Mycobacterium tuberculosis Exploits a Molecular Off Switch of the Immune System for Intracellular Survival

Mycobacterium tuberculosis (M. tuberculosis) survives and multiplies inside human macrophages by subversion of immune mechanisms. Although these immune evasion strategies are well characterised functionally, the underlying molecular mechanisms are poorly understood. Here we show that during infection of human whole blood with M. tuberculosis, host gene transcriptional suppression, rather than activation, is the predominant response. Spatial, temporal and functional characterisation of repressed genes revealed their involvement in pathogen sensing and phagocytosis, degradation within the phagolysosome and antigen processing and presentation. To identify mechanisms underlying suppression of multiple immune genes we undertook epigenetic analyses. We identified significantly differentially expressed microRNAs with known targets in suppressed genes. In addition, after searching regions upstream of the start of transcription of suppressed genes for common sequence motifs, we discovered novel enriched composite sequence patterns, which corresponded to Alu repeat elements, transposable elements known to have wide ranging influences on gene expression. Our findings suggest that to survive within infected cells, mycobacteria exploit a complex immune “molecular off switch” controlled by both miRNAs and Alu regulatory elements. 2 cohorts of blood samples infected with Mycobacterium tuberculosis and the same with Mycobacterium bovis BCG - Discovery and Validation. Experimental (discovery: n=4 donors; validation: n=6 donors for Mycobacterium tuberculosis), discovery set n=4; validation set n=5 for M. bovis BCG infection experiments). Replicates for each sample were not included but multiple timepoints for RNA extraction from each experimental donor were inlcuded. Timepoints for gene expression analysis included (Discovery set 0, 6, 24, 48, 72, 96 h; Validation set 0, 24, 48, 72, 96 h). Uninfected whole blood samples served as matched controls at each time point.