Comparative 'omics analyses differentiate Mycobacterium tuberculosis and Mycobacterium bovis and reveal distinct macrophage responses to infection with the human and bovine tubercle bacilli

Abstract

Members of the Mycobacterium tuberculosis complex (MTBC) are the causative agents of tuberculosis in a range of mammals, including humans. A key feature of MTBC pathogens is their high degree of genetic identity yet distinct host tropism. Notably, while Mycobacterium bovis is highly virulent and pathogenic for cattle, the human pathogen M. tuberculosis is attenuated in cattle. Previous research also suggests that host preference amongst MTBC members has a basis in host innate immune responses. To explore MTBC host tropism, we present in-depth profiling of the MTBC reference strains M. bovis AF2122/97 and M. tuberculosis H37Rv at both the global transcriptional and the translational level via RNA-sequencing and SWATH MS. Furthermore, a bovine alveolar macrophage infection time course model was used to investigate the shared and divergent host transcriptomic response to infection with M. tuberculosis H37Rv or M. bovis AF2122/97. Significant differential expression of virulence-associated pathways between the two bacilli was revealed, including the ESX-1 secretion system. A divergent transcriptional response was observed between M. tuberculosis H37Rv and M. bovis AF2122/97 infection of bovine alveolar macrophages, in particular cytosolic DNA-sensing pathways at 48 h post-infection, and highlights a distinct engagement of M. bovis with the bovine innate immune system. The work presented here therefore provides a basis for the identification of host innate immune mechanisms subverted by virulent host-adapted mycobacteria to promote their survival during the early stages of infection.

Alveolar macrophage chromatin is modified to orchestrate host response toMycobacterium bovisinfection

“…Previous studies have shown that bAM undergo extensive gene expression reprogramming following infection of M. bovis (Nalpas et al, 2015), with approximately one third of the genome significantly differentially expressed within bovine macrophages 24 hours after infection (Malone et al, 2018). Changes of this magnitude are comparable to those observed in previous experiments that have examined the chromatin remodelling that accompanies mycobacterial infection of macrophages, where trimethylation of lysine 4 of Histone H3 (H3K4me3) was shown to correlate with active transcription (Arts et al, 2018; Bouttier et al, 2016).…”

“…We demonstrate that chromatin is remodelled through differential H3K4me3 and that PolII occupancy is altered at key immune genes in M. bovis -infected bAM. This chromatin remodelling correlates with changes in the expression of genes that are pivotal for the innate immune response to mycobacteria (Alcaraz-Lopez et al, 2017; Malone et al, 2018; Nalpas et al, 2015). Our work supports the hypothesis that chromatin modifications of the host macrophage genome play an essential role during intracellular infections by mycobacterial pathogens (Cheng et al, 2014; LaMere et al, 2016).…”

“…Considering the dramatic perturbation of the vertebrate macrophage by intracellular mycobacteria, we and others have demonstrated that bovine and human alveolar macrophage transcriptomes are extensively reprogrammed in response to infection with M. bovis and M. tuberculosis (Jensen et al, 2018; Lavalett et al, 2017; Malone et al, 2018; Nalpas et al, 2015; Papp et al, 2018; Vegh et al, 2015). These studies have also revealed that differentially expressed gene sets and dysregulated cellular networks and pathways are functionally associated with many of the macrophage processes described above that can control or eliminate intracellular microbes.…”

The bovine alveolar macrophage DNA methylome is resilient to infection with Mycobacterium bovis

“…Finally, it has been proposed that, during chronic Helicobacter pylori infection 96 in humans, functional H. pylori DNA methyltransferases enter host epithelial cells and methylate 97 their recognition sequences in chromosomal DNA, potentially contributing to the pathogenesis of 98 gastric adenocarcinoma or lymphoma of the mucosa-associated lymphoid tissue 20 . 99 Our group has previously revealed the impact of M. bovis infection on the mammalian 100 alveolar macrophage gene expression, demonstrating that the bAM transcriptome is substantially 101 reprogrammed as a consequence of both host-driven defence responses and mycobacterial-102 6induced perturbation and manipulation of cellular processes [21][22][23][24] . However, the effect of M. bovis 103 on the bovine host epigenome, specifically the DNA methylome of bAM, remains unexplored.…”

“…induced perturbation and manipulation of cellular processes [21][22][23][24] . However, the effect of M. bovis 103 on the bovine host epigenome, specifically the DNA methylome of bAM, remains unexplored.…”