title: Analyzing Mycobacterium tuberculosis proteomes for candidate vaccine epitopes.
abstract: Secreted antigens of Mycobacterium tuberculosis (Mtb) induce strong T cell responses and interferon-gamma (IFN-gamma) secretion, both of which are integral in the defense against Mtb. We used web-based tools (SignaIP and Prosite) to identify putative secreted proteins from Mtb genomes CDC 1551 and H37Rv. We then used EpiMatrix, a proprietary pattern-matching algorithm, to do a preliminary analysis of these proteins for regions that contained a high number of class II MHC binding motif matches. The use of bioinformatics tools reduced the number of potential epitopes to be screened to 5% of the 1.3 million overlapping peptides. Peripheral blood mononuclear cells (PBMC) were obtained from healthy, asymptomatic tuberculin skin test-positive donors. Of the 17 highest-ranking peptide candidates that could be synthesized for this preliminary in vitro evaluation, 15 (88%) stimulated IFN-gamma response, and eight (47%) stimulated lymphocyte proliferation in vitro. IFN-gamma ELISpot assays were therefore a more sensitive test for T cell response to these peptides than were proliferation assays. One highly promiscuous epitope (MT2281-26-J, WRRRPLSSALLSFGLLLGGLPL) induced IFN-gamma secretion in PBMC from 11 of 25 Mtb immune subjects (44%). Overall, 15 epitopes, and MT2281-26-J in particular, are candidates for inclusion in a multi-epitope TB vaccine. These findings support the systematic application of bioinformatics tools to whole genomes when used in combination with in vitro methods for screening and confirming epitopes.
authors.affiliation: TB/HIV Research Laboratory, Brown University, Providence, RI 02912, USA.
authors.forename: J
authors.initials: J
authors.lastname: McMurry
authors.forename: H
authors.initials: H
authors.lastname: Sbai
authors.forename: M L
authors.initials: ML
authors.lastname: Gennaro
authors.forename: E J
authors.initials: EJ
authors.lastname: Carter
authors.forename: W
authors.initials: W
authors.lastname: Martin
authors.forename: A S
authors.initials: AS
authors.lastname: De Groot
mesh_terms: D000595:Amino Acid Sequence; D000942:Antigens, Bacterial / Q000276:immunology; D001426:Bacterial Proteins / Q000032:analysis / Q000276:immunology*; D019295:Computational Biology; D004797:Enzyme-Linked Immunosorbent Assay / Q000379:methods; D000939:Epitopes / Q000276:immunology*; D016680:Genome, Bacterial; D006801:Humans; D007371:Interferon-gamma / Q000276:immunology; D007963:Leukocytes, Mononuclear / Q000276:immunology; D008213:Lymphocyte Activation / Q000276:immunology; D009169:Mycobacterium tuberculosis / Q000276:immunology*; D010455:Peptides / Q000276:immunology; D020543:Proteome / Q000032:analysis / Q000276:immunology*; D013601:T-Lymphocytes / Q000276:immunology; D014376:Tuberculosis / Q000276:immunology; D032581:Tuberculosis Vaccines / Q000276:immunology*
chemical_list: D000942:Antigens, Bacterial; D001426:Bacterial Proteins; D000939:Epitopes; D010455:Peptides; D020543:Proteome; D032581:Tuberculosis Vaccines; D007371:Interferon-gamma