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Truong TN, Cheng LT. Development of a Subunit Vaccine against Duck Hepatitis A Virus Serotype 3. Vaccines (Basel) 2022; 10:vaccines10040523. [PMID: 35455272 PMCID: PMC9028120 DOI: 10.3390/vaccines10040523] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 02/01/2023] Open
Abstract
In this study, we sought to develop a subunit vaccine against the increasingly prevalent Duck hepatitis A virus serotype 3 (DHAV-3). The VP1 protein of DHAV-3 and a truncated version containing the C-terminal region of VP1, termed VP1-C, were expressed recombinantly in Escherichia coli as vaccine antigens. For enhanced immune response, a truncated version of flagellin, nFliC, was included as vaccine adjuvant. Ducklings were vaccinated once for immune response analysis and challenge test. Results showed that VP1-C elicited a higher level of virus-specific antibody response and neutralization titer than VP1. The addition of nFliC further enhanced the antibody response. In terms of cellular immune response, the VP1-C + nFliC vaccine elicited the highest level of T cell proliferation among the vaccine formulations tested. Examination of the cytokine expression profile showed that peripheral blood mononuclear cells from the VP1-C + nFliC vaccine group expressed the highest levels of pro-inflammatory (IL-6) and TH-1 type (IL-12 and IFN-γ) cytokines. Finally, in a DHAV-3 challenge test, the VP1-C + nFliC vaccine provided a 75% protection rate (n = 8), in contrast to 25% for the VP1 vaccine. In conclusion, E. coli-expressed VP1-C has been shown to be a promising antigen when combined with nFliC and may be further developed as a single-dose subunit vaccine against DHAV-3.
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Affiliation(s)
- Trang-Nhu Truong
- International Degree Program of Animal Vaccine Technology, International College, National Pingtung University of Science and Technology, 1, Shuefu Road, Neipu, Pingtung 91201, Taiwan;
- Institute of Veterinary Research and Development in Central Vietnam, Km 4, Road 2/4, Vinh Hoa, Nha Trang City 57000, Vietnam
| | - Li-Ting Cheng
- Graduate Institute of Animal Vaccine Technology, College of Veterinary Medicine, National Pingtung University of Science and Technology, 1, Shuefu Road, Neipu, Pingtung 91201, Taiwan
- Correspondence: ; Tel.: +886-8-770-3202 (ext. 5336); Fax: +886-8-7740178
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2
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Rong H, Wang L, Gao L, Fang Y, Chen Q, Hu J, Ye M, Liao Q, Zhang L, Dong C. Bioinformatics-based prediction of conformational epitopes for human parechovirus. PLoS One 2021; 16:e0247423. [PMID: 33793559 PMCID: PMC8016246 DOI: 10.1371/journal.pone.0247423] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 02/08/2021] [Indexed: 11/25/2022] Open
Abstract
Human parechoviruses (HPeVs) are human pathogens that usually cause diseases ranging from rash to neonatal sepsis in young children. HPeV1 and HPeV3 are the most frequently reported genotypes and their three-dimensional structures have been determined. However, there is a lack of systematic research on the antigenic epitopes of HPeVs, which are useful for understanding virus-receptor interactions, developing antiviral agents or molecular diagnostic tools, and monitoring antigenic evolution. Thus, we systematically predicted and compared the conformational epitopes of HPeV1 and HPeV3 using bioinformatics methods in the study. The results showed that both epitopes clustered into three sites (sites 1, 2 and 3). Site 1 was located on the "northern rim" near the fivefold vertex; site 2 was on the "puff"; and site 3 was divided into two parts, of which one was located on the "knob" and the other was close to the threefold vertex. The predicted epitopes highly overlapped with the reported antigenic epitopes, which indicated that the prediction results were accurate. Although the distribution positions of the epitopes of HPeV1 and HPeV3 were highly consistent, the residues varied largely and determined the genotypes. Three amino acid residues, VP3-91N, -92H and VP0-257S, were the key residues for monoclonal antibody (mAb) AM28 binding to HPeV1 and were also of great significance in distinguishing HPeV1 and HPeV3. We also found that two residues, VP1-85N and -87D, might affect the capability of mAb AT12-015 to bind to HPeV3.
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Affiliation(s)
- Hao Rong
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo, China
- Department of Preventive Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, School of Medicine, Ningbo University, Ningbo, China
| | - Liping Wang
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo, China
- Department of Preventive Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, School of Medicine, Ningbo University, Ningbo, China
| | - Liuying Gao
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo, China
- The Affiliated People’s Hospital of Ningbo University, Ningbo, China
| | - Yulu Fang
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo, China
- Department of Preventive Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, School of Medicine, Ningbo University, Ningbo, China
| | - Qin Chen
- HuaMei Hospital, University of Chinese Academy of Sciences, Ningbo, China
| | - Jianli Hu
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo, China
| | - Meng Ye
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo, China
- Department of Preventive Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, School of Medicine, Ningbo University, Ningbo, China
| | - Qi Liao
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo, China
- Department of Preventive Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, School of Medicine, Ningbo University, Ningbo, China
| | - Lina Zhang
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo, China
- Department of Preventive Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, School of Medicine, Ningbo University, Ningbo, China
| | - Changzheng Dong
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo, China
- Department of Preventive Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, School of Medicine, Ningbo University, Ningbo, China
- * E-mail:
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Detection of Parechovirus A1 with Monoclonal Antibody against Capsid Protein VP0. Microorganisms 2020; 8:microorganisms8111794. [PMID: 33207765 PMCID: PMC7696872 DOI: 10.3390/microorganisms8111794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/11/2020] [Accepted: 11/15/2020] [Indexed: 01/11/2023] Open
Abstract
Parechovirus A (PeV-A; human parechovirus) causes mild infections and severe diseases such as neonatal sepsis, encephalitis, and cardiomyopathy in young children. Among the 19 types of PeV-A, PeV-A1 is the most common type of infection. We have previously established an immunofluorescence assay for detecting multiple PeV-A types with a polyclonal antibody against the conserved epitope of VP0. Although the polyclonal antibody is useful for PeV-A diagnosis, it could not distinguish the PeV-A genotypes. Thus, the development of a specific monoclonal antibody for identifying the common infection of PeV-A1 would be beneficial in clinical diagnosis practice. In this study, the recombinant full-length PeV-A1 VP0 protein was used in mouse immunization; a total 10 hybridomas were established. After evaluation by immunoblotting and fluorescence assays, six hybridoma clones with monoclonal antibody (mAb) production were confirmed. These mAbs, which specifically recognize viral protein PeV-A1 VP0 without cross-reactivity to PeV-A3, will prove useful in research and PeV-A1 diagnosis.
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Real-Hohn A, Groznica M, Löffler N, Blaas D, Kowalski H. nanoDSF: In vitro Label-Free Method to Monitor Picornavirus Uncoating and Test Compounds Affecting Particle Stability. Front Microbiol 2020; 11:1442. [PMID: 32676065 PMCID: PMC7333345 DOI: 10.3389/fmicb.2020.01442] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 06/04/2020] [Indexed: 12/30/2022] Open
Abstract
Thermal shift assays measure the stability of macromolecules and macromolecular assemblies as a function of temperature. The Particle Stability Thermal Release Assay (PaSTRy) of picornaviruses is based on probes becoming strongly fluorescent upon binding to hydrophobic patches of the protein capsid (e.g., SYPRO Orange) or to the viral RNA genome (e.g., SYTO-82) that become exposed upon heating virus particles. PaSTRy has been exploited for studying the stability of viral mutants, viral uncoating, and the effect of capsid-stabilizing compounds. While the results were usually robust, the thermal shift assay with SYPRO Orange is sensitive to surfactants and EDTA and failed at least to correctly report the effect of excipients on an inactivated poliovirus 3 vaccine. Furthermore, interactions between the probe and capsid-binding antivirals as well as mutual competition for binding sites cannot be excluded. To overcome these caveats, we assessed differential scanning fluorimetry with a nanoDSF device as a label-free alternative. NanoDSF monitors the changes in the intrinsic tryptophan fluorescence (ITF) resulting from alterations of the 3D-structure of proteins as a function of the temperature. Using rhinovirus A2 as a model, we demonstrate that nanoDFS is well suited for recording the temperature-dependence of conformational changes associated with viral uncoating with minute amounts of sample. We compare it with orthogonal methods and correlate the increase in viral RNA exposure with PaSTRy measurements. Importantly, nanoDSF correctly identified the thermal stabilization of RV-A2 by pleconaril, a prototypic pocket-binding antiviral compound. NanoDFS is thus a label-free, high throughput-customizable, attractive alternative for the discovery of capsid-binding compounds impacting on viral stability.
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Affiliation(s)
- Antonio Real-Hohn
- Center for Medical Biochemistry, Max Perutz Labs, Vienna Biocenter, Medical University of Vienna, Vienna, Austria
| | - Martin Groznica
- Center for Medical Biochemistry, Max Perutz Labs, Vienna Biocenter, Medical University of Vienna, Vienna, Austria
| | - Nadine Löffler
- Center for Medical Biochemistry, Max Perutz Labs, Vienna Biocenter, Medical University of Vienna, Vienna, Austria
| | - Dieter Blaas
- Center for Medical Biochemistry, Max Perutz Labs, Vienna Biocenter, Medical University of Vienna, Vienna, Austria
| | - Heinrich Kowalski
- Center for Medical Biochemistry, Max Perutz Labs, Vienna Biocenter, Medical University of Vienna, Vienna, Austria
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Sridhar A, Karelehto E, Brouwer L, Pajkrt D, Wolthers KC. Parechovirus A Pathogenesis and the Enigma of Genotype A-3. Viruses 2019; 11:v11111062. [PMID: 31739613 PMCID: PMC6893760 DOI: 10.3390/v11111062] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 11/12/2019] [Accepted: 11/12/2019] [Indexed: 12/16/2022] Open
Abstract
Parechovirus A is a species in the Parechovirus genus within the Picornaviridae family that can cause severe disease in children. Relatively little is known on Parechovirus A epidemiology and pathogenesis. This review aims to explore the Parechovirus A literature and highlight the differences between Parechovirus A genotypes from a pathogenesis standpoint. In particular, the curious case of Parechovirus-A3 and the genotype-specific disease association will be discussed. Finally, a brief outlook on Parechovirus A research is provided.
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Affiliation(s)
- Adithya Sridhar
- Laboratory of Clinical Virology, Department of Medical Microbiology, Amsterdam UMC, location Academic Medical Center, University of Amsterdam, 1100 AZ Amsterdam, The Netherlands; (E.K.); (L.B.); (K.C.W.)
- Correspondence:
| | - Eveliina Karelehto
- Laboratory of Clinical Virology, Department of Medical Microbiology, Amsterdam UMC, location Academic Medical Center, University of Amsterdam, 1100 AZ Amsterdam, The Netherlands; (E.K.); (L.B.); (K.C.W.)
| | - Lieke Brouwer
- Laboratory of Clinical Virology, Department of Medical Microbiology, Amsterdam UMC, location Academic Medical Center, University of Amsterdam, 1100 AZ Amsterdam, The Netherlands; (E.K.); (L.B.); (K.C.W.)
| | - Dasja Pajkrt
- Department of Pediatrics, Emma Children’s Hospital, Amsterdam UMC, location Academic Medical Center, University of Amsterdam, 1100 AZ Amsterdam, The Netherlands;
| | - Katja C. Wolthers
- Laboratory of Clinical Virology, Department of Medical Microbiology, Amsterdam UMC, location Academic Medical Center, University of Amsterdam, 1100 AZ Amsterdam, The Netherlands; (E.K.); (L.B.); (K.C.W.)
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Li C, Jia Z, Chakravorty A, Pahari S, Peng Y, Basu S, Koirala M, Panday SK, Petukh M, Li L, Alexov E. DelPhi Suite: New Developments and Review of Functionalities. J Comput Chem 2019; 40:2502-2508. [PMID: 31237360 PMCID: PMC6771749 DOI: 10.1002/jcc.26006] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 05/07/2019] [Accepted: 06/09/2019] [Indexed: 12/25/2022]
Abstract
Electrostatic potential, energies, and forces affect virtually any process in molecular biology, however, computing these quantities is a difficult task due to irregularly shaped macromolecules and the presence of water. Here, we report a new edition of the popular software package DelPhi along with describing its functionalities. The new DelPhi is a C++ object-oriented package supporting various levels of multiprocessing and memory distribution. It is demonstrated that multiprocessing results in significant improvement of computational time. Furthermore, for computations requiring large grid size (large macromolecular assemblages), the approach of memory distribution is shown to reduce the requirement of RAM and thus permitting large-scale modeling to be done on Linux clusters with moderate architecture. The new release comes with new features, whose functionalities and applications are described as well. © 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.
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Affiliation(s)
- Chuan Li
- Department of MathematicsWest Chester University of PennsylvaniaWest ChesterPennsylvania19383
| | - Zhe Jia
- Department of Physics and AstronomyClemson UniversityClemsonSouth Carolina29634
| | - Arghya Chakravorty
- Department of Physics and AstronomyClemson UniversityClemsonSouth Carolina29634
| | - Swagata Pahari
- Department of Physics and AstronomyClemson UniversityClemsonSouth Carolina29634
| | - Yunhui Peng
- Department of Physics and AstronomyClemson UniversityClemsonSouth Carolina29634
| | - Sankar Basu
- Department of Physics and AstronomyClemson UniversityClemsonSouth Carolina29634
| | - Mahesh Koirala
- Department of Physics and AstronomyClemson UniversityClemsonSouth Carolina29634
| | | | - Marharyta Petukh
- Department of BiologyPresbyterian CollegeClintonSouth Carolina29325
| | - Lin Li
- Department of PhysicsUniversity of Texas at EI PasoTexas79968
| | - Emil Alexov
- Department of Physics and AstronomyClemson UniversityClemsonSouth Carolina29634
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Malasao R, Khamrin P, Kumthip K, Ushijima H, Maneekarn N. Molecular epidemiology and genetic diversity of human parechoviruses in children hospitalized with acute diarrhea in Thailand during 2011-2016. Arch Virol 2019; 164:1743-1752. [PMID: 30972593 DOI: 10.1007/s00705-019-04249-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 03/13/2019] [Indexed: 12/25/2022]
Abstract
Little is known about human parechovirus (HPeV) infection in Thailand. The genotype distribution of HPeV strains in children admitted to hospitals with acute gastroenteritis was investigated using polymerase chain reaction (PCR) and nucleotide sequencing of the VP1 region as the detection and genotype identification methods, respectively. Of a total of 2,002 stool samples, 49 (2.4%) were positive for HPeV. Of these, HPeV-1 was the most predominant genotype (40.8%), followed by HPeV-3 (16.3%) and HPeV-14 (16.3%), while HPeV-5, -6, -2, -4, and -8 strains were less frequently detected, at 10.2%, 8.2%, 2%, 2%, and 2%, respectively. HPeV infections were detected throughout the year with the biannual peaks of infection in the rainy (Jun-Jul-Aug) and winter (Nov-Dec-Jan) months in Thailand. Based on VP1 amino acid sequence alignment, the arginyl-glycyl-aspartic acid (RGD) motif was found in HPeV-1, -2, -4, and -6 strains. Additionally, an amino acid insertion at the N-terminus of VP1 was observed in HPeV-4 and HPeV-5 strains. Phylogenetic analysis revealed that small clades of HPeV-1 and HPeV-3 strains emerged in 2016 and 2015, respectively, and dominated in the year of their emergence. The HPeV strains detected in Thailand in this study were most closely related to reference strains from Asia and Europe. The evolutionary rate of HPeV strains was 2.87 × 10-4 (95% highest posterior density (HPD) 0.10-6.14 × 10-4) substitutions/site/year. These findings provide information about the genetic diversity and evolutionary dynamics of HPeV genotypes circulating in pediatric patients with acute gastroenteritis in Thailand.
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Affiliation(s)
- Rungnapa Malasao
- Department of Community Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
| | - Pattara Khamrin
- Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Suthep Rd, Si Phum, Amphoe Muang, Chiang Mai, 50200, Thailand
| | - Kattareeya Kumthip
- Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Suthep Rd, Si Phum, Amphoe Muang, Chiang Mai, 50200, Thailand
| | - Hiroshi Ushijima
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Niwat Maneekarn
- Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand.
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Suthep Rd, Si Phum, Amphoe Muang, Chiang Mai, 50200, Thailand.
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A 2.8-Angstrom-Resolution Cryo-Electron Microscopy Structure of Human Parechovirus 3 in Complex with Fab from a Neutralizing Antibody. J Virol 2019; 93:JVI.01597-18. [PMID: 30463974 DOI: 10.1128/jvi.01597-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 11/09/2018] [Indexed: 12/28/2022] Open
Abstract
Human parechovirus 3 (HPeV3) infection is associated with sepsis characterized by significant immune activation and subsequent tissue damage in neonates. Strategies to limit infection have been unsuccessful due to inadequate molecular diagnostic tools for early detection and the lack of a vaccine or specific antiviral therapy. Toward the latter, we present a 2.8-Å-resolution structure of HPeV3 in complex with fragments from a neutralizing human monoclonal antibody, AT12-015, using cryo-electron microscopy (cryo-EM) and image reconstruction. Modeling revealed that the epitope extends across neighboring asymmetric units with contributions from capsid proteins VP0, VP1, and VP3. Antibody decoration was found to block binding of HPeV3 to cultured cells. Additionally, at high resolution, it was possible to model a stretch of RNA inside the virion and, from this, identify the key features that drive and stabilize protein-RNA association during assembly.IMPORTANCE Human parechovirus 3 (HPeV3) is receiving increasing attention as a prevalent cause of sepsis-like symptoms in neonates, for which, despite the severity of disease, there are no effective treatments available. Structural and molecular insights into virus neutralization are urgently needed, especially as clinical cases are on the rise. Toward this goal, we present the first structure of HPeV3 in complex with fragments from a neutralizing monoclonal antibody. At high resolution, it was possible to precisely define the epitope that, when targeted, prevents virions from binding to cells. Such an atomic-level description is useful for understanding host-pathogen interactions and viral pathogenesis mechanisms and for finding potential cures for infection and disease.
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Kadambari S, Harvala H, Simmonds P, Pollard AJ, Sadarangani M. Strategies to improve detection and management of human parechovirus infection in young infants. THE LANCET. INFECTIOUS DISEASES 2019; 19:e51-e58. [DOI: 10.1016/s1473-3099(18)30288-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 04/11/2018] [Accepted: 04/27/2018] [Indexed: 12/13/2022]
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Human Parechovirus 1, 3 and 4 Neutralizing Antibodies in Dutch Mothers and Infants and Their Role in Protection Against Disease. Pediatr Infect Dis J 2018; 37:1304-1308. [PMID: 30382954 PMCID: PMC6239346 DOI: 10.1097/inf.0000000000001986] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Human parechoviruses (HPeVs) are common pathogens in young children, and in the Netherlands, HPeV1, HPeV3 and HPeV4 are the most frequently detected genotypes. HPeV3 in particular has been associated with severe disease in young infants below 3 months of age while the other genotypes more often infect older children and elicit mild symptoms. We investigated if maternal neutralizing antibodies (nAbs) against HPeV1, HPeV3 and HPeV4 protect young Dutch infants from severe disease related to HPeV infection. METHODS We conducted a prospective case-control study of Dutch mother-infant pairs. Thirty-eight HPeV-infected infants and their mothers were included as cases, and 65 HPeV-negative children and their mothers as controls. RESULTS In control infants, we observed nAb seropositivity rates of 41.4%, 33.3% and 27.6%, with median nAb titers of 1:16, 1:12 and 1:8, against HPeV1, HPeV3 and HPeV4, respectively. In control mothers, nAb seropositivity rates were 84.6%, 55.4% and 60.0% with median nAb titers of 1:128, 1:32 and 1:45 against HPeV1, HPeV3 and HPeV4, respectively. The HPeV3 nAb seroprevalence was significantly lower in HPeV3-infected infants and their mothers (0.0% with P < 0.05 and 10.0% with P < 0.001, respectively). In contrast, no differences in nAb seroprevalence against HPeV1 or HPeV4 could be detected between case and control infants or mothers. CONCLUSIONS Our results suggest that young Dutch infants are protected against severe disease related to HPeV1 and HPeV4 by maternal nAbs, but less so against HPeV3 explaining the distinct age distributions and disease severity profiles of children infected with these HPeV genotypes.
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Wolthers KC, Susi P, Jochmans D, Koskinen J, Landt O, Sanchez N, Palm K, Neyts J, Butcher SJ. Progress in human picornavirus research: New findings from the AIROPico consortium. Antiviral Res 2018; 161:100-107. [PMID: 30472162 DOI: 10.1016/j.antiviral.2018.11.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 11/17/2018] [Indexed: 01/29/2023]
Abstract
Several research groups in Europe are active on different aspects of human picornavirus research. The AIROPico (Academia-Industry R&D Opportunities for Picornaviruses) consortium combined the disciplines of pathogenesis, diagnostics and therapy development in order to fill the gaps in our understanding of how picornaviruses cause human disease and how to combat them. AIROPico was the first EU consortium dedicated to human picornavirus research and development, and has largely accelerated and improved R&D on picornavirus biology, diagnostics and therapy. In this article, we present the progress on pathogenesis, diagnostics and treatment strategy developments for human picornaviruses resulting from the structured, translational research approach of the AIROPico consortium. We here summarize new insights in protection against infection by maternal or cross-protective antibodies, the visualisation of interactions between virus and neutralizing antibodies by cryoEM structural imaging, and the outcomes from a picornavirus-infected human 3D organoid. Progress in molecular detection and a fast typing assay for rhinovirus species are presented, as well as the identification of new compounds potentially interesting as therapeutic compounds.
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Affiliation(s)
- Katja C Wolthers
- Department of Medical Microbiology, Laboratory of Clinical Virology, Amsterdam University Medical Centers, Location AMC, Amsterdam, the Netherlands.
| | - Petri Susi
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Dirk Jochmans
- Laboratory of Virology and Chemotherapy, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Janne Koskinen
- Research and Development Department, ArcDia International Ltd, Turku, Finland
| | | | | | | | - Johan Neyts
- Laboratory of Virology and Chemotherapy, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Sarah J Butcher
- HiLIFE -Institute of Biotechnology, and Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
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Intrinsically-disordered N-termini in human parechovirus 1 capsid proteins bind encapsidated RNA. Sci Rep 2018; 8:5820. [PMID: 29643409 PMCID: PMC5895611 DOI: 10.1038/s41598-018-23552-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 03/15/2018] [Indexed: 12/22/2022] Open
Abstract
Human parechoviruses (HPeV) are picornaviruses with a highly-ordered RNA genome contained within icosahedrally-symmetric capsids. Ordered RNA structures have recently been shown to interact with capsid proteins VP1 and VP3 and facilitate virus assembly in HPeV1. Using an assay that combines reversible cross-linking, RNA affinity purification and peptide mass fingerprinting (RCAP), we mapped the RNA-interacting regions of the capsid proteins from the whole HPeV1 virion in solution. The intrinsically-disordered N-termini of capsid proteins VP1 and VP3, and unexpectedly, VP0, were identified to interact with RNA. Comparing these results to those obtained using recombinantly-expressed VP0 and VP1 confirmed the virion binding regions, and revealed unique RNA binding regions in the isolated VP0 not previously observed in the crystal structure of HPeV1. We used RNA fluorescence anisotropy to confirm the RNA-binding competency of each of the capsid proteins’ N-termini. These findings suggests that dynamic interactions between the viral RNA and the capsid proteins modulate virus assembly, and suggest a novel role for VP0.
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Epidemiological and clinical characteristics of infants admitted to hospital due to human parechovirus infections: A prospective study in Spain. ANALES DE PEDIATRÍA (ENGLISH EDITION) 2018. [DOI: 10.1016/j.anpede.2017.02.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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14
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Martín del Valle F, Calvo C, Martinez-Rienda I, Cilla A, Romero MP, Menasalvas AI, Reis-Iglesias L, Roda D, Pena MJ, Rabella N, Portugués de la Red MDM, Megías G, Moreno-Docón A, Otero A, Cabrerizo M. Características epidemiológicas y clínicas de los lactantes hospitalizados por infecciones por parechovirus humanos. Estudio prospectivo en España. An Pediatr (Barc) 2018; 88:82-88. [DOI: 10.1016/j.anpedi.2017.02.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 02/06/2017] [Accepted: 02/24/2017] [Indexed: 10/19/2022] Open
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15
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Olijve L, Jennings L, Walls T. Human Parechovirus: an Increasingly Recognized Cause of Sepsis-Like Illness in Young Infants. Clin Microbiol Rev 2018; 31:e00047-17. [PMID: 29142080 PMCID: PMC5740974 DOI: 10.1128/cmr.00047-17] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Human parechovirus (HPeV) is increasingly being recognized as a potentially severe viral infection in neonates and young infants. HPeV belongs to the family Picornaviridae and is currently divided into 19 genotypes. HPeV-1 is the most prevalent genotype and most commonly causes gastrointestinal and respiratory disease. HPeV-3 is clinically the most important genotype due to its association with severe disease in younger infants, which may partly be explained by its distinct virological properties. In young infants, the typical clinical presentation includes fever, severe irritability, and rash, often leading to descriptions of "hot, red, angry babies." Infants with severe central nervous system (CNS) infections are at an increased risk of long-term sequelae. Considering the importance of HPeV as a cause of severe viral infections in young infants, we recommend that molecular diagnostic techniques for early detection be included in the standard practice for the investigation of sepsis-like illnesses and CNS infections in this age group.
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Affiliation(s)
- Laudi Olijve
- Department of Paediatrics, University of Otago, Christchurch School of Medicine, Christchurch, New Zealand
| | - Lance Jennings
- Canterbury Health Laboratories, Christchurch, New Zealand
| | - Tony Walls
- Department of Paediatrics, University of Otago, Christchurch School of Medicine, Christchurch, New Zealand
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16
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Strain-dependent neutralization reveals antigenic variation of human parechovirus 3. Sci Rep 2017; 7:12075. [PMID: 28935894 PMCID: PMC5608956 DOI: 10.1038/s41598-017-12458-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 09/08/2017] [Indexed: 11/09/2022] Open
Abstract
Human parechovirus 3 (HPeV3), a member of the Picornavirus family, is frequently detected worldwide. However, the observed seropositivity rates for HPeV3 neutralizing antibodies (nAbs) vary from high in Japan to low in the Netherlands and Finland. To study if this can be explained by technical differences or antigenic diversity among HPeV3 strains included in the serological studies, we determined the neutralizing activity of Japanese and Dutch intravenous immunoglobulin batches (IVIG), a rabbit HPeV3 hyperimmune polyclonal serum, and a human HPeV3-specific monoclonal antibody (mAb) AT12-015, against the HPeV3 A308/99 prototype strain and clinical isolates from Japan, the Netherlands and Australia, collected between 1989 and 2015. The rabbit antiserum neutralized all HPeV3 isolates whereas the neutralization capacity of the IVIG batches varied, and the mAb exclusively neutralized the A308/99 strain. Mapping of the amino acid variation among a subset of the HPeV3 strains on an HPeV3 capsid structure revealed that the majority of the surface-exposed amino acid variation was located in the VP1. Furthermore, amino acid mutations in a mAb AT12-015-resistant HPeV3 A308/99 variant indicated the location for potential antigenic determinants. Virus aggregation and the observed antigenic diversity in HPeV3 can explain the varying levels of nAb seropositivity reported in previous studies.
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17
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Anastasina M, Domanska A, Palm K, Butcher S. Human picornaviruses associated with neurological diseases and their neutralization by antibodies. J Gen Virol 2017. [PMID: 28631594 DOI: 10.1099/jgv.0.000780] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Picornaviruses are the most commonly encountered infectious agents in mankind. They typically cause mild infections of the gastrointestinal or respiratory tract, but sometimes also invade the central nervous system. There, they can cause severe diseases with long-term sequelae and even be lethal. The most infamous picornavirus is poliovirus, for which significant epidemics of poliomyelitis were reported from the end of the nineteenth century. A successful vaccination campaign has brought poliovirus close to eradication, but neurological diseases caused by other picornaviruses have increasingly been reported since the late 1990s. In this review we focus on enterovirus 71, coxsackievirus A16, enterovirus 68 and human parechovirus 3, which have recently drawn attention because of their links to severe neurological diseases. We discuss the clinical relevance of these viruses and the primary role of humoral immunity in controlling them, and summarize current knowledge on the neutralization of such viruses by antibodies.
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Affiliation(s)
- Maria Anastasina
- Institute of Biotechnology and Department of Biosciences, University of Helsinki, Viikinkaari 1, 00790 Helsinki, Finland.,Protobios LLC, Mäealuse 4, 12618 Tallinn, Estonia
| | - Aušra Domanska
- Institute of Biotechnology and Department of Biosciences, University of Helsinki, Viikinkaari 1, 00790 Helsinki, Finland
| | - Kaia Palm
- Protobios LLC, Mäealuse 4, 12618 Tallinn, Estonia.,Institute of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia
| | - Sarah Butcher
- Institute of Biotechnology and Department of Biosciences, University of Helsinki, Viikinkaari 1, 00790 Helsinki, Finland
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18
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Shakeel S, Dykeman EC, White SJ, Ora A, Cockburn JJB, Butcher SJ, Stockley PG, Twarock R. Genomic RNA folding mediates assembly of human parechovirus. Nat Commun 2017; 8:5. [PMID: 28232749 PMCID: PMC5431903 DOI: 10.1038/s41467-016-0011-z] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 11/16/2016] [Indexed: 01/04/2023] Open
Abstract
Assembly of the major viral pathogens of the Picornaviridae family is poorly understood. Human parechovirus 1 is an example of such viruses that contains 60 short regions of ordered RNA density making identical contacts with the protein shell. We show here via a combination of RNA-based systematic evolution of ligands by exponential enrichment, bioinformatics analysis and reverse genetics that these RNA segments are bound to the coat proteins in a sequence-specific manner. Disruption of either the RNA coat protein recognition motif or its contact amino acid residues is deleterious for viral assembly. The data are consistent with RNA packaging signals playing essential roles in virion assembly. Their binding sites on the coat proteins are evolutionarily conserved across the Parechovirus genus, suggesting that they represent potential broad-spectrum anti-viral targets.The mechanism underlying packaging of genomic RNA into viral particles is not well understood for human parechoviruses. Here the authors identify short RNA motifs in the parechovirus genome that bind capsid proteins, providing approximately 60 specific interactions for virion assembly.
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Affiliation(s)
- Shabih Shakeel
- Institute of Biotechnology and Department of Biosciences, University of Helsinki, Helsinki, 00790, Finland
| | - Eric C Dykeman
- Departments of Mathematics and Biology and York Centre for Complex Systems Analysis, University of York, York, YO10 5DD, UK
| | - Simon J White
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Ari Ora
- Institute of Biotechnology and Department of Biosciences, University of Helsinki, Helsinki, 00790, Finland
- Department of Applied Physics and Department of Biotechnology and Chemical Technology, Aalto University, Espoo, 02150, Finland
| | - Joseph J B Cockburn
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Sarah J Butcher
- Institute of Biotechnology and Department of Biosciences, University of Helsinki, Helsinki, 00790, Finland.
| | - Peter G Stockley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
| | - Reidun Twarock
- Departments of Mathematics and Biology and York Centre for Complex Systems Analysis, University of York, York, YO10 5DD, UK.
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19
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Cryo-electron Microscopy Study of the Genome Release of the Dicistrovirus Israeli Acute Bee Paralysis Virus. J Virol 2017; 91:JVI.02060-16. [PMID: 27928006 PMCID: PMC5286892 DOI: 10.1128/jvi.02060-16] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 11/21/2016] [Indexed: 01/09/2023] Open
Abstract
Viruses of the family Dicistroviridae can cause substantial economic damage by infecting agriculturally important insects. Israeli acute bee paralysis virus (IAPV) causes honeybee colony collapse disorder in the United States. High-resolution molecular details of the genome delivery mechanism of dicistroviruses are unknown. Here we present a cryo-electron microscopy analysis of IAPV virions induced to release their genomes in vitro. We determined structures of full IAPV virions primed to release their genomes to a resolution of 3.3 Å and of empty capsids to a resolution of 3.9 Å. We show that IAPV does not form expanded A particles before genome release as in the case of related enteroviruses of the family Picornaviridae. The structural changes observed in the empty IAPV particles include detachment of the VP4 minor capsid proteins from the inner face of the capsid and partial loss of the structure of the N-terminal arms of the VP2 capsid proteins. Unlike the case for many picornaviruses, the empty particles of IAPV are not expanded relative to the native virions and do not contain pores in their capsids that might serve as channels for genome release. Therefore, rearrangement of a unique region of the capsid is probably required for IAPV genome release.
IMPORTANCE Honeybee populations in Europe and North America are declining due to pressure from pathogens, including viruses. Israeli acute bee paralysis virus (IAPV), a member of the family Dicistroviridae, causes honeybee colony collapse disorder in the United States. The delivery of virus genomes into host cells is necessary for the initiation of infection. Here we present a structural cryo-electron microscopy analysis of IAPV particles induced to release their genomes. We show that genome release is not preceded by an expansion of IAPV virions as in the case of related picornaviruses that infect vertebrates. Furthermore, minor capsid proteins detach from the capsid upon genome release. The genome leaves behind empty particles that have compact protein shells.
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20
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Potent neutralization of hepatitis A virus reveals a receptor mimic mechanism and the receptor recognition site. Proc Natl Acad Sci U S A 2017; 114:770-775. [PMID: 28074040 PMCID: PMC5278457 DOI: 10.1073/pnas.1616502114] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Hepatitis A virus (HAV) infects ∼1.4 million people annually and, although there is a vaccine, there are no licensed therapeutic drugs. HAV is unusually stable (making disinfection problematic) and little is known of how it enters cells and releases its RNA. Here we report a potent HAV-specific monoclonal antibody, R10, which neutralizes HAV infection by blocking attachment to the host cell. High-resolution cryo-EM structures of HAV full and empty particles and of the complex of HAV with R10 Fab reveal the atomic details of antibody binding and point to a receptor recognition site at the pentamer interface. These results, together with our observation that the R10 Fab destabilizes the capsid, suggest the use of a receptor mimic mechanism to neutralize virus infection, providing new opportunities for therapeutic intervention.
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21
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Structural biology: A picornavirus unlike the others. Nat Microbiol 2016; 1:16217. [DOI: 10.1038/nmicrobiol.2016.217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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22
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Multiple capsid-stabilizing interactions revealed in a high-resolution structure of an emerging picornavirus causing neonatal sepsis. Nat Commun 2016; 7:11387. [PMID: 27435188 PMCID: PMC4961769 DOI: 10.1038/ncomms11387] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 03/18/2016] [Indexed: 12/28/2022] Open
Abstract
The poorly studied picornavirus, human parechovirus 3 (HPeV3) causes neonatal sepsis with no therapies available. Our 4.3-Å resolution structure of HPeV3 on its own and at 15 Å resolution in complex with human monoclonal antibody Fabs demonstrates the expected picornavirus capsid structure with three distinct features. First, 25% of the HPeV3 RNA genome in 60 sites is highly ordered as confirmed by asymmetric reconstruction, and interacts with conserved regions of the capsid proteins VP1 and VP3. Second, the VP0 N terminus stabilizes the capsid inner surface, in contrast to other picornaviruses where on expulsion as VP4, it forms an RNA translocation channel. Last, VP1's hydrophobic pocket, the binding site for the antipicornaviral drug, pleconaril, is blocked and thus inappropriate for antiviral development. Together, these results suggest a direction for development of neutralizing antibodies, antiviral drugs based on targeting the RNA–protein interactions and dissection of virus assembly on the basis of RNA nucleation. Human parechovirus 3 (HPeV3) can cause severe central nervous system infections and is a major cause of neonatal sepsis. Here the authors determine the structure of HPeV3 that provides a high-resolution view of the capsid's organization and shows multiple interactions of the RNA genome with coat proteins.
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23
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Kwakkenbos MJ, van Helden PM, Beaumont T, Spits H. Stable long-term cultures of self-renewing B cells and their applications. Immunol Rev 2016; 270:65-77. [PMID: 26864105 PMCID: PMC4755196 DOI: 10.1111/imr.12395] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Monoclonal antibodies are essential therapeutics and diagnostics in a large number of diseases. Moreover, they are essential tools in all sectors of life sciences. Although the great majority of monoclonal antibodies currently in use are of mouse origin, the use of human B cells to generate monoclonal antibodies is increasing as new techniques to tap the human B cell repertoire are rapidly emerging. Cloned lines of immortalized human B cells are ideal sources of monoclonal antibodies. In this review, we summarize our studies to the regulation of the replicative life span, differentiation, and maturation of B cells that led to the development of a platform that uses immortalization of human B cells by in vitro genetic modification for antibody development. We describe a number of human antibodies that were isolated using this platform and the application of the technique in other species. We also discuss the use of immortalized B cells as antigen-presenting cells for the discovery of tumor neoantigens.
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Affiliation(s)
| | | | - Tim Beaumont
- AIMM TherapeuticsAcademic Medical CenterAmsterdamThe Netherlands
| | - Hergen Spits
- AIMM TherapeuticsAcademic Medical CenterAmsterdamThe Netherlands
- Department of Cell Biology and HistologyAcademic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
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24
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López-Blanco JR, Chacón P. New generation of elastic network models. Curr Opin Struct Biol 2015; 37:46-53. [PMID: 26716577 DOI: 10.1016/j.sbi.2015.11.013] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 11/23/2015] [Accepted: 11/26/2015] [Indexed: 12/16/2022]
Abstract
The intrinsic flexibility of proteins and nucleic acids can be grasped from remarkably simple mechanical models of particles connected by springs. In recent decades, Elastic Network Models (ENMs) combined with Normal Model Analysis widely confirmed their ability to predict biologically relevant motions of biomolecules and soon became a popular methodology to reveal large-scale dynamics in multiple structural biology scenarios. The simplicity, robustness, low computational cost, and relatively high accuracy are the reasons behind the success of ENMs. This review focuses on recent advances in the development and application of ENMs, paying particular attention to combinations with experimental data. Successful application scenarios include large macromolecular machines, structural refinement, docking, and evolutionary conservation.
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Affiliation(s)
- José Ramón López-Blanco
- Department of Biological Chemical Physics, Rocasolano Physical Chemistry Institute C.S.I.C., Serrano 119, 28006 Madrid, Spain
| | - Pablo Chacón
- Department of Biological Chemical Physics, Rocasolano Physical Chemistry Institute C.S.I.C., Serrano 119, 28006 Madrid, Spain.
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