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

Thomas J Hall,John A Browne,Michael P Mullen,Stephen V Gordon,Douglas Vernimmen,Alan M O'Doherty,David E Machugh

doi:10.3389/fgene.2019.01386

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.

Highlights

Bovine tuberculosis is a chronic infectious disease of livestock, domestic cattle (Bos taurus, Bos indicus and Bos taurus/indicus hybrids), which causes more than $3 billion in losses to global agriculture annually (Steele, 1995; Waters et al, 2012)
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 (Bouttier et al, 2016; Arts et al, 2018)
Differential peaks between conditions were called, compared and visualised with Integrative Genomics Viewer (IGV) to determine where differences in histone H3 lysine tri-methylation (H3K4me3), H3K27me3 and Pol RNA Polymerase II (II) occupancy occur between control and infected bovine alveolar macrophages (bAM) (Figure 1)

Summary

Introduction

Bovine tuberculosis (bTB) is a chronic infectious disease of livestock, domestic cattle (Bos taurus, Bos indicus and Bos taurus/indicus hybrids), which causes more than $3 billion in losses to global agriculture annually (Steele, 1995; Waters et al, 2012). Disease-causing mycobacteria, can persist and replicate within alveolar macrophages via a bewildering range of evolved mechanisms that subvert and interfere with host immune responses (de Chastellier, 2009; Cambier et al, 2014; Schorey and Schlesinger, 2016; Awuh and Flo, 2017) These mechanisms include recruitment of cell surface receptors on the host macrophage; blocking of macrophage phagosome–lysosome fusion; detoxification of reactive oxygen and nitrogen intermediates (ROI and RNI); harnessing of intracellular nutrient supply and metabolism; inhibition of apoptosis and autophagy; suppression of antigen presentation; modulation of macrophage signalling pathways; cytosolic escape from the phagosome; and induction of necrosis, which leads to immunopathology and shedding of the pathogen from the host (Ehrt and Schnappinger, 2009; Hussain Bhat and Mukhopadhyay, 2015; Queval et al, 2017; BoseDasgupta and Pieters, 2018; Chaurasiya, 2018; Stutz et al, 2018)

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