Innovative Strategies to Identify M. tuberculosis Antigens and Epitopes Using Genome-Wide Analyses

Annemieke Geluk, Krista E. van Meijgaarden, Simone A. Joosten, Susanna Commandeur, Tom H. M. Ottenhoff

In view of the fact that only a small part of the Mtb expressome has been explored for identification of antigens capable of activating human T-cell responses, which is critically required for the design of better TB vaccination strategies, more emphasis should be placed on innovative ways to discover new Mtb antigens and explore their function at the several stages of infection. Better protective antigens for TB-vaccines are urgently needed, also in view of the disappointing results of the MVA85 vaccine, which failed to induce additional protection in BCG-vaccinated infants (1). Moreover, immune responses to relevant antigens may be useful to identify TB-specific biomarker signatures. Here, we describe the potency of novel tools and strategies to reveal such Mtb antigens. Using proteins specific for different Mtb infection phases, many new antigens of the latency-associated Mtb DosR-regulon as well as resuscitation promoting factor proteins, associated with resuscitating TB, were discovered that were recognized by CD4(+) and CD8(+) T-cells. Furthermore, by employing MHC binding algorithms and bioinformatics combined with high-throughput human T-cell screens and tetramers, HLA-class Ia restricted polyfunctional CD8(+) T-cells were identified in TB patients. Comparable methods, led to the identification of HLA-E-restricted Mtb epitopes recognized by CD8(+) T-cells. A genome-wide unbiased antigen discovery approach was applied to analyze the in vivo Mtb gene expression profiles in the lungs of mice, resulting in the identification of IVE-TB antigens, which are expressed during infection in the lung, the main target organ of Mtb. IVE-TB antigens induce strong T-cell responses in long-term latently Mtb infected individuals, and represent an interesting new group of TB antigens for vaccination. In summary, new tools have helped expand our view on the Mtb antigenome involved in human cellular immunity and provided new candidates for TB vaccination.