Multidonor analysis reveals structural elements, genetic determinants, and maturation pathway for HIV-1 neutralization by VRC01-class antibodies

Abstract

Antibodies of the VRC01 class neutralize HIV-1, arise in diverse HIV-1-infected donors, and are potential templates for an effective HIV-1 vaccine. However, the stochastic processes that generate repertoires in each individual of >10(12) antibodies make elicitation of specific antibodies uncertain. Here we determine the ontogeny of the VRC01 class by crystallography and next-generation sequencing. Despite antibody-sequence differences exceeding 50%, antibody-gp120 cocrystal structures reveal VRC01-class recognition to be remarkably similar. B cell transcripts indicate that VRC01-class antibodies require few specific genetic elements, suggesting that naive-B cells with VRC01-class features are generated regularly by recombination. Virtually all of these fail to mature, however, with only a few-likely one-ancestor B cell expanding to form a VRC01-class lineage in each donor. Developmental similarities in multiple donors thus reveal the generation of VRC01-class antibodies to be reproducible in principle, thereby providing a framework for attempts to elicit similar antibodies in the general population.

Figure 1. VRC01-Class Recognition of HIV-1 gp120

(A) Nine cocrystal structures of five VRC01-class antibodies from five donors in complex with HIV-1 gp120s from clades A, C, and AE. Macromolecules are shown in ribbon representation after alignment of gp120, which is shown in gray with CD4-binding loop (yellow), loop D (orange), and V5 (magenta) highlighted. Antibody light chains are colored light blue, and heavy chains are shown in pale green with CDR H2 (green), CDR L1 (blue), and CDR L3 (cyan) highlighted. (B) Class convergence of heavy chains. Upper panel shows interaction between CD4-binding loop of gp120 (yellow) and CDR H2s of VRC01 class (green) or C’C” ridge of CD4 (orange) with key interacting hydrogen bonds and salt bridges displayed as dotted lines. Lower panel shows mimicry of CD4 by VRC01 class-heavy chains. Rotation (vertical axis) and translation (horizontal axis) relative to CD4 are displayed for each antibody, with the nine new structures colored different hues of green according to the donor from which they were derived (and gray for previously published structures). (C) VRC01-class variation of light chain relative to heavy chain. Light-chain-variable domain (V_L) pivots around an axis that is close to both the CDR L3 and the interface between heavy and light chains. Other regions such as CDR L1 have larger degrees of structural variance. Upper panel shows light-chain positional variation displayed structurally. V_L in worm representation is colored to distinguish CDR and framework regions, with worm thickness corresponding to the per-residue variance in Cα position. Heavy-chain variable domain (V_H, cartoon) and gp120 (surface) are shown for reference, colored the same as in (A). Lower panel shows the average distance of each light-chain CDR (square) and framework (round) region relative to the centroid of the V_H (horizontal axis) is plotted related to the rmsd of the nine VRC01-class antibodies (vertical axis). The symbols and labels of CDR and framework regions are colored to match the worm colors in the upper panel. See also Figure S1 and Table S1.

Figure 2. VRC01 Class Exhibits Greater Structural Convergence than Other Antibody Classes

(A) Recognition by VH1-2-derived VRC01 class antibodies. Upper panel is shown in the same orientation as in Figure 1A with antigen gp120 depicted in gray surface and variable domains of nine VRC01 class antibodies from five donors displayed in cartoon (V_H in pale green and V_L in slate blue). (B) Recognition by VH1-69-derived anti-HIV-1 CD4i antibodies 17b (PDB ID 1RZK), 412d (PDB ID 2QAD), and X5 (PDB ID 2B4C). (C) Recognition by VH1-69-derived influenza stem antibodies CR6261 (PDB ID 3GBM), CR9114 (PDB ID 4FQI), and F10 (PDB ID 3FKU). In both (B) and (C), to allow comparisons between class members, the V_H of one member of each class was first aligned with the V_H region of VRC01 in (A) to provide a standard frame of reference. VRC01, 17b, and CR6261 were used to represent their respective classes. Other members of each class were then aligned by superposition of their bound antigen. Antigens are shown in gray, and antibodies are shown in pale green (V_H) and blue (V_L). Lower panels of (A), (B), and (C) are 90-degree views from upper panels, looking down onto the epitope from the antibody. (D) Intraclass positional variation of V_H domains are shown with average rotation angles and translation distances between antigen-superposed class members. VRC01 class show significantly lower positional variation compared to the other antibody classes. Data are represented as mean ± SEM.

Figure 3. Structural Signatures in CDR L1 and CDR L3

(A) CDR L1 sequences for VRC01-class antibodies that avoid loop D through deletion, with germline genes italicized and bold, current structures in green text (donor in blue subscript), and structures published elsewhere italicized. (B) Complex structures for VRC01-class antibodies with CDR L1 deletions. Antibodies are shown in ribbon representation and gp120 with a semitransparent surface, both colored the same as in Figure 1A. (C) CDR L1 sequences for VRC01-class antibodies that avoid loop D through mutation to glycine. Sequence highlighting scheme is the same as in (A). (D) Complex structures for VRC01-class antibodies with CDR L1 mutations to glycine. Antibodies are shown in ribbon representation and gp120 with a semitransparent surface, both colored the same as in (B). (E) Rotation of light chains (vertical axis) for VRC01-class antibodies that use deletion (left) and glycine (right) mechanisms of CDR L1 avoidance. Rotations calculated after gp120 superposition relative to the light chain of the 2010 VRC01-93TH057 gp120 complex structure. Data are represented as mean ± SEM. (F) CDR L3 sequences. In Kabat numbering, the third position of the CDR L3 is defined as residue 91 and the fourth position is defined as residue 96. Sequence highlighting scheme is the same as in (A). (G) CDR L3 (cyan) interaction with loop D (orange) of superimposed gp120s shown for VRC01-class antibodies with Leu91_LC (VRC-PG04_d74; left), Phe91_LC (VRC-PG20_d23 and 12A21_d57; middle), and Tyr91_LC (VRC01_d45, VRC-CH31_d0219 and 3BNC117_d3; right). (H) Relative decrease in affinity (vertical axis) of antibodies of the VRC01 class for gp120 (arranged horizontally) for wild-type (WT, white bars) and 91_LC to Ala substitutions (black bars). (I) Relative decrease in affinity (vertical axis) of antibodies of the VRC01 class for gp120 (arranged horizontally) for WT (white bars) and Gln or Glu 96_LC substitutions (black bars). See also Figure S2.

Figure 4. Genetic Records for the Development of CDR L1 and CDR L3 Signatures for the VRC01 Class

(A) Light-chain antibodyomes of donors with VRC01-class antibodies. Top row shows that for each donor, light-chain sequences are plotted as a function of sequence identity to an antibody of the VRC01 class identified in that donor (vertical axis) versus the sequence divergence from their assigned genomic V-gene alleles. Color coding indicates the number of sequences. Middle row shows heat map display of the amino-acid usage at each position of the CDR L3, for all light chains with 5-amino acid CDR L3s and greater than 15% germline divergence. Frequencies are colored from dark red (100% usage) to white (0%). Bottom row shows sequences with 5-residue CDR L3s with sequences that contain amino acids with at least 10% usage are plotted as dots. Orange (or purple) indicates the presence (or absence) of a CDR L1 deletion or mutation to glycine. Total numbers of sequences are listed in the corresponding colors. (B) Maximum-likelihood phylogenetic trees of light-chain sequences with mature genetic CDR L3 signature as defined in (A), colored orange (or purple) for sequences with (or without) CDR L1 signature. The nature of the CDR L1 signature is defined by “Δ” (deletion) or “GG” (mutation to glycine). See also Figure S3 and Table S2.

Figure 5. 454 Pyrosequencing-Derived Genetic Record of V- and J-Gene Usage for the VRC01 Class and Lineage Implications

Histograms of the assigned V-gene origin (top row) or J-gene origin (rows 2 and 3) are shown for VRC01-class transcripts identified from donor antibodyomes with the specific signatures provided in Figure 6B. Comparison of origin-gene assignments for VRC01-class transcripts (rows 1–3) versus those for all non-VRC01-class transcripts provides a measure of the skewing of origin genes used by the VRC01 class. Observations from six donors define genes compatible with the class (Figure 6B) and allow for an estimate of the skewing associated with functional selection. For skewing associated with clonal amplification from a limited number of ancestor-B cells, we estimated probabilities (bottom row) that different numbers of clonal lineages could have given rise to the 454-observed VRC01- class transcripts in each donor. Probability calculations based on both Bayesian and frequentist analyses are provided in Supplemental Experimental Procedures. See also Figure S4 and Table S3. (*Heavy chain J-gene distributions extracted from published antibody sequences for NIAID 45 and IAVI 74.)

Figure 6. B Cell Ontogeny of the VRC01 Class of HIV-1-Neutralizing Antibodies

(A) CDR L1 signature as a function of V-gene divergence in VRC01-class transcripts (top row) or non-VRC01-class transcripts (bottom row). Additional data provided in Table S4. (B) Observed B cell ontogeny in donors RU3, IAVI 23, NIAID 45, IAVI 57, and IAVI 74. Frequency is calculated from observed versus total number of elements. For example only 1 IGHV gene is observed (VH1-2) out of the ~50 V_H-germline alleles in each human. For IGKV or IGLV, frequentist analysis indicates 3–12 and Bayesian analysis 3–17 out of a total of ~80 V_L/K-germline alleles in each human. Specific recombination (to select the IGHV1-2 gene and a 5-amino acid CDR L3 with hydrophobic-Glu or Gln residue pair) and somatic mutation (to evolve heavy chain and CDR L1 signature) are observed in antibodies of the VRC01 class. (C) Schematic of B cell ontogeny of the VRC01 class. See also Figure S5 and Table S4.