Whole blood microarray analysis of pigs showing extreme phenotypes after a porcine reproductive and respiratory syndrome virus infection
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ABSTRACT:
ORGANISM(S): Sus scrofa
SUBMITTER: juan steibel
PROVIDER: E-GEOD-69515 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Porcine reproductive and respiratory disease (PRRS) is the most important disease in swine industry worldwide. However, strategies such as vaccination and good biosecurity are not consistently successful to eliminate PRRSV. Although some gene expression pathways have been explored recently, host molecular pathways blocked by PRRSV and the protective immune response expressed in pigs resistant to PRRSV are largely unknown. In order to answer these questions, we herein characterize changes in blood gene expression in pigs responding differentially to infection with a well characterized type 2 (North American) PRRSV isolate. Samples are those collected through the PRRS Host Genetics Consortium (PHGC). Samples were those from Tempus tube collected blood of PHGC pigs selected from four response groups according to their serum viral load (0-21 days post infection) and weight gain (0-42 dpi) and characterized as low vs. high viral load and low vs high weight gain . block reference design was used to accommodate samples from 4 treatment groups.
2012-09-26 | E-GEOD-41144 | biostudies-arrayexpress
Project description:The presence of variability in the response of pigs to Porcine Reproductive and Respiratory Syndrome virus (PRRSv) infection, and recent demonstration of significant genetic control of such responses, leads us to believe that selection towards more disease resistant pigs could be a valid strategy to reduce its economic impact on the swine industry. To find underlying molecular differences in PRRS susceptible versus more resistant pigs, 100 animals with extremely different growth rates and viremia levels after PRRSv infection were selected from a total of 600 infected pigs. A microarray experiment was conducted on whole blood RNA samples taken at 0, 4 and 7 days post infection (dpi) from these pigs. From these data, we examined associations of gene expression with weight gain and viral load phenotypes. The single nucleotide polymorphism (SNP) marker WUR10000125 (WUR) on the porcine 60K SNP chip was shown to be associated with viral load and weight gain after PRRSv infection, and so, additionally, the effect of the WUR10000125 (WUR) genotype was examined. Limited information was obtained through linear modeling of blood gene differential expression (DE) that contrasted pigs with extreme phenotypes, for growth or viral load or between animals with different WUR genotype. However, using network-based approaches, molecular pathway differences between extreme phenotypic classes could be identified. Several gene clusters of interest were found when Weighted Gene Co-expression Network Analysis (WGCNA) was applied to 4dpi contrasted with 0dpi data. The expression pattern of one such cluster of genes correlated with weight gain and WUR genotype, contained numerous immune response genes such as cytokines, chemokines, interferon type I stimulated genes, apoptotic genes and genes regulating complement activation. In addition, Partial Correlation and Information Theory (PCIT) identified differentially hubbed (DH) genes between the phenotypically divergent groups. GO enrichment revealed that the target genes of these DH genes are enriched in adaptive immune pathways. There are molecular differences in blood RNA patterns between pigs with extreme phenotypes or with a different WUR genotype in early responses to PRRSv infection, though they can be quite subtle and more difficult to discover with conventional DE expression analyses. Co-expression analyses such as WGCNA and PCIT can be used to reveal network differences between such extreme response groups. three timepoints from 100 animals are hibridized following a blocked reference design; Blood gene expression of pigs 7 days post infection
2015-06-04 | E-GEOD-69514 | biostudies-arrayexpress
Project description:The presence of variability in the response of pigs to Porcine Reproductive and Respiratory Syndrome virus (PRRSv) infection, and recent demonstration of significant genetic control of such responses, leads us to believe that selection towards more disease resistant pigs could be a valid strategy to reduce its economic impact on the swine industry. To find underlying molecular differences in PRRS susceptible versus more resistant pigs, 100 animals with extremely different growth rates and viremia levels after PRRSv infection were selected from a total of 600 infected pigs. A microarray experiment was conducted on whole blood RNA samples taken at 0, 4 and 7 days post infection (dpi) from these pigs. From these data, we examined associations of gene expression with weight gain and viral load phenotypes. The single nucleotide polymorphism (SNP) marker WUR10000125 (WUR) on the porcine 60K SNP chip was shown to be associated with viral load and weight gain after PRRSv infection, and so, additionally, the effect of the WUR10000125 (WUR) genotype was examined. Limited information was obtained through linear modeling of blood gene differential expression (DE) that contrasted pigs with extreme phenotypes, for growth or viral load or between animals with different WUR genotype. However, using network-based approaches, molecular pathway differences between extreme phenotypic classes could be identified. Several gene clusters of interest were found when Weighted Gene Co-expression Network Analysis (WGCNA) was applied to 4dpi contrasted with 0dpi data. The expression pattern of one such cluster of genes correlated with weight gain and WUR genotype, contained numerous immune response genes such as cytokines, chemokines, interferon type I stimulated genes, apoptotic genes and genes regulating complement activation. In addition, Partial Correlation and Information Theory (PCIT) identified differentially hubbed (DH) genes between the phenotypically divergent groups. GO enrichment revealed that the target genes of these DH genes are enriched in adaptive immune pathways. There are molecular differences in blood RNA patterns between pigs with extreme phenotypes or with a different WUR genotype in early responses to PRRSv infection, though they can be quite subtle and more difficult to discover with conventional DE expression analyses. Co-expression analyses such as WGCNA and PCIT can be used to reveal network differences between such extreme response groups. three timepoints from 100 animals are hibridized following a blocked reference design; Blood gene expression of pigs 4 days post infection
2015-06-04 | E-GEOD-69513 | biostudies-arrayexpress
Project description:Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) infection of pregnant females causes fetal death and increased piglet mortality, but there is substantial variation in the extent of reproductive pathology between individual dams. This study used RNA-sequencing to characterize the whole blood transcriptional response to PRRSV in pregnant gilts during the first week of infection, and attempted to identify gene expression signatures associated with a low or high level of fetal mortality at necropsy, 21 days post-inoculation. RNA-sequencing experiment compared whole blood gene expression in two groups of gilts: a low fetal mortality group (LFM) and a high fetal mortality (HFM) group (n=8 per group). Two sets of contrasts were perfromed. First, a time-course experiment in which gene expression at day 2 (D2) post-inoculation was compared to day 0 (D0-just prior to inoculation) and expression at day 6 post-inoculation was compared to D2. Second, a comparison of gene expression between LFM and HFM groups at each of the three time-points (D0, D2, and D6).
2016-05-17 | E-GEOD-75304 | biostudies-arrayexpress
Project description:Porcine reproductive and respiratory disease (PRRS) is the most important disease in swine industry worldwide. However, strategies such as vaccination and good biosecurity are not consistently successful to eliminate PRRSV. Though some interesting pathways have been tentatively examined recently, host molecular pathways utilized by PRRSV and the protective immune responses in resistant to PRRSV are largely unknown. In order to answer these questions, we herein characterize changes in global gene expressions in multiple tissues [tonsil, tracheobronchial lymph nodes (TBLN), Cranial lung (CR Lung), and distal lung (D Lung)] in response to PRRSV of high and low virulence. Both vaccinated and unvaccinated pigs are used for this study. Based on Ingenuity Pathway Analysis (IPA), molecule bases of some “black boxes” underlying immune responses are further identified. Our results indicate that cross talks among these pathways and immune balances/competition between host and virus are always happened during the pathogenesis of PRRS. connected loop design was used to accommodate samples from 4 treatment groups.
2011-01-15 | E-GEOD-26642 | biostudies-arrayexpress
Project description:The goal of this study was to produce a deep, global analysis of gene expression changes that occured following infection of normal porcine alveolar macrophages (PAMs) with PRRSV. The goal was to examine the gene expression changes to help determine the mechanisms that result in reduced function and immunosuppression observed in PRRSV-infected pigs. Keywords: time course of infection The PAMs were infected in culture at an MOI of 10 with PRRSV strains VR-2332 and incubated at 37C until 6, 12, 16 or 24 hours post infection. Total cellular RNA was collected from each at the appropriate time. SAGE libraries were prepared from each infected time point as well as from noninfected PAMs. The SAGE libraries were sequenced to at least 95,000 tags each.
2008-09-01 | E-GEOD-10346 | biostudies-arrayexpress
Project description:In this study we investigated whether there exists a genomic signature that can accurately predict the course of a respiratory syncytial virus (RSV) infection in hospitalized young infants. We used early blood microarray transcriptome profiles from 39 infants that were followed until recovery and of which the level of disease severity was determined retrospectively. Applying support vector machine learning on age by sex standardized transcriptomic data, an 84 gene signature was identified that discriminated hospitalized infants with eventually less severe RSV infection from infants that suffered from most severe RSV disease.
2016-11-11 | E-MTAB-5195 | biostudies-arrayexpress
Project description:This study compares differences in gene expression between RNAs from lung and bronchial lymph node (BLN) tissue of high (H), low (L) PRRSV burden pigs or a pooled reference (R) using the swine protein-annotated long oligonucleotide microarray. Pathway analyses were carried out on a large scale to determine biological processes, pathways and networks that differ between the H, L and R responses. Samples corresponding to animals with High and Low response to PRRSV infection were hyridized in a common reference design
2010-11-05 | E-GEOD-25120 | biostudies-arrayexpress
Project description:Porcine reproductive and respiratory syndrome caused by porcine reproductive and respiratory syndrome virus (PRRSV) is an infectious disease characterized by severe reproductive deficiency in pregnant sows, respiratory symptoms in piglets, and high mortality. In this study, we employed Affymetrix microarray chip technology to compare the gene expression profiles of lung tissue samples from Dapulian (DPL) pigs (a Chinese indigenous pig breed) and Duroc×Landrace×Yorkshire (DLY) pigs after infection with PRRSV. During infection with PRRSV, the DLY pigs exhibited the range of clinical features that typify the disease, while the DPL pigs exhibited only mild signs of the disease. The percentage of CD8+ T cells in the DPL pigs was significantly higher than that in the DLY pigs at 21 days post-infection (dpi) (p< 0.05). Interleukin (IL) 1 beta (IL-1β) and IL-2 levels showed significant differences between the DPL and DLY pigs at 0 and 7 dpi (p< 0.01). For IL-10, the DLY pigs had significantly higher values than the DPL pigs at 0 and 7 dpi (p< 0.01). Significant differences were apparent between the DPL and DLY pigs in terms of their tumor necrosis factor-alpha (TNF-α) and interferon (IFN)-gamma (IFN-γ) levels at 0 and 7 dpi (p< 0.01). Microarray data revealed 16 differentially expressed genes in the lung tissue samples from the DLY and DPL pigs (q≤5%), of which LOC100516029 and LOC100523005 were up-regulated in the PRRSV-infected DPL pigs, while the other 14 genes were down-regulated in the PRRSV-infected DPL pigs compared with the PRRSV-infected DLY pigs. The expression levels of 10 of the 16 genes, namely CCDC84, C6ORF52, THYMOSIN, PRVE, HSPCB, CYP2J2, AMPD3, TOR1AIP2, PTGES3, and ACOX3, were validated by real-time quantitative RT-PCR. This study provides a platform for further investigation of the molecular mechanisms underlying the differential immune responses to PRRSV infection in different breeds or lines of pig. We investigated the response of lung tissues from Dapulian (DPL) pigs (a Chinese indigenous pig breed) and Duroc×Landrace×Yorkshire (DLY) pigs infected with porcine reproductive and respiratory syndrome virus (strain JXA1) by using the Affymetrix Porcine Genome Array. Sixteen healthy 30-day-old weaned DPL pigs were selected from the Jiaxiang Dapulian farm, Jining City, China, and 15 healthy 30-day-old weaned DLY pigs were obtained from a commercial farm with high standards of animal health. These pigs were free from PRRSV, porcine circovirus type 2 (PCV2), pseudorabies virus (PRV), and classical swine fever virus (CSFV) as determined by ELISA tests for serum antibodies; the absence of PRRSV was also confirmed by real-time quantitative reverse transcription PCR (qRT-PCR). Pigs were randomly assigned into two groups and reared in separate places: the PRRSV-infected group consisted of 11 DPL and 10 DLY pigs, and the control group consisted of five DPL and five DLY pigs. Infections in the pigs proceeded via inoculation with 2 ml of a viral suspension of PRRSV (at a tissue culture infectious dose of 105) by dripping the solution into the nasal cavity of each pig. The control group was treated with an identical volume of PBS by the same method. Rectal temperatures and clinical examinations on the pigs were recorded daily during the experiment. Anticoagulant-treated blood and untreated blood samples were collected separately at 0, 7, 14, and 21 days post-infection (dpi) from the infected and control groups for assaying CD4+, CD8+, cytokine (interleukin (IL) 1 beta (IL-1β), IL-2, IL-10, interferon (IFN)-gamma (IFN-γ), tumor necrosis factor-alpha (TNF-α), and immunoglobulin G (IgG) protein levels. Lung samples for microarray analysis and real-time qRT-PCR analysis were collected from six infected DLY and DPL pigs (three pigs for each breed) immediately post-slaughter at 28 dpi. Total RNA was isolated from lung tissue samples and purified using an RNeasy Mini kit according to the manufacturer’s protocol. RNA was prepared using the GeneChip (AFF-900623) one cycle target for the labeling and control reagents, and the labeled RNA was hybridized in an Affymetrix Hybridization Oven 640 for sequencing.
2013-07-30 | E-GEOD-49306 | biostudies-arrayexpress
Project description:Time course data from porcine alveolar macrophages(PAM)collected from infected with PRRSV.
2011-03-03 | E-MTAB-505 | biostudies-arrayexpress