title: Genome-based in silico identification of new Mycobacterium tuberculosis antigens activating polyfunctional CD8+ T cells in human tuberculosis.
abstract: Although CD8(+) T cells help control Mycobacterium tuberculosis infection, their M. tuberculosis Ag repertoire, in vivo frequency, and functionality in human tuberculosis (TB) remains largely undefined. We have performed genome-based bioinformatics searches to identify new M. tuberculosis epitopes presented by major HLA class I supertypes A2, A3, and B7 (covering 80% of the human population). A total of 432 M. tuberculosis peptides predicted to bind to HLA-A*0201, HLA-A*0301, and HLA-B*0702 (representing the above supertypes) were synthesized and HLA-binding affinities determined. Peptide-specific CD8(+) T cell proliferation assays (CFSE dilution) in 41 M. tuberculosis-responsive donors identified 70 new M. tuberculosis epitopes. Using HLA/peptide tetramers for the 18 most prominently recognized HLA-A*0201-binding M. tuberculosis peptides, recognition by cured TB patients' CD8(+) T cells was validated for all 18 epitopes. Intracellular cytokine staining for IFN-γ, IL-2, and TNF-α revealed mono-, dual-, as well as triple-positive CD8(+) T cells, indicating these M. tuberculosis peptide-specific CD8(+) T cells were (poly)functional. Moreover, these T cells were primed during natural infection, because they were absent from M. tuberculosis-noninfected individuals. Control CMV peptide/HLA-A*0201 tetramers stained CD8(+) T cells in M. tuberculosis-infected and noninfected individuals equally, whereas Ebola peptide/HLA-A*0201 tetramers were negative. In conclusion, the M. tuberculosis-epitope/Ag repertoire for human CD8(+) T cells is much broader than hitherto suspected, and the newly identified M. tuberculosis Ags are recognized by (poly)functional CD8(+) T cells during control of infection. These results impact on TB-vaccine design and biomarker identification.
authors.affiliation: Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark.
authors.forename: Sheila T
authors.initials: ST
authors.lastname: Tang
authors.forename: Krista E
authors.initials: KE
authors.lastname: van Meijgaarden
authors.forename: Nadia
authors.initials: N
authors.lastname: Caccamo
authors.forename: Giuliana
authors.initials: G
authors.lastname: Guggino
authors.forename: Michèl R
authors.initials: MR
authors.lastname: Klein
authors.forename: Pascale
authors.initials: P
authors.lastname: van Weeren
authors.forename: Fatima
authors.initials: F
authors.lastname: Kazi
authors.forename: Anette
authors.initials: A
authors.lastname: Stryhn
authors.forename: Alexander
authors.initials: A
authors.lastname: Zaigler
authors.forename: Ugur
authors.initials: U
authors.lastname: Sahin
authors.forename: Søren
authors.initials: S
authors.lastname: Buus
authors.forename: Francesco
authors.initials: F
authors.lastname: Dieli
authors.forename: Ole
authors.initials: O
authors.lastname: Lund
authors.forename: Tom H M
authors.initials: TH
authors.lastname: Ottenhoff
mesh_terms: D000328:Adult; D000368:Aged; D000942:Antigens, Bacterial / Q000235:genetics* / Q000378:metabolism / Q000502:physiology; D018414:CD8-Positive T-Lymphocytes / Q000276:immunology* / Q000378:metabolism / Q000382:microbiology*; D019295:Computational Biology; D018984:Epitopes, T-Lymphocyte / Q000235:genetics / Q000378:metabolism / Q000502:physiology; D005260:Female; D016680:Genome, Bacterial; D015894:Genome, Human; D006801:Humans; D007424:Intracellular Fluid / Q000276:immunology / Q000378:metabolism / Q000382:microbiology; D008213:Lymphocyte Activation / Q000235:genetics / Q000276:immunology*; D008297:Male; D008875:Middle Aged; D009169:Mycobacterium tuberculosis / Q000235:genetics / Q000276:immunology*; D011237:Predictive Value of Tests; D014376:Tuberculosis / Q000235:genetics / Q000276:immunology* / Q000378:metabolism*
chemical_list: D000942:Antigens, Bacterial; D018984:Epitopes, T-Lymphocyte