Global Gene Expression and Systems Biology Analysis of Bovine Monocyte-Derived Macrophages in Response to <em>In Vitro</em> Challenge with <em>Mycobacterium bovis</em>

<div><h3>Background</h3><p><em>Mycobacterium bovis</em>, the causative agent of bovine tuberculosis, is a major cause of mortality in global cattle populations. Macrophages are among the first cell types to encounter <em>M. bovis</em> following exposure and the response elicited by these cells is pivotal in determining the outcome of infection. Here, a functional genomics approach was undertaken to investigate global gene expression profiles in bovine monocyte-derived macrophages (MDM) purified from seven age-matched non-related females, in response to <em>in vitro</em> challenge with <em>M. bovis</em> (multiplicity of infection 2∶1). Total cellular RNA was extracted from non-challenged control and <em>M. bovis</em>-challenged MDM for all animals at intervals of 2 hours, 6 hours and 24 hours post-challenge and prepared for global gene expression analysis using the Affymetrix® GeneChip® Bovine Genome Array.</p> <h3>Results</h3><p>Comparison of <em>M. bovis</em>-challenged MDM gene expression profiles with those from the non-challenged MDM controls at each time point identified 3,064 differentially expressed genes 2 hours post-challenge, with 4,451 and 5,267 differentially expressed genes detected at the 6 hour and 24 hour time points, respectively (adjusted <em>P</em>-value threshold ≤0.05). Notably, the number of downregulated genes exceeded the number of upregulated genes in the <em>M. bovis</em>-challenged MDM across all time points; however, the fold-change in expression for the upregulated genes was markedly higher than that for the downregulated genes. Systems analysis revealed enrichment for genes involved in: (1) the inflammatory response; (2) cell signalling pathways, including Toll-like receptors and intracellular pathogen recognition receptors; and (3) apoptosis.</p> <h3>Conclusions</h3><p>The increased number of downregulated genes is consistent with previous studies showing that <em>M. bovis</em> infection is associated with the repression of host gene expression. The results also support roles for MyD88-independent signalling and intracellular PRRs in mediating the host response to <em>M. bovis</em>.</p>