Plasma IgG to linear epitopes in the V2 and V3 regions of HIV-1 gp120 correlate with a reduced risk of infection in the RV144 vaccine efficacy trial

Abstract

Neutralizing and non-neutralizing antibodies to linear epitopes on HIV-1 envelope glycoproteins have potential to mediate antiviral effector functions that could be beneficial to vaccine-induced protection. Here, plasma IgG responses were assessed in three HIV-1 gp120 vaccine efficacy trials (RV144, Vax003, Vax004) and in HIV-1-infected individuals by using arrays of overlapping peptides spanning the entire consensus gp160 of all major genetic subtypes and circulating recombinant forms (CRFs) of the virus. In RV144, where 31.2% efficacy against HIV-1 infection was seen, dominant responses targeted the C1, V2, V3 and C5 regions of gp120. An analysis of RV144 case-control samples showed that IgG to V2 CRF01_AE significantly inversely correlated with infection risk (OR= 0.54, p=0.0042), as did the response to other V2 subtypes (OR=0.60-0.63, p=0.016-0.025). The response to V3 CRF01_AE also inversely correlated with infection risk but only in vaccine recipients who had lower levels of other antibodies, especially Env-specific plasma IgA (OR=0.49, p=0.007) and neutralizing antibodies (OR=0.5, p=0.008). Responses to C1 and C5 showed no significant correlation with infection risk. In Vax003 and Vax004, where no significant protection was seen, serum IgG responses targeted the same epitopes as in RV144 with the exception of an additional C1 reactivity in Vax003 and infrequent V2 reactivity in Vax004. In HIV-1 infected subjects, dominant responses targeted the V3 and C5 regions of gp120, as well as the immunodominant domain, heptad repeat 1 (HR-1) and membrane proximal external region (MPER) of gp41. These results highlight the presence of several dominant linear B cell epitopes on the HIV-1 envelope glycoproteins. They also generate the hypothesis that IgG to linear epitopes in the V2 and V3 regions of gp120 are part of a complex interplay of immune responses that contributed to protection in RV144.

Figure 1. Heatmaps of smoothed normalized peptide binding values for samples from RV144, Vax003, Vax004 and HIV-1-infected individuals as a function of HxB2 coordinates.

Each row represents a sample from a single individual, where stronger intensities of binding are shown as darker images. Columns represent amino acid positions using HxB2 numbering from the amino terminus (NH) to the carboxy terminus (COOH) as shown along the x-axis of each heatmap. Within the x-axis bar, areas of white and gray are used to show regions of strongest reactivity. Boxes are used to show group-specific regions of strongest reactivity. A. Gp120 peptides. B. Gp41 peptides.

Figure 2. Heatmap of smoothed normalized gp160 peptide binding values for samples from HIV-1-infected individuals as a function of genetic subtype and HxB2 coordinates.

Each row represents a sample from a single individual, where stronger intensities of binding are shown as darker images. Columns represent amino acid positions using HxB2 numbering from the amino terminus (NH) to the carboxy terminus (COOH) as shown along the x-axis. Within the x-axis bar, areas of white and gray are used to show regions of strongest reactivity from Figure 1. Boxes are used to show the regions of strongest reactivity from Figure 1, plus additional regions of interest.

Figure 3. IgG response rates by peptide genetic subtype.

Response rates (percent positive responses) are shown for major reactive regions in gp120, as color-coded in the legend.

Figure 4. Sequences of major reactive regions in gp120 and gp41.

Sequences are shown for individual genetic subtypes in the major IgG binding regions of gp120 and gp41. Borders were defined by overlapping peptide binding intensities (only reactive regions are shown). Amino acid residues that differ from the group M consensus are shown in boldface type. Boxed is a key position in V2 that was identified by genetic sieve analyses of breakthrough viruses in RV144. The HXB2 numbering system is used to identify amino acid sites.

Figure 5. Known conformations of reactive peptides.

A. Conformations of reactive peptides known from solved X-ray structures of gp120 core or fragments of gp120 in complex with antibodies. B. V2 peptide is shown with respect to different conformations it adopts depending on the bound antibody. Structures with antibodies PG9 (PDB: 3U4E), CH 58 (PDB: 4HPO) and CH 59 (PDB: 4HPY) are shown where tan and gray colors indicate the light and heavy chains of the antibody, respectively. C. The CD4 bound structure of gp120 with N-and C- terminal regions is used as a template to show the C1a, C5a, C5b peptides in the context of entire gp120 monomer structure (PDB: 3JWD). Also shown are the CD4 and CCR5 binding regions respect to these peptides. D. NMR structure of isolated region of C-terminal end of gp120 showing C5b and part of C5c peptides (PDB: 1MEQ). E. V3 peptide is shown with respect to the rest of the gp120 core (PDB: 2B4C).

Figure 6. Subtype-specific and aggregate V2 responses in RV144.

Boxplots are stratified by infection status for peptides centered at the maximum hotspot region (position 174). Individuals with different risk and gender categories (used in our correlate model) are shown with different symbols and grey shades.

Figure 7. Complementary cumulative distribution function (ccdf) for V3-CRF01_AE (V3.1) peptide binding in RV144.

The ccdf is broken down by infection status and by dichotomized IgA, neutralizing Ab and Avidity levels. Low/High dichotomized levels were defined by dividing the responses into two equal groups around the median. For a given V3.1 value, the ccdf gives the proportion of individuals who have a response above that value. At low levels of IgA, neutralizing Ab and Avidity, the infected groups have lower ccdf for nearly all values, supporting our correlates analysis. This pattern is inversed at high levels of IgA, neutralizing Ab and Avidity, supporting our interaction analysis.