title: Integrated computational prediction and experimental validation identifies promiscuous T cell epitopes in the proteome ofMycobacterium bovis.
abstract: The discovery of novel antigens is an essential requirement in devising new diagnostics or vaccines for use in control programmes against human tuberculosis (TB) and bovine tuberculosis (bTB). Identification of potential epitopes recognised by CD4+T cells requires prediction of peptide binding to MHC class-II, an obligatory prerequisite for T cell recognition. To comprehensively prioritise potential MHC-II-binding epitopes fromMycobacterium bovis, the agent of bTB and zoonotic TB in humans, we integrated three binding prediction methods with theM. bovisproteome using a subset of human HLA alleles to approximate the binding of epitope-containing peptides to the bovine MHC class II molecule BoLA-DRB3. Two parallel strategies were then applied to filter the resulting set of binders: identification of the top-scoring binders or clusters of binders. Our approach was tested experimentally by assessing the capacity of predicted promiscuous peptides to drive interferon-γ secretion from T cells ofM. bovisinfected cattle. Thus, 376 20-mer peptides, were synthesised (270 predicted epitopes, 94 random peptides with low predictive scores and 12 positive controls of known epitopes). The results of this validation demonstrated significant enrichment (>24 %) of promiscuously recognised peptides predicted in our selection strategies, compared with randomly selected peptides with low prediction scores. Our strategy offers a general approach to the identification of promiscuous epitopes tailored to target populations where there is limited knowledge of MHC allelic diversity.
authors.affiliation: 1​School of Veterinary Medicine, University College Dublin, Dublin D4, Ireland.
authors.forename: Damien
authors.initials: D
authors.lastname: Farrell
authors.affiliation: 2​Department of Bacteriology, Animal and Plant Health Agency, New Haw, Surrey KT15 3NB, UK.
authors.forename: Gareth
authors.initials: G
authors.lastname: Jones
authors.affiliation: 2​Department of Bacteriology, Animal and Plant Health Agency, New Haw, Surrey KT15 3NB, UK.
authors.forename: Christopher
authors.initials: C
authors.lastname: Pirson
authors.affiliation: 1​School of Veterinary Medicine, University College Dublin, Dublin D4, Ireland.
authors.forename: Kerri
authors.initials: K
authors.lastname: Malone
authors.affiliation: 1​School of Veterinary Medicine, University College Dublin, Dublin D4, Ireland.|3​School of Agriculture and Food Science, University College Dublin, Dublin 4, Ireland.
authors.forename: Kevin
authors.initials: K
authors.lastname: Rue-Albrecht
authors.affiliation: 4​School of Medicine, University College Dublin, Dublin D4, Ireland.
authors.forename: Anthony J
authors.initials: AJ
authors.lastname: Chubb
authors.affiliation: 2​Department of Bacteriology, Animal and Plant Health Agency, New Haw, Surrey KT15 3NB, UK.
authors.forename: Martin
authors.initials: M
authors.lastname: Vordermeier
authors.affiliation: 6​School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland.|5​Conway Institute of Biomolecular and Biomedical Science, University College Dublin, Dublin D4, Ireland.|1​School of Veterinary Medicine, University College Dublin, Dublin D4, Ireland.|4​School of Medicine, University College Dublin, Dublin D4, Ireland.
authors.forename: Stephen V
authors.initials: SV
authors.lastname: Gordon
mesh_terms: D000818:Animals; D002417:Cattle; D019295:Computational Biology; D018984:Epitopes, T-Lymphocyte / Q000235:genetics*; D006801:Humans; D009163:Mycobacterium bovis / Q000235:genetics*; D020543:Proteome / Q000235:genetics*; D015203:Reproducibility of Results; D014376:Tuberculosis / Q000382:microbiology / Q000517:prevention & control; D032581:Tuberculosis Vaccines / Q000276:immunology; D014380:Tuberculosis, Bovine / Q000382:microbiology* / Q000517:prevention & control
chemical_list: D018984:Epitopes, T-Lymphocyte; D020543:Proteome; D032581:Tuberculosis Vaccines
keywords: MHC; Mycobacterium bovis; Tuberculosis; bovine; epitope