title: Poor correlation between T-cell activation assays and HLA-DR binding prediction algorithms in an immunogenic fragment of Pseudomonas exotoxin A.
abstract: The ability to identify immunogenic determinants that activate T-cells is important for the development of new vaccines, allergy therapy and protein therapeutics. In silico MHC-II binding prediction algorithms are often used for T-cell epitope identification. To understand how well those programs predict immunogenicity, we computed HLA binding to peptides spanning the sequence of PE38, a fragment of an anti-cancer immunotoxin, and compared the predicted and experimentally identified T-cell epitopes. We found that the prediction for individual donors did not correlate well with the experimental data. Furthermore, prediction of T-cell epitopes in an HLA heterogenic population revealed that the two strongest epitopes were predicted at multiple cutoffs but the third epitope was predicted negative at all cutoffs and overall 4/9 epitopes were missed at several cutoffs. We conclude that MHC class-II binding predictions are not sufficient to predict the T-cell epitopes in PE38 and should be supplemented by experimental work.
authors.affiliation: Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA. Electronic address: mazorr@mail.nih.gov.
authors.forename: Ronit
authors.initials: R
authors.lastname: Mazor
authors.affiliation: Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA. Electronic address: TaiC@mail.nih.gov.
authors.forename: Chin-Hsien
authors.initials: CH
authors.lastname: Tai
authors.affiliation: Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA. Electronic address: BKLee@mail.nih.gov.
authors.forename: Byungkook
authors.initials: B
authors.lastname: Lee
authors.affiliation: Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA. Electronic address: pastani@mail.nih.gov.
authors.forename: Ira
authors.initials: I
authors.lastname: Pastan
mesh_terms: D036002:ADP Ribose Transferases / Q000276:immunology*; D000465:Algorithms; D000595:Amino Acid Sequence; D000917:Antibody Formation / Q000276:immunology; D001427:Bacterial Toxins / Q000276:immunology*; D001665:Binding Sites / Q000276:immunology; D018984:Epitopes, T-Lymphocyte / Q000276:immunology*; D005098:Exotoxins / Q000276:immunology*; D006684:HLA-DR Antigens / Q000276:immunology*; D006801:Humans; D008213:Lymphocyte Activation / Q000276:immunology*; D008969:Molecular Sequence Data; D010455:Peptides / Q000276:immunology; D011485:Protein Binding / Q000276:immunology*; D011549:Pseudomonas / Q000276:immunology*; D013601:T-Lymphocytes / Q000276:immunology*; D037521:Virulence Factors / Q000276:immunology*; D000097668:Pseudomonas aeruginosa Exotoxin A
chemical_list: D036002:ADP Ribose Transferases; D001427:Bacterial Toxins; D018984:Epitopes, T-Lymphocyte; D005098:Exotoxins; D006684:HLA-DR Antigens; D010455:Peptides; D037521:Virulence Factors; D000097668:Pseudomonas aeruginosa Exotoxin A
keywords: HLA binding algorithm; HLA binding prediction; Immunogenicity; MHC alleles; T-cell activation; T-cell epitope