Random Screening of Proteins for HLA-A*0201-Binding Nine-Amino Acid Peptides Is Not Sufficient for Identifying CD8 T Cell Epitopes Recognized in the Context of HLA-A*0201

Abstract

HLA-A2 is the most frequent HLA molecule in Caucasians with HLA-A*0201 representing the most frequent allele; it was also the first human HLA allele for which peptide binding prediction was developed. The Bioinformatics and Molecular Analysis Section of the National Institutes of Health (BIMAS) and the University of Tübingen (Syfpeithi) provide the most popular prediction algorithms of peptide/MHC interaction on the World Wide Web. To test these predictions, HLA-A*0201-binding nine-amino acid peptides were searched by both algorithms in 19 structural CMV proteins. According to Syfpeithi, the top 2% of predicted peptides should contain the naturally presented epitopes in 80% of predictions (www.syfpeithi.de). Because of the high number of predicted peptides, the analysis was limited to 10 randomly chosen proteins. The top 2% of peptides predicted by both algorithms were synthesized corresponding to 261 peptides in total. PBMC from 10 HLA-A*0201-positive and CMV-seropositive healthy blood donors were tested by ex vivo stimulation with all 261 peptides using crossover peptide pools. IFN-γ production in T cells measured by CFC was used as readout. However, only one peptide was found to be stimulating in one single donor. As a result of this work, we report a potential new T cell target protein, one previously unknown CD8-T cell-stimulating peptide, and an extensive list of CMV-derived potentially strong HLA-A*0201-binding peptides that are not recognized by T cells of HLA-A*0201-positive CMV-seropositive donors. We conclude that MHC/peptide binding predictions are helpful for locating epitopes in known target proteins but not necessarily for screening epitopes in proteins not known to be T cell targets.

Mapping of novel peptides of WT-1 and presenting HLA alleles that induce epitope-specific HLA-restricted T cells with cytotoxic activity against WT-1+ leukemias

“…This also held true in other direct comparisons of the immunogenicity of peptides when presented by AAPCs selectively expressing HLA-A0201. Therefore, as has also been shown for viral epitopes, 49 the capacity of a given peptide to elicit a T-cell response is not consistently correlated with its predicted potential to bind its presenting HLA allele.…”

Human Asymptomatic Epitopes Identified from the Herpes Simplex Virus Tegument Protein VP13/14 (UL47) Preferentially Recall Polyfunctional Effector Memory CD44highCD62LlowCD8+TEMCells and Protect Humanized HLA-A*02:01 Transgenic Mice against Ocular Herpesvirus Infection

“…Despite the 84-plus HSV-1 ORFs encoding hundreds of potential epitopes, protective CD8 ϩ T cells target only a few epitopes (48)(49)(50)(51). Tegument proteins are delivered to the cytoplasm of host cells during viral entry, resulting in immediate processing by APCs shortly after infection (9-12).…”

Recognition of HLA Class I–Restricted β-Cell Epitopes in Type 1 Diabetes

“…The discrepancy between the predicted and actual binding affinities of candidate ␤-cell epitopes is likely attributable to the fact that the three-dimensional structure of the peptide-HLA interaction cannot be accurately determined by existing algorithms. Nonetheless, computer-based prediction algorithms are helpful for identifying a pool of candidate epitopes in known target proteins that require confirmation of binding in vitro (23).…”