Bos taurus
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ABSTRACT:
PROVIDER: PRJNA253809 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Purpose: The goal of this RNA-seq study was to profile changes in miRNA expression in bovine alveolar macrophages isolated from Holstein-Friesian and challenged with M. bovis over a 48 hour time course. Background: Mycobacterium bovis, the causative agent of bovine tuberculosis, is a major infectious disease problem for global agriculture, resulting in losses of billions of Euros annually. The bacterium spreads via an airborne route and is taken up by alveolar macrophages in the lung. MicroRNAs (miRNAs) — short non-coding RNAs that post-transcriptionally regulate gene expression — are increasingly being recognised as key regulators of the immune system. There is mounting evidence for the role of miRNAs in regulating the early innate immune response to mycobacterial infections; however, the underlying processes are not fully understood yet. Results: In total, 2.5 billion raw sequencing reads were generated. 93% of post-filtered reads aligned to known miRNAs. The expression of miRNAs varied over a wide range: miR-21 was expressed at approximately 430,000 reads per million (RPM), but the majority were more lowly expressed (1000-10,000 RPM). One, six, and 40 miRNAs were identified as significantly differentially expressed at 2, 24 and 48 h post-infection (hpi), respectively (FDR < 0.05); the differential expression at 48 hpi of three (out of four) of these miRNAs was confirmed by RT-qPCR. No miRNAs were detected to be differentially expressed 6 hpi. Many of the differentially expressed miRNAs have been shown to have a role in the host response to mycobacterial pathogens and other infections in other species. MicroRNA-155, for example, which we observed to be upregulated in response to M. bovis has recently been shown to control autophagy in murine macrophages infected with the human pathogen Mycobacterium tuberculosis. Pathway analysis suggests that upregulated miRNAs target endocytosis and lysosome trafficking, thus potentially enhancing bacterial survival. An independent gene silencing experiment with a bovine macrophage cell line (Bomac) has confirmed downregulation of IRAK1 by miR-146a and miR-146b. Moreover, downregulation of another predicted target, TGFRB2, by miR-146a was also confirmed. These findings support the target prediction and pathway analysis results. Our results suggest that several miRNAs have an important role in the alveolar macrophage response to pathogenic mycobacteria.
2014-11-13 | GSE58883 | GEO
Project description:Mycobacterium bovis, the agent of bovine tuberculosis, causes an estimated $3 billion annual losses to global agriculture due, in part, to the limitations of current diagnostics. Development of next-generation diagnostics requires a greater understanding of the interaction between the pathogen and the bovine host. Therefore, to explore the early response of the alveolar macrophage to infection, we report the first application of RNA-sequencing to define, in exquisite detail, the transcriptomes of M. bovis-infected and non-infected alveolar macrophages from ten calves at 2, 6, 24 and 48 hours post-infection. Differentially expressed sense genes were detected at these time points that revealed enrichment of innate immune signalling functions, and transcriptional suppression of host defence mechanisms (e.g., lysosome maturation). We also detected differentially expressed natural antisense transcripts, which may play a role in subverting innate immune mechanisms following infection. Furthermore, we report differential expression of novel bovine genes, some of which have immune-related functions based on orthology with human proteins. This is the first in-depth transcriptomics investigation of the alveolar macrophage response to the early stages of M. bovis infection and reveals complex patterns of gene expression and regulation that underlie the immunomodulatory mechanisms used by M. bovis to evade host defence mechanisms.
2015-10-10 | GSE62506 | GEO
Project description:Mycobacterium bovis (M. bovis) and Mycobacterium avium subspecies paratuberculosis (MAP) are important pathogens of cattle, causing bovine tuberculosis and Johne’s disease respectively. M. bovis and MAP infect residential macrophages in the lung and intestines respectively and subvert the macrophage biology to create a survival niche. To investigate this interaction we simultaneously studied the transcriptional response of bovine monocyte-derived macrophages to infection with two strains of M. bovis (AF2122/97 and G18) and two strains of MAP (C & L1).
2017-09-30 | GSE104211 | GEO
Project description:Bovine tuberculosis, caused by Mycobacterium bovis, is a disease of considerable economic importance yet comparatively little is known about the bovine immune response to the disease. Alveolar macrophages are one of the first cells to encounter mycobacteria following infection. In this experiment we investigated the early transcriptional response of bovine alveolar macrophages following infection with M. bovis. The transcriptional response to heat-killed M. bovis was also investigated to look for genes that are only differentially transcribed in response to the live organism. Five-condition experiment, uninfected, live and heat-killed M. bovis-infected bovine alveolar macrophages from five cattle infected for two and four hours. Comparisons were within animal. Dye swaps were incorporated into the design.
2010-01-30 | E-GEOD-19237 | biostudies-arrayexpress
Project description:Bovine tuberculosis, caused by Mycobacterium bovis, is a disease of considerable economic importance yet comparatively little is known about the bovine immune response to the disease. Alveolar macrophages are one of the first cells to encounter mycobacteria following infection. In this experiment we investigated the early transcriptional response of bovine alveolar macrophages following infection with M. bovis. The transcriptional response to heat-killed M. bovis was also investigated to look for genes that are only differentially transcribed in response to the live organism.
2010-01-31 | GSE19237 | GEO
Project description:Mycobacterium bovis is an intracellular pathogen that causes tuberculosis in cattle. Following infection, the pathogen resides and persists inside host macrophages by subverting host immune responses via a diverse range of mechanisms. Here, a high-density bovine microarray platform was used to examine the bovine monocyte-derived macrophage transcriptome response to M. bovis infection relative to infection with the attenuated vaccine strain, M. bovis Bacille CalmetteM-bM-^@M-^SGuM-CM-)rin. Differentially expressed genes were identified (adjusted P-value M-bM-^IM-$ 0.01) and interaction networks generated across an infection time course of 2, 6 and 24 h. The largest number of biological interactions was observed in the 24 h network, which exhibited small-worldscale-free network properties. The 24 h network featured a small number of key hub and bottleneck gene nodes, including IKBKE, MYC, NFKB1 and EGR1 that differentiated the macrophage response to virulent and attenuated M. bovis strains, possibly via the modulation of host cell death mechanisms. These hub and bottleneck genes represent possible targets for immunomodulation of host macrophages by virulent mycobacterial species that enable their survival within a hostile environment. Affymetrix GeneChipM-BM-. Bovine Genome Arrays were used to examine gene expression from a paired comparison of bovine monocyte-derived macrophages (MDM) after in vitro challenge with Mycobacterium bovis versus M. bovis BCG across a time series of 2 hr, 6 hr and 24 hr post-challenge.
2014-08-01 | E-GEOD-59774 | biostudies-arrayexpress
Project description:Massive reprogramming of the host alveolar macrophage transcriptome occurs during the initial stages of tuberculosis. In bovine tuberculosis, Mcobacterium bovis can persist and replicate within alveolar macrophages through varied mechanisms to subvert or exploit host immune responses ( REF). To determine how these transcriptional changes are regulated we performed ChIPseq analysis of H3K4 and H3K27 methylation, established histone tail markers associated with permissive and repressive chromatin states, respectively. These analyses were carried out in parallel with RNA polymerase II ChIPseq, RNAseq and small non-coding RNAseq. This meta data file refers to the RNA-seq datasets.
2019-07-05 | GSE116732 | GEO
Project description:Massive reprogramming of the host alveolar macrophage transcriptome occurs during the initial stages of tuberculosis. In bovine tuberculosis, Mcobacterium bovis can persist and replicate within alveolar macrophages through varied mechanisms to subvert or exploit host immune responses ( REF). To determine how these transcriptional changes are regulated we performed ChIPseq analysis of H3K4 and H3K27 methylation, established histone tail markers associated with permissive and repressive chromatin states, respectively. These analyses were carried out in parallel with RNA polymerase II ChIPseq, RNAseq and small non-coding RNAseq. This meta data file refers to the miRNA-seq datasets.
2019-07-05 | GSE116733 | GEO
Project description:Massive reprogramming of the host alveolar macrophage transcriptome occurs during the initial stages of tuberculosis. In bovine tuberculosis, Mcobacterium bovis can persist and replicate within alveolar macrophages through varied mechanisms to subvert or exploit host immune responses ( REF). To determine how these transcriptional changes are regulated we performed ChIPseq analysis of H3K4 and H3K27 methylation, established histone tail markers associated with permissive and repressive chromatin states, respectively. These analyses were carried out in parallel with RNA polymerase II ChIPseq, RNAseq and small non-coding RNAseq. This meta data file refers to the ChIP-seq datasets.
2019-07-05 | GSE116731 | GEO
Project description:Mycobacterium bovis is an intracellular pathogen that causes tuberculosis in cattle. Following infection, the pathogen resides and persists inside host macrophages by subverting host immune responses via a diverse range of mechanisms. Here, a high-density bovine microarray platform was used to examine the bovine monocyte-derived macrophage transcriptome response to M. bovis infection relative to infection with the attenuated vaccine strain, M. bovis Bacille Calmette–Guérin. Differentially expressed genes were identified (adjusted P-value ≤ 0.01) and interaction networks generated across an infection time course of 2, 6 and 24 h. The largest number of biological interactions was observed in the 24 h network, which exhibited small-worldscale-free network properties. The 24 h network featured a small number of key hub and bottleneck gene nodes, including IKBKE, MYC, NFKB1 and EGR1 that differentiated the macrophage response to virulent and attenuated M. bovis strains, possibly via the modulation of host cell death mechanisms. These hub and bottleneck genes represent possible targets for immunomodulation of host macrophages by virulent mycobacterial species that enable their survival within a hostile environment.
2014-08-01 | GSE59774 | GEO