Alveolar Macrophage Chromatin Is Modified to Orchestrate Host Response to Mycobacterium bovis Infection

Abstract

Bovine tuberculosis is caused by infection with Mycobacterium bovis, which can also cause disease in a range of other mammals, including humans. Alveolar macrophages are the key immune effector cells that first encounter M. bovis and how the macrophage epigenome responds to mycobacterial pathogens is currently not well understood. Here, we have used chromatin immunoprecipitation sequencing (ChIP-seq), RNA-seq and miRNA-seq to examine the effect of M. bovis infection on the bovine alveolar macrophage (bAM) epigenome. We show that H3K4me3 is more prevalent, at a genome-wide level, in chromatin from M. bovis-infected bAM compared to control non-infected bAM; this was particularly evident at the transcriptional start sites of genes that determine programmed macrophage responses to mycobacterial infection (e.g. M1/M2 macrophage polarisation). This pattern was also supported by the distribution of RNA Polymerase II (Pol II) ChIP-seq results, which highlighted significantly increased transcriptional activity at genes demarcated by permissive chromatin. Identification of these genes enabled integration of high-density genome-wide association study (GWAS) data, which revealed genomic regions associated with resilience to infection with M. bovis in cattle. Through integration of these data, we show that bAM transcriptional reprogramming occurs through differential distribution of H3K4me3 and Pol II at key immune genes. Furthermore, this subset of genes can be used to prioritise genomic variants from a relevant GWAS data set.

Integrative genomics of the mammalian alveolar macrophage response to intracellular mycobacteria

“…In this regard, previous work has shown that macrophage PI3K/AKT signalling is key to a range of cellular processes associated with host-pathogen interaction in MTBC infections, including modulation of cell death pathways, manipulation of signalling downstream of TLRs, and initiation of granuloma formation (Maiti et al 2001;A et al 2012;Cho et al 2013;Liu et al 2016;Brace et al 2017;Yang et al 2018). We have also recently demonstrated that genes encoding protein products embedded in the PI3K/AKT pathway are primary targets for chromatin modifications that substantially alter bAM gene expression in response to M. bovis infection (Hall et al 2020).…”

“…In addition, these studies have been expanded to encompass surveys of the bAM epigenome using methylome sequencing and chromatin immunoprecipitation sequencing (ChIP-seq). This work has demonstrated that the transcriptional reprogramming of bAM caused by M. bovis infection is profoundly shaped by chromatin remodelling at gene loci associated with critical components of host-pathogen interaction (O'Doherty et al 2019;Hall et al 2020).…”

“…Since 2005, substantial efforts have been made to better understand host-pathogen interaction for bTB using transcriptomics technologies such as gene expression microarrays and RNA sequencing (RNA-seq) at the host cellular level-specifically the bovine AM (bAM) and initial innate immune responses to infection by M. bovis (Widdison et al 2008;Widdison et al 2011;Magee et al 2014;Nalpas et al 2015;Vegh et al 2015;Malone et al 2018;Hall et al 2020). These studies have helped to define a "pathogenic signature" (Falkow 2008;Cambier et al 2014) of M. bovis infection in bAM, which reflects the tension between macrophage responses to contain and kill intracellular pathogens and evasion and avoidance mechanisms evolved by these mycobacteria.…”

“…We have recently shown that integration of bAM functional genomics data sets-RNA-seq, microRNA-seq and ChIP-seq-with a GWAS data set for resistance to M. bovis infection can be used to enhance detection of genomic regions associated with reduced incidence of bTB disease (Hall et al 2020). For the present study, we substantially expand this work by leveraging gene-focused network-and pathway-based methods under a statistical framework based on a new software tool, extraction from M. bovis-infected and control non-infected alveolar macrophages, 78 strand-specific RNA-seq libraries were prepared (paired-end 2 × 90 nucleotide reads).…”

Integrative Genomics of the Mammalian Alveolar Macrophage Response to Intracellular Mycobacteria

“…In addition, these studies have been expanded to encompass surveys of the bAM epigenome using methylome sequencing and chromatin immunoprecipitation sequencing (ChIP-seq). This work has demonstrated that the transcriptional reprogramming of bAM caused by M. bovis infection is profoundly shaped by chromatin remodelling at gene loci associated with critical components of host-pathogen interaction [46,48].…”