SARS CTL vaccine candidates; HLA supertype-, genome-wide scanning and biochemical validation

Abstract

An effective Severe Acute Respiratory Syndrome (SARS) vaccine is likely to include components that can induce specific cytotoxic T-lymphocyte (CTL) responses. The specificities of such responses are governed by human leukocyte antigen (HLA)-restricted presentation of SARS-derived peptide epitopes. Exact knowledge of how the immune system handles protein antigens would allow for the identification of such linear sequences directly from genomic/proteomic sequence information (Lauemoller et al., Rev Immunogenet 2001: 2: 477-91). The latter was recently established when a causative coronavirus (SARS-CoV) was isolated and full-length sequenced (Marra et al., Science 2003: 300: 1399-404). Here, we have combined advanced bioinformatics and high-throughput immunology to perform an HLA supertype-, genome-wide scan for SARS-specific CTL epitopes. The scan includes all nine human HLA supertypes in total covering >99% of all individuals of all major human populations (Sette & Sidney, Immunogenetics 1999: 50: 201-12). For each HLA supertype, we have selected the 15 top candidates for test in biochemical binding assays. At this time (approximately 6 months after the genome was established), we have tested the majority of the HLA supertypes and identified almost 100 potential vaccine candidates. These should be further validated in SARS survivors and used for vaccine formulation. We suggest that immunobioinformatics may become a fast and valuable tool in rational vaccine design.

Figure 1

A representative example of the genome‐wide scanning for putative epitopes restricted to A1. (A) Predicted strong binding peptides (equilibrium dissociation constant, K_D < 50 nM); (B) predicted intermediate binding peptides (K_D < 500 nM); (C) predicted proteasomal cleavage (netchop 2.0 > 0.5); (D) sequence variation estimated from 12 SARS isolates; (E) assigned translated regions; and (F) combined selection of peptides (binding <500 nM, proteasomal cleavage >0.5, and sequence variation = 0).

Figure 2

The concentration of de novo‐folded peptide–human leukocyte antigen (HLA)‐A*1101 complexes was measured in a quantitative enzyme‐linked immunosorbent assay and plotted against the concentration of peptide offered ( 15 ). Peptides: LIGANYLGK (▵); MTNRQFHQK (◊); ITCVVIPSK (○); GVAMPNLYK (□).

Figure 3

A graphical representation of the predicted and validated human leukocyte antigen (HLA) binding of 119 selected SARS‐derived peptides binding to eight different HLA molecules. It illustrates combinations that were (A) predicted and confirmed binders (true positives, ▪); (B) predicted, but not confirmed, binders (false positives, ); (C) predicted, but not confirmed, non‐binders (false negatives, ); and (D) predicted and confirmed non‐binders (true negatives, □).