Electron-Microscopy-Based Epitope Mapping Defines Specificities of Polyclonal Antibodies Elicited during HIV-1 BG505 Envelope Trimer Immunization

Abstract

SummaryCharacterizing polyclonal antibody responses via currently available methods is inherently complex and difficult. Mapping epitopes in an immune response is typically incomplete, which creates a barrier to fully understanding the humoral response to antigens and hinders rational vaccine design efforts. Here, we describe a method of characterizing polyclonal responses by using electron microscopy, and we applied this method to the immunization of rabbits with an HIV-1 envelope glycoprotein vaccine candidate, BG505 SOSIP.664. We detected known epitopes within the polyclonal sera and revealed how antibody responses evolved during the prime-boosting strategy to ultimately result in a neutralizing antibody response. We uncovered previously unidentified epitopes, including an epitope proximal to one recognized by human broadly neutralizing antibodies as well as potentially distracting non-neutralizing epitopes. Our method provides an efficient and semiquantitative map of epitopes that are targeted in a polyclonal antibody response and should be of widespread utility in vaccine and infection studies.

HIV-1 Envelope and MPER antibody structures in lipid assemblies

“…Env-nanodisc immunization could then address three important open questions: first, the transmembrane version of Env has been shown to possess a glycan shield that is closer to the composition of the glycan shield presented on virus particles Rantalainen et al, 2018;Seabright et al, 2019;Torrents de la Pena et al, 2019). Second, a recent analysis of the polyclonal immune response against soluble SOSIP immunogen indicated that in the non-human primate model, a dominant response targeted the exposed base of the trimer (Bianchi et al, 2018). In membrane-embedded formulations, this immunodominant neoepitope would be protected by the bilayer.…”

Mapping polyclonal antibody responses in non-human primates vaccinated with HIV Env trimer subunit vaccines

“…, suggesting viral evolution away from the infecting virus and concomitant antibody evolution. The remaining three animals exhibited antibody responses in and around the N289/S241 glycan hole region (GH-1/GH-2) that is a highly immunogenic epitope in rabbits (McCoy et al, 2016;Bianchi et al, 2018;Klasse et al, 2018), and the C3/V5 region of gp120 that we have previously described as the "C3/T465 epitope" in NHPs. Thus, considering a sample of only six animals and a time span of just 20 weeks under viral challenge pressure, the infected control macaques exhibited a relatively narrow repertoire of antibody epitope responses to the founding virus, with five different 3D Fab phenotypes detected against two regions of Env ( Figure 1B and 1C).…”

Innovations in structure-based antigen design and immune monitoring for next generation vaccines

“…The combination of deep mutational scanning, viral growth in the presence of antibodies, and NGS of surviving viruses enables mapping of epitopes and functional mutations required for recognition by antibodies [50]*. Single particle electron microscopy polyclonal epitope mapping (EMPEM) is another exciting and recently developed technique that is able to visualize the antibody response directly from serum [51]*. These EM images provide immediate feedback regarding on-and off-target antibody responses in a time-dependent manner and reveal potential differences in the responses between individual animals, modes of immunogen delivery, adjuvants etc.…”