Designing a B Cell-Based Vaccine against a Highly Variable Hepatitis C Virus

Abstract

The ability to use structure-based design and engineering to control the molecular shape and reactivity of an immunogen to induce protective responses shows great promise, along with corresponding advancements in vaccine testing and evaluation systems. We describe in this review new paradigms for the development of a B cell-based HCV vaccine. Advances in test systems to measure in vitro and in vivo antibody-mediated virus neutralization include retroviral pseudotype particles expressing HCV E1E2 glycoproteins (HCVpp), infectious cell culture-derived HCV virions (HCVcc), and surrogate animal models mimicking acute HCV infection. Their applications have established the role of broadly neutralizing antibodies to control HCV infection. However, the virus has immunogenic regions in the viral envelope glycoproteins that are associated with viral escape or non-neutralizing antibodies. These regions serve as immunologic decoys that divert the antibody response from less prominent conserved regions mediating virus neutralization. This review outlines the immunogenic regions on E2, which are roughly segregated into the hypervariable region 1 (HVR1), and five clusters of overlapping epitopes designated as antigenic domains A-E. Understanding the molecular architecture of conserved neutralizing epitopes within these antigenic domains, and how other antigenic regions or decoys deflect the immune response from these conserved regions will provide a roadmap for the rational design of an HCV vaccine.

Keywords: antigenic domains; epitopes; hepatitis C virus; human monoclonal antibodies; vaccine design; virus neutralization.

Figure 1

Sequence variability of HCV in comparison with other viruses. Phylogenetic trees of HCV E1E2 (A), HIV env (gp41/gp120; B), and influenza hemagglutinin (HA; C) are shown. E1E2 amino acid reference sequences (N = 204) were downloaded from the LANL HCV database (Kuiken et al., 2005), HIV env reference sequences (N = 39) were downloaded from the LANL HIV database (http://www.hiv.lanl.gov), and influenza A HA clones were from Corti et al. (2011), with amino acid sequences downloaded from the Influenza Research Database (Zhang et al., 2017). Multiple sequence alignments were performed using MAFFT software (Katoh and Standley, 2013). Phylogenetic trees were built using the neighbor joining method, and visualized using the APE package (Paradis et al., 2004) in R. Sequence names are labeled, and are colored according to HCV genotype (A), HIV subtype (B), and influenza group (C; red = group 1, blue = group 2). Scale bar represents 5% sequence divergence.

Figure 2

Amino acid sequence variability of HCV envelope glycoproteins E1 and E2 Sequence logos (Crooks et al., 2004) were generated using a multiple sequence alignment of approximately 400 complete E1E2 amino acid sequences downloaded from the Los Alamos HCV database (Kuiken et al., 2005). This gives amino acid propensities at each E1 and E2 position (residues 192-383 and 384-746, respectively, based on the H77 isolate numbering), with total height at each position representing sequence conservation (more variable positions have lower height). Hypervariable regions of E2 are shown in red boxes, and hypervariable region 1 (HVR1; aa 384-410) is highlighted. Antigenic domain E (aa 412-423) is shown in blue box and highlighted. Figure adapted from Pierce et al. (2016a).

Figure 3

Global E2 alanine scanning, shown as heat map. E2 alanine mutants are on the vertical axis, while HMAbs are on the horizontal axis, colored by antigenic domain (domain A, red; domain B, magenta; domain C, cyan; domain D, green; domain E, blue). Heat map colors represent measured affinity compared with wild-type (H77) E2 as detailed in the legend. Figure adapted from Pierce et al. (2016b).

Figure 4

Antigenic domains mapped to the surface of E2. Antigenic domains are colored and labeled on the neutralizing (front layer; A) and non-neutralizing (back layer; B) face of the E2 core structure (PDB code 4MWF), with key epitope residues shown in space-fill and a subset of those residues labeled. Basic N-glycans were modeled at all 10 sites present in the E2 core structure (N1-N4, N6-N11) using the GlyProt web server (Bohne-Lang and von der Lieth, 2005), and are shown as orange sticks. As the E2 core structure does not include coordinates for the majority of domain E (residues 412-423; of which 412-420 are not present), the domain E coordinates from the domain E-HCV1 complex structure (PDB code 4DGY) were modeled at that site. Hypervariable region 1 (HVR1), which is located at the N-terminus of E2 and also is not represented in the E2 core structure, is shown as a black line for reference. Figure adapted from Fauvelle et al. (2016).