Transcription profiling of human NB4 cells treated with lethal Bacillus anthracis toxin
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Hans-Joachim Mollenkopf
PROVIDER: E-GEOD-5966 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Dinoflagellates have evolved a nuclear organization unlike that of any other eukaryotic group. Recent studies find a predominance of post-transcriptional control of dinoflagellate gene expression. This study investigated regulation of the environmental stress response in the red tide dinoflagellate, Karenia brevis using an Agilent custom oligonucleotide microarray. K. brevis cultures were exposed to 5°C or 10°C heat shock, or three different sources of oxidative stress: 60 µM H2O2, 10 mM NaNO2, or 12 µM PbCl2 over acute time courses. Ribosomal genes, genes involved in RNA processing, translation, and chaperones were among the classes of genes consistently downregulated across treatments, although within these functional classes the same genes did not always respond to different stressors. Genes involved in the photosystem and mitochondrial and chloroplast ATP generation dominated the down-regulated genes. Heat shock and oxidative stress response genes were not induced under any treatment, even under conditions that resulted in decreased viability. We subsequently identified the presence of a trans-spliced leader sequence on many stress response gene transcripts, which suggests that they may be transcribed constitutively and their expression regulated at the level of translation. Cultures of were grown to mid-log phase. For each treatment, five replicate untreated control cultures and five replicate treated cultures were harvested at several time points following treatment. The following time courses were used: 5°C heat shock - 5, 15, 30, 60, and 240 min; 10°C heat shock - 60 min; 60 µM H2O2 - 5, 15, 30, 60, and 240 min; 10 mM NaNO2 -1, 4, and 7 hours; 12 µM PbCl2 -1, 4, and 7 hours. For each treatment, RNA was pooled from the controls and treated cultures at each timepoint. Two color arrays were then run comparing each the transcriptome at timepoint with the pooled control for that treatment. A technical dye swap array was run at each timepoint.
2010-12-01 | E-GEOD-13961 | biostudies-arrayexpress
Project description:The fathead minnow (Pimephales promelas) is a small fish species widely used for ecotoxicology research and regulatory testing in North America. This study used a 2000 gene oligonucleotide microarray to evaluate the effects of the aromatase inhibitor, fadrozole, on gene expression in the liver and brain tissue of exposed females. Reproductive measures, plasma vitellogenin, and gene expression data for the brain isoform of aromatase (CYP19B), vitellogenin precursors, and transferrin all provided evidence supporting the efficacy of the fadrozole exposure. Unsupervised analysis of the microarray results identified 20 genes in brain and 41 in liver as significantly up-regulated and 7 genes in brain and around 45 in liver as significantly down-regulated. Differentially expressed genes were associated with a broad spectrum of biological functions, many with no obvious relationship to aromatase inhibition. However, in brain, fadrozole exposure elicited significant up-regulation of several genes involved in the cholesterol synthesis, suggesting it as one potentially impacted pathway. Gene ontology-based analysis of expression changes in liver suggested overall down-regulation of protein biosynthesis. While real-time PCR analyses supported some of the microarray responses, others could not be verified. Overall, results of this study provide a foundation for developing novel hypotheses regarding the system-wide effects of fadrozole, and other chemical stressors with similar modes of action, on fish biology. Keywords: chemical stress response --Fadrozole exposure-- Treatments: 0, 60 ug fadrozole/L Replication: 4 replicate tanks per treatment, 2 replicate pairs (1 male, one female per pair) per tank for a total of 8 male, 8 female per treatment. Route of exposure: Waterborne, continuous flow through, without the use of carrier solvents, flow rate approx. 45 ml/min. Tanks: 20 L tanks containing 10 L of exposure water Fadrozole (purity ⥠99%; Dr. H. Cooper Eckhardt, Summit, NJ, USA). Fish: Adult (ca. 6 month old) male (4.65±0.93 g) and female (1.90±0.44 g) Conditions: (25°C, 16:8 light:dark photoperiod, fed adult brine shrimp twice daily) Duration: 7 d (± 4 h) Sampling: Fish humanely euthanized in tricaine methanesulfonate (Finquel; Argent, Redmond, WA, USA). Liver, and brain samples transferred directly to pre-weighed vials of RNAlater® (Sigma, St. Louis, MO). Plasma samples were stored frozen at -80°C. Average water quality characteristics (±SD): temperature 25.5±0.1 °C; pH 7.21±0.04; dissolved oxygen 5.74±0.52 mg/L. --Microarray analysis-- n=3 microarrays per treatment and tissue Experimental samples: total RNA pooled from n=2 fish from the same treatment and replicate (except for pooled sample BC3 which included fish from two different replicate tanks). Reference sample: pooled liver, brain, and gonad samples from adult male and female fathead minnows Microarray design: Two color, reference design Hybridization: Experimental samples Cy5, reference sample Cy3
2010-05-22 | E-GEOD-10722 | biostudies-arrayexpress
Project description:Ciguatoxins (CTX) are polyether neurotoxins responsible for ciguatera, the most common fish-borne food poisoning in humans. This study characterizes the global transcriptional response of mouse liver to a symptomatic dose (0.26 ng/g) of the highly potent Pacific ciguatoxin-1 (P-CTX-1). At 1 h post exposure 2.4% of features on a 44K whole genome array were differentially expressed (p � 0.0001), increasing to 5.2% at 4 h and decreasing to 1.4% by 24 h post-CTX exposure. Early gene expression was likely influenced prominently by an acute 4 °C decline in core body temperature by 1 h, which resolved by 8 h following exposure. Cytochrome P450s were of particular interest due to their role in xenobiotic metabolism. Twenty-seven genes, mostly members of Cyp2 and Cyp4 families, showed significant changes in expression. Many Cyps underwent an initial down-regulation at 1 h but were quickly and strongly up-regulated at 4 and 24 h post exposure. In addition to Cyps, increases in several glutathione S-transferases were observed, an indication that both phase I and phase II metabolic reactions are involved in the hepatic response to CTX in mice. Experiment Overall Design: Individual C57/BL6 mice (n=3) exposed to 0.26 ng/g P-CTX-1 ip for 1, 4, or 24 h were compared to pooled time-matched controls (n=3). The triplicate arrays at each time point included a dye swap.
2008-06-20 | E-GEOD-10768 | biostudies-arrayexpress
Project description:The human pathogen Helicobacter pylori (Hp) colonizes the gastric epithelium as a unique niche in the stomach. Infections commonly occur in childhood and persist lifelong, leading in some cases to adenocarcinoma and MALT lymphoma. Several studies define mammalian microRNAs as key regulators of the immune system and of carcinogenesis processes. Here, we show Hp infection induces miR-155 expression in epithelial and hematopoietic cells in vitro and in vivo. This induction is mediated by at least two main bacterial virulence factors, the vacuolating toxin (VacA) and the gamma-glutamyl transpeptidase (GGT) in an LPS independent manner. Using adenylate cyclases agonists and inhibitor, we demonstrated that the miR-155 microRNA regulatory cascade in Hp infection involves the second messenger cyclic adenosine monophosphate (cAMP). Furthermore, the study showed that a knock-down of the Foxp3 transcription factor in T cells abolishes miR-155 expression. Together, these findings are the first demonstration of a direct interconnection between the regulatory T cell development factor Foxp3 and a microRNA. This study supports the link between Hp infection, regulation of cellular immunity, inflammation and cancer development. A color-swap dye reversal experimental setting was applied. Ratio profiles comprising single hybridizations were combined in an error-weighted fashion to create ratio experiments. A two-fold change expression cut off for ratio experiments was applied together with anti-correlation of ratio profiles rendering the microarray analysis set highly significant (P-value > 0.01), robust and reproducible.
2010-12-22 | E-GEOD-18616 | biostudies-arrayexpress
Project description:Azaspiracid-1 (AZA-1) is a marine phycotoxin that accumulates in shellfish and known to cause severe gastrointestinal intoxications in humans. As the mechanism of action of AZA-1 is currently unknown, human DNA microarrays were used to profile gene expression in human lymphocyte T cells following AZA-1 exposure. Highly significant early (1 hr) genes consisted of a T cell specific transcription factor, membrane proteins, receptors, and inflammatory genes. At 4 hr, responding genes included transcription factors and cell growth genes, in addition to 16 genes involved in fatty acid and cholesterol synthesis. Similarly, at 24 hr, 17 of the top 35 signature genes were involved in fatty acid and cholesterol synthesis. Gene Map Annotator and Pathway Profiler software confirmed cell signaling effects targeted toward lipid biosynthesis pathways. The transcriptional profile induced by AZA-1 shared high similarity to expression profiles of in vitro cholesterol synthesis inhibitor studies and in vitro and in vivo cholesterol synthesis gene knockout studies, suggesting a common transcriptional response and possible mechanism of action. Experiment Overall Design: Time course experiment comparing AZA treatment gene expression to vehicle control. Parallel cultures of cells (n=2) were exposed to AZA or vehicle control for 1, 4, 24hr and harvested for RNA extraction. dye swaps were used for the replicate time points. Experiment Overall Design: Log Ratio data are listed as Log10.
2008-04-08 | E-GEOD-5346 | biostudies-arrayexpress
Project description:The cellular microRNA, miR-155 has been shown to be involved in lymphocyte activation and is expressed in EBV infected cells displaying type III latency gene expression but not type I latency gene expression. We show here that the elevated levels of miR-155 in type III latency cells is due to EBV gene expression and not epigenetic differences in cell lines tested and we show that expression in EBV infected cells requires a conserved AP-1 element in the miR-155 promoter. Gene expression analysis was carried out in a type I latency cell line transduced with a miR-155 expressing retrovirus. This analysis identified both miR-155 suppressed and induced cellular mRNAs and suggested that in addition to direct targeting of 3’ UTRs, miR-155 alters gene expression in part through the alteration of signal transduction pathways. 3’ UTR reporter analysis of predicted miR-155 target genes identified the transcriptional regulatory genes, BACH1, ZIC3, HIVEP2, CEBPB, ZNF652, ARID2, and SMAD5 as miR-155 targets. Western blot analysis of the most highly suppressed of these, BACH1, showed lower expression in cells transduced with a miR-155 retrovirus. Inspection of the promoters from genes regulated in EBV infected cells and in cells infected with a miR-155 retrovirus identified potential binding sequences for BACH1 and ZIC3. Together, these experiments suggest that the induction of miR-155 by EBV contributes to EBV mediated signaling in part through the modulation of transcriptional regulatory factors. Keywords: Differential expression of miR-155 vs cntl expressing cells The EBV positive Burkitt's lymphoma cell line, Akata was infected with a control (pEhyg-miRCntl) or a microRNA-155 expressing (pEhyg-miR-155) retrovirus. Duplicate infections with the control retrovirus and with the miR-155 retrovirus were carried out. Control and miR-155 infection pair 1 were run on an array as well as a dye swap. Control and miR-155 infection pair 2 were similarly run on an array as well as a second array containing a dye swap.
2008-03-17 | E-GEOD-10864 | biostudies-arrayexpress
Project description:Helicobacter pylori is a human gastric pathogen associated with gastric and duodenal ulcers as well as specific gastric cancers. It is well-evidenced that motility is essential for this pathogen to colonize human gastric tissues. We found that the H. pylori G27 HP0518 mutant showed greater motility than the parental strain, leading to increased cell adhesion and subsequent CagA translocation and NF-κB activation in AGS cells. This mutant expressed a higher molecular mass flagellin A (FlaA) than the parental wild-type strain and the complemented HP0518 mutant, which correlated with differences in motility. Deglycosylation assays indicated that the increased molecular mass of the FlaA protein expressed by the mutant was due to O-linked glycoside modifications. Electron micrographs demonstrated that expression of bundle-formed flagellin filaments in the HP0518 mutant was enhanced in comparison to the wild-type strain. Different degrees of FlaA glycosylation between H. pylori strains suggested that glycosylation could affect both virulence and persistence in vivo. In conclusion, HP0518 inactivation resulted in FlaA hyper-glycosylation leading to increased virulence and motility. Microarray experiments were carried out as two-color hybridizations with a color-swap dye-reversal setting to compensate Cy-dye specific effects and to ensure statistically relevant data.
2010-12-22 | E-GEOD-14752 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE14861: Small_fish_comp_tox_ZF_haloperidol_96_h_ovary GSE15115: Small_fish_comp_tox_FHM_haloperidol_96_h_ovary Refer to individual Series
2010-05-17 | E-GEOD-15216 | biostudies-arrayexpress
Project description:Chlamydia trachomatis is the causative agent of sexually transmitted disease with the highest prevalence in the world today. Although, sensitive to antibiotic treatment, Ctr is also a major cause of infertility due to significant cell damage caused to the genital tract of affected women. Occlusion of Fallopian tubes is a frequent consequence of advanced ascending Ctr infection. So far the mechanisms of Ctr caused pathogensis are widely unclear. Here we show, by using an ex vivo infection model of human Fallopian tubes that Ctr causes changes in epithelial homeostasis within 2 days of inoculation, by disrupting cell adhesion and increasing cell proliferation. We demonstrate by imaging and expression analysis that tissue response to invading pathogen has also a paracrine component. We identify Wnt signalling activation as one of the hallmarks of Ctr infection which transmits effects of the infection beyond inclusion containing cells. Mechanisms of phenotypic changes involve up regulation of Epcam and Olfactomedin 4, biomarkers and regulators of cell adhesion and cell differentiation. Our findings bring focus to the pleiotropic effects of Ctr infection within epithelium and could be provide the basis for better understanding the pathological sequels in vivo. Microarray experiments were performed as dual-color hybridizations. To compensate for dye-specific effects, an independent dye-reversal color-swap was applied. Quality control and quantification of total RNA amount was assessed using an Agilent 2100 bioanalyzer (Agilent Technologies) and a NanoDrop 1000 spectrophotometer (Kisker).
2011-11-21 | E-GEOD-26692 | biostudies-arrayexpress
Project description:Human lymphocyte T cells in vitro were exposed to azaspiracid (1 or 10 nM) for 1, 4, or 24 hours. Time matched controls (methanol 0.1% v/v) was used. Experiment Overall Design: RNA was extracted and gene expression changes observed using Agilents whole genome array. n =2 at 1 hr and n = 3 at 4 and 24 hr. At least one array from each time point utilized a dye swap.
2008-04-08 | E-GEOD-8845 | biostudies-arrayexpress