Design of immunogens to elicit broadly neutralizing antibodies against HIV targeting the CD4 binding site

Identification of a mimotope of a complex gp41 human immunodeficiency virus epitope related to a non-structural protein of Hepacivirus previously implicated in Kawasaki disease

Current HIV vaccine strategies are hampered by difficulty with recapitulating heavily mutated broadly neutralizing antibodies. We have previously isolated a highly mutated antibody termed "group C 76-Q13-6F5" (6F5) that uses immunoglobulin heavy chain variable region (VH)1-02. 6F5 targets a conformational epitope on HIV gp41 and mediates Ab-dependent cell cytotoxicity (ADCC). Reverting the group C 76 antibodies' variable chain to VH1-02 germline in antibody 76Canc showed retained ADCC activity. A vaccine targeting an epitope functionally recognized by germline antibodies offers a distinct advantage. Due to the 76Canc germline antibody ability to retain anti-HIV function, we sought to identify a protein target that could form the basis of a vaccine. 76Canc specifically recognized a number of acidic peptides on a microarray containing 29,127 linear peptides. Meme analysis identified a peptide sequence similar to a non-structural protein of Hepacivirus previously implicated in Kawasaki disease (KD). Binding was confirmed to significant peptides, including the Hepacivirus-related and KD-related peptide. On serum competition studies using samples from children with KD compared to controls, targeting of this epitope showed no specific correlation to the clinical syndrome of KD. Yeast-displayed human protein microarray autoantigen screening was also reassuring. This study identifies a peptide that can mimic the gp41 epitope targeted by 76C group antibodies (i.e., a mimotope). We show little risk of autoimmune targeting inclusive of inflammation similar to KD, implying non-specific humoral immunity targeting of similar peptides during KD. Development of an HIV vaccine based on such peptides should proceed, but with continued caution.

IMPORTANCE

The development of protective HIV vaccines continues to remain a significant challenge. Many of the broadly neutralizing antibodies require a significant number of mutations, suggesting that traditional vaccines will not be able to recapitulate these types of responses. We have discovered an antibody that has Ab dependent cell cytotoxicity (ADCC) activity against HIV even when mutating the heavy chain of that antibody to germline. As a potential target for vaccines, this offers a distinct advantage: a few immunizations should directly stimulate B cells harboring those specific germline variable chains for expansion. This study sought to identify potential peptide targets that could be formulated into such a vaccine. We identified a peptide that both germline and mature antibodies can recognize. Initial autoantigen screens and consideration of inflammatory disorders suggest this identified antigen is a feasible approach to move forward into pre-clinical models.

An engineered antibody-lectin conjugate targeting the HIV glycan shield protects humanized mice against HIV challenge

Enveloped viruses responsible for global health pandemics often display a glycan shield on their surface envelope glycoproteins. In HIV, the glycan shield is formed by clusters of high-mannose glycans and plays essential roles in viral fitness and immune evasion. A few mannose-binding lectins potently inactivate HIV but have not been fully exploited due to poor pharmacokinetics and short serum half-lives. To address this, we engineered an antibody-lectin conjugate comprising the anti-HIV lectin griffithsin (GRFT) to the Fc region of human IgG1, with the aim of extending its serum half-life and augmenting anti-HIV activity by inducing immune effector responses. Engineered mGRFT-Fc produced in bacteria exhibited picomolar anti-HIV activity and an extended serum half-life, and mGRFT-Fc produced in mammalian cells (mGRFT-Fcglyc) elicited immune effector responses. In HIV-infected CD34+-humanized mice, both GRFT and mGRFT-Fcglyc effectively suppressed viral loads for up to 8 weeks after a single dose. Significantly, mGRFT-Fcglyc prevented HIV infection by neutralizing HIV and provided sustained protection from break-through infections via Fc-mediated immune effector responses, exhibiting a dual mode of protection. This study demonstrates the successful engineering of a lectin-based biologic and provides early evidence that a glycan-targeting agent alone can confer protection from viral infection in vivo.

Phenomenological Modeling of Antibody Response from Vaccine Strain Composition

The elicitation of broadly neutralizing antibodies (bnAbs) is a major goal of vaccine design for highly mutable pathogens, such as influenza, HIV, and coronavirus. Although many rational vaccine design strategies for eliciting bnAbs have been devised, their efficacies need to be evaluated in preclinical animal models and in clinical trials. To improve outcomes for such vaccines, it would be useful to develop methods that can predict vaccine efficacies against arbitrary pathogen variants. As a step in this direction, here, we describe a simple biologically motivated model of antibody reactivity elicited by nanoparticle-based vaccines using only antigen amino acid sequences, parametrized with a small sample of experimental antibody binding data from influenza or SARS-CoV-2 nanoparticle vaccinations. Results: The model is able to recapitulate the experimental data to within experimental uncertainty, is relatively insensitive to the choice of the parametrization/training set, and provides qualitative predictions about the antigenic epitopes exploited by the vaccine, which are testable by experiment. For the mosaic nanoparticle vaccines considered here, model results suggest indirectly that the sera obtained from vaccinated mice contain bnAbs, rather than simply different strain-specific Abs. Although the present model was motivated by nanoparticle vaccines, we also apply it to a mutlivalent mRNA flu vaccination study, and demonstrate good recapitulation of experimental results. This suggests that the model formalism is, in principle, sufficiently flexible to accommodate different vaccination strategies. Finally, we show how the model could be used to rank the efficacies of vaccines with different antigen compositions. Conclusions: Overall, this study suggests that simple models of vaccine efficacy parametrized with modest amounts of experimental data could be used to compare the effectiveness of designed vaccines.

Identification of a mimotope of a complex gp41 Human Immunodeficiency VIrus epitope related to a non-structural protein of Hepacivirus previously implicated in Kawasaki disease

Background

We have previously isolated a highly mutated VH1-02 antibody termed group C 76-Q13-6F5 (6F5) that targets a conformational epitope on gp41. 6F5 has the capacity to mediate Ab dependent cell cytotoxicity (ADCC). When the VH1-02 group C 76 antibodies variable chain sequence was reverted to germline (76Canc), this still retained ADCC activity. Due to this ability for the 76Canc germline antibody to functionally target this epitope, we sought to identify a protein target for vaccine development.

Methods

Initially, we interrogated peptide targeting by screening a microarray containing 29,127 linear peptides. Western blot and ELISAs were used to confirm binding and explore human serum targeting. Autoimmune targeting was further interrogated on a yeast-displayed human protein microarray.

Results

76Canc specifically recognized a number of acidic peptides. Meme analysis identified a peptide sequence similar to a non-structural protein of Hepacivirus previously implicated in Kawasaki disease (KD). Binding was confirmed to top peptides, including the Hepacivirus-related and KD-related peptide. On serum competitions studies using samples from children with KD compared to controls, targeting of this epitope showed no specific correlation to having KD. Human protein autoantigen screening was also reassuring.

Conclusions

This study identifies a peptide that can mimic the gp41 epitope targeted by 76C group antibodies (i.e. a mimotope). We show little risk of autoimmune targeting including any inflammation similar to KD, implying non-specific targeting of this peptide during KD. Development of such peptides as the basis for vaccination should proceed cautiously.

Guiding HIV-1 vaccine development with preclinical nonhuman primate research

PURPOSE OF THE REVIEW

Nonhuman primates (NHPs) are seen as the closest animal model to humans in terms of anatomy and immune system makeup. Here, we review how preclinical studies in this model system are teaching the field of HIV vaccinology the basic immunology that is needed to induce broadly neutralizing antibodies (bnAbs) with vaccination and elicit protective T cell responses. These lessons are being translated into clinical trials to advance towards protective active vaccination against HIV-1 infection.

RECENT FINDINGS

Preclinical vaccination studies in NHPs have shown that highly engineered HIV-1 immunogens can initiate bnAb precursors providing proof of concept for Phase I clinical trials. Additionally, NHP models of HIV-1 infection are elucidating the pathways for bnAb development while serving as systems to evaluate vaccine protection. Innovative immunization strategies have increased affinity maturation of HIV-1 antibodies in long-lived germinal centers. Preclinical studies in macaques have defined the protective level of neutralizing antibodies and have shown that T cell responses can synergize with antibody-mediated immunity to provide protection in the presence of lower neutralizing antibody titers.

SUMMARY

The NHP model provides vaccine regimens and desired antibody and T cell responses that serve as benchmarks for clinical trials, accelerating HIV vaccine design.

Evolutionary Landscapes of Host-Virus Arms Races

Vertebrate immune systems suppress viral infection using both innate restriction factors and adaptive immunity. Viruses mutate to escape these defenses, driving hosts to counterevolve to regain fitness. This cycle recurs repeatedly, resulting in an evolutionary arms race whose outcome depends on the pace and likelihood of adaptation by host and viral genes. Although viruses evolve faster than their vertebrate hosts, their proteins are subject to numerous functional constraints that impact the probability of adaptation. These constraints are globally defined by evolutionary landscapes, which describe the fitness and adaptive potential of all possible mutations. We review deep mutational scanning experiments mapping the evolutionary landscapes of both host and viral proteins engaged in arms races. For restriction factors and some broadly neutralizing antibodies, landscapes favor the host, which may help to level the evolutionary playing field against rapidly evolving viruses. We discuss the biophysical underpinnings of these landscapes and their therapeutic implications.

Multiscale affinity maturation simulations to elicit broadly neutralizing antibodies against HIV

The design of vaccines against highly mutable pathogens, such as HIV and influenza, requires a detailed understanding of how the adaptive immune system responds to encountering multiple variant antigens (Ags). Here, we describe a multiscale model of B cell receptor (BCR) affinity maturation that employs actual BCR nucleotide sequences and treats BCR/Ag interactions in atomistic detail. We apply the model to simulate the maturation of a broadly neutralizing Ab (bnAb) against HIV. Starting from a germline precursor sequence of the VRC01 anti-HIV Ab, we simulate BCR evolution in response to different vaccination protocols and different Ags, which were previously designed by us. The simulation results provide qualitative guidelines for future vaccine design and reveal unique insights into bnAb evolution against the CD4 binding site of HIV. Our model makes possible direct comparisons of simulated BCR populations with results of deep sequencing data, which will be explored in future applications.

Vaccination has saved more lives than any other medical procedure. But, we do not have robust ways to develop vaccines against highly mutable pathogens. For example, there is no effective vaccine against HIV, and a universal vaccine against diverse strains of influenza is also not available. The development of immunization strategies to elicit antibodies that can neutralize diverse strains of highly mutable pathogens (so-called ‘broadly neutralizing antibodies’, or bnAbs) would enable the design of universal vaccines against such pathogens, as well as other viruses that may emerge in the future. In this paper, we present an agent-based model of affinity maturation–the Darwinian process by which antibodies evolve against a pathogen–that, for the first time, enables the in silico investigation of real germline nucleotide sequences of antibodies known to evolve into potent bnAbs, evolving against real amino acid sequences of HIV-based vaccine-candidate proteins. Our results provide new insights into bnAb evolution against HIV, and can be used to qualitatively guide the future design of vaccines against highly mutable pathogens.

A Coarse-Grained Model of Affinity Maturation Indicates the Importance of B-Cell Receptor Avidity in Epitope Subdominance

The elicitation of broadly neutralizing antibodies (bnAbs) is a major goal in the design of vaccines against rapidly-mutating viruses. In the case of influenza, many bnAbs that target conserved epitopes on the stem of the hemagglutinin protein (HA) have been discovered. However, these antibodies are rare, are not boosted well upon reinfection, and often have low neutralization potency, compared to strain-specific antibodies directed to the HA head. Different hypotheses have been proposed to explain this phenomenon. We use a coarse-grained computational model of the germinal center reaction to investigate how B-cell receptor binding valency affects the growth and affinity maturation of competing B-cells. We find that receptors that are unable to bind antigen bivalently, and also those that do not bind antigen cooperatively, have significantly slower rates of growth, memory B-cell production, and, under certain conditions, rates of affinity maturation. The corresponding B-cells are predicted to be outcompeted by B-cells that bind bivalently and cooperatively. We use the model to explore strategies for a universal influenza vaccine, e.g., how to boost the concentrations of the slower growing cross-reactive antibodies directed to the stem. The results suggest that, upon natural reinfections subsequent to vaccination, the protectiveness of such vaccines would erode, possibly requiring regular boosts. Collectively, our results strongly support the importance of bivalent antibody binding in immunodominance, and suggest guidelines for developing a universal influenza vaccine.

Protein engineering strategies for rational immunogen design

Antibody immunodominance refers to the preferential and asymmetric elicitation of antibodies against specific epitopes on a complex protein antigen. Traditional vaccination approaches for rapidly evolving pathogens have had limited success in part because of this phenomenon, as elicited antibodies preferentially target highly variable regions of antigens, and thus do not confer long lasting protection. While antibodies targeting functionally conserved epitopes have the potential to be broadly protective, they often make up a minority of the overall repertoire. Here, we discuss recent protein engineering strategies used to favorably alter patterns of immunodominance, and selectively focus antibody responses toward broadly protective epitopes in the pursuit of next-generation vaccines for rapidly evolving pathogens.