PRRSV-infection of porcine alveolar macrophages
Ontology highlight
ABSTRACT:
ORGANISM(S): Sus scrofa
SUBMITTER: John Neill
PROVIDER: E-GEOD-10346 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Porcine reproductive and respiratory syndrome (PRRS), which caused by the porcine reproductive and respiratory syndrome virus (PRRSV), is a serious viral disease affecting global swine industry. At present, PRRSV vaccines fail to prevent this disease. Consequently, new antiviral strategies to compensate for the inefficacy of available vaccines are urgently required. Lysine acetylation is an important post-translational modification (PTM) regulating an array of pathological and physiological conditions. In this study, we profiled the global acetylome using acetylation specific antibody based enrichment and Tandem mass tag (TMT) label LC-MS in PRRSV-infected pulmonary alveolar macrophages (PAMs). As a result, 3731 lysine acetylation sites on 1421 cellular proteins were identified and quantified 6 hours post infection (hpi). Bioinformatics analysis of the differentially acetylated proteins revealed their involvement in various biological processes, including the host immune response and energy metabolism.
2020-12-11 | PXD016927 | Pride
Project description:We investigated for the first time the in vitro response of PRRSV-infected porcine DCs and monocytes to S. suis. We first assessed the effect of PRRSV infection on the phagocytosis and intracellular survival of S. suis by these two cell populations. We then used a genomic approach to compare the gene expression profiles of both type of cells infected with S. suis, with or without a previous infection with PRRSV. Total RNA obtained from porcine monocytes and dendritic cells infected with S. suis, PRRSV, or S. suis & PRRSV. Four replicates in all groups.
2016-06-01 | E-GEOD-75687 | biostudies-arrayexpress
Project description:Cell lines derived from Chlorocebus sabaeus kidney were infected with an isolate of PRRSV-1 or PRRSV-2 and RNASeq was performed (this entry) in parallel with ribosome profiling (see related accession numbers). These RNASeq datasets provide information on the transcriptome of PRRSV-infected cells and were used to detect novel viral transcripts and perform differential gene expression analysis on host transcripts. For the PRRSV-1 experiments, MA-104 cells were infected with an isolate based on the Porcilis vaccine strain (KJ127878.1 but with several accumulated mutations, see associated publication) and harvested at 8 hpi after pre-treatment with cycloheximide (CHX). For the PRRSV-2 experiments, MARC-145 cells were infected with SD95-21 PRRSV (KC469618.1), and a mutant thereof (KO2). One group of samples was harvested at 9 hpi after pre-treatment with CHX, and another group of samples was harvested at 3, 6, 9 and 12 hpi by flash-freezing without CHX pre-treatment. For all samples, RNA was extracted, ribosomal RNA was removed using Illumina's RiboZero kit, and remaining RNA was gel purified to select fragments 25-34 nt (PRRSV-1-infected samples, CHX-pre-treated PRRSV-2- or mock-infected samples, and non-CHX-pre-treated PRRSV-2- or mock-infected 9 hpi replicate one samples) or ~50 nt long (all other samples). Fragments were cloned into adapters based on the TruSeq small RNA adapters. For all PRRSV-2-infected (or mock-infected) libraries, adapters with an additional seven random nucleotides at the 5′-end of the 3′-adapter and the 3′-end of the 5′-adapter were used. For PRRSV-1 replicate one, no random nucleotides were present on the adapters, and for PRRSV-1 replicate two, 14 random nucleotides were present at the 5′-end of the 3′-adapter. Libraries were sequenced on the Illumina NextSeq 500 platform as a single-end run. For one NextSeq run, some potyvirus amplicons, indexed using TruSeq small RNA indices 1-48, was spiked in to the pool directly before sequencing, therefore some libraries (noCHX_RNA_9hpi_KO2_1, noCHX_RNA_9hpi_KO2_2, noCHX_RNA_9hpi_mock_1, noCHX_RNA_9hpi_mock_2, noCHX_RNA_9hpi_WT_1, noCHX_RNA_9hpi_WT_2) have a small proportion of potyvirus reads, but this does not represent co-infection in the biological sample and does not affect the conclusions of the study. Note that sample nomeclature (including replicate numbers) is consistent between this and the two related accessions, and RiboSeq libraries are matched with RNASeq libraries, which were prepared from the same lysate.
2022-03-09 | E-MTAB-10623 | biostudies-arrayexpress
Project description:Investigation of whole genome gene expression level changes in porcine alveolar macrophage response to co-infection of PRRSV and M. hyopneumoniae The results in this study will be further described in Bin li et al., 2013. BMC genomics. A 24 chip study using total RNA recovered from four separate group include control, PRRSV, M. hyopneumoniae and PRRSV+M. hyopneumoniae.
2014-05-30 | E-GEOD-49882 | biostudies-arrayexpress
Project description:Cell lines derived from Chlorocebus sabaeus kidney were infected with an isolate of PRRSV-1 or PRRSV-2 and ribosome profiling was performed (this entry) in parallel with RNASeq (see related accession number). These datasets were used to analyse the viral and host translatome, frameshifting on the viral genome, and putative frameshift-related ribosome pausing events. For the PRRSV-1 experiments, MA-104 cells were infected with an isolate based on the Porcilis vaccine strain (KJ127878.1 but with several accumulated mutations, see associated publication) and harvested at 8 hpi after pre-treatment with cycloheximide (CHX). For the PRRSV-2 experiments, MARC-145 cells were infected with SD95-21 PRRSV (KC469618.1), and a mutant thereof (KO2). One group of samples was harvested at 9 hpi after pre-treatment with CHX, and another group of samples was harvested at 3, 6, 9 and 12 hpi by flash-freezing without CHX pre-treatment. For all samples, RNase I treatment was carried out, following which ribosomes and enclosed RNA were isolated by centrifugation through a sucrose cushion. RNA was extracted, ribosomal RNA was removed using Illumina's RiboZero kit, and remaining RNA was gel purified to select fragments 25-34 nt (PRRSV-1-infected samples, CHX-pre-treated PRRSV-2- or mock-infected samples, and non-CHX-pre-treated PRRSV-2- or mock-infected 9 hpi replicate one samples) or 19-34 nt long (all other samples). Fragments were cloned into adapters based on the TruSeq small RNA adapters. For all PRRSV-2-infected (or mock-infected) libraries, adapters with an additional seven random nucleotides at the 5′-end of the 3′-adapter and the 3′-end of the 5′-adapter were used. For PRRSV-1 replicate one, no random nucleotides were present on the adapters, and for PRRSV-1 replicate two, 14 random nucleotides were present at the 5′-end of the 3′-adapter. Libraries were sequenced on the Illumina NextSeq 500 platform as a single-end run. Non-CHX-pre-treated PRRSV-2-infected 9 hpi replicate two libraries were uploaded under a separate accession number due to differences in the size selection and sequencing protocol - see associated paired-end entry. Note that sample nomeclature (including replicate numbers) is consistent between this and the two related accessions, and RiboSeq libraries are matched with RNASeq libraries, which were prepared from the same lysate. The noCHX_Ribo_9hpi_mock_3 library is deliberately absent as this was a poor quality library.
2022-03-09 | E-MTAB-10621 | biostudies-arrayexpress
Project description:Porcine reproductive and respiratory syndrome (PRRS), caused by PRRS virus (PRRSV), is the most economically important disease in pig populations. Lung damage is one major pathological condition following PRRSV infection, often leading to animal death. In vivo, PRRSV productive infection occurs predominately in alveolar macrophages of the lung. Here, transcriptome profiling of pulmonary alveolar macrophages (PAMs) from Tongcheng piglets pre- and post- infection of highly pathogenic PRRSV has been performed using porcine Affymetrix GeneChip. All animal procedures were performed according to protocols approved by the Biological Studies Animal Care and Use Committee of Hubei Province, China. Piglets used in this study were free from PRRSV, pseudorabies virus (PRV) and porcine circovirus type 2 (PCV2) determined by ELISA test for serum antibodies. Twelve of 5-week-old boars were obtained from three litters (four piglets per litter), and raised in pathogen-free facilities. In order to perform a paired experiment, every four full-sib individuals were divided equally into two groups: one infected group and one control group with 6 piglets in each group. The infected groups were challenged with PRRSV-Wuh2 (3 ml/15 kg, 10-5 TCID50/ml) by intramuscular inoculation. Slaughters were carried out at 0 days post-infection (dpi) for uninfected (control) groups, and at 5 or 7 dpi for infected groups. The PAMs for microarray analysis were collected by bronchoalveolar lavage from three uninfected pigs and three infected pigs at 5 dpi. Total of 6 microarrays have been hybridized in this experiment.
2012-06-30 | E-GEOD-22782 | 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:Porcine alveolar macrophages (PAMs) play impoartant role in innate immunity. Porcine circovirus type 2 (PCV2) has been identified as the causal agent of postweaning multisystemic wasting syndrome, an economically important multifactorial disease of the swine industry worldwide. We used microarrays to study the transcriptome of PAMs infection with PCV2. PAMs were collected by bronchoalveolar lavage from health piglets (free of PCV2, PRRSV, PRV, CSFV, PPV), and PAMs were cultured for 48 hours and inoculated with 5 moi of PCV2.
2011-07-26 | E-GEOD-30918 | biostudies-arrayexpress
Project description:By analyzing the changes of miRNAs of piglet PAMs 6h after PRRSV infection,we can find porcine miRNAs associated with viral infection and possible target sites in both PRRSV and pig genome and their roles in protection against viral infections. Then these targets will screened by bioinformatics methods to find the susceptibility genes, resistance genes and immune related genes, and formed molecular biology network of miRNAs at gene and protein level . PAM cells were isolated from 60d old healthy piglets and inoculated with HuN4,a strain of highly pathogenic porcine reproductive and respitory syndrome virus (HP-PRRSV) and were collected at 6h post-inoculation (pi). The uninfected cells served as mock-infected cells.The miRNA chip was according to the porcine miRNA sequences in Sanger miRBase Release 17.0 (http://www.sanger.ac.uk/Software/Rfam/mirna/)added with some miRNAs we found in reference. Microarray hybridization and data analysis helps to find the susceptibility genes, resistance genes and immune related genes, and formed molecular biology network of miRNAs at gene and protein level .
2013-11-01 | E-GEOD-52014 | biostudies-arrayexpress
Project description:Transcriptomes analysis of long noncoding RNA (lncRNA) and mRNA expression profiles of the porcine alveolar macrophages (PAMs) after porcine reproductive and respiratory syndrome virus (PRRSV) infection in vitro. We obtained 105,627,026 clean reads from 109,443,286 raw reads. A total of 951 annotated and 751 novel lncRNAs were identified. PAMs showed distinct transcriptome profiles after PRRSV infection. It was observed that 126 lncRNAs and 753 mRNAs were differentially expressed between PRRSV-infected and control group PAMs.
2019-06-20 | GSE132735 | GEO