Date Published: July 5, 2018
Publisher: Public Library of Science
Author(s): Adam S. Dingens, Priyamvada Acharya, Hugh K. Haddox, Reda Rawi, Kai Xu, Gwo-Yu Chuang, Hui Wei, Baoshan Zhang, John R. Mascola, Bridget Carragher, Clinton S. Potter, Julie Overbaugh, Peter D. Kwong, Jesse D. Bloom, Katie J Doores.
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 both delineate pathways of resistance to these fusion peptide-directed antibodies and provide a strategy to improve the breadth or potency of future vaccine-induced antibodies against Env’s fusion peptide.
The isolation of broadly neutralizing antibodies (bnAbs) capable of neutralizing diverse clades of HIV-1 has invigorated hopes of developing a broadly protective antibody-based HIV vaccine [1,2]. Epitope mapping of bnAbs has revealed a number of conserved sites of vulnerability on Env, and designing immunogens to elicit antibodies that target such sites is a promising vaccine strategy [3,4]. Structural characterization of the epitope of bnAb N123-VRC34.01 (subsequently referred to as VRC34.01) revealed that the N terminus of the fusion peptide (FP) is one such site of vulnerability . A number of additional bnAbs that also partially target this epitope have been characterized [6–10], suggesting it may be a promising vaccine target.
We used mutational antigenic profiling  to quantify how all single amino-acid mutations at each residue of Env affected the neutralization of replication-competent HIV by VRC34.01 and the two vaccine-induced antibodies, vFP16.02 and vFP20.01. Specifically, for each antibody, we neutralized libraries  of viruses carrying all amino-acid mutations to the ectodomain and transmembrane domain of the BG505.T332N Env at an ~IC95 antibody concentration. For each of the possible 12,730 Env mutations (670 mutagenized sites × 19 amino acid mutations), we calculated the enrichment of the mutation in the antibody-selected condition relative to a non-selected mutant virus library, a quantity that we term differential selection  (S1A Fig). This entire process was performed in full biological replicate, beginning with independent generation of the proviral plasmid mutant libraries. The results from the two replicates were well correlated (S1B and S1C Fig). For the remainder of the paper, we present the averaged data from these two replicates.
Overall, these in-depth delineations of the functional epitopes revealed similarities and differences between how VRC34.01 and the vaccine-elicited antibodies recognize Env. Escape from both vFP16.02 and vFP20.01 was mediated predominantly via mutations in the fusion peptide, whereas VRC34.01 neutralization was also affected by mutations at numerous additional sites.