Discovery and characterization of highly immunogenic and broadly recognized mimics of the HIV‐1 CTL epitope Gag_77–85

Abstract

Human immunodeficiency virus (HIV)-specific cytotoxic T lymphocytes (CTL) play an important role in HIV infection. Given the viral genetic diversity, the selection of suitable antigens and epitope variants will be important in the design of an effective vaccine. We have previously shown that combinatorial libraries are useful tools to identify epitope mimics as well as potentially cross-reactive natural sequences in protein databases. We have applied this approach to the HIV Gag p17-derived epitope SL9 (SLYNTVATL) to identify broadly recognized SL9 mimics and to assess the cross-recognition of naturally occurring SL9 variants. Nine nonapeptides were identified that were up to one order of magnitude more effective than SL9 in stimulating CTL responses in PBMC from HIVinfected subjects. Using transgenic mice, we demonstrate that a number of these epitope mimics were able to generate de novo T cell responses that cross-reacted with the original SL9 sequence. Particularly, mimics with changes at the relatively conserved Fpocket anchor residue were frequently cross-recognized. This approach may lead to vaccine candidates with higher in vivo immunogenicity and increased potential for cross-recognition of naturally occurring SL9 variants.

Design, Expression, and Processing of Epitomized Hepatitis C Virus-Encoded CTL Epitopes

“…Instead, it will possibly require carefully assessing the cross-reactivity potential by responses induced by subdominant variants. Although studies available to date have largely been limited to the induction of variant-specific responses in animal models, recent analyses in HIV have also documented the superior immunogenicity of certain subdominant sequence variants (12, 25–27). Importantly, the inclusion of such variants in vaccine immunogen sequences may not only provide potent immunogen components but may also facilitate the screening and reliable detection of responses in cohorts with particularly high viral diversity in the circulating viral population.…”

Impact of HLA-B Alleles, Epitope Binding Affinity, Functional Avidity, and Viral Coinfection on the Immunodominance of Virus-Specific CTL Responses

“…Among the 135 epitopes tested for binding, 41 did not show strong binding (IC 50 Ͼ 500 nM) to their described, restricting allele. Although this could potentially indicate wrongly assigned HLA restriction alleles (34), there are numerous examples of well-defined and frequently targeted epitopes with binding affinities Ͼ500 nM (2,7,14). In fact, when looking at epitopes with IC 50 Ͻ 500 or Ͼ 500 nM, there was no significant enrichment of rarely (Ͻ5%) or never-targeted epitopes in the group of epitopes with IC 50 Ͼ 500 nM.…”

“…Studies in HLA transgenic mice confirmed the relevance of this threshold, while also indicating some correlation between affinity and the propensity to be immunogenic (12,13). Furthermore, previous studies in the human system proposed a relationship between binding affinity and the magnitude and breadth of responses for variants of a single epitope but did not examine those relationships over a heterogeneous set of epitopes (7,14). Finally, studies in the context of the more complex system of malaria infection indicate that, provided that a peptide can bind to a specific HLA molecule, subsequent antigenicity and immunogenicity may not directly correlate with the affinity of epitope binding per se.…”

Degenerate T-cell Recognition of Peptides on MHC Molecules Creates Large Holes in the T-cell Repertoire

“…The principles of TCR-pMHC interactions that allow for this flexibility are not fully understood. CTL recognition-studies using peptide libraries with altered peptide ligands [9], [14]–[18] and pMHC-TCR structures [19], [20] allow some inferences to be made. The middle (P4–P6) part of the peptide forms the core of the interaction [9], [14]–[20], where the majority of amino acid substitutions (with exception of those with very similar amino acids) tend to perturb pMHC recognition.…”