Complete functional mapping of infection- and vaccine-elicited antibodies against the fusion peptide of HIV

Abstract

Eliciting broadly neutralizing antibodies (bnAbs) targeting envelope (Env) is a major goal of HIV vaccine development, but cross-clade breadth from immunization has only sporadically been observed. Recently, Xu et al (2018) elicited cross-reactive neutralizing antibody responses in a variety of animal models using immunogens based on the epitope of bnAb VRC34.01. The VRC34.01 antibody, which was elicited by natural human infection, targets the N terminus of the Env fusion peptide, a critical component of the virus entry machinery. Here we precisely characterize the functional epitopes of VRC34.01 and two vaccine-elicited murine antibodies by mapping all single amino-acid mutations to the BG505 Env that affect viral neutralization. While escape from VRC34.01 occurred via mutations in both fusion peptide and distal interacting sites of the Env trimer, escape from the vaccine-elicited antibodies was mediated predominantly by mutations in the fusion peptide. Cryo-electron microscopy of four vaccine-elicited antibodies in complex with Env trimer revealed focused recognition of the fusion peptide and provided a structural basis for development of neutralization breadth. Together, these functional and structural data suggest that the breadth of vaccine-elicited antibodies targeting the fusion peptide can be enhanced by specific interactions with additional portions of Env. Thus, our complete maps of viral escape provide a template to improve the breadth or potency of future vaccine-induced antibodies against Env's fusion peptide. Author summaryA major goal of HIV-1 vaccine design is to elicit antibodies that neutralize diverse strains of HIV-1. Recently, some of us elicited such antibodies in animal models using immunogens based on the epitope of a broad antibody (VRC34.01) isolated from an infected individual.Further improving these vaccine-elicited antibody responses will require a detailed understanding of how the resulting antibodies target HIV's envelope protein (Env). Here, we used mutational antigenic profiling to precisely map the epitope of two vaccine-elicited antibodies and the template VRC34.01 antibody. We did this by quantifying the effect of all possible amino acid mutations to Env on antibody neutralization. Although all antibodies target a similar region of Env, we found clear differences in the functional interaction of Env with the vaccine-and infection-elicited antibodies. We combined these functional data with structural analyses to identify antibody-Env interactions that could improve the breadth of vaccine-elicited antibodies, and thereby help to refine vaccination schemes to achieve broader responses.

Virus-Like Particle Based-Vaccines Elicit Neutralizing Antibodies against the HIV-1 Fusion Peptide

“…In addition, FP8 is not completely conserved in sequence across different subtypes of the HIV-1 Env 12,14 . Functional mapping of infectionand vaccine-elicited antibodies against the FP has identified escape mutants and common variant sequences within the FP8 epitope 14 . While functional mapping likely helps to re-center the protective domain on newly emerging HIV strains for subsequent rounds of immunogen design, the inherent structural diversity of FP may enable the design of conformationally diverse FP8 immunogens using multiple carrier protein or virus-like particle platforms, still capable of eliciting antibodies to recognize and neutralize FP in the context of native Env trimer.…”

“…The HIV-1 fusion peptide is a critical component of the viral entry machinery that is composed of 15-20 hydrophobic residues at the N-terminus of the gp41 subunit of HIV-1 Env 12 . A simple linear epitope consisting of 8 amino acids at the N-terminal region of the gp41 fusion peptide (called FP8) has been shown to be a primary target of a bnAb, VRC34.01, derived from an HIVpatient 12,14 . Recently, Xu et al designed an FP8-based vaccine in which the peptide is conjugated to keyhole limpet hemocyanin (KLH) through maleimide linkage chemistry 3 .…”

“…Antibodies targeting FP8 that have been elicited by infection or by vaccination exhibit broad neutralization 3,12,15 ; however, neutralization activity against specific HIV-1 isolates is dependent on the structural diversity of the fusion peptide (FP), sensitivity to mutations at specific antibody interaction sites of the Env trimer outside of the FP and the natural diversity in FP8 sequences 14,16 . FP, in the context of the native HIV Env trimer, adopts multiple conformations and orientations, which can both facilitate and complicate recognition of the FP8 epitope by bnAbs 12,16,17 .…”

“…Known FP8-targeting bnAbs approach the HIV Env trimer from diverse angles and recognize this epitope by penetrating through a highly conserved glycosylation site on gp120 (N88) 16 . Mutations within this region of gp120 potentially affect the neutralization breadth of FP8-specific bnAbs 14,16 . In addition, FP8 is not completely conserved in sequence across different subtypes of the HIV-1 Env 12,14 .…”

“…Mutations within this region of gp120 potentially affect the neutralization breadth of FP8-specific bnAbs 14,16 . In addition, FP8 is not completely conserved in sequence across different subtypes of the HIV-1 Env 12,14 . Functional mapping of infectionand vaccine-elicited antibodies against the FP has identified escape mutants and common variant sequences within the FP8 epitope 14 .…”