An Unbiased Genome-Wide Mycobacterium tuberculosis Gene Expression Approach To Discover Antigens Targeted by Human T Cells Expressed during Pulmonary Infection

Abstract

Mycobacterium tuberculosis is responsible for almost 2 million deaths annually. Mycobacterium bovis bacillus Calmette-Guérin, the only vaccine available against tuberculosis (TB), induces highly variable protection against TB, and better TB vaccines are urgently needed. A prerequisite for candidate vaccine Ags is that they are immunogenic and expressed by M. tuberculosis during infection of the primary target organ, that is, the lungs of susceptible individuals. In search of new TB vaccine candidate Ags, we have used a genome-wide, unbiased Ag discovery approach to investigate the in vivo expression of 2170 M. tuberculosis genes during M. tuberculosis infection in the lungs of mice. Four genetically related but distinct mouse strains were studied, representing a spectrum of TB susceptibility controlled by the supersusceptibility to TB 1 locus. We used stringent selection approaches to select in vivo–expressed M. tuberculosis (IVE-TB) genes and analyzed their expression patterns in distinct disease phenotypes such as necrosis and granuloma formation. To study the vaccine potential of these proteins, we analyzed their immunogenicity. Several M. tuberculosis proteins were recognized by immune cells from tuberculin skin test-positive, ESAT6/CFP10-responsive individuals, indicating that these Ags are presented during natural M. tuberculosis infection. Furthermore, TB patients also showed responses toward IVE-TB Ags, albeit lower than tuberculin skin test-positive, ESAT6/CFP10-responsive individuals. Finally, IVE-TB Ags induced strong IFN-γ+/TNF-α+ CD8+ and TNF-α+/IL-2+ CD154+/CD4+ T cell responses in PBMC from long-term latently M. tuberculosis–infected individuals. In conclusion, these IVE-TB Ags are expressed during pulmonary infection in vivo, are immunogenic, induce strong T cell responses in long-term latently M. tuberculosis–infected individuals, and may therefore represent attractive Ags for new TB vaccines.

Novel Vaccination Strategies against Tuberculosis

“…The need to go beyond the most popular antigens in TB vaccine, such as the Ag85 cognates, is also the subject of renewed interest, and recent discovery efforts have provided a number of very promising protective antigens selected to provide target molecules stably expressed also in LTBI (Bertholet et al 2010;Aagaard et al 2011;Knudsen et al 2014), a phase where Ag85-based vaccines may have their limitations because gene expression is shut down (Shi et al 2004;Bold et al 2011;Aagaard et al 2011;Commandeur et al 2013). …”

“…As Mtb adapts to the conditions in the immune host, the current data suggest that the bacteria transform from a growing metabolically active state to nonreplicating persistence with low metabolic activity (Andersen 2007;Barry et al 2009;Gengenbacher and Kaufmann 2012;Reece and Kaufmann 2012). In this process the bacteria change their gene expression profile, which results in a different or modified antigenic repertoire where, for example, the genes encoding the Ag85 family are down-regulated to very low levels (Shi et al 2004;Bold et al 2011;Aagaard et al 2011;Commandeur et al 2013). The changed antigen repertoire has been confirmed in human studies showing that the antigens preferentially recognized by the immune system in latently infected healthy individuals differed from patients with active TB disease (Demissie et al 2006;Leyten et al 2006;Schuck et al 2009).…”

Antigens for CD4 and CD8 T Cells in Tuberculosis

“…Several investigations have tried to identify immunodominant antigens through genomics and proteomics (Covert et al 2001;Malen et al 2008;Deenadayalan et al 2010), comparative genomics (Cockle et al 2002), or bioinformatics (Zvi et al 2008), none of which covered the entire genome. The majority of the MTB genome was covered in an investigation for in vivo expression of MTB genes during MTB infection in the lungs of mice (Commandeur et al 2013). Identified antigens were confirmed in humans with TB disease and may Lindestam Arlehamn et al represent antigen candidates for vaccine development.…”

Resuscitation-promoting factors are important determinants of the pathophysiology inMycobacterium tuberculosisinfection

“…As Rpf are secreted or cell wall attached proteins, they are potential targets for the host immune system (Commandeur et al, 2013;Kana & Mizrahi, 2010;Yeremeev et al, 2003). As previously mentioned, Rpf are key virulence factors for Mtb (Kana et al, 2008), thus responses directed to Rpf may be protective.…”