Whole Genome Methylation Analysis Reveals Role of DNA Methylation in Cow's Ileal and Ileal Lymph Node Responses to Mycobacterium avium subsp. paratuberculosis Infection.

Eveline M Ibeagha-Awemu,Mengqi Wang,Nathalie Bissonnette,Xin Zhao,Suraj Bhattarai,Pier-Luc Dudemaine,Stephanie Mckay

doi:10.3389/fgene.2021.797490

Eveline M Ibeagha-Awemu, Mengqi Wang + Show 5 more

Open Access

https://doi.org/10.3389/fgene.2021.797490

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Abstract

Johne’s Disease (JD), caused by Mycobacterium avium subsp paratuberculosis (MAP), is an incurable disease of ruminants and other animal species and is characterized by an imbalance of gut immunity. The role of MAP infection on the epigenetic modeling of gut immunity during the progression of JD is still unknown. This study investigated the DNA methylation patterns in ileal (IL) and ileal lymph node (ILLN) tissues from cows diagnosed with persistent subclinical MAP infection over a one to 4 years period. DNA samples from IL and ILLN tissues from cows negative (MAPneg) (n = 3) or positive for MAP infection (MAPinf) (n = 4) were subjected to whole genome bisulfite sequencing. A total of 11,263 and 62,459 differentially methylated cytosines (DMCs), and 1259 and 8086 differentially methylated regions (DMRs) (FDR<0.1) were found between MAPinf and MAPneg IL and ILLN tissues, respectively. The DMRs were found on 394 genes (denoted DMR genes) in the IL and on 1305 genes in the ILLN. DMR genes with hypermethylated promoters/5′UTR [3 (IL) and 88 (ILLN)] or hypomethylated promoters/5′UTR [10 (IL) and 25 (ILLN)] and having multiple functions including response to stimulus/immune response (BLK, BTC, CCL21, AVPR1A, CHRNG, GABRA4, TDGF1), cellular processes (H2AC20, TEX101, GLA, NCKAP5L, RBM27, SLC18A1, H2AC20BARHL2, NLGN3, SUV39H1, GABRA4, PPA1, UBE2D2) and metabolic processes (GSTO2, H2AC20, SUV39H1, PPA1, UBE2D2) are potential DNA methylation candidate genes of MAP infection. The ILLN DMR genes were enriched for more biological process (BP) gene ontology (GO) terms (n = 374), most of which were related to cellular processes (27.6%), biological regulation (16.6%), metabolic processes (15.4%) and response to stimulus/immune response (8.2%) compared to 75 BP GO terms (related to cellular processes, metabolic processes and transport, and system development) enriched for IL DMR genes. ILLN DMR genes were enriched for more pathways (n = 47) including 13 disease pathways compared with 36 enriched pathways, including 7 disease/immune pathways for IL DMR genes. In conclusion, the results show tissue specific responses to MAP infection with more epigenetic changes (DMCs and DMRs) in the ILLN than in the IL tissue, suggesting that the ILLN and immune processes were more responsive to regulation by methylation of DNA relative to IL tissue. Our data is the first to demonstrate a potential role for DNA methylation in the pathogenesis of MAP infection in dairy cattle.

Highlights

Infection with Mycobacterium avium subsp. paratuberculosis (MAP), the causative agent of Johne’s disease (JD) of bovine and other ruminants, is one of the major threats to cattle health and the economic profitability of the dairy industry (Whittington et al, 2019)
Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were enriched for ileal lymph node (ILLN) differentially methylated regions (DMRs) genes including immune (e.g., Bacterial invasion of epithelial cells, Transcriptional misregulation in cancer, Cell adhesion molecules (CAMs), Inflammatory mediator regulation of TRP channels and Platelet activation, etc.) and disease (e.g., Cushing syndrome, pathways in cancer, Small cell lung cancer, Gastric cancer and Arrhythmogenic right ventricular cardiomyopathy (ARVC), etc.) related pathways (Figure 7; Supplementary Table S7D)
Results of functional analysis of IL and ILLN DMR genes further portrayed the potent effect of MAP on DNA methylation in the ILLN tissue as compared to IL tissue, whereby more Gene ontology (GO) terms and KEGG pathways were enriched for ILLN DMR genes as compared to IL DMR genes

Summary

Introduction

Infection with Mycobacterium avium subsp. paratuberculosis (MAP), the causative agent of Johne’s disease (JD) of bovine and other ruminants, is one of the major threats to cattle health and the economic profitability of the dairy industry (Whittington et al, 2019). JD is a long progressive and chronic enteric disease which progresses through three phases upon MAP infection (silent, subclinical, and clinical/advanced stages) and is characterized by imbalance in gut immunity, and MAP’s ability to escape host immune surveillance, and subvert host cell responses to ensure its intracellular survival and replication (Whitlock and Buergelt, 1996; Arsenault et al, 2014; Koets et al, 2015). MAP acquired propensity to infect macrophages helps it to exquisitely adapt and survive in an aggressive host immune response environment. Pathogenic mycobacteria, including the Mycobacterium avium complex pathogens, respond to host immune responses with counterattack strategies, notably to escape the maturation of phagolysosomes of the phagocytotic cells, which function to destroy them (Liu and Modlin, 2008). The effect of JD on animals, the environment and the economy highlights the need for deeper understanding of the host cellular processes that are perturbed or manipulated by MAP, in order to develop robust disease control strategies

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