Abstract
ABSTRACTAll HIV-1-infected individuals develop strain-specific neutralizing antibodies to their infecting virus, which in some cases mature into broadly neutralizing antibodies. Defining the epitopes of strain-specific antibodies that overlap conserved sites of vulnerability might provide mechanistic insights into how broadly neutralizing antibodies arise. We previously described an HIV-1 clade C-infected donor, CAP257, who developed broadly neutralizing plasma antibodies targeting an N276 glycan-dependent epitope in the CD4 binding site. The initial CD4 binding site response potently neutralized the heterologous tier 2 clade B viral strain RHPA, which was used to design resurfaced gp120 antigens for single-B-cell sorting. Here we report the isolation and structural characterization of CAP257-RH1, an N276 glycan-dependent CD4 binding site antibody representative of the early CD4 binding site plasma response in donor CAP257. The cocrystal structure of CAP257-RH1 bound to RHPA gp120 revealed critical interactions with the N276 glycan, loop D, and V5, but not with aspartic acid 368, similarly to HJ16 and 179NC75. The CAP257-RH1 monoclonal antibody was derived from the immunoglobulin-variable IGHV3-33 and IGLV3-10 genes and neutralized RHPA but not the transmitted/founder virus from donor CAP257. Its narrow neutralization breadth was attributed to a binding angle that was incompatible with glycosylated V5 loops present in almost all HIV-1 strains, including the CAP257 transmitted/founder virus. Deep sequencing of autologous CAP257 viruses, however, revealed minority variants early in infection that lacked V5 glycans. These glycan-free V5 loops are unusual holes in the glycan shield that may have been necessary for initiating this N276 glycan-dependent CD4 binding site B-cell lineage.IMPORTANCE The conserved CD4 binding site on gp120 is a major target for HIV-1 vaccine design, but key events in the elicitation and maturation of different antibody lineages to this site remain elusive. Studies have shown that strain-specific antibodies can evolve into broadly neutralizing antibodies or in some cases act as helper lineages. Therefore, characterizing the epitopes of strain-specific antibodies may help to inform the design of HIV-1 immunogens to elicit broadly neutralizing antibodies. In this study, we isolate a narrowly neutralizing N276 glycan-dependent antibody and use X-ray crystallography and viral deep sequencing to describe how gp120 lacking glycans in V5 might have elicited these early glycan-dependent CD4 binding site antibodies. These data highlight how glycan holes can play a role in the elicitation of B-cell lineages targeting the CD4 binding site.
Highlights
All HIV-1-infected individuals develop strain-specific neutralizing antibodies to their infecting virus, which in some cases mature into broadly neutralizing antibodies
Analysis of donor CAP257 autologous viruses by deep sequencing revealed a minority population with glycan-free V5 loops similar to those of RHPA, which may have initiated this lineage or provided the antigenic stimuli that allowed it to mature. These findings provide a mechanism for the strain specificity of early CD4 binding site (CD4bs) neutralizing antibodies in donor CAP257, which target a rare glycan hole in V5 and have implications for the use of HIV-1 immunogens that are aimed at activating CD4bs bNAb precursors by removing key loop D and/or V5 loop glycans
We have previously shown that the CD4bs neutralizing antibodies in plasma from donor CAP257 were similar to HJ16 [36] and could not be adsorbed with the resurfaced stabilized gp120 core (RSC3) sorting antigen used to isolate VRC01
Summary
All HIV-1-infected individuals develop strain-specific neutralizing antibodies to their infecting virus, which in some cases mature into broadly neutralizing antibodies. We previously described an HIV-1 clade C-infected donor, CAP257, who developed broadly neutralizing plasma antibodies targeting an N276 glycan-dependent epitope in the CD4 binding site. Deep sequencing of autologous CAP257 viruses, revealed minority variants early in infection that lacked V5 glycans These glycan-free V5 loops are unusual holes in the glycan shield that may have been necessary for initiating this N276 glycandependent CD4 binding site B-cell lineage. VH gene-restricted bNAbs all develop from the germ line-encoded immunoglobulin heavy chain variable gene IGHV1-2 or IGHV1-46 and were defined by prototypical antibodies VRC01 and 8ANC131 [25, 26, 29, 30] This class has a germ line-encoded arginine residue at position 71 in CDR-H2 that mimics an arginine at position 59 in CD4 by interacting with aspartic acid 368 in the CD4 binding loop of gp120. These glycan deletions create large holes in the glycan shield, but their effects on Env antigenicity, and the immunogenicity of the CD4bs, remain to be determined
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