Mapping Polyclonal Antibody Responses in Non-human Primates Vaccinated with HIV Env Trimer Subunit Vaccines

Nogal, Bartek; Bianchi, Matteo; Cottrell, Christopher A.; Kirchdoerfer, Robert N.; Sewall, Leigh M.; Turner, Hannah L.; Zhao, Fangzhu; Sok, Devin; Burton, Dennis R.; Hangartner, Lars; Ward, Andrew B.

doi:10.1016/j.celrep.2020.02.061

Cited by 89 publications

(111 citation statements)

References 44 publications

(83 reference statements)

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“…The 43A2-bound BG505 V1 loop remains in the ground state conformation, which we define as the conformation observed in structures of Env that do not have an antibody bound to the N332 supersite or V2 apex epitopes, which influence the V1 conformation (28)(29)(30) The ground state conformation was also observed in the NHP V1-specific antibody revealed in a polyclonal imaging approach described elsewhere ( Figure 5D and S3F) (20,29,31). In bnAb structures, the V1 loop is lifted up, providing greater access to the GDIR motif (24,32).…”

Section: Electron Microscopy Studies Reveal the Details Of 43a Mab Epmentioning

confidence: 96%

HIV Envelope Trimer-Elicited Autologous Neutralizing Antibodies Bind a Region Overlapping the N332 Glycan Supersite

Nogal

McCoy²,

Gils

et al. 2019

Preprint

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To date, immunization studies of rabbits with the BG505 SOSIP.664 HIV envelope glycoprotein trimers have revealed the 241/289 glycan hole as the dominant neutralizing antibody epitope. Here, we isolated monoclonal antibodies from a rabbit that did not exhibit glycan hole-dependent autologous serum neutralization. The antibodies did not compete with a previously isolated glycan hole-specific antibody but did compete with N332 glycan supersite broadly neutralizing antibodies. A high resolution cryoEM structure of one of the antibodies in complex with the BG505 SOSIP.664 trimer demonstrated that, while the epitope recognized overlapped with the N332 glycan supersite by contacting the GDIR motif at the base of V3, the primary contacts were located in the variable V1 loop. These data suggest that strain-specific responses to V1 may interfere with broadly neutralizing responses to the N332 glycan supersite and vaccine immunogens may require engineering to minimize these off-target responses or steer them toward a more desirable pathway.

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Section: Electron Microscopy Studies Reveal the Details Of 43a Mab Epmentioning

confidence: 96%

HIV Envelope Trimer-Elicited Autologous Neutralizing Antibodies Bind a Region Overlapping the N332 Glycan Supersite

Nogal

McCoy²,

Gils

et al. 2019

Preprint

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“…We next used negative stain polyclonal electron microscopy (nsEMPEM) Nogal et al, 2020) to map epitopes from Fabs isolated from convalescent COVID-19 plasma IgGs onto the SARS-CoV-2 S protein. In this method, Fabs that bind to an antigenic target are separated from non-binding Fabs in a polyclonal mixture by size-exclusion chromatography (SEC), Fab-antigen complexes are imaged by EM, and 2D/3D classification are used to identify predominant epitopes Nogal et al, 2020) (Figure 2A-C). Typically, Fabs are incubated at 1000-2000x above EC50 values calculated from binding assays Nogal et al, 2020).…”

Section: Em Reveals Distinct Predominant Epitopes Targeted By Convalementioning

confidence: 99%

“…In this method, Fabs that bind to an antigenic target are separated from non-binding Fabs in a polyclonal mixture by size-exclusion chromatography (SEC), Fab-antigen complexes are imaged by EM, and 2D/3D classification are used to identify predominant epitopes Nogal et al, 2020) (Figure 2A-C). Typically, Fabs are incubated at 1000-2000x above EC50 values calculated from binding assays Nogal et al, 2020). For most COVID-19 plasmas, Anti-S Fab EC50 values were estimated to be >50 µg/mL ( Figure S2).…”

Section: Em Reveals Distinct Predominant Epitopes Targeted By Convalementioning

confidence: 99%

Structures of human antibodies bound to SARS-CoV-2 spike reveal common epitopes and recurrent features of antibodies

Barnes

West

Huey-Tubman

et al. 2020

Preprint

223

339

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Neutralizing antibody responses to coronaviruses focus on the trimeric spike, with most against the receptor-binding domain (RBD). Here we characterized polyclonal IgGs and Fabs from COVID-19 convalescent individuals for recognition of coronavirus spikes. Plasma IgGs differed in their degree of focus on RBD epitopes, recognition of SARS-CoV, MERS-CoV, and mild coronaviruses, and how avidity effects contributed to increased binding/neutralization of IgGs over Fabs. Electron microscopy reconstructions of polyclonal plasma Fab-spike complexes showed recognition of both S1 A and RBD epitopes. A 3.4Å cryo-EM structure of a neutralizing monoclonal Fab-S complex revealed an epitope that blocks ACE2 receptor-binding on "up" RBDs. Modeling suggested that IgGs targeting these sites have different potentials for interspike crosslinking on viruses and would not be greatly affected by identified SARS-CoV-2 spike mutations. These studies structurally define a recurrent anti-SARS-CoV-2 antibody class derived from VH3-53/VH3-66 and similarity to a SARS-CoV VH3-30 antibody, providing criteria for evaluating vaccine-elicited antibodies.

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“…In this study, we show that EMPEM can directly inform rational design of a universal influenza vaccine by extensive characterization of pAb responses to a vaccine derived from non-circulating IAV strains, such as H5N1. While we have performed EMPEM on rabbit and NHP sera, here we report the first study using our structure-based method to comprehensively map the polyclonal response to an avian influenza virus vaccine in humans (Bianchi et al, 2018;Cirelli et al, 2019;Moyer et al, 2020;Nogal et al, 2020).…”

Section: Discussionmentioning

confidence: 99%

“…The application of single particle electron microscopy (EM) to structurally characterize heterogenous pAb immune complexes from low to high resolution yields unprecedented insight into polyclonal immune responses following IAV vaccination. We previously designed and implemented EM polyclonal epitope mapping (EMPEM) to discern the polyclonal immune response of rabbits and non-human primates to vaccination with HIV immunogens (Bianchi et al, 2018;Cirelli et al, 2019;Moyer et al, 2020;Nogal et al, 2020). This structure-based strategy is highly efficient: sample preparation is straightforward and the pipeline from sample collection to structural results is streamlined and expeditious, making longitudinal assessment of polyclonal responses in multiple subjects over a vaccination trial feasible.…”

Section: Introductionmentioning

confidence: 99%

Polyclonal epitope cartography reveals the temporal dynamics and diversity of human antibody responses to H5N1 vaccination

Han

Schmitz

Richey

et al. 2020

Preprint

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Novel influenza A virus (IAV) strains elicit recall immune responses to conserved epitopes, making them favorable antigenic choices for universal influenza virus vaccines. Evaluating these immunogens requires a thorough understanding of the antigenic sites targeted by the polyclonal antibody (pAb) response, which single particle electron microscopy (EM) can sensitively detect. Here, we employed EM polyclonal epitope mapping (EMPEM) to extensively characterize the pAb response to hemagglutinin (HA) after H5N1 immunization in humans. Cross-reactive pAbs originating from memory B cells immediately bound the stem of HA and persisted for over a year post vaccination. In contrast, de novo pAb responses to multiple sites on the head of HA, which targeted previously determined key neutralizing sites on H5 HA, expanded after the second immunization and waned quickly. Thus, EMPEM provides a robust tool for comprehensively tracking the specificity and durability of immune responses elicited by novel universal influenza vaccine candidates.

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Mapping Polyclonal Antibody Responses in Non-human Primates Vaccinated with HIV Env Trimer Subunit Vaccines

Cited by 89 publications

References 44 publications

HIV Envelope Trimer-Elicited Autologous Neutralizing Antibodies Bind a Region Overlapping the N332 Glycan Supersite

HIV Envelope Trimer-Elicited Autologous Neutralizing Antibodies Bind a Region Overlapping the N332 Glycan Supersite

Structures of human antibodies bound to SARS-CoV-2 spike reveal common epitopes and recurrent features of antibodies

Polyclonal epitope cartography reveals the temporal dynamics and diversity of human antibody responses to H5N1 vaccination

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