Comprehensive Mapping of HIV-1 Escape from a Broadly Neutralizing Antibody

Dingens, Adam S.; Haddox, Hugh K.; Overbaugh, Julie; Bloom, Jesse D

doi:10.1016/j.chom.2017.05.003

Cited by 93 publications

(124 citation statements)

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“…We used mutational antigenic profiling [13] 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.…”

Section: Resultsmentioning

confidence: 99%

“…Specifically, for each antibody, we neutralized libraries [14] of viruses carrying all aminoacid mutations to the ectodomain and transmembrane domain of the BG505.T332N Env at an ~IC 95 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 [13] (Fig S1A). This entire process was performed in full biological replicate, beginning with independent generation of the proviral plasmid mutant libraries.…”

Section: Resultsmentioning

confidence: 99%

“…We have previously described Env mutational antigenic profiling using BF520 Env libraries [13]; a similar approach was taken here. Briefly, 5×10 5 infectious units of two independent mutant virus libraries were neutralized with VRC34.01, vFP16.02, or vFP20.01 at an ~IC 95 concentration (33 ug/mL, 500 ug/mL, or 500ug/mL of antibody, respectively) for one hour.…”

Section: Mutational Antigenic Profilingmentioning

confidence: 99%

“…We used dms_tools2 version 2.2.4 (https://jbloomlab.github.io/dms_tools2/) to analyze the deep sequencing data and calculate the differential selection [17]. The differential selection statistic has been described in detail [13,18] and is further documented at https://jbloomlab.github.io/dms_tools2/diffsel.html. Sequencing of wildtype proviral DNA plasmid was used as the error control during the calculation of differential selection.…”

Section: Analysis Of Deep Sequencing Datamentioning

confidence: 99%

“…File S2 | VRC34.01 differential selection The VRC34.01 differential selection values for all measured mutations. The format is described at https://jbloomlab.github.io/dms_tools2/diffsel.html and in Dingens et al 2017 [13].…”

Section: Supplemental Filesmentioning

confidence: 99%

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

Dingens

Acharya

Haddox

et al. 2018

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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.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Mutational Antigenic Profilingmentioning

confidence: 99%