Transcriptome profiling of mice lungs exposed to low-dose ricin .
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ABSTRACT:
PROVIDER: PRJNA669006 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12817776_1.fastq.gz | Fastqsanger.gz | |||
| SRR12817776_2.fastq.gz | Fastqsanger.gz | |||
| SRR12817777_1.fastq.gz | Fastqsanger.gz | |||
| SRR12817777_2.fastq.gz | Fastqsanger.gz | |||
| SRR12817778_1.fastq.gz | Fastqsanger.gz |
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Project description:The goal of this study is to explore the alterations in gene expression in lungs of mice 48 hours after exposure to low-dose ricin compared to lungs of naive mice, in order to provide a framework for comparative investigation of genes and mechanisms that may contribute to the developing lung disease. Methods: Total RNA was extracted from lungs of naive or ricin intoxicated mice (intranasally exposure to 1.7 µg/kg ricin), using the RNeasy mini kit (Qiagen). RNA-seq libraries were constructed and sequencing of 100bp paired-end was performed on the Illumina NovaSeq 6000 system. Sequencing yielded about 21M reads per sample that were mapped to the mouse genome. The expression of the infected sample was compared to mock sample, and RNA ratios were clustered using partitioning clustering. We next carried out GO term enrichment analysis. Results: Principal component analysis revealed distinct transcriptional signatures between naïve and ricin mice. We found 8545 differentially expressed genes in the ricin group, including 4394 upregulated and 4151 downregulated genes.
2020-10-14 | GSE159461 | GEO
Project description:For the purpose of establishing a mice model for sever COVID-19 , mice were infected intranasally with SARS-CoV-2 two days after pulmonary application of low-dose ricin. The goal of this study is to perform a comparative transcriptomic analysis by exploring the alterations in gene expression in lungs of mice exposed to low-dose ricin and SARS-CoV-2 (samples OR009-OR012) compared to lungs of mice infected solely with SARS-CoV-2 (48 hr after infection, samples OR021-OR024) or mice exposed to low-dose ricin (96 hr post exposure,samples OR005-OR008)) or mice exposed to lethal dose of ricin (48 hr post exposure, samples OR013-OR016). Methods: Total RNA was extracted from lungs of ricin intoxicated mice (intranasally exposure to 1.7 µg/kg or 10 µg/kg ricin ) or of SARS-CoV-2 infected mice (intranasal administration of 5 x 106 PFU), using the RNeasy mini kit (Qiagen). RNA-seq libraries were constructed and sequencing of 100bp paired-end was performed on the Illumina NovaSeq 6000 system. Sequencing yielded about 22M reads per sample that were mapped to the mouse genome. RNA ratios were clustered using partitioning clustering. We next carried out Ingenuity Pathway Analysis (IPA). Results: Principal component analysis revealed distinct transcriptional signatures between lungs mice exposed to low-dose ricin and infected with SARS-CoV-2 compared to lungs of mice infected solely with SARS-CoV-2 or mice exposed to low-dose ricin (96 hr post exposure) or mice exposed to lethal dose of ricin (48 hr post exposure). Differentially Expressed Genes (DEGs) were defined as such when having false discovery rate (FDR) value (p-adjusted) of ≤ 0.01 and a fold change (FC) of ≥ 1.5 or ≤ 0.66. Analysis of Low-dose-ricin-treated mice transcripts resulted in the detection of 6684 DEGs, 55% upregulated and 45% downregulated. Similarly, in Low-dose-ricin-treated mice infected with SARS-CoV-2, we found a total of 6044 differentially expressed genes, 52% induced and 48% repressed. Considerably fewer (797, 67% upregulated and 33% downregulated) differentially expressed genes were identified in lungs of mice infected only with SARS-CoV-2.
2021-11-18 | GSE189015 | GEO
Project description:Ricin is a potential bioweapon because of its toxicity, availability, and ease of production. When delivered to the lungs, ricin causes severe pulmonary damage with symptoms that are similar to those observed in acute lung injury and adult respiratory distress syndrome. The airway epithelium plays an important role in the pathogenesis of many lung diseases, but its role in ricin intoxication has not been elucidated. Exposure of cultured primary human airway epithelial cells to ricin resulted in the activation of stress-activated protein kinases (SAPKs) and NF-κB and in the increased expression of multiple proinflammatory molecules. Among the genes upregulated by ricin and identified by microarray analysis were those associated with transcription, nucleosome assembly, inflammation, and response to stress. Sequence analysis of the promoters of these genes identified NF-κB as one of the transcription factors whose binding sites were over-represented. Although airway cells secrete TNF-α in response to ricin, blocking TNF-α did not prevent ricin-induced activation of NF-κB. Inhibition of p38 MAPK by a chemical inhibitor and NF-κB by short interfering RNA resulted in a marked reduction in the expression of proinflammatory genes, demonstrating the importance of these two pathways in ricin intoxication. Therefore, the p38 MAPK and NF-κB pathways are potential therapeutic targets for reducing the inflammatory consequences of ricin poisoning. Experiment Overall Design: Control RNA from untreated primary human airway cells was compared to RNA from ricin-treated airway cells
2008-06-15 | E-GEOD-7845 | biostudies-arrayexpress
Project description:We are investigating the response of human lymphoblastoid cells to low-dose exposure of environmental metals We used microarrays to detail the global programme of gene expression upon response to low-dose metals Keywords: dose TK6 cells were grown to mid log-phase and exposed to low-doses of arsenic and cadmium. RNA was collected 24 hrs after exposure.
2010-04-14 | E-GEOD-20320 | biostudies-arrayexpress
Project description:The toxin ricin has been shown to cause inflammatory lung damage, leading to pulmonary oedema and, at higher doses, mortality. In order to understand the genetic basis of this inflammatory cascade a custom microarray platform (1509 genes) directed towards immune and inflammatory markers was used to investigate the temporal expression profiles of genes in a Balb/c mouse model of inhalational ricin exposure. To facilitate examination of those genes involved in both inflammatory cascades and wound repair the dose which was investigated was sub-lethal across a 96 hour time course. Histopathology of the lung was mapped across the time course and genetic responses considered in the context of overall lung pathology. 685 genes were found to be statistically significantly different compared to controls, across the time course and these genes have been investigated in the context of their biological function in ricin poisoning. As well as confirming key inflammatory markers associated with ricin intoxication (TNFa and Il1b) several pathways that are altered in expression were identified following pulmonary exposure to ricin. These genes included those involved in cytokine-cytokine signalling cascades (IL1, IL1r, IL1r2, Ccl 4, 6, 10), focal adhesion (Fn1, ICAM1) and tissue remodelling (VEGF, Pim1). Furthermore, the observed alteration in expression of matrix metalloproteinases (MMPs) and their inhibitors (TIMPs) indicates a key role in membrane integrity and cellular adhesion in ricin poisoning. Data captured using this transcriptomic approach could be used to develop a specific approach to the treatment of inhalational ricin exposure. This work was conducted as part of a wider programme of work to compare a number of militarily relevant lung damaging agents, with a view to establishing a rational basis for the identification of more generic medical countermeasures. Four groups of six mice were exposed to ricin and a further groups exposed to vehicle only control (PBS). Following exposure mice were culled at 6 timepoints (1, 4, 7, 24, 48 and 96h). RNA was extracted and run on the custom array.
2009-08-19 | E-GEOD-17431 | biostudies-arrayexpress
Project description:Expression profiles in mouse liver exposed to long-term gamma-irradiation were examined to assess in vivo effects of low dose-rate radiation. Three groups of male C57BL/6J mice were exposed to whole body irradiation at dose-rates of 17-20 mGy/day, 0.86-1.0 mGy/day or 0.042-0.050 mGy/day for 401-485 days (cumulative doses were approximately 8 Gy, 0.4 Gy or 0.02 Gy, respectively). Expression profiles were produced for RNA isolated from irradiated individual animals and for pooled RNA from sham-irradiated 3 animals for control. The expression levels of 6 irradiated animals for each dose were compared individually with those of 2 pooled controls (3 irradiated samples to one pooled control in first and second experiments).
2011-01-01 | GSE20562 | GEO
Project description:We are investigating the response of human lymphoblastoid cells to low-dose exposure of environmental metals We used microarrays to detail the global programme of gene expression upon response to low-dose metals Keywords: dose
2010-04-01 | GSE20320 | GEO
Project description:Ricin is a potential bioweapon because of its toxicity, availability, and ease of production. When delivered to the lungs, ricin causes severe pulmonary damage with symptoms that are similar to those observed in acute lung injury and adult respiratory distress syndrome. The airway epithelium plays an important role in the pathogenesis of many lung diseases, but its role in ricin intoxication has not been elucidated. Exposure of cultured primary human airway epithelial cells to ricin resulted in the activation of stress-activated protein kinases (SAPKs) and NF-κB and in the increased expression of multiple proinflammatory molecules. Among the genes upregulated by ricin and identified by microarray analysis were those associated with transcription, nucleosome assembly, inflammation, and response to stress. Sequence analysis of the promoters of these genes identified NF-κB as one of the transcription factors whose binding sites were over-represented. Although airway cells secrete TNF-α in response to ricin, blocking TNF-α did not prevent ricin-induced activation of NF-κB. Inhibition of p38 MAPK by a chemical inhibitor and NF-κB by short interfering RNA resulted in a marked reduction in the expression of proinflammatory genes, demonstrating the importance of these two pathways in ricin intoxication. Therefore, the p38 MAPK and NF-κB pathways are potential therapeutic targets for reducing the inflammatory consequences of ricin poisoning. Keywords: Comparative genomic hybridization
2007-05-22 | GSE7845 | GEO
Project description:Pulmonary exposure to high doses of nanoparticles (NP) leads to well characterized lung toxicity in addition to long-term NP retention. However, pulmonary NP accumulation and toxicity following low dose exposures are not well described. In the present study we sought to: (1) investigate particle retention in mouse lungs following intratracheal instillation of varying doses of nano-sized titanium dioxide (nano-TiO2) and (2) determine the effects of long-term particle accumulation on pulmonary systems. Female C57BL/6 mice were exposed to rutile nano-TiO2 (primary size of 20.6 nm and surface area of 107.7 m2/g) via single intratracheal instillations of 18, 54 and 162 µg/mouse and sampled 1, 3 and 28 days post-exposure. The deposition of nano-TiO2 in the lungs was assessed using Nanoscale Hyperspectral Microscope. DNA microarrays, pathway-specific real-time RT-PCR (qPCR) and gene-specific qPCR arrays, and tissue protein analyses were employed to characterize pulmonary responses. Hyperspectral mapping showed dose-dependent retention of nano-TiO2 in the lungs up to 28 days post-exposure time. Retention did not correlate with the extent of inflammatory neutrophil influx into the lungs. DNA microarray analysis showed altered expression of approximately 3000 genes across all treatment groups (±1.3 fold; p<0.1). Several inflammatory mediators changed in a dose- and time-dependent manner at both the mRNA and protein levels. Although the low dose exposure failed to induce observable inflammation, significant changes in the expression of genes and proteins associated with inflammation were observed. Moreover, diminished (or absent) neutrophil influx in the low and medium dose groups was correlated with negative regulation of genes associated with ion homeostasis and muscle regulation. Gene expression changes for several inflammatory mediators have previously been noted in mice exposed to the same nano-TiO2 via inhalation. Our results suggest that retention of nano-TiO2 in the absence of inflammation and effective clearance can perturb calcium and ion homeostasis, and affect smooth muscle activities over time.
2013-11-01 | GSE41041 | GEO
Project description:Expression profiles in mouse liver exposed to long-term gamma-irradiation were examined to assess in vivo effects of low dose-rate radiation. Three groups of male C57BL/6J mice were exposed to whole body irradiation at dose-rates of 17-20 mGy/day, 0.86-1.0 mGy/day or 0.042-0.050 mGy/day for 401-485 days (cumulative doses were approximately 8 Gy, 0.4 Gy or 0.02 Gy, respectively). Expression profiles were produced for RNA isolated from irradiated individual animals and for pooled RNA from sham-irradiated 3 animals for control. The expression levels of 6 irradiated animals for each dose were compared individually with those of 2 pooled controls (3 irradiated samples to one pooled control in first and second experiments). The experiments were conducted twice at similar dose-rates. In the first experiment, three groups of 8 weeks old male C57BL/6J mice were exposed to whole body irradiation at dose-rates of either 16.6 mGy/day (H1), 0.858 mGy/day (M1) or 0.042 mGy/day (L1) for 485 days (cumulative doses were 8030 mGy, 416 mGy or 20.6 mGy, respectively). In the second experiment, the doe-rates were slightly elevated as 20.0 mGy/day (H2), 1.000 mGy/day (M2) or 0.050 mGy/day (L2) for 401 days (doses were 8015 mGy, 401 mGy or 20 mGy, respectively). A group of control unirradiated mice were set for each experiment (C1, C2).
2011-01-01 | E-GEOD-20562 | biostudies-arrayexpress