Strategies to guide the antibody affinity maturation process

Abstract

Antibodies with protective activity are critical for vaccine efficacy. Affinity maturation increases antibody activity through multiple rounds of somatic hypermutation and selection in the germinal center. Identification of HIV-1 specific and influenza-specific antibody developmental pathways, as well as characterization of B cell and virus co-evolution in patients, has informed our understanding of antibody development. In order to counteract HIV-1 and influenza viral diversity, broadly neutralizing antibodies precisely target specific sites of vulnerability and require high levels of affinity maturation. We present immunization strategies that attempt to recapitulate these natural processes and guide the affinity maturation process.

Figure 1. Overview of affinity maturation

Left, Naïve or memory B cells are activated by exposure to viral antigens by infection or vaccination. Center, Activated naïve or memory B cells migrate to germinal centers within secondary lymphoid tissues such as lymph nodes [111, 112]. There, B cells cycle between a dark zone, where they undergo mutation and proliferate, and a light zone, where they undergo selection [1]. In the light zone, B cells compete for antigen on follicular dendritic cells, internalize the antigen, and present it to T follicular helper cells. The B cells with highest affinity internalize the most antigen, conferring an advantage in obtaining T cell help which in turn regulates survival, dwell time, and number of cycles of selection [105, 106]. Approximately 90% of selected cells return to the dark zone and repeat the cycle, while the remaining 10% exit to serve as memory cells or plasma cells [113]. Right, After sufficient time passes for multiple rounds of germinal center selection, the resulting antibodies may be highly mutated from their naïve precursors. While chronic infection may result in mutation levels upwards of 30% as seen in HIV-1 broadly neutralizing antibodies (bNAbs) [22], mutations of 10–20% may provide sufficient maturation to be effective [17, 18], and is more readily achieved by vaccination.

Figure 2. Development of broadly neutralizing antibodies following changes in the viral envelope HIV-1 gp140

(A) Multi-lineage cooperation. Autologous neutralizing antibodies develop early in infection and can neutralize many autologous viruses but do not neutralize heterologous Tier 2 viral strains. Mutations that confer viral escape from these early, autologous neutralizing antibodies create the epitope for later, broadly cross-reactive antibodies of the same [6] or different [40] lineages that can neutralize both the autologous strains and also many heterologous viral strains. (B) Virus-antibody co-evolution. Viral diversification through mechanisms such as viral mutation or super-infection leads to the development of an epitope on the virus which selects for a specific B cell that can target a known site of vulnerability and gives autologous neutralization. Following selection of this initial B cells, ongoing virus evolution drives the maturation of the B cell which results in antibodies capable of heterologous neutralization increases in neutralization breadth and potency [6, 7].

Figure 3. Structural definition of protein immunogens

Left, Respiratory Syncytial Virus fusion glycoprotein exists in two forms: a metastable, neutralization-sensitive, prefusion form [46] (PDB ID:4MMT) and a stable, postfusion form [114] (PDB ID:3RRR). Center, HIV-1 BG505 SOSIP.664 trimer structure displays the near-native viral prefusion form [26] (PDB ID:4TVP). Right, Full-length Influenza Hemagglutinin H1 trimer [115] (PDB ID:1RUZ) and a model of the designed H1 stem immunogen [74] based on PDB ID:1RU7. All molecules are shown in ribbon representation with glycans shown in stick representation.

Figure 4. Immunization strategies to target specific sites and generate affinity matured cross-specific immune responses

(A) Strategy based on antibody ontogeny as defined from mature antibody identification and subsequent deep-sequencing data [13, 22, 37]. Initial priming immunogens such as Lumazine synthase-eOD-GT6 (LS-eOD-GT6) or HIV-1 gp140 clade C strain 426cΔ3-Gly are selected and designed based on their ability to bind to specific UCA or germline antibodies in vitro [64, 65]. These priming molecules can be used to boost the immune response or modified to ensure binding to only intermediate or mature antibodies. (B) Strategy based on antibody-viral co-evolution study information. This strategy would mimic natural infection and antibody evolution where all immunogens are designed based on viral sequences identified in a donor. Given that the viral population is transient and not uniform at any given time, immunogens based on a number of sequences may be used to enable development of the desired immune response. (C) Strategy based on viral diversity. Either through a sequential or mixture type of immunization strategy, the immune system would be inundated with many epitopes of interest. The common sites of vulnerability on the viral target would inherently be the only conserved regions between the diverse molecules and thus over time would lead to a targeted and affinity matured response aimed at these sites.