Whole blood transcriptomic analysis in BoHV-1 experimentally challenged dairy calves and comparison to a Bovine Respiratory Syncytial Virus (BRSV) challenge
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ABSTRACT:
PROVIDER: PRJNA818417 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18425903_1.fastq.gz | Fastqsanger.gz | |||
| SRR18425903_2.fastq.gz | Fastqsanger.gz | |||
| SRR18425904_1.fastq.gz | Fastqsanger.gz | |||
| SRR18425904_2.fastq.gz | Fastqsanger.gz | |||
| SRR18425905_1.fastq.gz | Fastqsanger.gz |
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Project description:Bovine Herpesvirus 1 (BoHV-1) is a leading cause of Bovine Respiratory Disease (BRD) in young calves, which is responsible for substantial morbidity and mortality. Therefore, the objective of the current study was to elucidate the whole blood mRNA transcriptomic response to an experimental challenge with BoHV-1, in dairy calves. Holstein-Friesian calves were either challenged by intranasal atomisation with BoHV1 virus (6.3 x 10^7/mL x 1.35mL) (n=12) or mock challenged with sterile phosphate buffered saline (n=6). Clinical signs were scored daily until euthanasia at day 6 post-challenge. Total RNA was extracted and sequenced from whole blood (100 bp paired-end). Sequence reads were aligned to the ARS-UCD1.2 bovine reference genome and differential gene expression analysis was performed using EdgeR. An MDS plot displayed an obvious separation between BoHV-1 challenged and control calves based on the gene expression changes in whole blood. There were 488 differentially expressed (DE) genes (p < 0.05, FDR < 0.1, fold change > 2) between the BoHV-1 challenged and control calves.
2022-08-19 | GSE199108 | GEO
Project description:Bovine Respiratory Syncytial Virus (BRSV) is a cause of Bovine Respiratory Disease (BRD). The objective of this study was to elucidate the chromatin regions which were differentially open in the bronchial lymph nodes (BLN) of dairy calves experimentally challenged with BRSV, relative to unchallenged control calves. Holstein-Friesian calves were either challenged with BRSV inoculum (n=12) or mock challenged with PBS (n=6). Calves were euthanised on day 7 post-challenge. ATAC-Seq libraries were prepared from fresh BLN tissues and sequenced (75 bp paired-end). Sequence reads were aligned to the UMD3.1 reference genome and peak calling (q < 0.01) was performed with MACS2, employing the BAMPE model. Using Diffbind, 9,144 and 5,096 differentially accessible peaks were identified between BRSV challenged and control calves (P < 0.05, FDR < 0.05) using DeSeq2 and EdgeR, respectively. There were 169 and 110 genes previously found to be differentially expressed using RNA-Seq located within or up to 2kb upstream of the differentially accessible peaks identified by the DeSeq 2 and EdgeR analyses, respectively. There were 237 differentially accessible peaks positioned within 40 previously identified susceptibility loci for BRD. These open chromatin regions are likely involved in the gene transcriptional and regulatory response to infection by BRSV.
2021-01-13 | GSE148056 | GEO
Project description:Bovine Respiratory Syncytial Virus (BRSV) is a leading cause of Bovine Respiratory Disease (BRD) in young calves, which is responsible for substantial morbidity and mortality. Infection with BRSV induces global gene expression changes in respiratory tissues. If these changes are observed in tissues which are accessible in live animals, such as whole blood, they may be used as biomarkers of the disease. Therefore, the objective of the current study was to elucidate the whole blood transcriptomic response to an experimental challenge with BRSV, in dairy calves. Holstein-Friesian calves were either inoculated with virus (103.5 TCID50/ml x 15 ml) (n=12) or mock challenged with sterile phosphate buffered saline (n=6). Clinical signs were scored daily and whole blood was collected in Tempus RNA tubes immediately prior to euthanasia, at day 7 post-challenge. RNA was extracted from blood and sequenced (150 bp paired-end). Sequence reads were aligned to the UMD3.1 bovine reference genome and differential gene expression analysis was performed using EdgeR. An MDS plot displayed an obvious separation between BRSV challenged and control calves based on whole blood gene expression changes, despite an observed mild clinical manifestation of the disease. There were 281 differentially expressed (DE) genes (p < 0.05, FDR < 0.1, fold change > 2) between the BRSV challenged and control calves. The top enriched KEGG pathways and gene ontology terms were associated with viral infection and included “Influenza A”, “defense response to virus”, “regulation of viral life cycle” and “innate immune response”. Highly DE genes involved in these pathways are may be beneficial for the diagnosis of subclinical BRD from blood samples.
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Project description:Elucidation of the open chromatin regions in the bronchial lymph nodes of dairy calves experimentally challenged with bovine respiratory syncytial virus, using ATAC-Seq
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Project description:Bovine respiratory disease (BRD) is the leading cause of morbidity and mortality in calves over one month of age. In a controlled challenge study in artificially-reared dairy calves, the influence of the host response to bovine respiratory syncytial virus (BRSV) was examined. Holstein-Friesian calves were either inoculated with BRSV (10^5/ml × 15 ml/animal) (n=12) or mock challenged with phosphate buffer saline (10ml/animal) (n=6). Calves were euthanised on day 7 post-challenge. Bronchial lymph nodes were collected; RNA was extracted and sequenced (75bp paired-end). Sequenced reads were adapter trimmed, quality assessed (FastQC) and aligned to the bovine genome (UMD 3.1) using STAR. Differential gene expression analysis was performed using EdgeR, and pathway and gene ontology analyses were carried out using g:Profiler, IPA and DAVID. There was a clear separation between BRSV challenged and control calves based on log2 fold gene expression changes, despite an observed mild clinical manifestation of the disease. There were 934 differentially expressed genes (DEG) (p < 0.05, FDR < 0.1, fold change > 2) between the BRSV challenged and control calves. Over-represented gene ontology terms, pathways and molecular functions, among the DEG, were associated with immune responses and defense responses to a virus.
2019-10-29 | GSE131452 | GEO
Project description:Calves are highly susceptible to gastrointestinal infection with Cryptosporidium parvum (C. parvum), which can result in watery diarrhea and eventually death or impaired development. With little to no effective therapeutics, understanding the host’s microbiota and pathogen interaction at the mucosal immune system has been critical to identify and test novel control strategies. We used an experimental model of C. parvum challenge in neonatal calves to describe the clinical signs and mucosal innate immune and microbiota hallmarks in the ileum and colon during cryptosporidiosis and investigated the impact of supplemental colostrum feeding on C. parvum infection. The C. parvum challenged calves experienced clinical signs including pyrexia and diarrhea 5 days post challenge. These calves showed ulcerative neutrophil ileitis with a proteomic signature driven by inflammatory effectors, including reactive oxygen species and myeloperoxidases. Colitis was also noticed with an aggravated mucin barrier depletion and lack of full filled mucin granule in goblet cells. The C. parvum challenged calves also displayed a pronounced dysbiosis with a high prevalence of Clostridium species (spp.) and number of exotoxins, adherence factors, and secretion systems related to Clostridium spp. and other enteropathogens, including Campylobacter spp., Escherichia sp., Shigella spp., and Listeria spp. Daily supplementation with a high-quality bovine colostrum product mitigated some of the clinical signs and modulated the gut immune response and concomitant microbiota to a pattern more similar to that of healthy unchallenged calves.
2023-04-27 | PXD040269 | Pride
Project description:We report the analysis of nasal curettage cells by RNAseq collected at pre-symptomatic timepoints in healthy adults experimentally challenged with respiratory syncytial virus (RSV). Following inoculation, 57% of participants developed PCR-confirmed infection. Prior to viral challenge, 80 differentially expressed genes were identified that associated with susceptibility to symptomatic infection. At day 3, 87 differentially expressed genes were associated with protection. Thus, we showed that the nasal mucosa at the time of virus exposure and during the incubation phase correlate with susceptibiltiy and protection from respiratory viral infection.
2020-09-01 | GSE155237 | GEO
Project description:Bovine Respiratory Disease (BRD) is responsible for the majority of calf morbidity and mortality. One of the main causes of BRD is initial infection with Bovine Respiratory Syncytial Virus (BRSV). The objective of this study was to elucidate the changes in the host's bronchial lymph node miRNA transcriptome in response to BRSV in a controlled viral challenge. Holstein-Friesian calves were either inoculated with BRSV (103.5 TCID50/ml x 15 ml) (n=12) or mock challenged with phosphate buffered saline (n=6). Clinical signs were scored daily until euthanasia at day 7 post-challenge. Total RNA was extracted and sequenced (75 bp) from bronchial lymph nodes. Sequences were filtered for contaminant short RNA species, and subsequently read counts for known miRNAS were generated using the miRDeep2 package with the UMD 3.1 version of the genome and the bovine mature miRNA sequences from the miRBase database (release 22). EdgeR was used for differential expression analysis and Targetscan was used to identify target genes for the differentially expressed (DE) miRNAs. Pathway and gene ontology analyses on target genes were carried out using Ingenuity Pathway analysis (Qiagen). There was a clear separation between BRSV challenged and control calves based on miRNA gene expression changes, despite an observed mild clinical manifestation of the disease. There were 119 DE miRNAs (p<0.05, FDR<0.1, fold change>1.5) between the BRSV challenged and control calves. The DE miRNAs were predicted to target 465 genes which were previously found to be DE in bronchial lymph node tissue, between these BRSV challenged and control calves. Out of the DE predicted target genes, 455 genes had inverse fold changes to that of the DE miRNAs. There were 8 enriched pathways among the DE predicted target genes with inverse fold changes to that of the DE miRNA including: granulocyte and agranulocyte adhesion and diapedesis, interferon signaling and role of pathogen recognition receptors in recognition of bacteria and viruses. Functions predicted to be increased included: T cell response, apoptosis of leukocytes, immune response of cells and stimulation of cells. Pathogen recognition and proliferation of cytotoxic T cells are vital for the recognition and subsequent elimination of the virus.
2021-04-19 | GSE151033 | GEO
Project description:BackgroundBovine Respiratory Syncytial Virus (BRSV) is a cause of Bovine Respiratory Disease (BRD). DNA-based biomarkers contributing to BRD resistance are potentially present in non-protein-coding regulatory regions of the genome, which can be determined using ATAC-Seq. The objectives of this study were to: (i) identify regions of open chromatin in DNA extracted from bronchial lymph nodes (BLN) of healthy dairy calves experimentally challenged with BRSV and compare them with those from non-challenged healthy control calves, (ii) elucidate the chromatin regions that were differentially or uniquely open in the BRSV challenged relative to control calves, and (iii) compare the genes found in regions proximal to the differentially open regions to the genes previously found to be differentially expressed in the BLN in response to BRSV and to previously identified BRD susceptibility loci. This was achieved by challenging clinically healthy Holstein-Friesian calves (mean age 143 ± 14 days) with either BRSV inoculum (n = 12) or with sterile phosphate buffered saline (PBS) (n = 6) and preparing and sequencing ATAC-Seq libraries from fresh BLN tissues.ResultsUsing Diffbind, 9,144 and 5,096 differentially accessible regions (P < 0.05, FDR < 0.05) were identified between BRSV challenged and control calves employing DeSeq2 and EdgeR, respectively. Additionally, 8,791 chromatin regions were found to be uniquely open in BRSV challenged calves. Seventy-six and 150 of the genes that were previously found to be differentially expressed using RNA-Seq, were located within 2 kb downstream of the differentially accessible regions, and of the regions uniquely open in BRSV challenged calves, respectively. Pathway analyses within ClusterProfiler indicated that these genes were involved in immune responses to infection and participated in the Th1 and Th2 pathways, pathogen recognition and the anti-viral response. There were 237 differentially accessible regions positioned within 40 previously identified BRD susceptibility loci.ConclusionsThe identified open chromatin regions are likely to be involved in the regulatory response of gene transcription induced by infection with BRSV. Consequently, they may contain variants which impact resistance to BRD that could be used in breeding programmes to select healthier, more robust cattle.
| S-EPMC7789798 | biostudies-literature