Mapping Neutralizing Antibody Epitope Specificities to an HIV Env Trimer in Immunized and in Infected Rhesus Macaques

Zhao, Fangzhu; Joyce, Collin; Burns, Alison; Nogal, Bartek; Ramos, Alejandra; Biddle, Trevor; Pauthner, Matthias; Nedellac, Rebecca; Qureshi, Huma; Mason, Rosemarie D.; Landais, Elise; Ward, Andrew B.; Burton, Dennis R.; Sok, Devin

doi:10.2139/ssrn.3578689

Cited by 6 publications

(15 citation statements)

References 56 publications

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“…EC 50 values from ELISA experiments with IgGs were 1.93 and 2.64 μg/ml, and the dissociation constants ( K d ) from BLI were 890 and 180 nM for Rh.33104 mAb.1 and Rh.33172 mAb.1, respectively. These binding affinities are comparable to mAbs isolated from BG505-immunized rhesus macaques in published studies ( 6 , 19 ).…”

Section: Resultssupporting

confidence: 75%

“…S2 to reduce heterogeneity and reconstruct higher-quality map of the V1 pAb. mAbs recognizing this epitope have recently been isolated from the same rhesus macaque ( 19 ). Two antibodies from the same clonal family, Rh4O9.7 and Rh4O9.8, neutralized the wild-type BG505 pseudovirus and were found to target the V1 loop through mutagenesis.…”

Section: Resultsmentioning

confidence: 99%

“…S1) has been uploaded to the EM Data Bank (EMDB), entry identification (ID): EMD-23779. The structural model of the complex, comprising BG505 SOSIP.v5.2 ( 28 ) and Rh4O9.8 mAb ( 19 ), was built into the EM map. ABodyBuilder ( 29 ) was applied to create an initial model of the Fab.…”

Section: Methodsmentioning

confidence: 99%

“…Antibody samples were concentrated, buffer exchanged to TBS buffer (Alfa Aesar), and then subjected to SEC purification (HiLoad 16/600 Superdex S200 pg column; GE Healthcare Life Sciences). nsEM of BG505 SOSIP in complex with Rh4O9.8 mAb Rh4O9.8 mAb (19) was provided by the D. Sok lab (International AIDS Vaccine Initiative-Neutralizing Antibody Center, La Jolla, CA, USA). Fifteen micrograms of BG505 SOSIP MD39 was incubated with 15 g of the Rh4O9.8 antibody (as Fab fragment) for 1 hour at room temperature.…”

Section: Antibody Expression and Purificationmentioning

confidence: 99%

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From structure to sequence: Antibody discovery using cryoEM

et al. 2022

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One of the rate-limiting steps in analyzing immune responses to vaccines or infections is the isolation and characterization of monoclonal antibodies. Here, we present a hybrid structural and bioinformatic approach to directly assign the heavy and light chains, identify complementarity-determining regions, and discover sequences from cryoEM density maps of serum-derived polyclonal antibodies bound to an antigen. When combined with next-generation sequencing of immune repertoires, we were able to specifically identify clonal family members, synthesize the monoclonal antibodies, and confirm that they interact with the antigen in a manner equivalent to the corresponding polyclonal antibodies. This structure-based approach for identification of monoclonal antibodies from polyclonal sera opens new avenues for analysis of immune responses and iterative vaccine design.

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Section: Resultssupporting

confidence: 75%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Antibody Expression and Purificationmentioning

confidence: 99%

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From structure to sequence: Antibody discovery using cryoEM

et al. 2022

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“…Computational mapping analysis to predict genetic signatures associated with plasma neutralization breadth suggested AIIMS709 plasma nAbs were dependent on several residues within the C3V4 region of gp120 (figure 5). The C3V4 region has been reported as a major nAb target in early subtype C infection, presumably due to its high immunogenicity as a result of increased exposure, being a component of the CD4-binding site as well as the presence of several conserved glycans such as N339, N355 and N363 in the C3 region and N393 and N398 in the V4 region of the viral envelope glycoprotein (15)(16)(17)(18). Overall, our findings suggest the presence of plasma nAbs in AIIMS709, of undescribed specificity that are glycan dependent and plausibly target the C3V4 region and can neutralize the hyperglycosylated Env.…”

Section: Resultsmentioning

confidence: 99%

Plasma neutralizing antibodies in an infant with interclade HIV-1 superinfection preferentially neutralize superinfecting HIV-1 strains

Mishra

Sharma

Dobhal

et al. 2020

Preprint

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HIV-1 superinfection is defined as infection by an unrelated second strain of HIV-1 after seroconversion due to primary infecting strain and has been associated with development of breadth in the neutralizing antibody (nAb) response, altered disease progression and efficacy of antiretrovirals; though conflicting observations have also been reported. Superinfection has been reported in HIV-1 infected adults. Recently we observed that multivariant infection in infants was associated with early induction of plasma broadly neutralizing antibodies (bnAbs) targeting diverse autologous viruses, however, there is paucity of information on infants with HIV-1 superinfection. Furthermore, the mechanisms by which superinfection in an infant, after priming by an initial infection, potentiate the evolution of a bnAb response have not been evaluated. Herein, we performed a longitudinal analysis and observed evolution of nAb responses in an antiretroviral naïve perinatally HIV-1 infected infant, with interclade superinfection (clade C followed by a unique A1C recombinant). The nAb responses broadened rapidly after superinfection targeted an undefined glycan-dependent epitope on the superinfecting variant, while no enrichment of nAb response against the primary infecting strain occurred. Defining virological features in infants with sequential infection with highly divergent circulating viruses that improve nAb responses will contribute information that could be leveraged for optimization of multicomponent candidate vaccines.ImportanceHIV-1 infected infants develop bnAbs rapidly suggesting factors governing bnAb induction in infants are distinct from adults. HIV-1 superinfection is more common in adults whereas the stringent genetic bottleneck for transmission in infants often leads to infection by a single transmitted/founder HIV-1 strain. Longitudinal studies in infants with HIV-1 superinfection can provide key information on the viral factors that induce a bnAb response towards development of a polyvalent vaccine. Herein, we show that in infant who was sequentially infected with two HIV-1 strains from different clades, antibody responses were primarily generated against the superinfecting, second strain of HIV-1.These antibody responses were dependent on glycans, and targeted an undefined epitope in the C3V4 region of HIV-1 Env. A better understanding of how neutralizing antibody responses develop during natural HIV-1 superinfection in infants will provide information relevant to HIV Env vaccine development and evaluation.

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Molecular insights into antibody-mediated protection against the prototypic simian immunodeficiency virus

et al. 2022

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SIVmac239 infection of macaques is a favored model of human HIV infection. However, the SIVmac239 envelope (Env) trimer structure, glycan occupancy, and the targets and ability of neutralizing antibodies (nAbs) to protect against SIVmac239 remain unknown. Here, we report the isolation of SIVmac239 nAbs that recognize a glycan hole and the V1/V4 loop. A high-resolution structure of a SIVmac239 Env trimer-nAb complex shows many similarities to HIV and SIVcpz Envs, but with distinct V4 features and an extended V1 loop. Moreover, SIVmac239 Env has a higher glycan shield density than HIV Env that may contribute to poor or delayed nAb responses in SIVmac239-infected macaques. Passive transfer of a nAb protects macaques from repeated intravenous SIVmac239 challenge at serum titers comparable to those described for protection of humans against HIV infection. Our results provide structural insights for vaccine design and shed light on antibody-mediated protection in the SIV model.

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Mapping Neutralizing Antibody Epitope Specificities to an HIV Env Trimer in Immunized and in Infected Rhesus Macaques

Cited by 6 publications

References 56 publications

From structure to sequence: Antibody discovery using cryoEM

From structure to sequence: Antibody discovery using cryoEM

Plasma neutralizing antibodies in an infant with interclade HIV-1 superinfection preferentially neutralize superinfecting HIV-1 strains

Molecular insights into antibody-mediated protection against the prototypic simian immunodeficiency virus

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