title: Bioinformatic and empirical analysis of novel hypoxia-inducible targets of the human antituberculosis T cell response.
abstract: We analyzed whole genome-based transcriptional profiles of Mycobacterium tuberculosis subjected to prolonged hypoxia to guide the discovery of novel potential Ags, by a combined bioinformatic and empirical approach. We analyzed the fold induction of the 100 most highly induced genes at 7 d of hypoxia, as well as transcript abundance, peptide-binding prediction (ProPred) adjusted for population-specific MHC class II allele frequency, and by literature search. Twenty-six candidate genes were selected by this bioinformatic approach and evaluated empirically using IFN-γ and IL-2 ELISPOT using immunodominant Ags (Acr-1, CFP-10, ESAT-6) as references. Twenty-three of twenty-six proteins induced an IFN-γ response in PBMCs of persons with active or latent tuberculosis. Five novel immunodominant proteins-Rv1957, Rv1954c, Rv1955, Rv2022c, and Rv1471-were identified that induced responses similar to CFP-10 and ESAT-6 in both magnitude and frequency. IL-2 responses were of lower magnitude than were those of IFN-γ. Only moderate evidence of infection stage-specific recognition of Ags was observed. Reconciliation of bioinformatic and empirical hierarchies of immunodominance revealed that Ags could be predicted, providing transcriptomic data were combined with peptide-binding prediction adjusted by population-specific MHC class II allele frequency.
authors.affiliation: Clinical Infectious Diseases Research Initiative, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
authors.forename: Hannah P
authors.initials: HP
authors.lastname: Gideon
authors.forename: Katalin A
authors.initials: KA
authors.lastname: Wilkinson
authors.forename: Tige R
authors.initials: TR
authors.lastname: Rustad
authors.forename: Tolu
authors.initials: T
authors.lastname: Oni
authors.forename: Heinner
authors.initials: H
authors.lastname: Guio
authors.forename: David R
authors.initials: DR
authors.lastname: Sherman
authors.forename: H Martin
authors.initials: HM
authors.lastname: Vordermeier
authors.forename: Brian D
authors.initials: BD
authors.lastname: Robertson
authors.forename: Douglas B
authors.initials: DB
authors.lastname: Young
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Wilkinson
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D019295:Computational Biology / Q000379:methods*; D018390:Gene Targeting; D016680:Genome, Bacterial / Q000235:genetics / Q000276:immunology; D006801:Humans; D000860:Hypoxia / Q000235:genetics* / Q000276:immunology* / Q000382:microbiology; D008875:Middle Aged; D009169:Mycobacterium tuberculosis / Q000235:genetics* / Q000254:growth & development / Q000276:immunology*; D011237:Predictive Value of Tests; D016176:T-Lymphocyte Subsets / Q000276:immunology* / Q000378:metabolism / Q000382:microbiology*; D014397:Tuberculosis, Pulmonary / Q000276:immunology / Q000382:microbiology / Q000517:prevention & control*; D055815:Young Adult