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Clark T, Subramanian V, Jayaraman A, Fitzpatrick E, Gopal R, Pentakota N, Rurak T, Anand S, Viglione A, Raman R, Tharakaraman K, Sasisekharan R. Enhancing antibody affinity through experimental sampling of non-deleterious CDR mutations predicted by machine learning. Commun Chem 2023; 6:244. [PMID: 37945793 PMCID: PMC10636138 DOI: 10.1038/s42004-023-01037-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 10/20/2023] [Indexed: 11/12/2023] Open
Abstract
The application of machine learning (ML) models to optimize antibody affinity to an antigen is gaining prominence. Unfortunately, the small and biased nature of the publicly available antibody-antigen interaction datasets makes it challenging to build an ML model that can accurately predict binding affinity changes due to mutations (ΔΔG). Recognizing these inherent limitations, we reformulated the problem to ask whether an ML model capable of classifying deleterious vs non-deleterious mutations can guide antibody affinity maturation in a practical setting. To test this hypothesis, we developed a Random Forest classifier (Antibody Random Forest Classifier or AbRFC) with expert-guided features and integrated it into a computational-experimental workflow. AbRFC effectively predicted non-deleterious mutations on an in-house validation dataset that is free of biases seen in the publicly available training datasets. Furthermore, experimental screening of a limited number of predictions from the model (<10^2 designs) identified affinity-enhancing mutations in two unrelated SARS-CoV-2 antibodies, resulting in constructs with up to 1000-fold increased binding to the SARS-COV-2 RBD. Our findings indicate that accurate prediction and screening of non-deleterious mutations using machine learning offers a powerful approach to improving antibody affinity.
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Affiliation(s)
- Thomas Clark
- Altus Enterprises, 900 Middlesex Turnpike, Billerica, MA, USA
| | | | - Akila Jayaraman
- Altus Enterprises, 900 Middlesex Turnpike, Billerica, MA, USA
| | | | - Ranjani Gopal
- Altus Enterprises, 900 Middlesex Turnpike, Billerica, MA, USA
| | | | - Troy Rurak
- Altus Enterprises, 900 Middlesex Turnpike, Billerica, MA, USA
| | - Shweta Anand
- Altus Enterprises, 900 Middlesex Turnpike, Billerica, MA, USA
| | | | - Rahul Raman
- Department of Biological Engineering, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA.
| | | | - Ram Sasisekharan
- Department of Biological Engineering, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA.
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2
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Lata K, Charles S, Mangala Prasad V. Advances in computational approaches to structure determination of alphaviruses and flaviviruses using cryo-electron microscopy. J Struct Biol 2023; 215:107993. [PMID: 37414374 DOI: 10.1016/j.jsb.2023.107993] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 05/15/2023] [Accepted: 07/03/2023] [Indexed: 07/08/2023]
Abstract
Advancements in the field of cryo-electron microscopy (cryo-EM) have greatly contributed to our current understanding of virus structures and life cycles. In this review, we discuss the application of single particle cryo-electron microscopy (EM) for the structure elucidation of small enveloped icosahedral viruses, namely, alpha- and flaviviruses. We focus on technical advances in cryo-EM data collection, image processing, three-dimensional reconstruction, and refinement strategies for obtaining high-resolution structures of these viruses. Each of these developments enabled new insights into the alpha- and flavivirus architecture, leading to a better understanding of their biology, pathogenesis, immune response, immunogen design, and therapeutic development.
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Affiliation(s)
- Kiran Lata
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, Karnataka 560012, India
| | - Sylvia Charles
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, Karnataka 560012, India
| | - Vidya Mangala Prasad
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, Karnataka 560012, India; Center for Infectious Disease Research, Indian Institute of Science, Bengaluru, Karnataka 560012, India
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3
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Gulland A. 'Gagged and blindsided': how an allegation of research misconduct affected our lab. Nature 2023:10.1038/d41586-023-02711-5. [PMID: 37626219 DOI: 10.1038/d41586-023-02711-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/27/2023]
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4
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Watanabe S, Vasudevan SG. Clinical and experimental evidence for transplacental vertical transmission of flaviviruses. Antiviral Res 2023; 210:105512. [PMID: 36572192 DOI: 10.1016/j.antiviral.2022.105512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 12/24/2022]
Abstract
The Zika virus (ZIKV) epidemic outbreak in Americas in 2016 attracted global attention because of the association of the virus infection with severe birth defects such as microcephaly, mediated through transplacental virus transmission during pregnancy. Less well-known, but also reported is the increasing evidence that prenatal vertical transmission can be caused by other flaviviruses such as dengue virus (DENV). Currently, the mechanism(s) that cause the vertical transmission of flaviviruses is understudied. Here we review the published reports of clinical evidence of intrauterine transmission of ZIKV and other flaviviruses. We also discuss the animal models for flavivirus infection during pregnancy that have been developed to study the mechanisms underlying the transplacental transmission of flaviviruses in order to develop potential countermeasures for its prevention.
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Affiliation(s)
- Satoru Watanabe
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8-College Road, 169857, Singapore.
| | - Subhash G Vasudevan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8-College Road, 169857, Singapore
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5
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Miller NL, Clark T, Raman R, Sasisekharan R. Learned features of antibody-antigen binding affinity. Front Mol Biosci 2023; 10:1112738. [PMID: 36895805 PMCID: PMC9989197 DOI: 10.3389/fmolb.2023.1112738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 01/18/2023] [Indexed: 02/23/2023] Open
Abstract
Defining predictors of antigen-binding affinity of antibodies is valuable for engineering therapeutic antibodies with high binding affinity to their targets. However, this task is challenging owing to the huge diversity in the conformations of the complementarity determining regions of antibodies and the mode of engagement between antibody and antigen. In this study, we used the structural antibody database (SAbDab) to identify features that can discriminate high- and low-binding affinity across a 5-log scale. First, we abstracted features based on previously learned representations of protein-protein interactions to derive 'complex' feature sets, which include energetic, statistical, network-based, and machine-learned features. Second, we contrasted these complex feature sets with additional 'simple' feature sets based on counts of contacts between antibody and antigen. By investigating the predictive potential of 700 features contained in the eight complex and simple feature sets, we observed that simple feature sets perform comparably to complex feature sets in classification of binding affinity. Moreover, combining features from all eight feature-sets provided the best classification performance (median cross-validation AUROC and F1-score of 0.72). Of note, classification performance is substantially improved when several sources of data leakage (e.g., homologous antibodies) are not removed from the dataset, emphasizing a potential pitfall in this task. We additionally observe a classification performance plateau across diverse featurization approaches, highlighting the need for additional affinity-labeled antibody-antigen structural data. The findings from our present study set the stage for future studies aimed at multiple-log enhancement of antibody affinity through feature-guided engineering.
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Affiliation(s)
- Nathaniel L Miller
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States.,Koch Institute of Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Thomas Clark
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States.,Koch Institute of Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Rahul Raman
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States.,Koch Institute of Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Ram Sasisekharan
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States.,Koch Institute of Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
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6
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Gopal R, Fitzpatrick E, Pentakota N, Jayaraman A, Tharakaraman K, Capila I. Optimizing Antibody Affinity and Developability Using a Framework-CDR Shuffling Approach-Application to an Anti-SARS-CoV-2 Antibody. Viruses 2022; 14:2694. [PMID: 36560698 PMCID: PMC9784564 DOI: 10.3390/v14122694] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/21/2022] [Accepted: 11/25/2022] [Indexed: 12/03/2022] Open
Abstract
The computational methods used for engineering antibodies for clinical development have undergone a transformation from three-dimensional structure-guided approaches to artificial-intelligence- and machine-learning-based approaches that leverage the large sequence data space of hundreds of millions of antibodies generated by next-generation sequencing (NGS) studies. Building on the wealth of available sequence data, we implemented a computational shuffling approach to antibody components, using the complementarity-determining region (CDR) and the framework region (FWR) to optimize an antibody for improved affinity and developability. This approach uses a set of rules to suitably combine the CDRs and FWRs derived from naturally occurring antibody sequences to engineer an antibody with high affinity and specificity. To illustrate this approach, we selected a representative SARS-CoV-2-neutralizing antibody, H4, which was identified and isolated previously based on the predominant germlines that were employed in a human host to target the SARS-CoV-2-human ACE2 receptor interaction. Compared to screening vast CDR libraries for affinity enhancements, our approach identified fewer than 100 antibody framework-CDR combinations, from which we screened and selected an antibody (CB79) that showed a reduced dissociation rate and improved affinity against the SARS-CoV-2 spike protein (7-fold) when compared to H4. The improved affinity also translated into improved neutralization (>75-fold improvement) of SARS-CoV-2. Our rapid and robust approach for optimizing antibodies from parts without the need for tedious structure-guided CDR optimization will have broad utility for biotechnological applications.
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Affiliation(s)
- Ranjani Gopal
- Discovery and Diagnostics Division, Peritia Inc., 12 Gill Street, Woburn, MA 01801, USA
| | - Emmett Fitzpatrick
- Discovery and Diagnostics Division, Peritia Inc., 12 Gill Street, Woburn, MA 01801, USA
| | - Niharika Pentakota
- Discovery and Diagnostics Division, Peritia Inc., 12 Gill Street, Woburn, MA 01801, USA
| | - Akila Jayaraman
- Discovery and Diagnostics Division, Peritia Inc., 12 Gill Street, Woburn, MA 01801, USA
| | - Kannan Tharakaraman
- Discovery and Diagnostics Division, Peritia Inc., 12 Gill Street, Woburn, MA 01801, USA
| | - Ishan Capila
- Celltas Biosciences, 900 Middlesex Turnpike, Billerica, MA 01821, USA
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França RKADO, Silva JM, Rodrigues LS, Sokolowskei D, Brigido MM, Maranhão AQ. New Anti-Flavivirus Fusion Loop Human Antibodies with Zika Virus-Neutralizing Potential. Int J Mol Sci 2022; 23:ijms23147805. [PMID: 35887153 PMCID: PMC9321016 DOI: 10.3390/ijms23147805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/05/2022] [Accepted: 07/11/2022] [Indexed: 02/04/2023] Open
Abstract
Zika virus infections exhibit recurrent outbreaks and can be responsible for disease complications such as congenital Zika virus syndrome. Effective therapeutic interventions are still a challenge. Antibodies can provide significant protection, although the antibody response may fail due to antibody-dependent enhancement reactions. The choice of the target antigen is a crucial part of the process to generate effective neutralizing antibodies. Human anti-Zika virus antibodies were selected by phage display technology. The antibodies were selected against a mimetic peptide based on the fusion loop region in the protein E of Zika virus, which is highly conserved among different flaviviruses. Four rounds of selection were performed using the synthetic peptide in two strategies: the first was using the acidic elution of bound phages, and the second was by applying a competing procedure. After panning, the selected VH and VL domains were determined by combining NGS and bioinformatic approaches. Three different human monoclonal antibodies were expressed as scFvs and further characterized. All showed a binding capacity to Zika (ZIKV) and showed cross-recognition with yellow fever (YFV) and dengue (DENV) viruses. Two of these antibodies, AZ1p and AZ6m, could neutralize the ZIKV infection in vitro. Due to the conservation of the fusion loop region, these new antibodies can potentially be used in therapeutic intervention against Zika virus and other flavivirus illnesses.
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Affiliation(s)
- Renato Kaylan Alves de Oliveira França
- Molecular Immunology Laboratory, Department of Cellular Biology, Institute of Biological Sciences, University of Brasilia, Brasilia 70910-900, Brazil; (R.K.A.d.O.F.); (J.M.S.); (L.S.R.); (D.S.); (A.Q.M.)
- Graduation Program in Molecular Pathology, University of Brasilia, Brasilia 70910-900, Brazil
| | - Jacyelle Medeiros Silva
- Molecular Immunology Laboratory, Department of Cellular Biology, Institute of Biological Sciences, University of Brasilia, Brasilia 70910-900, Brazil; (R.K.A.d.O.F.); (J.M.S.); (L.S.R.); (D.S.); (A.Q.M.)
| | - Lucas Silva Rodrigues
- Molecular Immunology Laboratory, Department of Cellular Biology, Institute of Biological Sciences, University of Brasilia, Brasilia 70910-900, Brazil; (R.K.A.d.O.F.); (J.M.S.); (L.S.R.); (D.S.); (A.Q.M.)
- Graduation Program in Molecular Pathology, University of Brasilia, Brasilia 70910-900, Brazil
| | - Dimitri Sokolowskei
- Molecular Immunology Laboratory, Department of Cellular Biology, Institute of Biological Sciences, University of Brasilia, Brasilia 70910-900, Brazil; (R.K.A.d.O.F.); (J.M.S.); (L.S.R.); (D.S.); (A.Q.M.)
- Graduation Program in Molecular Biology, University of Brasilia, Brasilia 70910-900, Brazil
| | - Marcelo Macedo Brigido
- Molecular Immunology Laboratory, Department of Cellular Biology, Institute of Biological Sciences, University of Brasilia, Brasilia 70910-900, Brazil; (R.K.A.d.O.F.); (J.M.S.); (L.S.R.); (D.S.); (A.Q.M.)
- Graduation Program in Molecular Pathology, University of Brasilia, Brasilia 70910-900, Brazil
- Graduation Program in Molecular Biology, University of Brasilia, Brasilia 70910-900, Brazil
- III-Immunology Investigation Institute–CNPq-MCT, São Paulo 05403-000, Brazil
- Correspondence:
| | - Andrea Queiroz Maranhão
- Molecular Immunology Laboratory, Department of Cellular Biology, Institute of Biological Sciences, University of Brasilia, Brasilia 70910-900, Brazil; (R.K.A.d.O.F.); (J.M.S.); (L.S.R.); (D.S.); (A.Q.M.)
- Graduation Program in Molecular Pathology, University of Brasilia, Brasilia 70910-900, Brazil
- Graduation Program in Molecular Biology, University of Brasilia, Brasilia 70910-900, Brazil
- III-Immunology Investigation Institute–CNPq-MCT, São Paulo 05403-000, Brazil
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8
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Miller NL, Raman R, Clark T, Sasisekharan R. Complexity of Viral Epitope Surfaces as Evasive Targets for Vaccines and Therapeutic Antibodies. Front Immunol 2022; 13:904609. [PMID: 35784339 PMCID: PMC9247215 DOI: 10.3389/fimmu.2022.904609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 05/16/2022] [Indexed: 11/29/2022] Open
Abstract
The dynamic interplay between virus and host plays out across many interacting surfaces as virus and host evolve continually in response to one another. In particular, epitope-paratope interactions (EPIs) between viral antigen and host antibodies drive much of this evolutionary race. In this review, we describe a series of recent studies examining aspects of epitope complexity that go beyond two interacting protein surfaces as EPIs are typically understood. To structure our discussion, we present a framework for understanding epitope complexity as a spectrum along a series of axes, focusing primarily on 1) epitope biochemical complexity (e.g., epitopes involving N-glycans) and 2) antigen conformational/dynamic complexity (e.g., epitopes with differential properties depending on antigen state or fold-axis). We highlight additional epitope complexity factors including epitope tertiary/quaternary structure, which contribute to epistatic relationships between epitope residues within- or adjacent-to a given epitope, as well as epitope overlap resulting from polyclonal antibody responses, which is relevant when assessing antigenic pressure against a given epitope. Finally, we discuss how these different forms of epitope complexity can limit EPI analyses and therapeutic antibody development, as well as recent efforts to overcome these limitations.
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Affiliation(s)
- Nathaniel L. Miller
- Harvard Massachusetts Institute of Technology (MIT) Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Rahul Raman
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Thomas Clark
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Ram Sasisekharan
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
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9
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Tsuji I, Vang F, Dominguez D, Karwal L, Sanjali A, Livengood JA, Davidson E, Fouch ME, Doranz BJ, Das SC, Dean HJ. Somatic Hypermutation and Framework Mutations of Variable Region Contribute to Anti-Zika Virus-Specific Monoclonal Antibody Binding and Function. J Virol 2022; 96:e0007122. [PMID: 35575481 PMCID: PMC9175631 DOI: 10.1128/jvi.00071-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 04/04/2022] [Indexed: 11/20/2022] Open
Abstract
Zika virus (ZIKV) is a global public health concern due to its ability to cause congenital Zika syndrome and lack of approved vaccine, therapeutic, or other control measures. We discovered eight novel rabbit monoclonal antibodies (MAbs) that bind to distinct ZIKV envelope protein epitopes. The majority of the MAbs were ZIKV specific and targeted the lateral ridge of the envelope (E) protein domain III, while the MAb with the highest neutralizing activity recognized a putative quaternary epitope spanning E protein domains I and III. One of the non-neutralizing MAbs specifically recognized ZIKV precursor membrane protein (prM). Somatic hypermutation of immunoglobulin variable regions increases antibody affinity maturation and triggers antibody class switching. Negative correlations were observed between the somatic hypermutation rate of the immunoglobulin heavy-chain variable region and antibody binding parameters such as equilibrium dissociation constant, dissociation constant, and half-maximal effective concentration value of MAb binding to ZIKV virus-like particles. Complementarity-determining regions recognize the antigen epitopes and are scaffolded by canonical framework regions. Reversion of framework region amino acids to the rabbit germ line sequence decreased anti-ZIKV MAb binding activity of some MAbs. Thus, antibody affinity maturation, including somatic hypermutation and framework region mutations, contributed to the binding and function of these anti-ZIKV MAbs. IMPORTANCE ZIKV is a global health concern against which no vaccine or therapeutics are available. We characterized eight novel rabbit monoclonal antibodies recognizing ZIKV envelope and prM proteins and studied the relationship between somatic hypermutation of complementarity-determining regions, framework regions, mutations, antibody specificity, binding, and neutralizing activity. The results contribute to understanding structural features and somatic mutation pathways by which potent Zika virus-neutralizing antibodies can evolve, including the role of antibody framework regions.
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Affiliation(s)
- Isamu Tsuji
- Vaccine Business Unit, Takeda Pharmaceutical Ltd., Cambridge, Massachusetts, USA
| | - Fue Vang
- Vaccine Business Unit, Takeda Pharmaceutical Ltd., Cambridge, Massachusetts, USA
| | - David Dominguez
- Vaccine Business Unit, Takeda Pharmaceutical Ltd., Cambridge, Massachusetts, USA
| | - Lovkesh Karwal
- Vaccine Business Unit, Takeda Pharmaceutical Ltd., Cambridge, Massachusetts, USA
| | - Ankita Sanjali
- Vaccine Business Unit, Takeda Pharmaceutical Ltd., Cambridge, Massachusetts, USA
| | - Jill A. Livengood
- Vaccine Business Unit, Takeda Pharmaceutical Ltd., Cambridge, Massachusetts, USA
| | | | | | | | - Subash C. Das
- Vaccine Business Unit, Takeda Pharmaceutical Ltd., Cambridge, Massachusetts, USA
| | - Hansi J. Dean
- Vaccine Business Unit, Takeda Pharmaceutical Ltd., Cambridge, Massachusetts, USA
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10
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Watanabe S, Chan KWK, Tan NWW, Mahid MBA, Chowdhury A, Chang KTE, Vasudevan SG. Experimental evidence for a high rate of maternal-fetal transmission of dengue virus in the presence of antibodies in immunocompromised mice. EBioMedicine 2022; 77:103930. [PMID: 35290828 PMCID: PMC8921544 DOI: 10.1016/j.ebiom.2022.103930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 02/15/2022] [Accepted: 02/24/2022] [Indexed: 11/18/2022] Open
Abstract
Background Congenital disorders associated with prenatal vertical transmission of Zika virus (ZIKV) is well established since the 2016 outbreak in the Americas. However, despite clinical reports of similar mode of transmission for other flaviviruses such as dengue virus (DENV), the phenomenon has not been experimentally explored. Methods Pregnant AG129 mice were infected with DENV1 in the presence or absence of enhancing antibodies at different gestational time points. ZIKV was used for comparison. We quantified viral load in fetus and placentas and performed comprehensive gene expression profiling in the maternal (decidua) and fetal portion of placenta separately. Findings We demonstrate in a laboratory experimental setting that DENV can be transmitted vertically in a gestation stage-dependent manner similar to ZIKV, and this incidence drastically increases in the presence of enhancing antibodies. Interestingly, a high rate of DENV fetal infection occurs even though the placental viral load is significantly lower than that found in ZIKV-infected dams. Comprehensive gene expression profiling revealed DENV infection modulates a variety of inflammation-associated genes comparable to ZIKV in decidua and fetal placenta in early pregnancy. Interpretation Our findings suggest that the virus-induced modulation of host gene expression may facilitate DENV to cross the placental barrier in spite of lower viral burden compared to ZIKV. This mouse model may serve to identify the host determinants required for the vertical transmission of flaviviruses and develop appropriate countermeasures. Funding National Medical Research Council/Open Fund Individual Research Grant MOH-000524 (SW), MOH-000086 and OFIRG20nov-0017 (SGV).
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Affiliation(s)
- Satoru Watanabe
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8-College Road 169857, Singapore.
| | - Kitti Wing Ki Chan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8-College Road 169857, Singapore
| | - Nicole Wei Wen Tan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8-College Road 169857, Singapore
| | | | - Avisha Chowdhury
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8-College Road 169857, Singapore
| | - Kenneth Tou En Chang
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8-College Road 169857, Singapore; Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, 100 Bukit Timah Road 229899, Singapore
| | - Subhash G Vasudevan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8-College Road 169857, Singapore; Institute for Glycomics, Griffith University, Gold Coast Campus, Queensland 4222, Australia.
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11
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Lee DCP, Raman R, Ghafar NA, Budigi Y. An antibody engineering platform using amino acid networks: A case study in development of antiviral therapeutics. Antiviral Res 2021; 192:105105. [PMID: 34111505 DOI: 10.1016/j.antiviral.2021.105105] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 11/29/2022]
Abstract
We present here a case study of an antibody-engineering platform that selects, modifies, and assembles antibody parts to construct novel antibodies. A salient feature of this platform includes the role of amino acid networks in optimizing framework regions (FRs) and complementarity determining regions (CDRs) to engineer new antibodies with desired structure-function relationships. The details of this approach are described in the context of its utility in engineering ZAb_FLEP, a potent anti-Zika virus antibody. ZAb_FLEP comprises of distinct parts, including heavy chain and light chain FRs and CDRs, with engineered features such as loop lengths and optimal epitope-paratope contacts. We demonstrate, with different test antibodies derived from different FR-CDR combinations, that despite these test antibodies sharing high overall sequence similarity, they yield diverse functional readouts. Furthermore, we show that strategies relying on one dimensional sequence similarity-based analyses of antibodies miss important structural nuances of the FR-CDR relationship, which is effectively addressed by the amino acid networks approach of this platform.
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Affiliation(s)
| | - Rahul Raman
- Department of Biological Engineering, And Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
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12
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Miller NL, Clark T, Raman R, Sasisekharan R. Glycans in Virus-Host Interactions: A Structural Perspective. Front Mol Biosci 2021; 8:666756. [PMID: 34164431 PMCID: PMC8215384 DOI: 10.3389/fmolb.2021.666756] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 05/19/2021] [Indexed: 11/13/2022] Open
Abstract
Many interactions between microbes and their hosts are driven or influenced by glycans, whose heterogeneous and difficult to characterize structures have led to an underappreciation of their role in these interactions compared to protein-based interactions. Glycans decorate microbe glycoproteins to enhance attachment and fusion to host cells, provide stability, and evade the host immune system. Yet, the host immune system may also target these glycans as glycoepitopes. In this review, we provide a structural perspective on the role of glycans in host-microbe interactions, focusing primarily on viral glycoproteins and their interactions with host adaptive immunity. In particular, we discuss a class of topological glycoepitopes and their interactions with topological mAbs, using the anti-HIV mAb 2G12 as the archetypical example. We further offer our view that structure-based glycan targeting strategies are ready for application to viruses beyond HIV, and present our perspective on future development in this area.
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Affiliation(s)
- Nathaniel L Miller
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, United States.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Thomas Clark
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Rahul Raman
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Ram Sasisekharan
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
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13
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A potent neutralizing mouse monoclonal antibody specific to dengue virus type 1 Mochizuki strain recognized a novel epitope around the N-67 glycan on the envelope protein: A possible explanation of dengue virus evolution regarding the acquisition of N-67 glycan. Virus Res 2020; 294:198278. [PMID: 33388392 DOI: 10.1016/j.virusres.2020.198278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 12/20/2020] [Accepted: 12/21/2020] [Indexed: 12/15/2022]
Abstract
The analysis of neutralizing epitope of dengue virus (DENV) is important for the development of an effective dengue vaccine. A potent neutralizing mouse monoclonal antibody named 7F4 was previously reported and, here, we further analyzed the detailed epitope of this antibody. 7F4 recognized a novel conformational epitope close to the N-67 glycan on the envelope protein. This antibody was specific to the DENV that lacks N-67 glycan, including the Mochizuki strain. Interestingly, the Mochizuki strain acquired N-67 glycan by 7F4 selective pressure. Considering that most of the currently circulating DENVs possess N-67 glycan, DENVs may have evolved to escape from antibodies targeting 7F4 epitope, suggesting the potency of this neutralizing epitope. In addition, this study demonstrated the existence of the epitopes close to 7F4 epitope and their crucial role in neutralization. In conclusion, the epitopes close to the N-67 glycan are attractive targets for the dengue vaccine antigen. Further analysis of this epitope is warranted.
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Gasco S, Muñoz-Fernández MÁ. A Review on the Current Knowledge on ZIKV Infection and the Interest of Organoids and Nanotechnology on Development of Effective Therapies against Zika Infection. Int J Mol Sci 2020; 22:ijms22010035. [PMID: 33375140 PMCID: PMC7792973 DOI: 10.3390/ijms22010035] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/18/2020] [Accepted: 12/18/2020] [Indexed: 12/11/2022] Open
Abstract
Zika virus (ZIKV) acquired a special relevance due to the pandemic that occurred in the Americas in 2015, when an important number of fetal microcephaly cases occurred. Since then, numerous studies have tried to elucidate the pathogenic mechanisms and the potential therapeutic approaches to combat the virus. Cellular and animal models have proved to be a basic resource for this research, with the more recent addition of organoids as a more realistic and physiological 3D culture for the study of ZIKV. Nanotechnology can also offer a promising therapeutic tool, as the nanoparticles developed by this field can penetrate cells and deliver a wide array of drugs in a very specific and controlled way inside the cells. These two state-of-the-art scientific tools clearly provide a very relevant resource for the study of ZIKV, and will help researchers find an effective treatment or vaccine against the virus.
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Affiliation(s)
- Samanta Gasco
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), 28001 Madrid, Spain;
- Laboratorio InmunoBiología Molecular (HGUGM), 28001 Madrid, Spain
| | - María Ángeles Muñoz-Fernández
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), 28001 Madrid, Spain;
- Laboratorio InmunoBiología Molecular (HGUGM), 28001 Madrid, Spain
- Spanish HIV-HGM BioBank, 28001 Madrid, Spain
- Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), 28001 Madrid, Spain
- Correspondence: or ; Tel.: +34-91-462-4684
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15
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Yau C, Gan ES, Kwek SS, Tan HC, Ong EZ, Hamis NZ, Rivino L, Chan KR, Watanabe S, Vasudevan SG, Ooi EE. Live vaccine infection burden elicits adaptive humoral and cellular immunity required to prevent Zika virus infection. EBioMedicine 2020; 61:103028. [PMID: 33045466 PMCID: PMC7553235 DOI: 10.1016/j.ebiom.2020.103028] [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: 07/22/2020] [Revised: 08/31/2020] [Accepted: 09/10/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The emergence of Zika virus (ZIKV) as an important cause of congenital and childhood developmental disorders presents another challenge to global health. Efforts to develop a Zika vaccine have begun although vaccine development against flaviviruses, of which ZIKV belongs to, has proven to be time-consuming and challenging. Defining the vaccine attributes that elicit adaptive immune response necessary for preventing ZIKV infection could provide an evidence-based guide to Zika vaccine development. METHODS We used a previously described attenuated ZIKV DN-2 strain in a type-I interferon receptor deficient mouse model and tested the hypothesis that duration of vaccine burden rather than peak level of infection, is a determinant of immunogenicity. We quantified both humoral and cellular responses against ZIKV using plaque reduction neutralisation test and flow cytometry with ELISPOT assays, respectively. Vaccinated mice were challenged with wild-type ZIKV (H/PF/2013 strain) to determine the level of protection against infection. FINDINGS We found that the overall vaccine burden is directly correlated with neutralising antibody titres. Reduced duration of vaccine burden lowered neutralising antibody titres that resulted in subclinical infection, despite unchanged peak vaccine viraemia levels. We also found that sterilising immunity is dependant on both neutralising antibody and CD8+T cell responses; depletion of CD8+T cells in vaccinated animals led to wild-type ZIKV infection, especially in the male reproductive tract. INTERPRETATION Our findings indicate that duration of attenuated virus vaccine burden is a determinant of humoral and cellular immunity and also suggest that vaccines that elicit both arms of the adaptive immune response are needed to fully prevent ZIKV transmission. FUNDING This study was supported by the National Medical Research Council through the Clinician-Scientist Award (Senior Investigator) to E.E.O. Salary support for S.W. was from a Competitive Research Programme grant awarded by the National Research Foundation of Singapore.
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Affiliation(s)
- Clement Yau
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Esther Shuyi Gan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Swee Sen Kwek
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Hwee Cheng Tan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Eugenia Z Ong
- Programme 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
| | - Noor Zayanah Hamis
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Laura Rivino
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Kuan Rong Chan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Satoru Watanabe
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Subhash G Vasudevan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Eng Eong Ooi
- Programme 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; Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore.
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16
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Low JG, Ng JHJ, Ong EZ, Kalimuddin S, Wijaya L, Chan YFZ, Ng DHL, Tan HC, Baglody A, Chionh YH, Lee DCP, Budigi Y, Sasisekharan R, Ooi EE. Phase 1 Trial of a Therapeutic Anti-Yellow Fever Virus Human Antibody. N Engl J Med 2020; 383:452-459. [PMID: 32726531 DOI: 10.1056/nejmoa2000226] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND Insufficient vaccine doses and the lack of therapeutic agents for yellow fever put global health at risk, should this virus emerge from sub-Saharan Africa and South America. METHODS In phase 1a of this clinical trial, we assessed the safety, side-effect profile, and pharmacokinetics of TY014, a fully human IgG1 anti-yellow fever virus monoclonal antibody. In a double-blind, phase 1b clinical trial, we assessed the efficacy of TY014, as compared with placebo, in abrogating viremia related to the administration of live yellow fever vaccine (YF17D-204; Stamaril). The primary safety outcomes were adverse events reported 1 hour after the infusion and throughout the trial. The primary efficacy outcome was the dose of TY014 at which 100% of the participants tested negative for viremia within 48 hours after infusion. RESULTS A total of 27 healthy participants were enrolled in phase 1a, and 10 participants in phase 1b. During phase 1a, TY014 dose escalation to a maximum of 20 mg per kilogram of body weight occurred in 22 participants. During phases 1a and 1b, adverse events within 1 hour after infusion occurred in 1 of 27 participants who received TY014 and in none of the 10 participants who received placebo. At least one adverse event occurred during the trial in 22 participants who received TY014 and in 8 who received placebo. The mean half-life of TY014 was approximately 12.8 days. At 48 hours after the infusion, none of the 5 participants who received the starting dose of TY014 of 2 mg per kilogram had detectable YF17D-204 viremia; these participants remained aviremic throughout the trial. Viremia was observed at 48 hours after the infusion in 2 of 5 participants who received placebo and at 72 hours in 2 more placebo recipients. Symptoms associated with yellow fever vaccine were less frequent in the TY014 group than in the placebo group. CONCLUSIONS This phase 1 trial of TY014 did not identify worrisome safety signals and suggested potential clinical benefit, which requires further assessment in a phase 2 trial. (Funded by Tysana; ClinicalTrials.gov number, NCT03776786.).
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Affiliation(s)
- Jenny G Low
- From the Duke-National University of Singapore Medical School (J.G.L., E.Z.O., H.-C.T., E.-E.O.), Singapore General Hospital (J.G.L., S.K., L.W., Y.F.Z.C., D.H.L.N.), Tysana (J.H.J.N., A.B., Y.-H.C., D.C.P.L., Y.B.), and the Singapore-MIT (Massachusetts Institute of Technology) Alliance for Research and Technology (R.S., E.-E.O.) - all in Singapore; and the Massachusetts Institute of Technology, Cambridge (R.S.)
| | - Justin H J Ng
- From the Duke-National University of Singapore Medical School (J.G.L., E.Z.O., H.-C.T., E.-E.O.), Singapore General Hospital (J.G.L., S.K., L.W., Y.F.Z.C., D.H.L.N.), Tysana (J.H.J.N., A.B., Y.-H.C., D.C.P.L., Y.B.), and the Singapore-MIT (Massachusetts Institute of Technology) Alliance for Research and Technology (R.S., E.-E.O.) - all in Singapore; and the Massachusetts Institute of Technology, Cambridge (R.S.)
| | - Eugenia Z Ong
- From the Duke-National University of Singapore Medical School (J.G.L., E.Z.O., H.-C.T., E.-E.O.), Singapore General Hospital (J.G.L., S.K., L.W., Y.F.Z.C., D.H.L.N.), Tysana (J.H.J.N., A.B., Y.-H.C., D.C.P.L., Y.B.), and the Singapore-MIT (Massachusetts Institute of Technology) Alliance for Research and Technology (R.S., E.-E.O.) - all in Singapore; and the Massachusetts Institute of Technology, Cambridge (R.S.)
| | - Shirin Kalimuddin
- From the Duke-National University of Singapore Medical School (J.G.L., E.Z.O., H.-C.T., E.-E.O.), Singapore General Hospital (J.G.L., S.K., L.W., Y.F.Z.C., D.H.L.N.), Tysana (J.H.J.N., A.B., Y.-H.C., D.C.P.L., Y.B.), and the Singapore-MIT (Massachusetts Institute of Technology) Alliance for Research and Technology (R.S., E.-E.O.) - all in Singapore; and the Massachusetts Institute of Technology, Cambridge (R.S.)
| | - Limin Wijaya
- From the Duke-National University of Singapore Medical School (J.G.L., E.Z.O., H.-C.T., E.-E.O.), Singapore General Hospital (J.G.L., S.K., L.W., Y.F.Z.C., D.H.L.N.), Tysana (J.H.J.N., A.B., Y.-H.C., D.C.P.L., Y.B.), and the Singapore-MIT (Massachusetts Institute of Technology) Alliance for Research and Technology (R.S., E.-E.O.) - all in Singapore; and the Massachusetts Institute of Technology, Cambridge (R.S.)
| | - Yvonne F Z Chan
- From the Duke-National University of Singapore Medical School (J.G.L., E.Z.O., H.-C.T., E.-E.O.), Singapore General Hospital (J.G.L., S.K., L.W., Y.F.Z.C., D.H.L.N.), Tysana (J.H.J.N., A.B., Y.-H.C., D.C.P.L., Y.B.), and the Singapore-MIT (Massachusetts Institute of Technology) Alliance for Research and Technology (R.S., E.-E.O.) - all in Singapore; and the Massachusetts Institute of Technology, Cambridge (R.S.)
| | - Dorothy H L Ng
- From the Duke-National University of Singapore Medical School (J.G.L., E.Z.O., H.-C.T., E.-E.O.), Singapore General Hospital (J.G.L., S.K., L.W., Y.F.Z.C., D.H.L.N.), Tysana (J.H.J.N., A.B., Y.-H.C., D.C.P.L., Y.B.), and the Singapore-MIT (Massachusetts Institute of Technology) Alliance for Research and Technology (R.S., E.-E.O.) - all in Singapore; and the Massachusetts Institute of Technology, Cambridge (R.S.)
| | - Hwee-Cheng Tan
- From the Duke-National University of Singapore Medical School (J.G.L., E.Z.O., H.-C.T., E.-E.O.), Singapore General Hospital (J.G.L., S.K., L.W., Y.F.Z.C., D.H.L.N.), Tysana (J.H.J.N., A.B., Y.-H.C., D.C.P.L., Y.B.), and the Singapore-MIT (Massachusetts Institute of Technology) Alliance for Research and Technology (R.S., E.-E.O.) - all in Singapore; and the Massachusetts Institute of Technology, Cambridge (R.S.)
| | - Anjali Baglody
- From the Duke-National University of Singapore Medical School (J.G.L., E.Z.O., H.-C.T., E.-E.O.), Singapore General Hospital (J.G.L., S.K., L.W., Y.F.Z.C., D.H.L.N.), Tysana (J.H.J.N., A.B., Y.-H.C., D.C.P.L., Y.B.), and the Singapore-MIT (Massachusetts Institute of Technology) Alliance for Research and Technology (R.S., E.-E.O.) - all in Singapore; and the Massachusetts Institute of Technology, Cambridge (R.S.)
| | - Yok-Hian Chionh
- From the Duke-National University of Singapore Medical School (J.G.L., E.Z.O., H.-C.T., E.-E.O.), Singapore General Hospital (J.G.L., S.K., L.W., Y.F.Z.C., D.H.L.N.), Tysana (J.H.J.N., A.B., Y.-H.C., D.C.P.L., Y.B.), and the Singapore-MIT (Massachusetts Institute of Technology) Alliance for Research and Technology (R.S., E.-E.O.) - all in Singapore; and the Massachusetts Institute of Technology, Cambridge (R.S.)
| | - Debbie C P Lee
- From the Duke-National University of Singapore Medical School (J.G.L., E.Z.O., H.-C.T., E.-E.O.), Singapore General Hospital (J.G.L., S.K., L.W., Y.F.Z.C., D.H.L.N.), Tysana (J.H.J.N., A.B., Y.-H.C., D.C.P.L., Y.B.), and the Singapore-MIT (Massachusetts Institute of Technology) Alliance for Research and Technology (R.S., E.-E.O.) - all in Singapore; and the Massachusetts Institute of Technology, Cambridge (R.S.)
| | - Yadunanda Budigi
- From the Duke-National University of Singapore Medical School (J.G.L., E.Z.O., H.-C.T., E.-E.O.), Singapore General Hospital (J.G.L., S.K., L.W., Y.F.Z.C., D.H.L.N.), Tysana (J.H.J.N., A.B., Y.-H.C., D.C.P.L., Y.B.), and the Singapore-MIT (Massachusetts Institute of Technology) Alliance for Research and Technology (R.S., E.-E.O.) - all in Singapore; and the Massachusetts Institute of Technology, Cambridge (R.S.)
| | - Ram Sasisekharan
- From the Duke-National University of Singapore Medical School (J.G.L., E.Z.O., H.-C.T., E.-E.O.), Singapore General Hospital (J.G.L., S.K., L.W., Y.F.Z.C., D.H.L.N.), Tysana (J.H.J.N., A.B., Y.-H.C., D.C.P.L., Y.B.), and the Singapore-MIT (Massachusetts Institute of Technology) Alliance for Research and Technology (R.S., E.-E.O.) - all in Singapore; and the Massachusetts Institute of Technology, Cambridge (R.S.)
| | - Eng-Eong Ooi
- From the Duke-National University of Singapore Medical School (J.G.L., E.Z.O., H.-C.T., E.-E.O.), Singapore General Hospital (J.G.L., S.K., L.W., Y.F.Z.C., D.H.L.N.), Tysana (J.H.J.N., A.B., Y.-H.C., D.C.P.L., Y.B.), and the Singapore-MIT (Massachusetts Institute of Technology) Alliance for Research and Technology (R.S., E.-E.O.) - all in Singapore; and the Massachusetts Institute of Technology, Cambridge (R.S.)
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17
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Tyagi A, Ahmed T, Shi J, Bhushan S. A complex between the Zika virion and the Fab of a broadly cross-reactive neutralizing monoclonal antibody revealed by cryo-EM and single particle analysis at 4.1 Å resolution. JOURNAL OF STRUCTURAL BIOLOGY-X 2020; 4:100028. [PMID: 32647830 PMCID: PMC7337043 DOI: 10.1016/j.yjsbx.2020.100028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 06/10/2020] [Accepted: 06/11/2020] [Indexed: 11/30/2022]
Abstract
Zika virus (ZIKV) recently emerged as a major public health concern because it can cause fetal microcephaly and neurological disease such as the Guillain-Barré syndrome. A particularly potent class of broadly neutralizing antibodies (nAbs) targets a quaternary epitope located at the interface of two envelope proteins monomers, exposed at the surface of the mature virion. This “E-dimer-dependent epitope” (EDE), comprises the fusion loop of one monomer at the tip of domain II of E and a portion of the domains I and III of the adjacent monomer. Since this epitope largely overlaps with the binding site of the precursor membrane protein (prM) during Zika virion maturation, its molecular surface is evolutionary conserved in flaviviruses such as Dengue and Zika viruses, and can elicit antibodies that broadly neutralize various ZIKV strains. Here, we present a cryo-EM reconstruction at 4.1 Å resolution of the virion bound to the antigen binding fragment (Fab) of an antibody that targets this mutationally-constrained quaternary epitope. The Fab incompletely covers the surface of the virion as it does not bind next to its 5-fold icosahedral axes. The structure reveals details of the binding mode of this potent neutralizing class of antibodies and can inform the design of immunogens and vaccines targeting this conserved epitope.
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Affiliation(s)
- Anu Tyagi
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Tofayel Ahmed
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Jian Shi
- Center for Bio-Imaging Sciences, National University of Singapore, Singapore
| | - Shashi Bhushan
- School of Biological Sciences, Nanyang Technological University, Singapore
- Nanyang Institute of Structural Biology, Experimental Medicine Building, 59 Nanyang Drive, 636921, Singapore
- Corresponding author at: School of Biological Sciences, Nanyang Technological University, Singapore.
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18
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Fuzo CA, de Araujo LFL, Pontes RDS, Évora PM, Stabeli RG. Adjacent dimer epitope of envelope protein as an important region for Zika virus serum neutralization: a computational investigation. J Biomol Struct Dyn 2020; 39:1082-1092. [PMID: 32090677 DOI: 10.1080/07391102.2020.1728385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The recent emergence of Zika virus (ZIKV) has affected many countries, with severe clinical manifestations such as fetal microcephaly and Guillain-Barré syndrome. However, even though it is a major public health concern, there is no approved treatment available. Structural knowledge of the main neutralization regions of the envelope (E) protein of ZIKV and its interactions with neutralizing antibodies (nAbs) are crucial for the rational development of subunit vaccines and establishment of antibody-based interventions. In this study we screened from public data hot spot epitopes in conserved regions of ZIKV E protein that are nAbs targets. The result points to a conserved epitope located at domain II of the ZIKV E protein, namely adjacent dimer epitope, which is the ZIKV-117 and Z20 nAbs target. Although these two nAbs have been isolated from different donors, we have demonstrated, from structural and energetic details obtained by molecular dynamics of native and mutants, that hot spots residues of the epitope are the same for these nAbs, thereby indicating that they may share similar binding and neutralization mechanism. This convergence of information between these nAbs is important because both are potential targets for the development of therapies against ZIKV and only Z20 has its sequence and its complex structure with ZIKV E protein determined. Finally, these findings also contribute to existing knowledge, by fine mapping of the epitope/paratope residue pairs that are important for biotechnological development of therapies such as epitope mimetics for subunit vaccines and the rational design for antibody-based interventions against ZIKV. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Carlos Alessandro Fuzo
- Plataforma de Pesquisa em Medicina Translacional, Fundação Oswaldo Cruz - Fiocruz SP, São Paulo, Brazil.,Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Luiz Felipe Lemes de Araujo
- Plataforma de Pesquisa em Medicina Translacional, Fundação Oswaldo Cruz - Fiocruz SP, São Paulo, Brazil.,Departamento de Bioquímica e Imunologia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Rafael de Souza Pontes
- Plataforma de Pesquisa em Medicina Translacional, Fundação Oswaldo Cruz - Fiocruz SP, São Paulo, Brazil.,Departamento de Bioquímica e Imunologia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Patricia Martinez Évora
- Plataforma de Pesquisa em Medicina Translacional, Fundação Oswaldo Cruz - Fiocruz SP, São Paulo, Brazil.,Departamento de Bioquímica e Imunologia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Rodrigo Guerino Stabeli
- Plataforma de Pesquisa em Medicina Translacional, Fundação Oswaldo Cruz - Fiocruz SP, São Paulo, Brazil.,Departamento de Bioquímica e Imunologia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
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19
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Finlay WJ, Lugovskoy AA. De novo discovery of antibody drugs - great promise demands scrutiny. MAbs 2019; 11:809-811. [PMID: 31122133 PMCID: PMC6601558 DOI: 10.1080/19420862.2019.1622926] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 05/01/2019] [Accepted: 05/21/2019] [Indexed: 01/10/2023] Open
Abstract
We live in an era of rapidly advancing computing capacity and algorithmic sophistication. "Big data" and "artificial intelligence"find progressively wider use in all spheres of human activity, including healthcare. A diverse array of computational technologies is being applied with increasing frequency to antibody drug research and development (R&D). Their successful applications are met with great interest due to the potential for accelerating and streamlining the antibody R&D process. While this excitement is very likely justified in the long term, it is less likely that the transition from the first use to routine practice will escape challenges that other new technologies had experienced before they began to blossom. This transition typically requires many cycles of iterative learning that rely on the deconstruction of the technology to understand its pitfalls and define vectors for optimization. The study by Vasquez et al. identifies a key obstacle to such learning: the lack of transparency regarding methodology in computational antibody design reports, which has the potential to mislead the community efforts.
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20
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Ng IHW, Chan KWK, Tan MJA, Gwee CP, Smith KM, Jeffress SJ, Saw WG, Swarbrick CMD, Watanabe S, Jans DA, Grüber G, Forwood JK, Vasudevan SG. Zika Virus NS5 Forms Supramolecular Nuclear Bodies That Sequester Importin-α and Modulate the Host Immune and Pro-Inflammatory Response in Neuronal Cells. ACS Infect Dis 2019; 5:932-948. [PMID: 30848123 DOI: 10.1021/acsinfecdis.8b00373] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The Zika virus (ZIKV) epidemic in the Americas was alarming because of its link with microcephaly in neonates and Guillain-Barré syndrome in adults. The unusual pathologies induced by ZIKV infection and the knowledge that the flaviviral nonstructural protein 5 (NS5), the most conserved protein in the flavivirus proteome, can modulate the host immune response during ZIKV infection prompted us to investigate the subcellular localization of NS5 during ZIKV infection and explore its functional significance. A monopartite nuclear localization signal (NLS) sequence within ZIKV NS5 was predicted by the cNLS Mapper program, and we observed localization of ZIKV NS5 in the nucleus of infected cells by immunostaining with specific antibodies. Strikingly, ZIKV NS5 forms spherical shell-like nuclear bodies that exclude DNA. The putative monopartite NLS 390KRPR393 is necessary to direct FLAG-tagged NS5 to the nucleus as the NS5 390ARPA393 mutant protein accumulates in the cytoplasm. Furthermore, coimmunostaining experiments reveal that NS5 localizes with and sequesters importin-α, but not importin-β, in the observed nuclear bodies during virus infection. Structural and biochemical data demonstrate binding of ZIKV NS5 with importin-α and reveal important binding determinants required for their interaction and formation of complexes that give rise to the supramolecular nuclear bodies. Significantly, we demonstrate a neuronal-specific activation of the host immune response to ZIKV infection and a possible role of ZIKV NS5's nuclear localization toward this activation. This suggests that ZIKV pathogenesis may arise from a tissue-specific host response to ZIKV infection.
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Affiliation(s)
- Ivan H. W. Ng
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857
| | - Kitti Wing-Ki Chan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857
- Department of Microbiology and Immunology, National University of Singapore, 5 Science Drive 2, Singapore 117545
| | - Min Jie Alvin Tan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857
- Genome Institute of Singapore, Agency for Science & Technology Research (A*STAR), 60 Biopolis Street, Singapore 138672
| | - Chin Piaw Gwee
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857
| | - Kate M. Smith
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, New South Wales 2650, Australia
| | - Sarah J. Jeffress
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, New South Wales 2650, Australia
| | - Wuan-Geok Saw
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Crystall M. D. Swarbrick
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857
| | - Satoru Watanabe
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857
| | - David A. Jans
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Gerhard Grüber
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Jade K. Forwood
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, New South Wales 2650, Australia
| | - Subhash G. Vasudevan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
- Department of Microbiology and Immunology, National University of Singapore, 5 Science Drive 2, Singapore 117545
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21
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Vásquez M, Krauland E, Walker L, Wittrup D, Gerngross T. Connecting the sequence dots: shedding light on the genesis of antibodies reported to be designed in silico. MAbs 2019; 11:803-808. [PMID: 31107637 PMCID: PMC6601546 DOI: 10.1080/19420862.2019.1611172] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Two recent publications out of the same research laboratory report on structure-based in silico design of antibodies against viral targets without sequence disclosure. Cross-referencing the published data to patent databases, we established the sequence identity of said computationally designed antibodies. In both cases, the antibodies align with high sequence identity to previously reported antibodies of the same specificity. This clear underlying sequence relationship, which is far closer than the antibody templates reported to seed the computational design, suggests an alternative origin of the computationally designed antibodies. The lack of both reproducible computational algorithms and of output sequences in the initial publications obscures the relationship to previously reported antibodies, and sows doubt as to the genesis narrative described therein.
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Affiliation(s)
| | | | | | - Dane Wittrup
- a Adimab LLC , Lebanon , NH , USA.,b Massachusetts Institute of Technology , Cambridge , MA , USA
| | - Tillman Gerngross
- a Adimab LLC , Lebanon , NH , USA.,c Thayer School of Engineering , Dartmouth College , Hanover , NH , USA
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22
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Watanabe S, Tan NWW, Chan KWK, Vasudevan SG. Assessing the utility of antivirals for preventing maternal-fetal transmission of zika virus in pregnant mice. Antiviral Res 2019; 167:104-109. [PMID: 31051186 DOI: 10.1016/j.antiviral.2019.04.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 04/24/2019] [Accepted: 04/25/2019] [Indexed: 11/18/2022]
Abstract
Zika virus (ZIKV) infection during pregnancy has been associated with adverse outcomes and birth defects such as microcephaly in newborn children. Congenital malformations associated with ZIKV are believed to occur via direct infection of the fetus. Unfortunately, there are no licensed therapeutic or preventative tools to block maternal-fetal transmission of ZIKV. In this study, we developed a mouse model of ZIKV infection that specifically establishes vertical maternal-fetal transmission of ZIKV in 40-60% of fetuses when the dams acquire ZIKV infection during pregnancy. This mouse model somewhat mirrors the experience in humans at the peak of the epidemic in the Americas. Using this model, we demonstrate that a well-documented directly acting antiviral (DAA) compound that targets flaviviral RNA synthesis can completely prevent fetal infection when the treatment is started at the time of infection. Notably, we show that the treatment commenced at the time of peak viremia is still able to reduce the risk of fetal infection concomitant with significant reduction in placental viral load. Our results show for the first time the potential for clinical development of antiviral drugs for preventing vertical maternal-fetal transmission of ZIKV.
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Affiliation(s)
- Satoru Watanabe
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8-College Road, 169857, Singapore.
| | - Nicole Wei Wen Tan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8-College Road, 169857, Singapore
| | - Kitti Wing Ki Chan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8-College Road, 169857, Singapore
| | - Subhash G Vasudevan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8-College Road, 169857, Singapore.
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23
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Fink K. Can We Improve Vaccine Efficacy by Targeting T and B Cell Repertoire Convergence? Front Immunol 2019; 10:110. [PMID: 30814993 PMCID: PMC6381292 DOI: 10.3389/fimmu.2019.00110] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 01/15/2019] [Indexed: 01/31/2023] Open
Abstract
Traditional vaccine development builds on the assumption that healthy individuals have virtually unlimited antigen recognition repertoires of receptors in B cells and T cells [the B cell receptor (BCR) and TCR respectively]. However, there are indications that there are "holes" in the breadth of repertoire diversity, where no or few B or T cell are able to bind to a given antigen. Repertoire diversity may in these cases be a limiting factor for vaccine efficacy. Assuming that it is possible to predict which B and T cell receptors will respond to a given immunogen, vaccine strategies could be optimized and personalized. In addition, vaccine testing could be simplified if we could predict responses through sequencing BCR and TCRs. Bulk sequencing has shown putatively specific converging sequences after infection or vaccination. However, only single cell technologies have made it possible to capture the sequence of both heavy and light chains of a BCR or the alpha and beta chains the TCR. This has enabled the cloning of receptors and the functional validation of a predicted specificity. This review summarizes recent evidence of converging sequences in infectious diseases. Current and potential future applications of single cell technology in immune repertoire analysis are then discussed. Finally, possible short- and long- term implications for vaccine research are highlighted.
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Affiliation(s)
- Katja Fink
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore, Singapore
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24
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Badolo A, Burt F, Daniel S, Fearns R, Gudo ES, Kielian M, Lescar J, Shi Y, von Brunn A, Weiss SR, Hilgenfeld R. Third Tofo Advanced Study Week on Emerging and Re-emerging Viruses, 2018. Antiviral Res 2018; 162:142-150. [PMID: 30597184 PMCID: PMC7132404 DOI: 10.1016/j.antiviral.2018.12.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 12/24/2018] [Indexed: 11/23/2022]
Abstract
The Third Tofo Advanced Study Week on Emerging and Re-Emerging Viruses (3rd TASW) was held in Praia do Tofo, Mozambique, from September 02 to 06, 2018. It brought together 55 participants from 10 African countries as well as from Belgium, China, Germany, Singapore, and the USA. Meeting sessions covered aspects of the epidemiology, diagnosis, molecular and structural biology, vaccine development, and antiviral drug discovery for emerging RNA viruses that are current threats in Africa and included flaviviruses (dengue and Zika), alphaviruses (chikungunya), coronaviruses, filoviruses (Ebola), influenza viruses, Crimean Congo hemorrhagic fever virus, Rift Valley fever Virus, Lassa virus, and others. Data were presented on recent flavivirus and/or chikungunyavirus outbreaks in Angola, Burkina Faso, and Mozambique. In addition, these viruses are endemic in many sub-Saharan countries. The TASW series on emerging viruses is unique in Africa and successful in promoting collaborations between researchers in Africa and other parts of the world, as well as among African scientists. This report summarizes the lectures held at the meeting and highlights advances in the field. The 3rd Tofo Advanced Study Week on Emerging and Re-emerging Viruses took place from September 2–6, 2018. African attendees came from Angola, Botswana, Burkina Faso, the CAR, Mozambique, Nigeria, S Africa, Tanzania and Zimbabwe. Other participants were from Europe, China, Singapore, and the USA. This unique meeting enabled scientists from Africa and elsewhere to discuss problems and initiate new collaborations. Presentations covered dengue virus, Zika, chikungunya, coronaviruses, Ebola, influenza, Rift Valley fever, CCHF, and RSV.
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Affiliation(s)
- Athanase Badolo
- Laboratory of Fundamental and Applied Entomology, University Ouaga, Ouagadougou, Burkina Faso.
| | - Felicity Burt
- Division of Virology, National Health Laboratory Services and Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa.
| | - Susan Daniel
- Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA.
| | - Rachel Fearns
- Boston University School of Medicine, Boston, MA, USA.
| | | | - Margaret Kielian
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA.
| | - Julien Lescar
- Structural Biology and Biochemistry, Nanyang Technological University, Singapore.
| | - Yi Shi
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
| | - Albrecht von Brunn
- Max von Pettenkofer-Institute, Ludwig-Maximilians-University of Munich, Munich, Germany; German Center for Infection Research (DZIF), Munich Site, Munich, Germany.
| | - Susan R Weiss
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Rolf Hilgenfeld
- Institute of Biochemistry, University of Lübeck, Lübeck, Germany; German Center for Infection Research (DZIF), Hamburg - Lübeck - Borstel - Riems Site, Lübeck, Germany.
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25
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Lim MQ, Kumaran EAP, Tan HC, Lye DC, Leo YS, Ooi EE, MacAry PA, Bertoletti A, Rivino L. Cross-Reactivity and Anti-viral Function of Dengue Capsid and NS3-Specific Memory T Cells Toward Zika Virus. Front Immunol 2018; 9:2225. [PMID: 30327651 PMCID: PMC6174860 DOI: 10.3389/fimmu.2018.02225] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 09/07/2018] [Indexed: 12/01/2022] Open
Abstract
Zika virus (ZIKV), a flavivirus with homology to dengue virus (DENV), is spreading to areas of DENV hyper-endemicity. Heterologous T cell immunity, whereby virus-specific memory T cells are activated by variant peptides derived from a different virus, can lead to enhanced viral clearance or diminished protective immunity and altered immunopathology. In mice, CD8+ T cells specific for DENV provide in vivo protective efficacy against subsequent ZIKV infection. In humans, contrasting studies report complete absence or varying degrees of DENV/ZIKV T cell cross-reactivity. Moreover, the impact of cross-reactive T cell recognition on the anti-viral capacity of T cells remains unclear. Here, we show that DENV-specific memory T cells display robust cross-reactive recognition of ZIKV NS3 ex vivo and after in vitro expansion in respectively n = 7/10 and n = 9/9 dengue-immune individuals tested. In contrast, cross-reactivity toward ZIKV capsid is low or absent. Cross-reactive recognition of DENV or ZIKV NS3 peptides elicits similar production of the anti-viral effector mediators IFN-γ, TNF-α, and CD107a. We identify 9 DENV/ZIKV cross-reactive epitopes, 7 of which are CD4+ and 2 are CD8+ T cell epitopes. We also show that cross-reactive CD4+ and CD8+ T cells targeting novel NS3 epitopes display anti-viral effector potential toward ZIKV-infected cells, with CD8+ T cells mediating direct lyses of these cells. Our results demonstrate that DENV NS3-specific memory T cells display anti-viral effector capacity toward ZIKV, suggesting a potential beneficial effect in humans of pre-existing T cell immunity to DENV upon ZIKV infection.
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Affiliation(s)
- Mei Qiu Lim
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Emmanuelle A P Kumaran
- Immunology Programme, Department of Microbiology and Immunology, Life Science Institute, National University of Singapore, Singapore, Singapore
| | - Hwee Cheng Tan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - David C Lye
- Communicable Disease Centre, Institute of Infectious Disease and Epidemiology, Tan Tock Seng Hospital, Singapore, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Yee Sin Leo
- Communicable Disease Centre, Institute of Infectious Disease and Epidemiology, Tan Tock Seng Hospital, Singapore, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,National Centre for Infectious diseases, NCID, Singapore, Singapore
| | - Eng Eong Ooi
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore.,Immunology Programme, Department of Microbiology and Immunology, Life Science Institute, National University of Singapore, Singapore, Singapore
| | - Paul A MacAry
- Immunology Programme, Department of Microbiology and Immunology, Life Science Institute, National University of Singapore, Singapore, Singapore
| | - Antonio Bertoletti
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore.,Singapore Immunology Network, Singapore Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Laura Rivino
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
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