Genetic and structural insights into broad neutralization of hepatitis C virus by human V
            <sub>H</sub>
            1-69 antibodies

Tzarum, N.; Kong, Leopold; He, Linling; Prentoe, Jannick; Augestad, Elias H.; Hua, Yuanzi; Castillo, Shaun; Lauer, Georg M.; Bukh, Jens; Zhu, Jiang; Wilson, Ian A.; Law, Mansun

doi:10.1126/sciadv.aav1882

Cited by 76 publications

(155 citation statements)

References 69 publications

(130 reference statements)

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“…Consistent with a previous study of DENV-infected individuals (Appanna et al, 2016), many of the DENV-specific mAbs originating from plasmablasts of patient 013 also derived from IGVH1-69 (Table S3), which is commonly used among bNAbs against other viruses such as influenza and Hepatitis C virus (Chen, Tzarum, Wilson, & Law, 2019). Many of these bNAbs can achieve neutralization breadth and potency with limited SHM (Lingwood et al, 2012;Tzarum et al, 2019). Despite a moderately high degree of SHM for J8 VH (9.9% at the nucleotide level, Figure S1), five early amino acid mutations in CDR-H2 and CDR-H3 were sufficient for neutralization breadth and potency ( Figure 7).…”

Section: Discussionsupporting

confidence: 73%

Functional characterization and lineage analysis of broadly neutralizing human antibodies against dengue virus identified by single B cell transcriptomics

Durham

Agrawal

Waltari

et al. 2019

Preprint

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Eliciting broadly neutralizing antibodies (bNAbs) against the four dengue virus serotypes (DENV1-4) that are spreading into new territories is an important goal of vaccine design. To delineate bNAb targets, we characterized 28 monoclonal antibodies belonging to expanded and hypermutated clonal families identified by transcriptomic analysis of single plasmablasts from DENV-infected individuals. Among these, we identified two somatically related bNAbs that potently neutralized DENV1-4. Mutagenesis studies revealed that the major recognition determinants of these bNAbs are in E protein domain I, distinct from the only known class of human bNAbs against flaviviruses with a well-defined epitope. B cell repertoire analysis from acute-phase peripheral blood suggested a memory origin and divergent somatic hypermutation pathways for these bNAbs, and a limited number of mutations was sufficient for neutralizing activity. Our study suggests multiple B cell evolutionary pathways leading to DENV bNAbs targeting a novel epitope that can be exploited for vaccine design. E monomeric subunits within the dimer. A subset of these E dimer epitope (EDE)-specific bNAbs potently neutralize not only DENV1-4, but also ZIKV, owing to the high conservation of the EDE, which overlaps the prM binding site on E ( Barba-Spaeth et al., 2016;Dejnirattisai et al., 2015;Rouvinski et al., 2015). The exciting discovery of the EDE class of bNAbs highlights the potential for an epitope-focused flavivirus vaccine strategy.As multiple specificities are likely required to provide maximum coverage of diverse circulating viral variants (Bell et al., 2019;Doria-Rose et al., 2012;Goo, Jalalian-Lechak, Richardson, & Overbaugh, 2012;Katzelnick et al., 2015; Keeffe et al., 2018; Kong et al., 2015), in this study, we aimed to define novel sites on the flavivirus E protein that can be targeted by bNAbs. By characterizing 28 monoclonal antibodies from the plasmablasts of two DENV-infected individuals, we identified J8 and J9, clonally related bNAbs that neutralized DENV1-4 in the low picomolar range. The major recognition determinants for J8 and J9 were in E protein DI, distinct from previously characterized bNAbs. Analysis of the corresponding B cell repertoire revealed divergent evolution of J8 and J9, suggesting multiple evolutionary pathways to generate bNAbs within this lineage. Our work identifies both viral and host determinants of the development of DENV bNAbs that can guide immunogen design and evaluation. Results Identification of cross-reactive neutralizing antibodies from clonally expanded plasmablasts of DENV-infected individualsWe previously profiled the single-cell transcriptomics of peripheral blood mononuclear cells (PBMCs) from six dengue patients and four healthy individuals (Zanini et al., 2018). In two DENV-infected patients (013 and 020), we identified 15 clonal families comprising a total of 38 unique paired heavy (VH) and light (VL) chain IgG1 plasmablast sequences, some of which were hypermutated (1.67% to 10.77% for VH, 0.67% to 7.22% for...

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Section: Discussionsupporting

confidence: 73%

Functional characterization and lineage analysis of broadly neutralizing human antibodies against dengue virus identified by single B cell transcriptomics

Durham

Agrawal

Waltari

et al. 2019

Preprint

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“…S1A). Notably, the tip (amino acids 543 to 546) of the -sandwich loop (amino acids 540 to 552) was also truncated to focus immune response to bNAb epitopes, because non-NAbs, such as AR1B, E1, and HEPC46, bind to this region (34,36,37). The crystal structure of HK6a E2c3 in complex with non-NAb E1 confirms the role of the -sandwich loop in E1 recognition (fig.…”

Section: Structure-based Optimization Of Hcv Envelope Glycoprotein E2mentioning

confidence: 58%

“…The overall fold of E2mc3 variants is highly similar to that of H77 E2c and HK6a E2c3 [Protein Data Bank (PDB): 4MWF and 6BKB] ( Fig. 2A) but with notable differences in the C-terminal part of the back layer (amino acids 629 to 640) (34) and in an FL loop (amino acids 430 to 438) ( fig. S3A) that connects 1 and 1 (13) and interacts with the HCDR3 (heavy-chain complementarity-determining region 3) loops of bNAbs AR3A/B/C/D.…”

Section: Structural Characterization Of Minimized Cores Derived From mentioning

confidence: 84%

“…Culture supernatants were harvested 5 days after transfection, clarified by centrifugation at 1800 rpm for 20 min, and filtered using a 0.45-m filter (Thermo Fisher Scientific). E2 proteins were extracted from the supernatants using an AR3A antibody column as previously described (13,34). Bound proteins were eluted three times, each with 5 ml of 0.2 M glycine (pH 2.2), and neutralized with 0.5 ml of tris base (pH 9.0).…”

Section: Expression and Purification Of E2 Antigensmentioning

confidence: 99%

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Proof of concept for rational design of hepatitis C virus E2 core nanoparticle vaccines

et al. 2020

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Hepatitis C virus (HCV) envelope glycoproteins E1 and E2 are responsible for cell entry, with E2 being the major target of neutralizing antibodies (NAbs). Here, we present a comprehensive strategy for B cell–based HCV vaccine development through E2 optimization and nanoparticle display. We redesigned variable region 2 in a truncated form (tVR2) on E2 cores derived from genotypes 1a and 6a, resulting in improved stability and antigenicity. Crystal structures of three optimized E2 cores with human cross-genotype NAbs (AR3s) revealed how the modified tVR2 stabilizes E2 without altering key neutralizing epitopes. We then displayed these E2 cores on 24- and 60-meric nanoparticles and achieved substantial yield and purity, as well as enhanced antigenicity. In mice, these nanoparticles elicited more effective NAb responses than soluble E2 cores. Next-generation sequencing (NGS) defined distinct B cell patterns associated with nanoparticle-induced antibody responses, which target the conserved neutralizing epitopes on E2 and cross-neutralize HCV genotypes.

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“…Deep sequencing yielded a total of 14.2 million heavy chains and 14.1 million light (κ and λ) chains in two separate NGS runs on the Ion S5 GeneStudio platform ( Table S1). The Antibodyomics 2.0 pipeline was used to process, annotate, and analyze the NGS data, rendering 1.3 to 2.9 million reads per time point (Table S1) (35,49). Of these sequences, 55.3 to 71.2% are high-quality, full-length antibody variable regions which were used for the in-depth analysis of B cell repertoire profiles (Table S1).…”

Section: Dynamic B Cell Repertoire Response Throughout Zikv Infectionmentioning

confidence: 99%

Development of a Potent and Protective Germline-Like Antibody Lineage Against Zika Virus in a Convalescent Human

Gao

Lin

et al. 2019

Front. Immunol.

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Zika virus (ZIKV) specific neutralizing antibodies hold great promise for antibody-based interventions and vaccine design against ZIKV infection. However, their development in infected patients remains unclear. Here, we applied next-generation sequencing (NGS) to probe the dynamic development of a potent and protective ZIKV E DIII-specific antibody ZK2B10 isolated from a ZIKV convalescent individual. The unbiased repertoire analysis showed dramatic changes in the usage of antibody variable region germline genes. However, lineage tracing of ZK2B10 revealed limited somatic hypermutation and transient expansion during the 12 months following the onset of symptoms. The NGS-derived, germline-like ZK2B10 somatic variants neutralized ZIKV potently and protected mice from lethal challenge of ZIKV without detectable cross-reactivity with Dengue virus (DENV). Site-directed mutagenesis identified two residues within the λ chain, N31 and S91, that are essential to the functional maturation of ZK2B10. The repertoire and lineage features unveiled here will help elucidate the developmental process and protective potential of E DIII-directed antibodies against ZIKV infection.

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Genetic and structural insights into broad neutralization of hepatitis C virus by human V _H 1-69 antibodies

Abstract: We elucidate the role of human VH1-69 antibodies in broad neutralization of HCV to facilitate rational vaccine design.

Cited by 76 publications

References 69 publications

Functional characterization and lineage analysis of broadly neutralizing human antibodies against dengue virus identified by single B cell transcriptomics

Functional characterization and lineage analysis of broadly neutralizing human antibodies against dengue virus identified by single B cell transcriptomics

Proof of concept for rational design of hepatitis C virus E2 core nanoparticle vaccines

Development of a Potent and Protective Germline-Like Antibody Lineage Against Zika Virus in a Convalescent Human

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Genetic and structural insights into broad neutralization of hepatitis C virus by human V H 1-69 antibodies

Abstract: We elucidate the role of human VH1-69 antibodies in broad neutralization of HCV to facilitate rational vaccine design.

Cited by 76 publications

References 69 publications

Functional characterization and lineage analysis of broadly neutralizing human antibodies against dengue virus identified by single B cell transcriptomics

Functional characterization and lineage analysis of broadly neutralizing human antibodies against dengue virus identified by single B cell transcriptomics

Proof of concept for rational design of hepatitis C virus E2 core nanoparticle vaccines

Development of a Potent and Protective Germline-Like Antibody Lineage Against Zika Virus in a Convalescent Human

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Product

Resources

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Genetic and structural insights into broad neutralization of hepatitis C virus by human V _H 1-69 antibodies