, Guthals A, Beckman JS, Voinov VG. Direct Determination of Antibody Chain Pairing by Top-down and Middle-down Mass Spectrometry Using Electron Capture Dissociation and Ultraviolet Photodissociation. Anal Chem 2020; 92:766-773. [PMID: 31769659 PMCID: PMC7819135 DOI: 10.1021/acs.analchem.9b03129] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
One challenge associated with the discovery and development of monoclonal antibody (mAb) therapeutics is the determination of heavy chain and light chain pairing. Advances in MS instrumentation and MS/MS methods have greatly enhanced capabilities for the analysis of large intact proteins yielding much more detailed and accurate proteoform characterization. Consequently, direct interrogation of intact antibodies or F(ab')2 and Fab fragments has the potential to significantly streamline therapeutic mAb discovery processes. Here, we demonstrate for the first time the ability to efficiently cleave disulfide bonds linking heavy and light chains of mAbs using electron capture dissociation (ECD) and 157 nm ultraviolet photodissociation (UVPD). The combination of intact mAb, Fab, or F(ab')2 mass, intact LC and Fd masses, and CDR3 sequence coverage enabled determination of heavy chain and light chain pairing from a single experiment and experimental condition. These results demonstrate the potential of top-down and middle-down proteomics to significantly streamline therapeutic antibody discovery.
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Affiliation(s)
- Jared B. Shaw
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Boulevard, Richland, Washington 99354, United States
| | - Weijing Liu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Boulevard, Richland, Washington 99354, United States
| | - Yury V. Vasil′ev
- e-MSion Inc., 2121 NE Jack London Drive, Corvallis, Oregon 97330, United States
- Linus Pauling Institute and the Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
| | - Carter C. Bracken
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Boulevard, Richland, Washington 99354, United States
| | - Neha Malhan
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Boulevard, Richland, Washington 99354, United States
| | - Adrian Guthals
- Mapp Biopharmaceutical Inc., 6160 Lusk Boulevard #105, San Diego, California 92121, United States
| | - Joseph S. Beckman
- e-MSion Inc., 2121 NE Jack London Drive, Corvallis, Oregon 97330, United States
- Linus Pauling Institute and the Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
| | - Valery G. Voinov
- e-MSion Inc., 2121 NE Jack London Drive, Corvallis, Oregon 97330, United States
- Linus Pauling Institute and the Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
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17
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Swanstrom JA, Henein S, Plante JA, Yount BL, Widman DG, Gallichotte EN, Dean HJ, Osorio JE, Partidos CD, de Silva AM, Baric RS. Analyzing the Human Serum Antibody Responses to a Live Attenuated Tetravalent Dengue Vaccine Candidate. J Infect Dis 2019; 217:1932-1941. [PMID: 29800370 DOI: 10.1093/infdis/jiy063] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Background Dengue virus serotypes 1-4 (DENV-1-4) are the most common vector-borne viral pathogens of humans and the etiological agents of dengue fever and dengue hemorrhagic syndrome. A live-attenuated tetravalent dengue vaccine (TDV) developed by Takeda Vaccines has recently progressed to phase 3 safety and efficacy evaluation. Methods We analyzed the qualitative features of the neutralizing antibody (nAb) response induced in naive and DENV-immune individuals after TDV administration. Using DENV-specific human monoclonal antibodies (mAbs) and recombinant DENV displaying different serotype-specific Ab epitopes, we mapped the specificity of TDV-induced nAbs against DENV-1-3. Results Nearly all subjects had high levels of DENV-2-specific nAbs directed to epitopes centered on domain III of the envelope protein. In some individuals, the vaccine induced nAbs that tracked with a DENV-1-specific neutralizing epitope centered on domain I of the envelope protein. The vaccine induced binding Abs directed to a DENV-3 type-specific neutralizing epitope, but findings of mapping of DENV-3 type-specific nAbs were inconclusive. Conclusion Here we provide qualitative measures of the magnitude and epitope specificity of the nAb responses to TDV. This information will be useful for understanding the performance of TDV in clinical trials and for identifying correlates of protective immunity.
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Affiliation(s)
- Jesica A Swanstrom
- Department of Epidemiology, School of Public Health, University of North Carolina, Chapel Hill
| | - Sandra Henein
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill
| | - Jessica A Plante
- Department of Epidemiology, School of Public Health, University of North Carolina, Chapel Hill
| | - Boyd L Yount
- Department of Epidemiology, School of Public Health, University of North Carolina, Chapel Hill
| | - Douglas G Widman
- Department of Epidemiology, School of Public Health, University of North Carolina, Chapel Hill
| | - Emily N Gallichotte
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill
| | | | | | | | - Aravinda M de Silva
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill
| | - Ralph S Baric
- Department of Epidemiology, School of Public Health, University of North Carolina, Chapel Hill.,Department of Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill
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18
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Halstead SB, Dans LF. Dengue infection and advances in dengue vaccines for children. THE LANCET CHILD & ADOLESCENT HEALTH 2019; 3:734-741. [PMID: 31378686 DOI: 10.1016/s2352-4642(19)30205-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 05/23/2019] [Accepted: 06/10/2019] [Indexed: 12/26/2022]
Abstract
Dengue viruses are endemic in most tropical and subtropical countries where they produce disease ranging from a mild fever to a severe, potentially fatal vascular permeability syndrome. We reviewed the status of development and testing in children of three vaccines designed to protect against the four dengue viruses. The first dengue virus vaccine, Dengvaxia, now licensed in 20 endemic countries, the EU and the USA, provides protection against severe dengue in seropositive individuals but increases the risk for naive recipients to develop severe dengue and to be hospitalised. We discuss mechanisms and implications of shortcomings of the licensed vaccine and describe the structure and attributes of two other dengue virus vaccines. Based upon human dengue challenge studies, one of these vaccines promises to deliver solid, long-lasting immunity after a single dose. Because dengue virus infections are ubiquitous in residents and visitors to tropical countries, in the absence of a protective vaccine paediatricians should recognise the early signs and clinical presentation of severe dengue, understand its pathophysiology and appropriate management.
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Affiliation(s)
- Scott B Halstead
- Uniformed Services University of the Health Sciences, Bethesda, MD, USA.
| | - Leonila F Dans
- Departments of Pediatrics and Clinical Epidemiology, College of Medicine, University of the Philippines, Manila, Philippines
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19
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Abstract
This is a selective review of recent publications on dengue clinical features, epidemiology, pathogenesis, and vaccine development placed in a context of observations made over the past half century. Four dengue viruses (DENVs) are transmitted by urban cycle mosquitoes causing diseases whose nature and severity are influenced by interacting factors such as virus, age, immune status of the host, and human genetic variability. A phenomenon that controls the kinetics of DENV infection, antibody-dependent enhancement, best explains the correlation of the vascular permeability syndrome with second heterotypic DENV infections and infection in the presence of passively acquired antibodies. Based on growing evidence in vivo and in vitro, the tissue-damaging DENV non-structural protein 1 (NS1) is responsible for most of the pathophysiological features of severe dengue. This review considers the contribution of hemophagocytic histiocytosis syndrome to cases of severe dengue, the role of movement of humans in dengue epidemiology, and modeling and planning control programs and describes a country-wide survey for dengue infections in Bangladesh and efforts to learn what controls the clinical outcome of dengue infections. Progress and problems with three tetravalent live-attenuated vaccines are reviewed. Several research mysteries remain: why is the risk of severe disease during second heterotypic DENV infection so low, why is the onset of vascular permeability correlated with defervescence, and what are the crucial components of protective immunity?
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Affiliation(s)
- Scott Halstead
- Emeritus Professor, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
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20
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Lyski ZL, Messer WB. Approaches to Interrogating the Human Memory B-Cell and Memory-Derived Antibody Repertoire Following Dengue Virus Infection. Front Immunol 2019; 10:1276. [PMID: 31244836 PMCID: PMC6562360 DOI: 10.3389/fimmu.2019.01276] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 05/20/2019] [Indexed: 12/21/2022] Open
Abstract
Memory B-cells (MBCs) are potential antibody secreting immune cells that differentiate and mature following host exposure to a pathogen. Following differentiation, MBCs remain in peripheral circulation after recovery and are poised to secrete antigen-specific antibodies if and when they are re-exposed to their cognate antigen. Consequently, MBCs form the founder population and provide one of the first lines of pathogen-specific defense against reinfection. The role MBCs play is complicated for viruses that are heterologous, such as dengue virus (DENV), which exist as antigenically different serotypes. On second infection with a different serotype, MBCs from initial dengue infection rapidly proliferate and secrete antibodies: many of these MBC derived antibodies will be cross-reactive and weakly neutralizing, while some antibodies may recognize epitopes conserved across serotypes and have the capacity to broadly neutralize 2 or more serotypes. It is also possible that a new population of MBCs and antibodies specific for the second virus serotype need to arise for long-term broader immunity to develop. Methods to interrogate and track memory B cell responses are important for evaluating both natural immunity and vaccine response. However, the low abundance of MBCs for any specific pathogen makes it challenging to interrogate frequency, specificity, and breadth for the pathogen of interest. This review discusses current approaches that have been used to interrogate the memory B cell immune response against viral pathogens in general and DENV specifically. Including strengths, limitations, and future directions. Single-cell approaches could help uncover the DENV specific MBC antibody repertoire, and improved methods for isolating DENV specific monoclonal antibodies from human peripheral blood cells would allow for a functional analysis of the anti-DENV repertoire.
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Affiliation(s)
- Zoe L Lyski
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, Portland, OR, United States
| | - William B Messer
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, Portland, OR, United States
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21
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Nivarthi UK, Tu HA, Delacruz MJ, Swanstrom J, Patel B, Durbin AP, Whitehead SS, Pierce KK, Kirkpatrick BD, Baric RS, Nguyen N, Emerling DE, de Silva AM, Diehl SA. Longitudinal analysis of acute and convalescent B cell responses in a human primary dengue serotype 2 infection model. EBioMedicine 2019; 41:465-478. [PMID: 30857944 PMCID: PMC6444124 DOI: 10.1016/j.ebiom.2019.02.060] [Citation(s) in RCA: 20] [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: 12/18/2018] [Revised: 02/18/2019] [Accepted: 02/28/2019] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Acute viral infections induce a rapid and transient increase in antibody-secreting plasmablasts. At convalescence, memory B cells (MBC) and long-lived plasma cells (LLPC) are responsible for long-term humoral immunity. Following an acute viral infection, the specific properties and relationships between antibodies produced by these B cell compartments are poorly understood. METHODS We utilized a controlled human challenge model of primary dengue virus serotype 2 (DENV2) infection to study acute and convalescent B-cell responses. FINDINGS The level of DENV2 replication was correlated with the magnitude of the plasmablast response. Functional analysis of plasmablast-derived monoclonal antibodies showed that the DENV2-specific response was dominated by cells producing DENV2 serotype-specific antibodies. DENV2-neutralizing antibodies targeted quaternary structure epitopes centered on domain III of the viral envelope protein (EDIII). Functional analysis of MBC and serum antibodies from the same subjects six months post-challenge revealed maintenance of the serotype-specific response in both compartments. The serum response mainly targeted DENV2 serotype-specific epitopes on EDIII. INTERPRETATION Our data suggest overall functional alignment of DENV2-specific responses from the plasmablast, through the MBC and LLPC compartments following primary DENV2 inflection. These results provide enhanced resolution of the temporal and specificity of the B cell compartment in viral infection and serve as framework for evaluation of B cell responses in challenge models. FUNDING This study was supported by the Bill and Melinda Gates Foundation and the National Institutes of Health.
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Affiliation(s)
- Usha K Nivarthi
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, USA
| | - Huy A Tu
- Department of Microbiology and Molecular Genetics, Vaccine Testing Center, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA; Cellular, Molecular, and Biomedical Sciences Graduate Program, University of Vermont, Burlington, VT 05405, USA
| | - Matthew J Delacruz
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, USA
| | - Jesica Swanstrom
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, USA
| | - Bhumi Patel
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, USA
| | - Anna P Durbin
- Department of International Health, Center for Immunization Research, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Stephen S Whitehead
- Laboratory of Infectious Diseases, NIAID, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kristen K Pierce
- Department of Microbiology and Molecular Genetics, Vaccine Testing Center, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Beth D Kirkpatrick
- Department of Microbiology and Molecular Genetics, Vaccine Testing Center, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Ralph S Baric
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, USA
| | - Ngan Nguyen
- Atreca, Inc. Redwood City, California 94063, USA
| | | | - Aravinda M de Silva
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, USA.
| | - Sean A Diehl
- Department of Microbiology and Molecular Genetics, Vaccine Testing Center, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA.
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22
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Andrade P, Gimblet-Ochieng C, Modirian F, Collins M, Cárdenas M, Katzelnick LC, Montoya M, Michlmayr D, Kuan G, Balmaseda A, Coloma J, de Silva AM, Harris E. Impact of pre-existing dengue immunity on human antibody and memory B cell responses to Zika. Nat Commun 2019; 10:938. [PMID: 30808875 PMCID: PMC6391383 DOI: 10.1038/s41467-019-08845-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 02/04/2019] [Indexed: 12/21/2022] Open
Abstract
Little is known about enduring memory B cell (MBC) responses to Zika virus (ZIKV) and their relationship with circulating antibodies. Here we comprehensively assess MBC frequency and specificity alongside serum binding and neutralizing antibody responses to ZIKV ~2 weeks and ~8 months postinfection in 31 pediatric subjects with 0, 1 or >1 prior infections with the related dengue virus (DENV). ZIKV infection elicits a robust type-specific MBC response, and the majority of late convalescent anti-ZIKV serum neutralizing activity is attributable to ZIKV-specific antibodies. The number of prior DENV infections does not influence type-specific or cross-reactive MBC responses, although ZIKV has the highest cross-reactivity with DENV3. DENV cross-reactive MBCs expanded by ZIKV infection decline in number and proportion by late convalescence. Finally, ZIKV induces greater cross-reactivity in the MBC pool than in serum antibodies. Our data suggest immunity to DENV only modestly shapes breadth and magnitude of enduring ZIKV antibody responses.
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Affiliation(s)
- Paulina Andrade
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, 94720-3370, USA
- Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, EC170157, Ecuador
| | - Ciara Gimblet-Ochieng
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, 27599-7292, USA
| | - Faraz Modirian
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, 94720-3370, USA
| | - Matthew Collins
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, 27599-7292, USA
- Hope Clinic of the Emory Vaccine Center, Division of Infectious Diseases, Department of Medicine, School of Medicine, Emory University, Decatur, GA, 30030, USA
| | - Maritza Cárdenas
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, 94720-3370, USA
| | - Leah C Katzelnick
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, 94720-3370, USA
| | - Magelda Montoya
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, 94720-3370, USA
| | - Daniela Michlmayr
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, 94720-3370, USA
| | - Guillermina Kuan
- Centro de Salud Sócrates Flores Vivas, Ministry of Health, Managua, 12014, Nicaragua
- Sustainable Sciences Institute, Managua, 14007, Nicaragua
| | - Angel Balmaseda
- Sustainable Sciences Institute, Managua, 14007, Nicaragua
- Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Managua, 16064, Nicaragua
| | - Josefina Coloma
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, 94720-3370, USA
| | - Aravinda M de Silva
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, 27599-7292, USA
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, 94720-3370, USA.
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23
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Katzelnick LC, Coello Escoto A, McElvany BD, Chávez C, Salje H, Luo W, Rodriguez-Barraquer I, Jarman R, Durbin AP, Diehl SA, Smith DJ, Whitehead SS, Cummings DAT. Viridot: An automated virus plaque (immunofocus) counter for the measurement of serological neutralizing responses with application to dengue virus. PLoS Negl Trop Dis 2018; 12:e0006862. [PMID: 30356267 PMCID: PMC6226209 DOI: 10.1371/journal.pntd.0006862] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 11/09/2018] [Accepted: 09/20/2018] [Indexed: 12/12/2022] Open
Abstract
The gold-standard method for quantifying neutralizing antibody responses to many viruses, including dengue virus (DENV), is the plaque reduction neutralization test (PRNT, also called the immunofocus reduction neutralization test). The PRNT conducted on 96-well plates is high-throughput and requires a smaller volume of antiserum than on 6- or 24-well plates, but manual plaque counting is challenging and existing automated plaque counters are expensive or difficult to optimize. We have developed Viridot (Viridot package), a program for R with a user interface in shiny, that counts viral plaques of a variety of phenotypes, estimates neutralizing antibody titers, and performs other calculations of use to virologists. The Viridot plaque counter includes an automatic parameter identification mode (misses <10 plaques/well for 87% of diverse DENV strains [n = 1521]) and a mode that allows the user to fine-tune the parameters used for counting plaques. We compared standardized manual and Viridot plaque counting methods applied to the same wells by two analyses and found that Viridot plaque counts were as similar to the same analyst's manual count (Lin’s concordance correlation coefficient, ρc = 0.99 [95% confidence interval: 0.99–1.00]) as manual counts between analysts (ρc = 0.99 [95% CI: 0.98–0.99]). The average ratio of neutralizing antibody titers based on manual counted plaques to Viridot counted plaques was 1.05 (95% CI: 0.98–1.14), similar to the average ratio of antibody titers based on manual plaque counts by the two analysts (1.06 [95% CI: 0.84–1.34]). Across diverse DENV and ZIKV strains (n = 14), manual and Viridot plaque counts were mostly consistent (range of ρc = 0.74 to 1.00) and the average ratio of antibody titers based on manual and Viridot counted plaques was close to 1 (0.94 [0.86–1.02]). Thus, Viridot can be used for plaque counting and neutralizing antibody titer estimation of diverse DENV strains and potentially other viruses on 96-well plates as well as for formalization of plaque-counting rules for standardization across experiments and analysts. Although the plaque reduction neutralization test (PRNT) is an important assay for measuring neutralizing antibody responses against many viruses, no free, open-source programs specifically designed for virus plaque counting and neutralizing antibody titer estimation are available. We have developed Viridot, a package for R with a user-interface in shiny, which is designed for use by laboratory-based virologists and researchers with minimal coding experience. The program includes: automatic and user-specification of settings for plaque counting; saving of plaque counting settings; counting of many plates at once; and easy output of plaque counts, plaque sizes, and images with counted plaques circled. Viridot also includes programs to analyze plaque counts, including estimation of: neutralizing antibody titers, pfu/mL of a virus stock, and the dilution factor of virus needed for an experiment. Viridot can be used to standardize plaque-counting methods within and between laboratories, helping researchers formalize an important aspect of the PRNT method that is often subjective. Viridot thus provides laboratory researchers around the world with a free tool to improve the speed and consistency with which the PRNT is conducted, aiding the public health response to emerging viral diseases.
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Affiliation(s)
- Leah C. Katzelnick
- Department of Biology, University of Florida, Gainesville, FL, United States
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, United States
- * E-mail:
| | - Ana Coello Escoto
- Department of Biology, University of Florida, Gainesville, FL, United States
| | - Benjamin D. McElvany
- Department of Medicine-Infectious Disease, Vaccine Testing Center, University of Vermont Larner College of Medicine, Burlington, VT, United States
| | - Christian Chávez
- Department of Biology, University of Florida, Gainesville, FL, United States
| | - Henrik Salje
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, Paris, France
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Wensheng Luo
- Center for Immunization Research, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Isabel Rodriguez-Barraquer
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
- School of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Richard Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Anna P. Durbin
- Center for Immunization Research, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Sean A. Diehl
- Department of Medicine-Infectious Disease, Vaccine Testing Center, University of Vermont Larner College of Medicine, Burlington, VT, United States
| | - Derek J. Smith
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Stephen S. Whitehead
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Derek A. T. Cummings
- Department of Biology, University of Florida, Gainesville, FL, United States
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States
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24
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Lu J, Wang R, Xia B, Yu Y, Zhou X, Yang Z, Huang P. Potent Neutralization Ability of a Human Monoclonal Antibody Against Serotype 1 Dengue Virus. Front Microbiol 2018; 9:1214. [PMID: 29928270 PMCID: PMC5997965 DOI: 10.3389/fmicb.2018.01214] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 05/18/2018] [Indexed: 11/13/2022] Open
Abstract
The incidence of dengue virus (DENV) infections has been escalating in tropical and subtropical countries, but there are still no effective therapeutic options. In the present study, a DENV-1-specific human monoclonal antibody (HMAb), 1G5, isolated from single plasma cells obtained from the peripheral blood mononuclear cells of dengue patients was found to have potent neutralization activity against serotype 1 DENV (DENV-1). Its neutralization activity against DENV-2 was not as strong, and it was almost absent for DENV-3 and DENV-4. The results showed that HMAb 1G5 only binds to the envelop protein of intact DENV-1 or the envelop protein under unheated and non-reducing conditions, and that it does not bind to recombinant envelope protein. This could mean that the antibody recognizes a conformational epitope of the envelope protein. Further, the findings showed that HMAb 1G5 potently neutralizes DENV-1 in both the pre- and post-attachment phases of the virus at low concentrations. In vivo studies showed that HMAb 1G5 provides protection from DENV-1 infection in a murine model. In addition, antibody-dependent enhancement that occurs at lower doses of the antibody was completely abrogated by the introduction of Leu-to-Ala mutations (1G5-LALA) or deletion of nine amino acids (1G5-9del) in the Fc region. Therefore, HMAb 1G5 shows promise as a safe and effective agent for prophylactic and therapeutic treatment of DENV-1 infection.
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Affiliation(s)
- Jiansheng Lu
- Laboratory of Protein Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Rong Wang
- Laboratory of Protein Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Binghui Xia
- Laboratory of Protein Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Yunzhou Yu
- Laboratory of Protein Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Xiaowei Zhou
- Laboratory of Protein Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Zhixin Yang
- Laboratory of Protein Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Peitang Huang
- Laboratory of Protein Engineering, Beijing Institute of Biotechnology, Beijing, China
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25
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Halstead SB. Which Dengue Vaccine Approach Is the Most Promising, and Should We Be Concerned about Enhanced Disease after Vaccination? There Is Only One True Winner. Cold Spring Harb Perspect Biol 2018; 10:a030700. [PMID: 28716893 PMCID: PMC5983193 DOI: 10.1101/cshperspect.a030700] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The scientific community now possesses information obtained directly from human beings that makes it possible to understand why breakthrough-enhanced dengue virus (DENV) infections occurred in children receiving Sanofi Pasteur's Dengvaxia tetravalent live attenuated vaccine and to predict the possibility of breakthrough-enhanced DENV infections following immunization with two other tetravalent live attenuated vaccines now in phase III testing. Based upon recent research, Dengvaxia, lacking DENV nonstructural protein antigens, did not protect seronegatives because it failed to raise a competent T-cell response and/or antibodies to NS1. It is also possible that chimeric structure does not present the correct virion conformation permitting the development of protective neutralizing antibodies. A premonitory signal shared by the Sanofi Pasteur and the Takeda vaccines was the failure of fully immunized subhuman primates to prevent low-level viremia and/or anamnestic antibody responses to live DENV challenge. The vaccine developed by the National Institute of Allergy and Infectious Diseases (National Institutes of Health [NIH]) has met virtually all of the goals needed to demonstrate preclinical efficacy and safety for humans. Each monovalent vaccine was comprehensively studied for reactogenicity and immunogenicity in human volunteers. Protective immunity in subjects receiving tetravalent candidate vaccines was evidenced by the fact that when vaccinated subjects were given further doses of vaccine or different strains of DENV the result was "solid immunity," a nonviremic and nonanamnestic immune response.
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Affiliation(s)
- Scott B Halstead
- Department of Preventive Medicine and Biometrics, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20817
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26
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Crowe JE. Principles of Broad and Potent Antiviral Human Antibodies: Insights for Vaccine Design. Cell Host Microbe 2018; 22:193-206. [PMID: 28799905 DOI: 10.1016/j.chom.2017.07.013] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Antibodies are the principal immune effectors that mediate protection against reinfection following viral infection or vaccination. Robust techniques for human mAb isolation have been developed in the last decade. The study of human mAbs isolated from subjects with prior immunity has become a mainstay for rational structure-based, next-generation vaccine development. The plethora of detailed molecular and genetic studies coupling the structure of antigen-antibody complexes with their antiviral function has begun to reveal common principles of critical interactions on which we can build better vaccines and therapeutic antibodies. This review outlines the approaches to isolating and studying human antiviral mAbs and discusses the common principles underlying the basis for their activity. This review also examines progress toward the goal of achieving a comprehensive understanding of the chemical and physical basis for molecular recognition of viral surface proteins in order to build predictive molecular models that can be used for vaccine design.
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Affiliation(s)
- James E Crowe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, TN 37232, USA; Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
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27
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Hegde NR, Gauthami S, Sampath Kumar HM, Bayry J. The use of databases, data mining and immunoinformatics in vaccinology: where are we? Expert Opin Drug Discov 2017; 13:117-130. [PMID: 29226722 DOI: 10.1080/17460441.2018.1413088] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
INTRODUCTION Vaccinology has evolved from a sub-discipline focussed on simplistic vaccine development based on antibody-mediated protection to a separate discipline involving epidemiology, host and pathogen biology, immunology, genomics, proteomics, structure biology, protein engineering, chemical biology, and delivery systems. Data mining in combination with bioinformatics has provided a scaffold linking all these disciplines to the design of vaccines and vaccine adjuvants. Areas covered: This review provides background knowledge on immunological aspects which have been exploited with informatics for the in silico analysis of immune responses and the design of vaccine antigens. Furthermore, the article presents various databases and bioinformatics tools, and discusses B and T cell epitope predictions, antigen design, adjuvant research and systems immunology, highlighting some important examples, and challenges for the future. Expert opinion: Informatics and data mining have not only reduced the time required for experimental immunology, but also contributed to the identification and design of novel vaccine candidates and the determination of biomarkers and pathways of vaccine response. However, more experimental data is required for benchmarking immunoinformatic tools. Nevertheless, developments in immunoinformatics and reverse vaccinology, which are nascent fields, are likely to hasten vaccine discovery, although the path to regulatory approval is likely to remain a necessary impediment.
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Affiliation(s)
| | - S Gauthami
- b Ella Foundation, Turkapally , Hyderabad , India
| | - H M Sampath Kumar
- c Council of Scientific and Industrial Research - Indian Institute of Chemical Technology , Hyderabad , India
| | - Jagadeesh Bayry
- d Institut National de la Santé et de la Recherche Médicale (INSERM) Unité 1138 , Centre de Recherche des Cordeliers, Paris , France
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28
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Potent Plasmablast-Derived Antibodies Elicited by the National Institutes of Health Dengue Vaccine. J Virol 2017; 91:JVI.00867-17. [PMID: 28878078 DOI: 10.1128/jvi.00867-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 08/17/2017] [Indexed: 12/21/2022] Open
Abstract
Exposure to dengue virus (DENV) is thought to elicit lifelong immunity, mediated by DENV-neutralizing antibodies (nAbs). However, Abs generated by primary infections confer serotype-specific protection, and immunity against other serotypes develops only after subsequent infections. Accordingly, the induction of these nAb responses acquired after serial DENV infections has been a long-sought-after goal for vaccination. Nonetheless, it is still unclear if tetravalent vaccines can elicit or recall nAbs. In this study, we have characterized the responses from a volunteer who had been previously exposed to DENV and was immunized with the live attenuated tetravalent vaccine Butantan-DV, developed by the NIH and Butantan Institute. Eleven days after vaccination, we observed an ∼70-fold expansion of the plasmablast population. We generated 21 monoclonal Abs (MAbs) from singly sorted plasmablasts. These MAbs were the result of clonal expansions and had significant levels of somatic hypermutation (SHM). Nineteen MAbs (90.5%) neutralized at least one DENV serotype at concentrations of 1 μg/ml or less; 6 of the 21 MAbs neutralized three or more serotypes. Despite the tetravalent composition of the vaccine, we observed a neutralization bias in the induced repertoire: DENV3 was targeted by 18 of the 19 neutralizing MAbs (nMAbs). Furthermore, the P3D05 nMAb neutralized DENV3 with extraordinary potency (concentration to achieve half-maximal neutralization [Neut50] = 0.03 μg/ml). Thus, the Butantan-DV vaccine engendered a mature, antigen-selected B cell repertoire. Our results suggest that preexisting responses elicited by a previous DENV3 infection were recalled by immunization.IMPORTANCE The dengue epidemic presents a global public health challenge that causes widespread economic burden and remains largely unchecked by existing control strategies. Successful control of the dengue epidemic will require effective prophylactic and therapeutic interventions. Several vaccine clinical efficacy trials are approaching completion, and the chances that one or more live attenuated tetravalent vaccines (LATVs) will be introduced worldwide is higher than ever. While it is widely accepted that dengue virus (DENV)-neutralizing antibody (nAb) titers are associated with protection, the Ab repertoire induced by LATVs remain uncharacterized. Here, we describe the isolation of potent (Neut50 < 0.1 μg/ml) nAbs from a DENV-seropositive volunteer immunized with the tetravalent vaccine Butantan-DV, which is currently in phase III trials.
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29
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Shrivastava A, Tripathi NK, Dash PK, Parida M. Working towards dengue as a vaccine-preventable disease: challenges and opportunities. Expert Opin Biol Ther 2017; 17:1193-1199. [PMID: 28707486 DOI: 10.1080/14712598.2017.1356284] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
INTRODUCTION Dengue is an emerging viral disease that affects the human population around the globe. Recent advancements in dengue virus research have opened new avenues for the development of vaccines against dengue. The development of a vaccine against dengue is a challenging task because any of the four serotypes of dengue viruses can cause disease. The development of a dengue vaccine aims to provide balanced protection against all the serotypes. Several dengue vaccine candidates are in the developmental stages such as inactivated, live attenuated, recombinant subunit, and plasmid DNA vaccines. Area covered: The authors provide an overview of the progress made in the development of much needed dengue vaccines. The authors include their expert opinion and their perspectives for future developments. Expert opinion: Human trials of a live attenuated tetravalent chimeric vaccine have clearly demonstrated its potential as a dengue vaccine. Other vaccine candidate molecules such as DENVax, a recombinant chimeric vaccine andTetraVax, are at different stages of development at this time. The authors believe that the novel strategies for testing and improving the immune response of vaccine candidates in humans will eventually lead to the development of a successful dengue vaccine in future.
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Affiliation(s)
- Ambuj Shrivastava
- a Division of Virology , Defence Research and Development Establishment , Gwalior , India
| | - Nagesh K Tripathi
- a Division of Virology , Defence Research and Development Establishment , Gwalior , India
| | - Paban K Dash
- a Division of Virology , Defence Research and Development Establishment , Gwalior , India
| | - Manmohan Parida
- a Division of Virology , Defence Research and Development Establishment , Gwalior , India
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30
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Tsai WY, Lin HE, Wang WK. Complexity of Human Antibody Response to Dengue Virus: Implication for Vaccine Development. Front Microbiol 2017; 8:1372. [PMID: 28775720 PMCID: PMC5517401 DOI: 10.3389/fmicb.2017.01372] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 07/06/2017] [Indexed: 01/21/2023] Open
Abstract
The four serotypes of dengue virus (DENV) are the leading cause of arboviral diseases in humans. Decades of efforts have made remarkable progress in dengue vaccine development. Despite the first dengue vaccine (dengvaxia from Sanofi Pasteur), a live-attenuated tetravalent chimeric yellow fever-dengue vaccine, has been licensed by several countries since 2016, its overall moderate efficacy (56.5–60.8%) in the presence of neutralizing antibodies during the Phase 2b and 3 trials, lower efficacy among dengue naïve compared with dengue experienced individuals, and increased risk of hospitalization among young children during the follow-up highlight the need for a better understanding of humoral responses after natural DENV infection. Recent studies of more than 300 human monoclonal antibodies (mAbs) against DENV have led to the discovery of several novel epitopes on the envelope protein recognized by potent neutralizing mAbs. This information together with in-depth studies on polyclonal sera and B-cells following natural DENV infection has tremendous implications for better immunogen design for a safe and effective dengue vaccine. This review outlines the progress in our understanding of mouse mAbs, human mAbs, and polyclonal sera against DENV envelope and precursor membrane proteins, two surface proteins involved in vaccine development, following natural infection; analyses of these discoveries have provided valuable insight into new strategies involving molecular technology to induce more potent neutralizing antibodies and less enhancing antibodies for next-generation dengue vaccine development.
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Affiliation(s)
- Wen-Yang Tsai
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii at ManoaHonolulu, HI, United States
| | - Hong-En Lin
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii at ManoaHonolulu, HI, United States
| | - Wei-Kung Wang
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii at ManoaHonolulu, HI, United States
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31
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Covalently linked dengue virus envelope glycoprotein dimers reduce exposure of the immunodominant fusion loop epitope. Nat Commun 2017; 8:15411. [PMID: 28534525 PMCID: PMC5457521 DOI: 10.1038/ncomms15411] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Accepted: 03/23/2017] [Indexed: 12/22/2022] Open
Abstract
A problem in the search for an efficient vaccine against dengue virus is the immunodominance of the fusion loop epitope (FLE), a segment of the envelope protein E that is buried at the interface of the E dimers coating mature viral particles. Anti-FLE antibodies are broadly cross-reactive but poorly neutralizing, displaying a strong infection enhancing potential. FLE exposure takes place via dynamic ‘breathing' of E dimers at the virion surface. In contrast, antibodies targeting the E dimer epitope (EDE), readily exposed at the E dimer interface over the region of the conserved fusion loop, are very potent and broadly neutralizing. We here engineer E dimers locked by inter-subunit disulfide bonds, and show by X-ray crystallography and by binding to a panel of human antibodies that these engineered dimers do not expose the FLE, while retaining the EDE exposure. These locked dimers are strong immunogen candidates for a next-generation vaccine. The immunodominant epitope of dengue virus envelope protein (E) induces poorly neutralizing antibodies, which poses a problem for vaccine development. Here, the authors engineer covalently locked E dimers exposing an epitope that has been shown to induce potent and broadly neutralizing antibodies.
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32
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Mire CE, Geisbert JB, Borisevich V, Fenton KA, Agans KN, Flyak AI, Deer DJ, Steinkellner H, Bohorov O, Bohorova N, Goodman C, Hiatt A, Kim DH, Pauly MH, Velasco J, Whaley KJ, Crowe JE, Zeitlin L, Geisbert TW. Therapeutic treatment of Marburg and Ravn virus infection in nonhuman primates with a human monoclonal antibody. Sci Transl Med 2017; 9:eaai8711. [PMID: 28381540 PMCID: PMC5719873 DOI: 10.1126/scitranslmed.aai8711] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 03/03/2017] [Indexed: 12/26/2022]
Abstract
As observed during the 2013-2016 Ebola virus disease epidemic, containment of filovirus outbreaks is challenging and made more difficult by the lack of approved vaccine or therapeutic options. Marburg and Ravn viruses are highly virulent and cause severe and frequently lethal disease in humans. Monoclonal antibodies (mAbs) are a platform technology in wide use for autoimmune and oncology indications. Previously, we described human mAbs that can protect mice from lethal challenge with Marburg virus. We demonstrate that one of these mAbs, MR191-N, can confer a survival benefit of up to 100% to Marburg or Ravn virus-infected rhesus macaques when treatment is initiated up to 5 days post-inoculation. These findings extend the small but growing body of evidence that mAbs can impart therapeutic benefit during advanced stages of disease with highly virulent viruses and could be useful in epidemic settings.
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Affiliation(s)
- Chad E Mire
- Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX 77555, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Joan B Geisbert
- Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX 77555, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Viktoriya Borisevich
- Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX 77555, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Karla A Fenton
- Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX 77555, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Krystle N Agans
- Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX 77555, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Andrew I Flyak
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Daniel J Deer
- Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX 77555, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Herta Steinkellner
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | | | | | | | - Andrew Hiatt
- Mapp Biopharmaceutical Inc., San Diego, CA 92121, USA
| | - Do H Kim
- Mapp Biopharmaceutical Inc., San Diego, CA 92121, USA
| | | | - Jesus Velasco
- Mapp Biopharmaceutical Inc., San Diego, CA 92121, USA
| | - Kevin J Whaley
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - James E Crowe
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Larry Zeitlin
- Mapp Biopharmaceutical Inc., San Diego, CA 92121, USA.
| | - Thomas W Geisbert
- Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX 77555, USA.
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
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Chaudhury S, Gromowski GD, Ripoll DR, Khavrutskii IV, Desai V, Wallqvist A. Dengue virus antibody database: Systematically linking serotype-specificity with epitope mapping in dengue virus. PLoS Negl Trop Dis 2017; 11:e0005395. [PMID: 28222130 PMCID: PMC5336305 DOI: 10.1371/journal.pntd.0005395] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 03/03/2017] [Accepted: 02/06/2017] [Indexed: 12/27/2022] Open
Abstract
Background A majority infections caused by dengue virus (DENV) are asymptomatic, but a higher incidence of severe illness, such as dengue hemorrhagic fever, is associated with secondary infections, suggesting that pre-existing immunity plays a central role in dengue pathogenesis. Primary infections are typically associated with a largely serotype-specific antibody response, while secondary infections show a shift to a broadly cross-reactive antibody response. Methods/Principal findings We hypothesized that the basis for the shift in serotype-specificity between primary and secondary infections can be found in a change in the antibody fine-specificity. To investigate the link between epitope- and serotype-specificity, we assembled the Dengue Virus Antibody Database, an online repository containing over 400 DENV-specific mAbs, each annotated with information on 1) its origin, including the immunogen, host immune history, and selection methods, 2) binding/neutralization data against all four DENV serotypes, and 3) epitope mapping at the domain or residue level to the DENV E protein. We combined epitope mapping and activity information to determine a residue-level index of epitope propensity and cross-reactivity and generated detailed composite epitope maps of primary and secondary antibody responses. We found differing patterns of epitope-specificity between primary and secondary infections, where secondary responses target a distinct subset of epitopes found in the primary response. We found that secondary infections were marked with an enhanced response to cross-reactive epitopes, such as the fusion-loop and E-dimer region, as well as increased cross-reactivity in what are typically more serotype-specific epitope regions, such as the domain I-II interface and domain III. Conclusions/Significance Our results support the theory that pre-existing cross-reactive memory B cells form the basis for the secondary antibody response, resulting in a broadening of the response in terms of cross-reactivity, and a focusing of the response to a subset of epitopes, including some, such as the fusion-loop region, that are implicated in poor neutralization and antibody-dependent enhancement of infection. Dengue virus (DENV) infections are typically asymptomatic, but severe and potentially lethal disease symptoms, such as dengue hemorrhagic fever, are associated with secondary infections. This suggests that pre-existing immunity from primary infection plays a central role in DENV pathogenesis. In order to characterize the antibody response in primary and secondary infections, we assembled the Dengue Virus Antibody Database, a freely accessible online repository (http://denvabdb.bhsai.org) storing over 400 unique monoclonal dengue-specific antibodies annotated by their 1) origin and host immune history, 2) activity information against all four dengue serotypes, and 3) epitope mapping information. Here we demonstrate the utility of the database by carrying out a large-scale analysis to characterize shifts in epitope fine-specificity and serotype cross-reactivity in primary and secondary infections. In particular, we show how the antibody response in secondary infections displays a systematic shift towards increased serotype cross-reactivity by focusing on a subset of cross-reactive epitopes on the dengue E protein. Our findings suggest a mechanistic basis for this shift in epitope and serotype specificity and demonstrate how a detailed understanding of the antibody response can provide insight into the mechanisms of dengue pathogenesis.
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Affiliation(s)
- Sidhartha Chaudhury
- Biotechnology HPC Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, Maryland, United States of America
- * E-mail:
| | - Gregory D. Gromowski
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Daniel R. Ripoll
- Biotechnology HPC Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, Maryland, United States of America
| | - Ilja V. Khavrutskii
- Biotechnology HPC Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, Maryland, United States of America
| | - Valmik Desai
- Biotechnology HPC Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, Maryland, United States of America
| | - Anders Wallqvist
- Biotechnology HPC Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, Maryland, United States of America
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Mapping the Human Memory B Cell and Serum Neutralizing Antibody Responses to Dengue Virus Serotype 4 Infection and Vaccination. J Virol 2017; 91:JVI.02041-16. [PMID: 28031369 DOI: 10.1128/jvi.02041-16] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 12/21/2016] [Indexed: 01/02/2023] Open
Abstract
The four dengue virus (DENV) serotypes are mosquito-borne flaviviruses responsible for dengue fever and dengue hemorrhagic fever. People exposed to DENV develop antibodies (Abs) that strongly neutralize the serotype responsible for infection. Historically, infection with DENV serotype 4 (DENV4) has been less common and less studied than infections with the other three serotypes. However, DENV4 has been responsible for recent large and sustained epidemics in Asia and Latin America. The neutralizing antibody responses and the epitopes targeted against DENV4 have not been characterized in human infection. In this study, we mapped and characterized epitopes on DENV4 recognized by neutralizing antibodies in people previously exposed to DENV4 infections or to a live attenuated DENV4 vaccine. To study the fine specificity of DENV4 neutralizing human antibodies, B cells from two people exposed to DENV4 were immortalized and screened to identify DENV-specific clones. Two human monoclonal antibodies (MAbs) that neutralized DENV4 were isolated, and their epitopes were finely mapped using recombinant viruses and alanine scan mutation array techniques. Both antibodies bound to quaternary structure epitopes near the hinge region between envelope protein domain I (EDI) and EDII. In parallel, to characterize the serum neutralizing antibody responses, convalescence-phase serum samples from people previously exposed to primary DENV4 natural infections or a monovalent DENV4 vaccine were analyzed. Natural infection and vaccination also induced serum-neutralizing antibodies that targeted similar epitope domains at the EDI/II hinge region. These studies defined a target of neutralizing antigenic site on DENV4 targeted by human antibodies following natural infection or vaccination.IMPORTANCE The four serotypes of dengue virus are the causative agents of dengue fever and dengue hemorrhagic fever. People exposed to primary DENV infections develop long-term neutralizing antibody responses, but these principally recognize only the infecting serotype. An effective vaccine against dengue should elicit long-lasting protective antibody responses to all four serotypes simultaneously. We and others have defined antigenic sites on the envelope (E) protein of viruses of dengue virus serotypes 1, 2, and 3 targeted by human neutralizing antibodies. The epitopes on DENV4 E protein targeted by the human neutralizing antibodies and the mechanisms of serotype 4 neutralization are poorly understood. Here, we report the properties of human antibodies that neutralize dengue virus serotype 4. People exposed to serotype 4 infections or a live attenuated serotype 4 vaccine developed neutralizing antibodies that bound to similar sites on the viral E protein. These studies have provided a foundation for developing and evaluating DENV4 vaccines.
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The Antigenic Structure of Zika Virus and Its Relation to Other Flaviviruses: Implications for Infection and Immunoprophylaxis. Microbiol Mol Biol Rev 2017; 81:81/1/e00055-16. [PMID: 28179396 DOI: 10.1128/mmbr.00055-16] [Citation(s) in RCA: 131] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Zika virus was discovered ∼70 years ago in Uganda and maintained a low profile as a human disease agent in Africa and Asia. Only recently has it caused explosive outbreaks in previously unaffected regions, first in Oceania and then in the Americas since 2015. Of special concern is the newly identified link between congenital malformations (especially microcephaly) and Zika virus infections during pregnancy. At present, it is unclear whether Zika virus changed its pathogenicity or whether the huge number of infections allowed the recognition of a previously cryptic pathogenic property. The purpose of this review is to discuss recent data on the molecular antigenic structure of Zika virus in the context of antibody-mediated neutralization and antibody-dependent enhancement (ADE) of infection, a phenomenon that has been implicated in the development of severe disease caused by the related dengue viruses. Emphasis is given to epitopes of antibodies that potently neutralize Zika virus and also to epitopes that provide antigenic links to other important human-pathogenic flaviviruses such as dengue, yellow fever, West Nile, Japanese encephalitis, and tick-borne encephalitis viruses. The antigenic cross talk between Zika and dengue viruses appears to be of special importance, since they cocirculate in many regions of endemicity and sequential infections are likely to occur frequently. New insights into the molecular antigenic structure of Zika virus and flaviviruses in general have provided the foundation for great progress made in developing Zika virus vaccines and antibodies for passive immunization.
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36
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Identification of a New Broadly Cross-reactive Epitope within Domain III of the Duck Tembusu Virus E Protein. Sci Rep 2016; 6:36288. [PMID: 27824100 PMCID: PMC5099753 DOI: 10.1038/srep36288] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 10/13/2016] [Indexed: 01/02/2023] Open
Abstract
In 2010, a pathogenic flavivirus termed duck Tembusu virus (DTMUV) caused widespread outbreak of egg-drop syndrome in domesticated ducks in China. Although the glycoprotein E of DTMUV is an important structural component of the virus, the B-cell epitopes of this protein remains uncharacterized. Using phage display and mutagenesis, we identified a minimal B-cell epitope, 374EXE/DPPFG380, that mediates binding to a nonneutralizing monoclonal antibody. DTMUV-positive duck serum reacted with the epitope, and amino acid substitutions revealed the specific amino acids that are essential for antibody binding. Dot-blot assays of various flavivirus-positive sera indicated that EXE/DPPFG is a cross-reactive epitope in most flaviviruses, including Zika, West Nile, Yellow fever, dengue, and Japanese encephalitis viruses. These findings indicate that the epitope sequence is conserved among many strains of mosquito-borne flavivirus. Protein structure modeling revealed that the epitope is located in domain III of the DTMUV E protein. Together, these results provide new insights on the broad cross-reactivity of a B-cell binding site of the E protein of flaviviruses, which can be exploited as a diagnostic or therapeutic target for identifying, studying, or treating DTMUV and other flavivirus infections.
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Guthals A, Gan Y, Murray L, Chen Y, Stinson J, Nakamura G, Lill JR, Sandoval W, Bandeira N. De Novo MS/MS Sequencing of Native Human Antibodies. J Proteome Res 2016; 16:45-54. [PMID: 27779884 DOI: 10.1021/acs.jproteome.6b00608] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
One direct route for the discovery of therapeutic human monoclonal antibodies (mAbs) involves the isolation of peripheral B cells from survivors/sero-positive individuals after exposure to an infectious reagent or disease etiology, followed by single-cell sequencing or hybridoma generation. Peripheral B cells, however, are not always easy to obtain and represent only a small percentage of the total B-cell population across all bodily tissues. Although it has been demonstrated that tandem mass spectrometry (MS/MS) techniques can interrogate the full polyclonal antibody (pAb) response to an antigen in vivo, all current approaches identify MS/MS spectra against databases derived from genetic sequencing of B cells from the same patient. In this proof-of-concept study, we demonstrate the feasibility of a novel MS/MS antibody discovery approach in which only serum antibodies are required without the need for sequencing of genetic material. Peripheral pAbs from a cytomegalovirus-exposed individual were purified by glycoprotein B antigen affinity and de novo sequenced from MS/MS data. Purely MS-derived mAbs were then manufactured in mammalian cells to validate potency via antigen-binding ELISA. Interestingly, we found that these mAbs accounted for 1 to 2% of total donor IgG but were not detected in parallel sequencing of memory B cells from the same patient.
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Affiliation(s)
- Adrian Guthals
- Mapp Biopharmaceutical, Inc. , 6160 Lusk Boulevard #C105, San Diego, California 92121, United States
| | - Yutian Gan
- Department of Proteomics & Biological Resources, Genentech, Inc. , South San Francisco, California 94080, United States
| | - Laura Murray
- Department of Protein Chemistry, Genentech, Inc. , South San Francisco, California 94080, United States
| | - Yongmei Chen
- Department of Antibody Engineering, Genentech, Inc. , South San Francisco, California 94080, United States
| | - Jeremy Stinson
- Department of Molecular Biology, Genentech, Inc. , South San Francisco, California 94080, United States
| | - Gerald Nakamura
- Department of Antibody Engineering, Genentech, Inc. , South San Francisco, California 94080, United States
| | - Jennie R Lill
- Department of Proteomics & Biological Resources, Genentech, Inc. , South San Francisco, California 94080, United States
| | - Wendy Sandoval
- Department of Proteomics & Biological Resources, Genentech, Inc. , South San Francisco, California 94080, United States
| | - Nuno Bandeira
- Department of Computer Science and Engineering, University of California, San Diego , 9500 Gilman Drive, Mail Code 0404, La Jolla, California 92093, United States.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego , 9500 Gilman Drive, Mail Code 0657, La Jolla, California 92093, United States
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Deconstructing the Antiviral Neutralizing-Antibody Response: Implications for Vaccine Development and Immunity. Microbiol Mol Biol Rev 2016; 80:989-1010. [PMID: 27784796 DOI: 10.1128/mmbr.00024-15] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The antibody response plays a key role in protection against viral infections. While antiviral antibodies may reduce the viral burden via several mechanisms, the ability to directly inhibit (neutralize) infection of cells has been extensively studied. Eliciting a neutralizing-antibody response is a goal of many vaccine development programs and commonly correlates with protection from disease. Considerable insights into the mechanisms of neutralization have been gained from studies of monoclonal antibodies, yet the individual contributions and dynamics of the repertoire of circulating antibody specificities elicited by infection and vaccination are poorly understood on the functional and molecular levels. Neutralizing antibodies with the most protective functionalities may be a rare component of a polyclonal, pathogen-specific antibody response, further complicating efforts to identify the elements of a protective immune response. This review discusses advances in deconstructing polyclonal antibody responses to flavivirus infection or vaccination. Our discussions draw comparisons to HIV-1, a virus with a distinct structure and replication cycle for which the antibody response has been extensively investigated. Progress toward deconstructing and understanding the components of polyclonal antibody responses identifies new targets and challenges for vaccination strategies.
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Taylor A, Foo SS, Bruzzone R, Dinh LV, King NJC, Mahalingam S. Fc receptors in antibody-dependent enhancement of viral infections. Immunol Rev 2016; 268:340-64. [PMID: 26497532 PMCID: PMC7165974 DOI: 10.1111/imr.12367] [Citation(s) in RCA: 176] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Sensitization of the humoral immune response to invading viruses and production of antiviral antibodies forms part of the host antiviral repertoire. Paradoxically, for a number of viral pathogens, under certain conditions, antibodies provide an attractive means of enhanced virus entry and replication in a number of cell types. Known as antibody‐dependent enhancement (ADE) of infection, the phenomenon occurs when virus‐antibody immunocomplexes interact with cells bearing complement or Fc receptors, promoting internalization of the virus and increasing infection. Frequently associated with exacerbation of viral disease, ADE of infection presents a major obstacle to the prevention of viral disease by vaccination and is thought to be partly responsible for the adverse effects of novel antiviral therapeutics such as intravenous immunoglobulins. There is a growing body of work examining the intracellular signaling pathways and epitopes responsible for mediating ADE, with a view to aiding rational design of antiviral strategies. With in vitro studies also confirming ADE as a feature of infection for a growing number of viruses, challenges remain in understanding the multilayered molecular mechanisms of ADE and its effect on viral pathogenesis.
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Affiliation(s)
- Adam Taylor
- Emerging Viruses and Inflammation Research Group, Institute for Glycomics, Griffith University, Gold Coast, Qld, Australia
| | - Suan-Sin Foo
- Emerging Viruses and Inflammation Research Group, Institute for Glycomics, Griffith University, Gold Coast, Qld, Australia
| | - Roberto Bruzzone
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong SAR, Hong Kong.,Department of Cell Biology and Infection, Institut Pasteur, Paris, France
| | - Luan Vu Dinh
- Discipline of Pathology, Bosch Institute, School of Medical Sciences, Sydney Medical School, Charles Perkins Centre, University of Sydney, Sydney, NSW, Australia
| | - Nicholas J C King
- Discipline of Pathology, Bosch Institute, School of Medical Sciences, Sydney Medical School, Charles Perkins Centre, University of Sydney, Sydney, NSW, Australia
| | - Suresh Mahalingam
- Emerging Viruses and Inflammation Research Group, Institute for Glycomics, Griffith University, Gold Coast, Qld, Australia
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40
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Smith SA, Silva LA, Fox JM, Flyak AI, Kose N, Sapparapu G, Khomandiak S, Khomadiak S, Ashbrook AW, Kahle KM, Fong RH, Swayne S, Doranz BJ, McGee CE, Heise MT, Pal P, Brien JD, Austin SK, Diamond MS, Dermody TS, Crowe JE. Isolation and Characterization of Broad and Ultrapotent Human Monoclonal Antibodies with Therapeutic Activity against Chikungunya Virus. Cell Host Microbe 2016; 18:86-95. [PMID: 26159721 DOI: 10.1016/j.chom.2015.06.009] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 05/27/2015] [Accepted: 06/22/2015] [Indexed: 11/25/2022]
Abstract
Chikungunya virus (CHIKV) is a mosquito-transmitted RNA virus that causes acute febrile infection associated with polyarthralgia in humans. Mechanisms of protective immunity against CHIKV are poorly understood, and no effective therapeutics or vaccines are available. We isolated and characterized human monoclonal antibodies (mAbs) that neutralize CHIKV infectivity. Among the 30 mAbs isolated, 13 had broad and ultrapotent neutralizing activity (IC50 < 10 ng/ml), and all of these mapped to domain A of the E2 envelope protein. Potent inhibitory mAbs blocked post-attachment steps required for CHIKV membrane fusion, and several were protective in a lethal challenge model in immunocompromised mice, even when administered at late time points after infection. These highly protective mAbs could be considered for prevention or treatment of CHIKV infection, and their epitope location in domain A of E2 could be targeted for rational structure-based vaccine development.
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Affiliation(s)
- Scott A Smith
- Department of Medicine, Vanderbilt University Medical Center, Vanderbilt University, Nashville, TN 37232, USA; Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Vanderbilt University, Nashville, TN 37232, USA
| | - Laurie A Silva
- Department of Pediatrics, Vanderbilt University Medical Center, Vanderbilt University, Nashville, TN 37232, USA; Elizabeth B. Lamb Center for Pediatric Research, Vanderbilt University Medical Center, Vanderbilt University, Nashville, TN 37232, USA
| | - Julie M Fox
- Departments of Medicine, Molecular Microbiology, Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Andrew I Flyak
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Vanderbilt University, Nashville, TN 37232, USA
| | - Nurgun Kose
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Vanderbilt University, Nashville, TN 37232, USA
| | - Gopal Sapparapu
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Vanderbilt University, Nashville, TN 37232, USA
| | | | - Solomiia Khomadiak
- Department of Pediatrics, Vanderbilt University Medical Center, Vanderbilt University, Nashville, TN 37232, USA; Elizabeth B. Lamb Center for Pediatric Research, Vanderbilt University Medical Center, Vanderbilt University, Nashville, TN 37232, USA
| | - Alison W Ashbrook
- Department of Pediatrics, Vanderbilt University Medical Center, Vanderbilt University, Nashville, TN 37232, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Vanderbilt University, Nashville, TN 37232, USA; Elizabeth B. Lamb Center for Pediatric Research, Vanderbilt University Medical Center, Vanderbilt University, Nashville, TN 37232, USA
| | | | | | | | | | - Charles E McGee
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Mark T Heise
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Pankaj Pal
- Departments of Medicine, Molecular Microbiology, Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - James D Brien
- Departments of Medicine, Molecular Microbiology, Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - S Kyle Austin
- Departments of Medicine, Molecular Microbiology, Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michael S Diamond
- Departments of Medicine, Molecular Microbiology, Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Terence S Dermody
- Department of Pediatrics, Vanderbilt University Medical Center, Vanderbilt University, Nashville, TN 37232, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Vanderbilt University, Nashville, TN 37232, USA; Elizabeth B. Lamb Center for Pediatric Research, Vanderbilt University Medical Center, Vanderbilt University, Nashville, TN 37232, USA
| | - James E Crowe
- Department of Pediatrics, Vanderbilt University Medical Center, Vanderbilt University, Nashville, TN 37232, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Vanderbilt University, Nashville, TN 37232, USA; Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Vanderbilt University, Nashville, TN 37232, USA.
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Use of Human Hybridoma Technology To Isolate Human Monoclonal Antibodies. Microbiol Spectr 2016; 3:AID-0027-2014. [PMID: 26104564 DOI: 10.1128/microbiolspec.aid-0027-2014] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The human hybridoma technique offers an important approach for isolation of human monoclonal antibodies. A diversity of approaches can be used with varying success. Recent technical advances in expanding the starting number of human antigen-specific B cells, improving fusion efficiency, and isolating new myeloma partners and new cell cloning methods have enabled the development of protocols that make the isolation of human monoclonal antibodies from blood samples feasible. Undoubtedly, additional innovations that could improve efficiency are possible.
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42
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New insights into the immunopathology and control of dengue virus infection. Nat Rev Immunol 2015; 15:745-59. [DOI: 10.1038/nri3916] [Citation(s) in RCA: 232] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Dengue Virus prM-Specific Human Monoclonal Antibodies with Virus Replication-Enhancing Properties Recognize a Single Immunodominant Antigenic Site. J Virol 2015; 90:780-9. [PMID: 26512092 DOI: 10.1128/jvi.01805-15] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 10/19/2015] [Indexed: 02/02/2023] Open
Abstract
UNLABELLED The proposed antibody-dependent enhancement (ADE) mechanism for severe dengue virus (DENV) disease suggests that non-neutralizing serotype cross-reactive antibodies generated during a primary infection facilitate entry into Fc receptor bearing cells during secondary infection, resulting in enhanced viral replication and severe disease. One group of cross-reactive antibodies that contributes considerably to this serum profile target the premembrane (prM) protein. We report here the isolation of a large panel of naturally occurring human monoclonal antibodies (MAbs) obtained from subjects following primary DENV serotype 1, 2, or 3 or secondary natural DENV infections or following primary DENV serotype 1 live attenuated virus vaccination to determine the antigenic landscape on the prM protein that is recognized by human antibodies. We isolated 25 prM-reactive human MAbs, encoded by diverse antibody-variable genes. Competition-binding studies revealed that all of the antibodies bound to a single major antigenic site on prM. Alanine scanning-based shotgun mutagenesis epitope mapping studies revealed diverse patterns of fine specificity of various clones, suggesting that different antibodies use varied binding poses to recognize several overlapping epitopes within the immunodominant site. Several of the antibodies interacted with epitopes on both prM and E protein residues. Despite the diverse genetic origins of the antibodies and differences in the fine specificity of their epitopes, each of these prM-reactive antibodies was capable of enhancing the DENV infection of Fc receptor-bearing cells. IMPORTANCE Antibodies may play a critical role in the pathogenesis of enhanced DENV infection and disease during secondary infections. A substantial proportion of enhancing antibodies generated in response to natural dengue infection are directed toward the prM protein. The fine specificity of human prM antibodies is not understood. Here, we isolated a panel of dengue prM-specific human monoclonal antibodies from individuals after infection in order to define the mode of molecular recognition by enhancing antibodies. We found that only a single antibody molecule can be bound to each prM protein at any given time. Distinct overlapping epitopes were mapped, but all of the epitopes lie within a single major antigenic site, suggesting that this antigenic domain forms an immunodominant region of the protein. Neutralization and antibody-dependent enhanced replication experiments showed that recognition of any of the epitopes within the major antigenic site on prM was sufficient to cause enhanced infection of target cells.
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Hadjilaou A, Green AM, Coloma J, Harris E. Single-Cell Analysis of B Cell/Antibody Cross-Reactivity Using a Novel Multicolor FluoroSpot Assay. THE JOURNAL OF IMMUNOLOGY 2015; 195:3490-6. [PMID: 26320246 DOI: 10.4049/jimmunol.1500918] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 07/28/2015] [Indexed: 11/19/2022]
Abstract
Dengue is a major public health problem globally. It is caused by four antigenically distinct serotypes of dengue virus (DENV1-4), and although serotype-specific and strongly neutralizing cross-reactive immune responses against the four DENV serotypes are thought to be protective, subneutralizing Abs can contribute to increased disease severity upon secondary infection with a different DENV serotype. Understanding the breadth of the immune response in natural DENV infections and in vaccinees is crucial for determining the correlates of protection or disease severity. Transformation of B cell populations to generate mAbs and ELISPOT assays have been used to determine B cell and Ab specificity to DENV; however, both methods have technical limitations. We therefore modified the conventional ELISPOT to develop a Quad-Color FluoroSpot to provide a means of examining B cell/Ab serotype specificity and cross-reactivity on a single-cell basis. Abs secreted by B cells are captured by an Fc-specific Ab on a filter plate. Subsequently, standardized concentrations of all four DENV serotypes are added to allow equal stoichiometry for Ag binding. After washing, the spots, representing individual B cells, are visualized using four fluorescently labeled DENV serotype-specific detection mAbs. This method can be used to better understand the breadth and magnitude of B cell responses following primary and secondary DENV infection or vaccination and their role as immune correlates of protection from subsequent DENV infections. Furthermore, the Quad-Color FluoroSpot assay can be applied to other diseases caused by multiple pathogen serotypes in which determining the serotype or subtype-specific B cell response is important.
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Affiliation(s)
- Alexandros Hadjilaou
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA 94720
| | - Angela M Green
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA 94720
| | - Josefina Coloma
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA 94720
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA 94720
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Abstract
Dengue is the most prevalent mosquito-borne viral disease worldwide. Yet, there are no vaccines or specific antivirals available to prevent or treat the disease. Several dengue vaccines are currently in clinical or preclinical stages. The most advanced vaccine is the chimeric tetravalent CYD-TDV vaccine of Sanofi Pasteur. This vaccine has recently cleared Phase III, and efficacy results have been published. Excellent tetravalent seroconversion was seen, yet the protective efficacy against infection was surprisingly low. Here, we will describe the complicating factors involved in the generation of a safe and efficacious dengue vaccine. Furthermore, we will discuss the human antibody responses during infection, including the epitopes targeted in humans. Also, we will discuss the current understanding of the assays used to evaluate antibody response. We hope this review will aid future dengue vaccine development as well as fundamental research related to the phenomenon of antibody-dependent enhancement of dengue virus infection.
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Affiliation(s)
- Jacky Flipse
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Jolanda M. Smit
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
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Callaway JB, Smith SA, McKinnon KP, de Silva AM, Crowe JE, Ting JPY. Spleen Tyrosine Kinase (Syk) Mediates IL-1β Induction by Primary Human Monocytes during Antibody-enhanced Dengue Virus Infection. J Biol Chem 2015; 290:17306-20. [PMID: 26032420 DOI: 10.1074/jbc.m115.664136] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Indexed: 11/06/2022] Open
Abstract
Approximately 500,000 people are hospitalized with severe dengue illness annually. Antibody-dependent enhancement (ADE) of dengue virus (DENV) infection is believed to contribute to the pathogenic cytokine storm described in severe dengue patients, but the precise signaling pathways contributing to elevated cytokine production are not elucidated. IL-1β is a potent inflammatory cytokine that is frequently elevated during severe dengue, and the unique dual regulation of IL-1β provides an informative model to study ADE-induced cytokines. This work utilizes patient-derived anti-DENV mAbs and primary human monocytes to study ADE-induced IL-1β and other cytokines. ADE of DENV serotype 2 (DENV-2) elevates mature IL-1β secretion by monocytes independent of DENV replication by 4 h postinoculation (hpi). Prior to this, DENV immune complexes activate spleen tyrosine kinase (Syk) within 1 hpi. Syk induces elevated IL1B, TNF, and IL6 mRNA by 2 hpi. Syk mediates elevated IL-1β secretion by activating ERK1/2, and both Syk and ERK1/2 inhibitors ablated ADE-induced IL-1β secretion. Maturation of pro-IL-1β during ADE requires caspase-1 and NLRP3, but caspase-1 is suboptimally increased by ADE and can be significantly enhanced by a typical inflammasome agonist, ATP. Importantly, this inflammatory Syk-ERK signaling axis requires DENV immune complexes, because DENV-2 in the presence of serotype-matched anti-DENV-2 mAb, but not anti-DENV-1 mAb, activates Syk, ERK, and IL-1β secretion. This study provides evidence that DENV-2 immune complexes activate Syk to mediate elevated expression of inflammatory cytokines. Syk and ERK may serve as new therapeutic targets for interfering with ADE-induced cytokine expression during severe dengue.
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Affiliation(s)
- Justin B Callaway
- From the Department of Microbiology and Immunology, Lineberger Comprehensive Cancer Center
| | - Scott A Smith
- the Vanderbilt Vaccine Center and the Departments of Medicine
| | | | | | - James E Crowe
- the Vanderbilt Vaccine Center and Pathology, Microbiology, and Immunology, and Pediatrics, Vanderbilt Medical Center, Nashville, Tennessee 37232
| | - Jenny P-Y Ting
- From the Department of Microbiology and Immunology, Lineberger Comprehensive Cancer Center, Department of Genetics, and Institute of Inflammatory Diseases, University of North Carolina, Chapel Hill, North Carolina 27599 and
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Fibriansah G, Tan JL, Smith SA, de Alwis R, Ng TS, Kostyuchenko VA, Jadi RS, Kukkaro P, de Silva AM, Crowe JE, Lok SM. A highly potent human antibody neutralizes dengue virus serotype 3 by binding across three surface proteins. Nat Commun 2015; 6:6341. [PMID: 25698059 PMCID: PMC4346626 DOI: 10.1038/ncomms7341] [Citation(s) in RCA: 167] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 01/21/2015] [Indexed: 12/12/2022] Open
Abstract
Dengue virus (DENV) infects ~400 million people annually. There is no licensed vaccine or therapeutic drug. Only a small fraction of the total DENV-specific antibodies in a naturally occurring dengue infection consists of highly neutralizing antibodies. Here we show that the DENV-specific human monoclonal antibody 5J7 is exceptionally potent, neutralizing 50% of virus at nanogram-range antibody concentration. The 9 Å resolution cryo-electron microscopy structure of the Fab 5J7–DENV complex shows that a single Fab molecule binds across three envelope proteins and engages three functionally important domains, each from a different envelope protein. These domains are critical for receptor binding and fusion to the endosomal membrane. The ability to bind to multiple domains allows the antibody to fully coat the virus surface with only 60 copies of Fab, that is, half the amount compared with other potent antibodies. Our study reveals a highly efficient and unusual mechanism of molecular recognition by an antibody. There is no licensed vaccine or therapeutic for dengue virus (DENV) infection. Here, the authors show that a highly potent human monoclonal antibody binds to DENV particles in an unusual and very effective way by interacting with three viral envelope proteins.
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Affiliation(s)
- Guntur Fibriansah
- 1] Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, 8 College Road, Singapore 169857, Singapore [2] Centre for BioImaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117557, Singapore
| | - Joanne L Tan
- 1] Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, 8 College Road, Singapore 169857, Singapore [2] Centre for BioImaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117557, Singapore
| | - Scott A Smith
- 1] Department of Medicine, Vanderbilt University, 1161 21st Avenue South, D-3100 Medical Center North, Nashville, Tennessee 37232-2358, USA [2] The Vanderbilt Vaccine Center, Vanderbilt University,Vanderbilt University Medical Center, 11475 MRB IV-2213 Garland Avenue, Nashville, Tennessee 37232-0417, USA
| | - Ruklanthi de Alwis
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, CB#7292, 9024 Burnett Womack, Chapel Hill, North Carolina 27599-7292, USA
| | - Thiam-Seng Ng
- 1] Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, 8 College Road, Singapore 169857, Singapore [2] Centre for BioImaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117557, Singapore
| | - Victor A Kostyuchenko
- 1] Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, 8 College Road, Singapore 169857, Singapore [2] Centre for BioImaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117557, Singapore
| | - Ramesh S Jadi
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, CB#7292, 9024 Burnett Womack, Chapel Hill, North Carolina 27599-7292, USA
| | - Petra Kukkaro
- 1] Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, 8 College Road, Singapore 169857, Singapore [2] Centre for BioImaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117557, Singapore
| | - Aravinda M de Silva
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, CB#7292, 9024 Burnett Womack, Chapel Hill, North Carolina 27599-7292, USA
| | - James E Crowe
- 1] The Vanderbilt Vaccine Center, Vanderbilt University,Vanderbilt University Medical Center, 11475 MRB IV-2213 Garland Avenue, Nashville, Tennessee 37232-0417, USA [2] Departments of Pediatrics and Pathology, Microbiology and Immunology, Vanderbilt University, Vanderbilt University Medical Center, 11475 MRB IV-2213 Garland Avenue, Nashville, Tennessee 37232-0417, USA
| | - Shee-Mei Lok
- 1] Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, 8 College Road, Singapore 169857, Singapore [2] Centre for BioImaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117557, Singapore
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Libraty DH, Zhang L, Obcena A, Brion JD, Capeding RZ. Anti-dengue virus envelope protein domain III IgG ELISA among infants with primary dengue virus infections. Acta Trop 2015; 142:103-7. [PMID: 25460346 DOI: 10.1016/j.actatropica.2014.11.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 10/27/2014] [Accepted: 11/17/2014] [Indexed: 11/19/2022]
Abstract
Dengue is the most prevalent arthropod-borne viral illness in humans. The current gold standard serologic test for dengue virus (DENV) infection is a neutralizing antibody assay. We examined a DENV recombinant (r)E protein domain III IgG ELISA among infants with primary DENV infections. Infants experience a primary DENV infection in the presence of maternally derived anti-DENV IgG. The estimated DENV rE protein domain III IgG levels to the infecting serotype at the time of infant primary symptomatic DENV2 and DENV3 infections correlated with the 50% plaque reduction neutralization reciprocal antibody titers (PRNT50). Anti-DENVs 1-4 rE protein domain III IgG levels all correlated with each other, and the estimated rE protein domain III IgG level to the infecting serotype at the time of infection inversely correlated with dengue disease severity. The anti-DENV rE protein domain III IgG ELISA may be a useful and potentially high-throughput alternative to traditional DENV neutralizing antibody assays.
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Affiliation(s)
- Daniel H Libraty
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA.
| | - Lei Zhang
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - AnaMae Obcena
- Department of Medicine, Research Institute for Tropical Medicine, Manila, Philippines
| | - Job D Brion
- San Pablo City Health Office, San Pablo, Philippines
| | - Rosario Z Capeding
- Department of Medicine, Research Institute for Tropical Medicine, Manila, Philippines; Department of Microbiology, Research Institute for Tropical Medicine, Manila, Philippines
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49
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Lisova O, Belkadi L, Bedouelle H. Direct and indirect interactions in the recognition between a cross-neutralizing antibody and the four serotypes of dengue virus. J Mol Recognit 2014; 27:205-14. [PMID: 24591178 DOI: 10.1002/jmr.2352] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 12/16/2013] [Accepted: 12/16/2013] [Indexed: 11/11/2022]
Abstract
Dengue fever is the most important vector-borne viral disease. Four serotypes of dengue virus, DENV1 to DENV4, coexist. Secondary infection by a different serotype is a risk factor for severe dengue. Monoclonal antibody mAb4E11 neutralizes the four serotypes of DENV with varying efficacies by recognizing an epitope located within domain-III (ED3) of the viral envelope (E) protein. To better understand the cross-reactivities between mAb4E11 and the four serotypes of DENV, we constructed mutations in both Fab4E11 fragment and ED3, and we searched for indirect interactions in the crystal structures of the four complexes. According to the serotype, 7 to 12 interactions are mediated by one water molecule, 1 to 10 by two water molecules, and several of these interactions are conserved between serotypes. Most interfacial water molecules make hydrogen bonds with both antibody and antigen. Some residues or atomic groups are engaged in both direct and water-mediated interactions. The doubly-indirect interactions are more numerous in the complex of lowest affinity. The third complementarity determining region of the light chain (L-CDR3) of mAb4E11 does not contact ED3. The structures and double-mutant thermodynamic cycles showed that the effects of (hyper)-mutations in L-CDR3 on affinity were caused by conformational changes and indirect interactions with ED3 through other CDRs. Exchanges of residues between ED3 serotypes showed that their effects on affinity were context dependent. Thus, conformational changes, structural context, and indirect interactions should be included when studying cross-reactivity between antibodies and different serotypes of viral antigens for a better design of diagnostics, vaccine, and therapeutic tools against DENV and other Flaviviruses.
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Affiliation(s)
- Olesia Lisova
- Institut Pasteur, Unit of Molecular Prevention and Therapy of Human Diseases, Department of Infection and Epidemiology, rue du Dr. Roux, F-75015, Paris, France; CNRS, URA3012, rue du Dr. Roux, F-75015, Paris, France
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50
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Pitcher TJ, Sarathy VV, Matsui K, Gromowski GD, Huang CYH, Barrett ADT. Functional analysis of dengue virus (DENV) type 2 envelope protein domain 3 type-specific and DENV complex-reactive critical epitope residues. J Gen Virol 2014; 96:288-293. [PMID: 25351518 DOI: 10.1099/vir.0.070813-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The dengue virus (DENV) envelope protein domain 3 (ED3) is the target of potent virus neutralizing antibodies. The DENV-2 ED3 contains adjacent type-specific and DENV complex-reactive antigenic sites that are composed of a small number of residues that were previously demonstrated to be critical for antibody binding. Site-directed mutagenesis of a DENV-2 16681 infectious clone was used to mutate critical residues in the DENV-2 type-specific (K305A and P384A) and DENV complex-reactive (K310A) antigenic sites. The K305A mutant virus multiplied like the parent virus in mosquito and mammalian cells, as did the P384A mutant virus, which required a compensatory mutation (G330D) for viability. However, the K310A mutant virus could not be recovered. The DENV-2 type-specific critical residue mutations K305A and P384A+G330D reduced the ability of DENV-2 type-specific, but not DENV complex-reactive, mAbs to neutralize virus infectivity and this was directly correlated with mAb binding affinity to the rED3 mutants.
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Affiliation(s)
- Trevor J Pitcher
- Center for Biodefense and Emerging Infectious Diseases, Sealy Center for Vaccine Development, Institute for Human Infections and Immunity, and Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555-0436, USA
| | - Vanessa V Sarathy
- Center for Biodefense and Emerging Infectious Diseases, Sealy Center for Vaccine Development, Institute for Human Infections and Immunity, and Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555-0436, USA
| | - Kiyohiko Matsui
- Center for Biodefense and Emerging Infectious Diseases, Sealy Center for Vaccine Development, Institute for Human Infections and Immunity, and Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555-0436, USA
| | - Gregory D Gromowski
- Center for Biodefense and Emerging Infectious Diseases, Sealy Center for Vaccine Development, Institute for Human Infections and Immunity, and Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555-0436, USA
| | - Claire Y-H Huang
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Public Health Service, US Department of Health and Human Services, Fort Collins, CO 80521, USA
| | - Alan D T Barrett
- Center for Biodefense and Emerging Infectious Diseases, Sealy Center for Vaccine Development, Institute for Human Infections and Immunity, and Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555-0436, USA
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