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New strategies are needed to develop better tools to control TB, including identification of novel antigens for vaccination. Such  Mtb  antigens must be expressed during  Mtb  infection in the major target organ, the lung, and must be capable of eliciting human immune responses. Using genome-wide transcriptomics of  Mtb  infected lungs we developed data sets and methods to identify IVE-TB ( in-vivo  expressed  Mtb ) antigens expressed in the lung. Quantitative expression analysis of 2,068  Mtb  genes from the predicted first operons identified the most upregulated IVE-TB genes during  in-vivo  pulmonary infection. By further analysing high-level conservation among whole-genome sequenced  Mtb -complex strains ( n  = 219) and algorithms predicting HLA-class-Ia and II presented epitopes, we selected the most promising IVE-TB candidate antigens. Several of these were recognized by T-cells from  in-vitro Mtb- PPD and ESAT6/CFP10-positive donors by proliferation and multi-cytokine production. This was validated in an independent cohort of latently  Mtb -infected individuals. Significant T-cell responses were observed in the absence of IFN-γ-production. Collectively, the results underscore the power of our novel antigen discovery approach in identifying  Mtb  antigens, including those that induce unconventional T-cell responses, which may provide important novel tools for TB vaccination and biomarker profiling. Our generic approach is applicable to other infectious diseases.

scientific reports

New Genome-Wide Algorithm Identifies Novel In-Vivo Expressed Mycobacterium Tuberculosis Antigens Inducing Human T-Cell Responses with Classical and Unconventional Cytokine Profiles