Interferon Alpha (IFNα) Induction and Knockout Analysis of ISGs in Atlantic Salmon SHK-1 Cells Challenged with ISAV and IPNV
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina NovaSeq 6000
ORGANISM(S): Salmo salar
SUBMITTER: Mohammad Ali Noman Reza
PROVIDER: E-MTAB-13068 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Infectious pancreatic necrosis virus (IPNV) is an aquatic virus that causes acute infection in freshwater and marine fish. The stage-specific expression of TNFα regulates Bad/Bid-mediated apoptosis and RIP1/ROS-mediated secondary necrosis in IPNV-infected fish cells. Using microRNA microarray and real-time quantitative PCR assays, the expression patterns of microRNA were characterized in different replication stages of IPNV or stimulation of LPS. Two-condition experiment, normal vs IPNV-infected cells (at 6, 12 or 24 hr post-infection), or normal vs LPS-stimulated cells (at 6, 12 or 24 h post-treatment).
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Project description:Infectious pancreatic necrosis virus (IPNV) is an aquatic virus that causes acute infection in freshwater and marine fish. The stage-specific expression of TNFα regulates Bad/Bid-mediated apoptosis and RIP1/ROS-mediated secondary necrosis in IPNV-infected fish cells. Using microRNA microarray and real-time quantitative PCR assays, the expression patterns of microRNA were characterized in different replication stages of IPNV or stimulation of LPS.
2011-12-31 | GSE30262 | GEO
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2020-11-06 | E-MTAB-9419 | biostudies-arrayexpress
Project description:Infectious pancreatic necrosis virus (IPNV) is a fish-derived pathogen and possess a bi-segmented, double-stranded RNA genome. By using zebrafish 14K oligo-microarray and quantitative RT-PCR, we identified differential expression of a defined subset of genes involved in apoptosis and immunity at 6-, 12- and 24- hour after IPNV infection. Transcripts divided into 11 functional categories were significantly modulated by IPNV, including immune response, apoptosis, transcription, signal transduction, lipid and cholesterol metabolism, carbohydrate metabolism, oxidative phosphorylation, cell cycle, protein degradation, protein folding and stress response, protein synthesis, nucleoside metabolism and synthesis. Most of pro-apoptotic bcl-2 family members were up-regulated after IPNV infection. Activation of pro-apoptotic members might disrupt potential of mitochondria and leaded to the mitochondria-mediated apoptosis in the late stage of IPNV infection. After treating the IPNV-infected cells with TNFα inhibitor AP126, expression of two bcl-2 family genes Bad and Bid and activation of caspase-8 and -3 had been inhibited significantly in early stage of IPNV infection. Expression of RIP-1 and Bmf-1 these two necroptosis-related genes and production of ROS were diminished in virus-infected cells which pre-treated with AP126. Our study shows the interactions between host cells and IPNV, the molecular mechanisms involved in IPNV-induced pathogenesis, and the variation of transcriptome through TNFα during infection which shows the important component of host defense. TNFα might lead to apoptosis in early stage and necrosis in late stage in ZF4 cells infected by IPNV. TNFα is crucial to apoptosis and ROS-mediated necrosis caused by IPNV in zebrafish cells.
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Project description:We described a striking divergence between the phenotypes arising from acute (siDOCK6) and chronic (DOCK6 KO cells) depletion is highly suggestive of a suppression mechanism that buffers the prolonged absence of DOCK6. To identify the factor(s) that compensate for the lack of DOCK6 activity, we compared the expression profiles of two independent DOCK6 KO HeLa clones (KO1 and KO45) with wild type control cells. See related experiment: E-MTAB-5067
2016-09-29 | E-MTAB-5068 | biostudies-arrayexpress
Project description:Infectious pancreatic necrosis virus (IPNV) is a fish-derived pathogen and possess a bi-segmented, double-stranded RNA genome. By using zebrafish 14K oligo-microarray and quantitative RT-PCR, we identified differential expression of a defined subset of genes involved in apoptosis and immunity at 6-, 12- and 24- hour after IPNV infection. Transcripts divided into 11 functional categories were significantly modulated by IPNV, including immune response, apoptosis, transcription, signal transduction, lipid and cholesterol metabolism, carbohydrate metabolism, oxidative phosphorylation, cell cycle, protein degradation, protein folding and stress response, protein synthesis, nucleoside metabolism and synthesis. Most of pro-apoptotic bcl-2 family members were up-regulated after IPNV infection. Activation of pro-apoptotic members might disrupt potential of mitochondria and leaded to the mitochondria-mediated apoptosis in the late stage of IPNV infection. After treating the IPNV-infected cells with TNFM-NM-1 inhibitor AP126, expression of two bcl-2 family genes Bad and Bid and activation of caspase-8 and -3 had been inhibited significantly in early stage of IPNV infection. Expression of RIP-1 and Bmf-1 these two necroptosis-related genes and production of ROS were diminished in virus-infected cells which pre-treated with AP126. Our study shows the interactions between host cells and IPNV, the molecular mechanisms involved in IPNV-induced pathogenesis, and the variation of transcriptome through TNFM-NM-1 during infection which shows the important component of host defense. TNFM-NM-1 might lead to apoptosis in early stage and necrosis in late stage in ZF4 cells infected by IPNV. TNFM-NM-1 is crucial to apoptosis and ROS-mediated necrosis caused by IPNV in zebrafish cells. Zebrafish ZF4 cell line was derived from 24h post-fertilization zebrafish embryos. Previous studies have been shown that adult zebrafish and zebrafish cell line could be infected with IPNV. In the present study, ZF4 cells were infected with IPNV, and total RNA was isolated from infected and uninfected control cells at 0 h, 6 h, 12 h, 24 h post-infection. Microarray analysis gene expression between IPNV-infected and uninfected cells relative to internal control on slides. The zebrafish 14K oligo microarray we used comprise 1800 zebrafish gene sequences from the NCBI and a database of 12768 putative open reading frames using NCBI zebrafish EST sequence information. Data files were imported into GeneSpring GX 7.3 for further analysis. Expression data sets must pass all the following quality control categories before used for cluster analysis. Clustering analysis allowed us to observe differences in cellular gene expression. A similar expression pattern was seen when comparing differentially expressed host cell genes between 12 and 24 h post-infection. The expression profiles were significantly different between 6 and 12 h post-infection. Therefore, we conclude that the regulation of host gene expression was changed after 12 h post-infection, and progressed into the late stage. To understand the interactions between host cells and IPNV and the molecular mechanisms involved in IPNV-induced pathogenesis, we used zebrafish oligo microarrays to investigate the gene expression profiles of IPNV-infected zebrafish embryonic cells. We also studied expression of specific genes related to immune response and apoptosis which were not present on the microarray we used by real-time quantitative RT-PCR. We used Pathway StudioM-bM-^@M-^Ys software to analyze the altered genes in cellular pathway for IPNV, TNFM-NM-1 was shown to be crucial to these genes of host response. Our study proved the variation of transcriptome during infection, which shows the activation of important component of host defense, apoptosis and necrosis through TNFM-NM-1 mediate pathway.
2011-02-01 | E-GEOD-21077 | biostudies-arrayexpress
Project description:Renal hypoxia is widespread in acute kidney injury (AKI) of various aetiologies. Hypoxia adaptation, conferred through the hypoxia-inducible factor (HIF), appears to be insufficient. Here we show that HIF activation in renal tubules through Pax8-rtTA-based inducible knockout of von Hippel-Lindau protein (VHL-KO) protects from rhabdomyolysis-induced AKI. In this model, histological observations indicate that injury mainly affects proximal convoluted tubules, with 5% necrosis at d1 and 40% necrosis at d2. HIF-1alpha up-regulation in distal tubules reflects renal hypoxia. However, lack of HIF in proximal tubules suggests insufficient adaptation by HIF. AKI in VHL-KO mice leads to prominent HIF activation in all nephron segments, as well as to reduced serum creatinine, serum urea, tubular necrosis, and apoptosis marker caspase-3 protein. At d1 after rhabdomyolysis, when tubular injury is potentially reversible, HIF mediated protection in AKI is associated with activated glycolysis, cellular glucose uptake and utilization, autophagy, vasodilation, and proton removal as demonstrated by qPCR, pathway enrichment analysis and immunohistochemistry. Together, our data provide evidence for a HIF-orchestrated multi-level shift towards glycolysis as a major mechanism for protection against acute tubular injury. All experiments were carried out in transgenic mice in which selective renal tubular VHL knockout (VHL-KO) was inducible by doxycycline (Reference: Mathia S, Paliege A, Koesters R, Peters H, Neumayer HH, Bachmann S, Rosenberger C. Action of hypoxia-inducible factor in liver and kidney from mice with Pax8-rtTA-based deletion of von Hippel-Lindau protein. Acta Physiol (Oxf). 2013; 207(3):565-76.). Four groups of animals were used: 1) controls: untreated mice; 2) VHL-KO: injected with doxycycline (0.1 mg per 10 g body weight SC), 4 days prior to sacrifice; 3) AKI: rhabdomyolysis; 4) VHL-KO/AKI: doxycycline plus rhabdomyolysis. To induce AKI, 50% glycerol (0.05 ml per 10 g body weight) was injected IM into the left hind limb under isoflurane narcosis. Drinking water was withdrawn between 20 h prior and 24 h after glycerol injection.
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