Rational Design of DNA-Expressed Stabilized Native-Like HIV-1 Envelope Trimers

Abstract

The HIV-1-envelope glycoprotein (Env) is the main target of antigen design for antibody-based prophylactic vaccines. The generation of broadly neutralizing antibodies (bNAb) likely requires the appropriate presentation of stabilized trimers preventing exposure of non-neutralizing antibody (nNAb) epitopes. We designed a series of membrane-bound Envs with increased trimer stability through the introduction of key stabilization mutations. We derived a stabilized HIV-1 trimer, ConSOSL.UFO.750, which displays a dramatic reduction in nNAb binding while maintaining high quaternary and MPER-specific bNAb binding. Its soluble counterpart, ConSOSL.UFO.664, displays similar antigenicity, and its native-like Env structure is confirmed by negative stain-EM and glycosylation profiling of the soluble ConSOSL.UFO.664 trimer. A rabbit immunization study demonstrated that the ConSOSL.UFO.664 can induce autologous tier 2 neutralization. We have successfully designed a stabilized native-like Env trimer amenable to nucleic acid or viral vector-based vaccination strategies.

Keywords: DNA; Env; HIV-1; bNAb; cell-based ELISA; cytoplasmic tail; muscle cells; transmembrane; trimer.

Graphical abstract

Figure 1

HIV-1 Env Membrane-Bound Stabilized Trimer Designs Cleavage-dependent (A) and cleavage-independent (B) Env trimers depicted here as gp120-gp41 monomers for clarity. The designs are chronologically organized from left to right at bottom. Features from published gp140 stabilized trimers were introduced as indicated: SOS (Binley et al., 2000) and SOSIP (Sanders et al., 2002); AP and AC+IC (Kwon et al., 2015); VD (Kesavardhana and Varadarajan, 2014); Linker L (Kovacs et al., 2014); Linker Lw (Sharma et al., 2015); UFO: HR1 redesign from uncleaved pre-fusion optimized (Kong et al., 2016). The cytoplasmic tail is truncated at amino acid 712 or 750 (HXB2 numbering). See also Supplemental Data.

Figure 2

Linker-Stabilized Env Presents a Favorable Quaternary Stabilized Structure (A) Cleavage-dependent (ConSOSVD.712, ConSOSIP.712) and cleavage-independent (ConSL.712) Envs were tested by flow cytometry for surface epitope exposure in 293T.17 cells. (B) Stabilization of cleavage-independent Env with I559P mutation (ConSLIP.712) compared to A433C+I201C+V570D (ConSLVD.712). Data are displayed as mean fluorescence intensity (MFI) ratios (mAb:2G12), using 2G12 to normalize the data. Error bars represent means ± SEMs, with n ≥ 2 independent experiments. One-way ANOVA with Sidak’s multiple comparisons. ^∗p < 0.05, ^∗∗p < 0.01, ^∗∗∗p < 0.001, ns, not significant. Quat. cleav. dpt., quaternary cleavage dependent. See also Supplemental Data.

Figure 3

The Adhesion Status, Cellular Host Model, and Cytoplasmic Tail of Env Affect the Epitope Presentation (A) Comparison of the BaL gp160 and modified BaL Env CT. Mutation of the recycling/endocytosis motifs are indicated in red. The impact on expression levels is reported as mean MFI (± SD) fold increase over BaL gp160 (n ≥ 2). (B) Mean MFI values of Env surface expression assessed by FC, representative of n ≥ 2 independent experiments. (C) mAb:2G12 ratios as in Figure 2 (n ≥ 2). (D and E) Comparison of mAb:2G12 ratios obtained from 293T.17 Cell ELISA (CE) and FC using (D) BaL Y712I.750 and (E) BaL gp160 (n = 3). (F) Comparison of BaL SSS.712 epitope profile in muscle cell CE, 293T.17 CE, and FC (n ≥ 2). (G) Muscle cell CE mAb:2G12 of ConSL.712, ConSLIP.712, and ConSLVD.712 (n ≥ 3). For all of the graphs, error bars represent means ± SEMs. One-way ANOVA with Sidak’s multiple comparisons. ^∗p < 0.05, ^∗∗p < 0.01, ^∗∗∗p < 0.001 for (C), (F), and (G), where each sign in (F) compares ^∗muscle cells versus 293T.17 FC, †muscle cells CE versus 293T.17 CE, and ‡293T.17 FC versus 293T CE. Unpaired t test for (D) and (E). FACS, fluorescence-activated cell sorting; LLP, lentiviral lytic peptide domains; MSD, membrane-spanning domain; ns, not significant; SSS, secretion signal sequence. See also Figures S1A, S3, S4, and S5.

Figure 4

Enhancement of bNAb Binding and Subsequent Reduction of nNAb Binding by gp41 HR1 Stabilization (A) mAb:2G12 binding profile as in Figure 2, comparing ConSLwIP.712 to subsequent stabilized constructs for gp120-specific mAbs (n ≥ 2, ConSOSL.UFO.750, n ≥ 3). (B) Same as in (A) for gp41 and gp120-gp41 interface-specific mAbs. (C) Comparison of ConSLwIP.712 and ConSOSL.UFO.750 epitope profiles in muscle cell CE, 293T.17 CE, and FC (n ≥ 2). (D) Muscle cell CE mAb:2G12 (n ≥ 3, ConSOSLIP.750 PGT135, n = 2). (E) mAb:2G12 ratios obtained from 293T.17 CE (n ≥ 3, except PGT135, n ≥ 2). For all of the graphs, error bars represent means ± SEMs. One-way ANOVA with Sidak’s multiple comparisons. ^∗p < 0.05, ^∗∗p < 0.01, ^∗∗∗p < 0.001, where each sign in (C) compares ^∗muscle cells versus 293T.17 FC, †muscle cells CE versus 293T.17 CE, and ‡293T.17 FC versus 293T CE. ns, not significant. See also Figures S4 and S5.

Figure 5

BNAbs Bind More Efficiently to ConSOSL.UFO.750 than nNAbs (A) Mean MFI values of ConSOSL.UFO.750 surface expression assessed by FC using a panel of mAbs. These Abs were titrated starting at 10 μg/mL in a 10-fold dilution series. Titration curves grouped by Env domain specificity. 2G12 plotted on all graphs for comparison. Solid lines, bNAbs; dotted lines, nNAbs. Representative of n = 2 independent experiments. (B) mAb:2G12 binding profile as in Figure 2, comparing ConS.750 for a panel of 15 mAbs (original ConS sequence truncated at position 750) to ConSOSL.UFO.750 (n ≥ 2; ConSOSL.UFO.750, n ≥ 3). (C) Same as in (B) for an additional 20 mAbs. For (B) and (C), error bars represent means ± SEMs. Unpaired t test. ^∗p < 0.05, ^∗∗p < 0.01, ^∗∗∗p < 0.001. ns, not significant. See also Figure S6A.

Figure 6

ConSOSL.UFO.664 Env Trimers Present a Native-Like Pre-fusion Conformation (A) Size exclusion chromatography (SEC) profile of the ConSOSL.UFO.664 produced in 293T.17 cells. (B) Native PAGE-western blotting of SEC fractions from (A), detected with 2G12. (C) Hydrophilic interaction-ultra-performance liquid chromatography (HILIC-UPLC) profile of N-linked glycans from SEC purified ConSOSL.UFO.664 trimers. Oligomannose-type (green) and complex-type (pink) glycans were identified by endoglycosidase H (Endo H) digestion. Rel., relative. (D) Relative N-glycosylation sites. (E) mAbs titration against ConSOSL.UFO.664 Myc-HIS trimers captured by anti-cMyc 9E10 Ab. Representative of at least n = 2 independent experiments. The titration curves are grouped by Env domain specificity, and 2G12 is plotted on all of the graphs for comparison. Solid lines, bNAbs; dotted lines, nNAbs. OD, optical density. (F) Same as in (E) for gp41-specific mAbs. (G and H) Negative stain-electron microscopy (NS-EM) images showing views of (G) the propeller shape of the ligand-free trimer and (H) in complex with VRC01 Fab. See also Figures S6B–S6I.

Figure 7

Immunogenicity of ConSOSL.UFO Design in Rabbits (A) Antigen-specific serum IgG binding assessed by 9E10 capture ELISA for DNA immunized rabbits with ConSOSL.UFO.750 plasmid (gray) and ConSOSL.UFO.664 plasmid (black) both boosted with protein (DDDP) and for ConSOSL.UFO.664 protein alone (blue) (PPP). ConSOSL.UFO.664 Myc-HIS trimers were used as captured antigen, and IgG concentration determined using a captured standard rabbit IgG. Gray arrows, DNA IM+EP immunization; red arrows, protein immunization. (B) Proportion of V3 response as assessed by competitive ELISA using matching V3 cys-cyclized peptide. (C) Neutralization of HIV-1 pseudoviruses in TZM-bl assay by rabbit sera from weeks 10 and 22. Data plotted as ID₅₀ values (serum dilution that inhibits by 50% infectivity). MW965.26, MN, SF162, and ConM are tier 1 viruses; ConS and TV1.29 are tier 2. n = 6 animals per group, except for groups ConSOSL.UFO.750 DDDP and 664 PPP at week 22, where n = 5. Error bars represent means ± SEMs. Unpaired t test. ^∗p < 0.05, ^∗∗p < 0.01. For (A), ^∗750 DDDP versus 664 DDDP; †664 PPP versus 664 DDDP; ‡664 PPP versus 750 DDDP. DDDP, DNA/DNA/DNA/protein immunization; PPP, protein/protein/protein. See also Figures S7A–S7F.