Unknown,Transcriptomics,Genomics,Proteomics

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MiRNA-seq analysis of 15 year old bovine serum miRNAs in the presence of Mycobacterium avium paratuberculosis infection.

ABSTRACT: Mycobacterium avium subspecies paratuberculosis (MAP) is capable of causing a chronic enteritis known as Johne's disease (JD) in ruminants, notably resulting in substantial economic losses within the dairy industry. Prognostic and diagnostic assays that are both sensitive and specific are required to limit the spread of infection. Circulating microRNAs (miRNAs) have shown potential as biomarkers for various pathologies. We had access to a MAP infection model that consisted of serum samples from unchallenged, silent and subclinical phases in cattle collected across a four year period. Hence, the first aim of this study was to determine whether small RNAs could be sequenced from one ml volumes of serum using this model. We sought to identify potential prognostic miRNA biomarkers of MAP infection. We also had the opportunity to confirm the stability and longevity of circulating miRNAs as the serum samples that had been stored at -20degree C for approximately 10-15 years.

INSTRUMENT(S): Agilent 2100 Bioanalyzer, Illumina HiSeq 2500

ORGANISM(S): Bos taurus

SUBMITTER: Damien Farrell

PROVIDER: E-MTAB-3355 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Mycobacterium avium ssp. paratuberculosis (MAP) is the causative agent of Johne’s disease (JD), which is also known as paratuberculosis, in ruminants. The mechanisms of JD pathogenesis are still unclear, but it is known that MAP subverts the host immune system for years by using macrophages as its primary reservoir. The effect of MAP infection on macrophages is often studied in healthy or experimentally infected cows, but reports on primary macrophages from naturally infected cows are lacking. In our study, the transcriptome of primary monocyte-derived macrophages challenged with live MAP was analyzed using next-generation sequencing (RNA‑seq). The gene expression signatures of macrophages from cows diagnosed as negative or positive for JD [JD(–) or JD(+), respectively] revealed differential host–pathogen interplay, highlighting long-term mechanisms established during mycobacterial disease. In JD(–) cows, a considerable number of genes (1,436) were differentially expressed at 8 h post-infection (hpi). Interestingly, while expected inflammatory immune response pathways were among the significant pathways, others related to Hepatic fibrosis/hepatic stellate cell activation, lipid homeostasis, such as the LXR/RXR [liver X receptor/retinoid X receptor] activation, and autoimmune diseases such as atherosclerosis and rheumatoid arthritis were consistently among the top significant pathways. Unexpectedly, the macrophages from JD(+) cows did not present a clear response pattern to ex vivo MAP infection, neither during the early period nor at 24 hpi. Analyzing of the transcriptomic profile of the uninfected macrophages, revealed 868 genes that were differentially expressed in JD(+) versus JD(–) cows. The down-regulated genes particularly modified the general cell metabolism by down-regulating amino acid synthesis, cholesterol biosynthesis, and other energy production pathways while introducing a pro-fibrotic pattern associated with foam cells. These modifications show the apparent importance of the metabolic pathways hijacked by MAP to subvert the immune cells. Our findings support the hypothesis that MAP could induce a tolerant-like state in circulating peripheral blood monocytes when they are differentiating into macrophages, which could further promote the persistence. Similar to other mycobacteria and pathogen-associated molecular patterns, MAP could influence macrophage behavior in the long term. This report contributes to a better understanding of MAP control of immune cells and its mechanisms of survival.

Dataset Information

MiRNA-seq analysis of 15 year old bovine serum miRNAs in the presence of Mycobacterium avium paratuberculosis infection.

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