Research ArticleVIROLOGY

A VH1-69 antibody lineage from an infected Chinese donor potently neutralizes HIV-1 by targeting the V3 glycan supersite

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Science Advances  16 Sep 2020:
Vol. 6, no. 38, eabb1328
DOI: 10.1126/sciadv.abb1328
  • Fig. 1 Isolation of neutralizing antibodies 438-B11 and 438-D5 from donor CBJC438.

    (A) The number of CD4+ T cells (blue) and viral loads (represented on y axes) were measured from 2005 to 2012 and represented in the line graph. The mAbs were isolated in 2008. (B) The neutralizing activity of donor CBJC438 serum from seven time points from 2005 to 2012 was tested against pseudoviruses on a global panel. (C) Antigen-specific single B cells were isolated by flow cytometry. Around 10 million PBMCs from CBJC438 were incubated with the sorting probe and cell markers. The gated cells were sorted into a 96-well PCR plate. (D) The neutralizing breadth and potency of 438-B11 were tested on a 129-virus panel. The N332-specific bNAbs PGT121 and PGT128 were used as controls. (E) Sequence analysis of mAbs 438-B11 and 438-D5 with alignment to their respective germline genes. FR and CDR are based on Kabat nomenclature. The symbol “.” denotes conserved amino acids.

  • Fig. 2 Structural epitope mapping of 438-B11 on HIV-1 Env.

    (A) Crystal structure at 3.8 Å of the BG505 UFO.664 (gp120, blue; gp41, pink) Env trimer in complex with Fabs 438-B11 (green) at the N332/V3 supersite and 35O22 (yellow) at the gp120/gp41 interface. (B) Side view of one protomer of the BG505 UFO.664 trimer in complex with Fab 438-B11 (HC, green; and LC, gray) and Fab 35O22 (yellow) Fabs. The cartoon representation of the structure is overlaid on the transparent molecular surface. The right inset shows the interaction of the 438-B11 Fab with Asn301 and Asn332 glycans (pink). The glycans are shown in sticks and overlaid on the transparent molecular surface. Below the inset is a schematic of Asn301 and Asn332 glycans observed in the structure with GlcNAc moieties as dark blue squares and mannose residues as green circles. The surface area (Å2) on each glycan moiety that is buried by 438-B11 (HC, green; LC, gray) is shown. (C) Recognition of the GDIR motif (blue) at the base of V3 by Fab 438-B11. The heavy chain (HC) 438-B11 is represented in cartoon and sticks with the CDRs and FRs (H1, green; H2, brown; H3, pink; FR1, cyan; and FR3, gray) that interact with gp120 (blue). (D) Buried surface area (Å2) of residues on the CDR loops and FRs of 438-B11 when bound to gp120 on Env. (E) Comparison of the mode of binding of N332/V3-class bNAbs to the surface of gp120 (blue) of HIV-1 Env. A distinct orientation of 438-B11 (HC, green; LC, gray) on HIV-Env is observed compared to other bNAbs of this class. HCDR3 loops (pink) are shown in cartoon representation. (F) Alignment of the amino acid sequences of HCDR3 of various N332/V3-class bNAbs.

  • Fig. 3 Structural analysis of unbound 438-B11 and 438-D5.

    (A) Crystal structure of 438-D5 Fab at 2.0 Å is shown in cartoon. The variable domain of the 438-D5 Fab is shown with HCDR loops labeled and colored for H1 (orange), H2 (blue), and H3 (pink) and LCDR loops for L1 (yellow), L2 (cyan), and L3 (green). The right inset shows the 2FoFc composite omit map (contoured at 1.0σ) of HCDR3. VL, variable region of immunoglobulin light chain. (B) Crystal structure of 438-B11 Fab in complex with protein G (gray) at 2.7 Å shown in cartoon. The right inset shows the 2FoFc composite omit map (contoured at 1.0 s) of HCDR3. (C) Superposition of 438-B11 (green) and 438-D5 (blue) Fab crystal structures with single-residue differences in heavy-chain FR1 and light-chain (LC) FR3 (see insets). (D) Superposition of variable domains of protein G-bound 438-B11 (green) and 438-D5 (blue) illustrates some differences at the HCDR3 apex that may be due to differences in crystal packing (see insets). (E) The variable domains from the various N332/V3-class bNAbs are shown with HCDR loops labeled and colored for H1 (blue), H2 (green), and H3 (red) and LCDR loops for L1 (light blue), L2 (light green), and L3 (light pink). (F) Crystal structure of 438-B11ΔSS Fab at 2.1 Å shown in cartoon and overlaid with transparent molecular surface representation of heavy chain (HC; green) and light chain (LC; gray). The right panel shows the superposition of unbound 438-B11 (blue) and 438-B11ΔSS (green). The inset shows the superposition of HCDR3. The disordered HCDR3 tip is shown as a dashed line. (G) (Top) Binding kinetics of 438-B11 and 438-B11ΔSS Fabs to soluble BG505 UFO.664. (Bottom) Neutralization breadth (%) and potency (μg/ml) of 438-B11 and 438-B11ΔSS on a global panel.

  • Fig. 4 Longitudinal analysis of the 438-B11/D5 lineage development.

    (A) Identity-divergence analysis of the unbiased heavy-chain (H) and light-chain (κ) repertoires of donor CBJC438 at time points 2005, 2008, and 2012. For the whole-repertoire analysis (rows 1 and 3), sequences are plotted as a function of sequence identity to 438-B11 and sequence divergence from putative germline genes. Color coding denotes sequence density. For analysis of the 438-B11–encoding germline gene families (rows 2 and 4), sequences are plotted as a function of sequence identity to 438-B11 and sequence divergence from IgHV1-69 and IgKV3-20 for the heavy and light chains, respectively. The germline gene family distribution is presented as black contour lines. 438-B11 and sequences identified on the basis of various criteria (see legend below figure) are shown on the black contours with the number of sequences labeled accordingly. (B) Dendrograms of functionally tested heavy and light chains are rooted by their respective germline allelic genes, IgHV1-69 and IgKV3-20, respectively. Heavy chains from 2005, 2008, and 2012 are presented in three separate dendrograms, while light chains from all three time points are shown in one dendrogram. (C) Neutralization breadth (%) and potency (μg/ml) of NGS-derived heavy and light chains paired with their respective 438-D5 partner chains on a global panel. The color-coding scheme is based on their potency.

  • Fig. 5 Virus escape through glycan shift revealed by SGA and mutations.

    (A) NJ phylogenetic tree of 53 HIV-1 Env sequences isolated from donor CBJC438 by SGA. (B) Percent neutralization breadth and median IC50 in μg/ml were determined at an IC50 cutoff of 10 μg/ml for 438-B11. Viruses were separated into those containing an N-linked glycan at N332 but not N334 (N332+N334), at N334 but not N332 (N332N334+), at both N332 and N334 (N332+N334+), and at neither N332 nor N334 (N332N334). NA, not applicable. (C) Interaction of 438-B11 with the N332 and N301 glycans. (D) Sequence logo of the V3 region from three time points. (E) Binding affinity of 438-B11 antibodies to glycan mutants of CBJC438 UFO Env trimer and BG505 UFO Env trimer. Sensorgrams were obtained from an Octet RED96 instrument using a trimer titration series of six concentrations (200 to 6.25 nM by twofold dilution). For the CBJC438 Env, the D332N/N334S mutation restored the N332 supersite, whereas for the BG505 Env, the T332N mutation restored the N332 supersite. For BG505, a panel of glycan mutants was used to determine which glycan(s) surrounding the N332 supersite may be involved in epitope recognition. (F) Glycans surrounding the N332 supersite on the surface of BG505 Env trimer. A top view of the BG505 UFO.664 trimer surface with the GDIR motif colored pink. Glycans N137, N156, N295, N301, and N332 are represented with stick models and labeled.

Supplementary Materials

  • Supplementary Materials

    A VH1-69 antibody lineage from an infected Chinese donor potently neutralizes HIV-1 by targeting the V3 glycan supersite

    Sonu Kumar, Bin Ju, Benjamin Shapero, Xiaohe Lin, Li Ren, Lei Zhang, Dan Li, Zehua Zhou, Yi Feng, Cindy Sou, Colin J. Mann, Yanling Hao, Anita Sarkar, Jiali Hou, Christian Nunnally, Kunxue Hong, Shuo Wang, Xiangyang Ge, Bin Su, Elise Landais, Devin Sok, Michael B. Zwick, Linling He, Jiang Zhu, Ian A. Wilson, Yiming Shao

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