The three stages of tuberculosis.

<p><b>Stage 1</b>: Infection of <i>Mycobacterium tuberculosis</i> (<i>Mtb</i>) frequently occurs at a young age. Metabolically active <i>Mtb</i> are inhaled and subsequently T-cells are stimulated which carry the major burden of acquired immunity. These include major histocompatability complex class II (MHC II)-restricted CD4 T-cells and MHC I-restricted CD8 T-cells. B cells are also activated but their protective role in TB remains elusive. Pre-exposure vaccines are given at this early stage. Novel pre-exposure vaccine candidates are given very soon after birth and thus generally before infection with <i>Mtb</i>. They either substitute for Bacille Calmette Guérin (BCG) or boost immunity induced by BCG. <b>Stage 2</b>: Acquired immunity comprising CD4 and CD8 T-cells contains <i>Mtb</i> in a dormant stage within solid granulomas. T-cells produce type I cytokines and cytolytic effector molecules. They become memory T-cells which concomitantly produce multiple cytokines. Individuals remain latently infected without clinical signs of active tuberculosis (TB). Post-exposure vaccines are given to adolescents or adults who are latently infected but healthy. <b>Stage 3</b>: Mechanisms leading to deficient immunity and disease reactivation are numerous and include production of suppressive cytokines such as interleukin (IL)-10 and transforming growth factor-beta (TGFβ) by T helper 2 (Th2) cells and regulatory T(reg) cells as well as T-cell exhaustion mediated by inhibitory receptor-coreceptor interactions on antigen presenting cells (APCs) and T-cells. <i>Mtb</i> becomes metabolically active and granulomas become caseous. <i>Mtb</i> can be spread to other organs and to other individuals. Therapeutic vaccines are given to TB patients in adjunct to chemotherapy.</p

Most advanced TB vaccine candidates in clinical trials.

<p>Most advanced TB vaccine candidates in clinical trials.</p

Genes identified by more than 1 independent study.

<p>Genes identified by more than 1 independent global genome-wide gene expression analysis. Manuscript numbers refer to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0073230#pone-0073230-t002" target="_blank">Table 2</a>. Classification into modules, functional groups according to Ingenuity and GSEA was performed according to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0073230#pone-0073230-t003" target="_blank">Tables 3</a> & <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0073230#pone-0073230-t004" target="_blank">4</a> and identical to Genes identified by more than 1 independent global genome-wide gene expression analysis. Manuscript numbers refer to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0073230#pone-0073230-t002" target="_blank">Table 2</a>. Classification into modules, functional groups according to Ingenuity and GSEA was performed according to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0073230#pone-0073230-t003" target="_blank">Tables 3</a> & <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0073230#pone-0073230-t004" target="_blank">4</a> and identical to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0073230#pone.0073230.s001" target="_blank">Table S1</a>.</p

Functional classification of individual genes identified by gene expression analysis on TB patients.

<p>Categories have been based on combined output from Ingenuity and GSEA software modules and may include multiple canonical pathways or cell processes. Myeloid cells includes the following canonical pathways: role of macrophages, fibroblasts and endothelial cells in rheumatoid arthritis; Fcg Receptor mediated phagocytosis in macrophages and monocytes; role of pattern recognition receptors in recognition of bacteria and viruses; IL12 signaling and production in macrophages; Dendritic cell maturation; production of Nitrox Oxide and Reactive Oxygen Species in Macrophages; Toll like receptor signaling. T cells includes: T cell receptor signaling; CD28 signaling in T helper cells; iCOS-iCOSL signaling in T helper cells. B cells includes: B cell receptor signaling; PI3K signaling in B lymphocytes. Interferon related pathways include: Interferon signaling, role of jak1, jak2 and tyk2 in interferon signaling, role of PKR in interferon induction and antiviral response. Inflammation includes: IL-8 signaling; NF-kB signaling; altered T cell and B cell signaling in Rheumatoid Arthritis; systemic lupus erythematosus signaling; chemokine signaling; IL-6 signaling. TREM1 includes specifically TREM1 signaling and mitochondrial dysfunction also only contains mitochondrial dysfunction. Finally, hematopoiesis includes: erythropoietin signaling; IL-3 signaling; FLT3 signaling in hematopoietic progenitor cells; prolactin signaling; HGF signaling.</p

Results from GSEA.

<p>Gene sets with an FDR <5% were included in this analysis. SIZE indicates the number of genes in both the gene set and the expression dataset. NES the primary result of the gene set enrichment analysis is the enrichment score (ES), which reflects the degree to which a gene set is overrepresented in a list of genes. Normalizing the enrichment score (NES) accounts for differences in gene set size and in correlations between gene sets and the expression dataset.</p

Ingenuity pathway analysis of all genes identified by unbiased methods related to TB disease.

<p>All 409 biomarkers were analysed by integrated pathway analysis using Ingenuity and the most dominant network is depicted here. Signalling pathways were coloured according to functional classification into myeloid cells, T cells and B cells and type I interferon related genes.</p

TREM1 canonical pathway.

<p>Genes involved in TREM1 signaling canonical pathway according to Ingenuity Integrated Pathway analysis. Genes identified in our 409 gene total geneset are indicated in the right column. * TLR genes include TLR2,4,5,6,7,8 and were identified by multiple studies, all genes identified count in overlap with pathway count according to Ingenuity</p

Information on studies included.

<p>Information on studies included.</p

Schematic representation of events during active TB Disease.

<p>Pathway and process based analysis suggests that these processes are key players in TB disease pathogenesis.</p

Factors that may affect TB Biomarkers.

<p>Factors that may affect TB Biomarkers.</p