Profiling differentially expressed earthworm genes in response to TNT exposure.
Ontology highlight
ABSTRACT:
ORGANISM(S): Eisenia fetida
PROVIDER: GSE7024 | GEO | 2007/10/15
SECONDARY ACCESSION(S): PRJNA98375
REPOSITORIES: GEO
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Project description:To understand molecular mechanisms of the joint effects of 2,4,6-trinitrotoluene (TNT) and hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), both widely used ordnance compounds, we constructed a microarray consisting of 4,032 cDNA isolated from the earthworm Eisenia fetida using the suppressive subtractive hybridization technique. Worms were exposed to TNT-, RDX-, or TNT+RDX-spiked soil for 28 days (TNT 50 mg/kg, RDX 30 mg/kg). Keywords: Combined toxicity of TNT and RDX to earthworm (Eisenia fetida)
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Project description:To understand molecular mechanisms of the joint effects of 2,4,6-trinitrotoluene (TNT) and hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), both widely used ordnance compounds, we constructed a microarray consisting of 4,032 cDNA isolated from the earthworm Eisenia fetida using the suppressive subtractive hybridization technique. Worms were exposed to TNT-, RDX-, or TNT+RDX-spiked soil for 28 days (TNT 50 mg/kg, RDX 30 mg/kg). Keywords: Combined toxicity of TNT and RDX to earthworm (Eisenia fetida) We analyzed 40 arrays for 4 treatments (control, TNT 50ppm, RDX 30ppm, TNT 50ppm + RDX 30ppm) with 5 biological replicates per treatment using an interwoven loop design.
2008-08-28 | E-GEOD-8909 | biostudies-arrayexpress
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2009-11-17 | E-GEOD-18983 | biostudies-arrayexpress
Project description:The use of a systems biology approach to analyze common and specific mechanisms of liver toxicity induced by munitions compounds TNT, 2,6-DNT, 2,4-DNT, 4A-DNT, and 2A-DNT The munitions compound 2,4,6-trinitrotoluene (TNT), its environmental degradation products 2-amino-4,6-dinitrotoluene (2A-DNT) and 4-amino-2,6-dinitrotoulene (4A-DNT), and two other munitions, 2,4-dinitrotoluene (2,4-DNT) and 2,4-dinitrotoluene (2,6-DNT) contaminate contaminate land, water and retired ammunitions plants. The release of these compounds to the environment is due to military activities and a series of manufacturing processes. Although toxicity has been characterized for these compounds, little is known of their mechanism of action. Here we describe to use an integrative systems biology approach including toxicology, pathology, transcriptomics, metabolomics, gene function classification, pathway analysis and gene network modeling to try to understand the mechanisms of toxicity of these compounds.
2009-12-25 | GSE19628 | GEO
Project description:Abstract - Current in vitro hazard assessment techniques lack the systems context necessary to holistically describe in vivo toxicity. To remedy this shortcoming, we have employed the Integrated discrete Multiple Organ Co-Culture (IdMOC) system in conjunction with global-transcriptomic expression assessment to provide a systems context of interactive organ and toxicity pathway responses. Specifically, IdMOC exposures containing hµMan cells representative of five organ types (kidney, liver, lung, vascular endotheliµM and heart muscle) were compared to mono-culture exposures, to evaluate toxic effects in a well-studied legacy munition, 2,4,6-trinitrotoluene (TNT) compared to a structurally similar insensitive munition, 2,4-dinitroanisole (DNAN) having sparsely described toxicity. DNAN toxicity, based on cell viability, was significantly lower than TNT for three cell lines: liver, vascular endotheliµM, and heart. Toxicity pathways enriched in transcriptional analysis of kidney cells exposed to TNT and DNAN through the IdMOC system reflected the literature-based in vivo mammalian toxicity of parent compounds and metabolites where multiple screening values matched chronic dosing levels within 1 order of magnitude. Enriched pathways were primarily unique to each chemical where TNT exposures affected xenobiotic metabolism, oxidative stress, and cell cycle pathways in addition to pathways providing potential screening for hematotoxicity, renal toxicity and urinary cancer. Ten pathway-level responses from IdMOC suggested that DNAN elicited toxicity representative of the primary metabolite, 2,4-dinitrophenol (2,4-DNP). Relative to monoculture, IdMOC results provided a higher nµMber and more robust enrichment of pathways involved in known in vivo toxicity mechanisms for TNT and a profile indicative of in vivo systemic toxicity of DNAN and metabolite 2,4-DNP.
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Project description:Motivation: Monitoring, assessment and prediction of environmental risks that chemicals pose demand rapid and accurate diagnostic assays. A variety of toxicological effects have been associated with explosive compounds TNT and RDX. One important goal of microarray experiments is to discover novel biomarkers for toxicity evaluation. We have developed an earthworm microarray containing 15,208 unique oligo probes. Our objective was to identify biomarker genes that can separate earthworm samples into three groups: control, TNT-treated, and RDX-treated. Results: We developed a discriminant analysis and cluster (DAC) pipeline to analyze a 248-array dataset. First, a total of 869 significantly changed genes in response to TNT or RDX exposure were inferred by class comparison statistical algorithms. Then, nine decision tree-based algorithms were applied to generate classification rules and a set of 286 classifier genes. These classifier genes were ranked by their overall weight of significance, and were used to build support vector machines (SVMs). An SVM containing all 286 classifier genes had the highest classification accuracy (91.5%). An unsupervised clustering method was used to cluster the worm samples and results show that the use of the top 100 classifier genes can assign the largest number of worm samples into the three reference clusters obtained by using all the 14,188 filtered genes, suggesting that these top-ranked genes may be potential candidates for biomarkers. This study demonstrates that the DAC pipeline can be used to identify a small set of biomarker genes from high dimensional datasets and generate a reliable SVM classification model for multiple classes. Adult earthworms (E. fetida) were exposed in soil spiked with TNT (0, 6, 12, 24, 48, or 96 mg/kg) or RDX (8, 16, 32, 64, or 128 mg/kg) for 0, 4 or 14 days. The 4-day treatment was repeated with RDX concentration being 2, 4, 8, 16 or 32 mg/kg soil. Each treatment originally had 10 replicate worms with 8-10 survivors at the end of exposure. Total RNA was isolated from the surviving worms. A total of 248 worm RNA samples were hybridized to a custom-designed oligo array using Agilentâs one-color Low RNA Input Linear Amplification Kit. The array contains 15,208 non-redundant 60-mer probes, each targeting a unique E. fetida transcript (Gong et al. 2009). After hybridization and scanning, gene expression data were acquired using Agilentâs Feature Extraction Software (v.9.1.3). The 248-array dataset consists of three worm groups: 32 untreated controls, 96 TNT-treated, and 120 RDX-treated.
2010-10-08 | E-GEOD-18495 | biostudies-arrayexpress
Project description:The earthworm Eisenia fetida is one of the most used species in standardized soil ecotoxicity tests. Endpoints such as survival, growth and reproduction are ecologically relevant but provide little mechanistic insight into the toxicity pathways, especially at the molecular level. To better understand toxicological modes of action and to facilitate the development of molecular biomarkers, we have obtained 30,245 unique EST sequences from E. fetida and have designed a novel microarray with 15,119 60-mer oligonucleotide probes. These probes target the unique non-redundant EST sequences identified in E. fetida. Using this array we have profiled gene expression of E. fetida after exposure to CL-20, a cage cyclic nitramine previously found exhibiting reversible neurotoxicity to worms. Worms were exposed for 6 days to CL-20. Half of the exposed worms were allowed to recover in a clean environment for 7 days. Electrophysiological analysis showed that the conduction velocity of worm medial giant nerve fiber was significantly decreased after 6-d exposure to CL-20, and that giant nerve fiber function was restored at the end of the 7-d recovery period. Total RNA samples isolated from four treatment groups (6 replicates per group), i.e., 6-d control, 6-d exposed, 13-d control and 6-d exposed with 7-d recovery, were analyzed using the new 15K oligo array. Bioinformatics and statistical analyses have identified specific neurological pathways affected by CL-20 and recovery of these pathways after CL-20 removal. These results provide significant insights on the CL-20 toxic mode of action and how earthworms can recover from chemical stressors.
2009-10-14 | GSE18536 | GEO
Project description:Purpose: The objective of this study was to investigate the TnBP-induced intestinal toxicity mechanism on earthworm Eisenia fetida. Methods: The intestinal tissues of nine earthworms under control and 10 mg/kg TnBP treatments were separately pooled into three replicates (three earthworms per replication) to obtain sufficient amounts of RNA for transcriptomic assessments, using BGISEQ-500. qRT–PCR validation was performed using SYBR Green assays. Results: A total of 10,401 contig sequences, mapped to 313 KEGG pathways,were classified. Scatter plots of DEGs based on the results showed that 3786 genes were significantly up regulated and 1084 genes were significantly downregulated at a P-value cut off of 0.01 . Pathway enrichment analysis of DEGs was performed to identify the potential biological functions for the interaction of genes based on the KEGG database. Pathways of the Digestive system were severely affected in the transcriptome dataset for the pathways of Protein digestion and absorption, Salivary secretion, Gastric acid secretion, and Bile secretion disruption. This is in accordance with the intestinal injury results of the digestive tract degradation and the alteration of digestive activities.
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Project description:Purpose: We studied the potential effects of lindane aging in soil on model earthworm Eisenia fetida at the transcriptomic level. Methods: transcriptomes of earthworms were generated by RNA sequencing using Illumina Hiseq Xten platform. Results: There were 1325 DE unigenes in G2 (1074 up and 251 down), 784 DE unigenes in G3 (457 up and 327 down), 3658 DE unigenes in G4 (2294 up and 1364 down), and 1511 DE unigenes in G5 (929 up and 582 down) compared with G1. Except in G2, lindane exposure caused significant impacts on cholinergic and GABAergic synaptic transmission in earthworms in other groups. The metabolic processes of ACh were also altered. It was of note that the term positive regulation of locomotion (GO:0040017) in G5 could be regarded as the phenotype of the interaction of two NTs. Conclusions: We found that aging of lindane prior to exposure promoted the disrupting effects of lindane on earthworm neurotransmission.
2020-08-16 | GSE118678 | GEO
Project description:The earthworm Eisenia fetida is one of the most used species in standardized soil ecotoxicity tests. Endpoints such as survival, growth and reproduction are ecologically relevant but provide little mechanistic insight into the toxicity pathways, especially at the molecular level. To better understand toxicological modes of action and to facilitate the development of molecular biomarkers, we have obtained 30,245 unique EST sequences from E. fetida and have designed a novel microarray with 15,119 60-mer oligonucleotide probes. These probes target the unique non-redundant EST sequences identified in E. fetida. Using this array we have profiled gene expression of E. fetida after exposure to CL-20, a cage cyclic nitramine previously found exhibiting reversible neurotoxicity to worms. Worms were exposed for 6 days to CL-20. Half of the exposed worms were allowed to recover in a clean environment for 7 days. Electrophysiological analysis showed that the conduction velocity of worm medial giant nerve fiber was significantly decreased after 6-d exposure to CL-20, and that giant nerve fiber function was restored at the end of the 7-d recovery period. Total RNA samples isolated from four treatment groups (6 replicates per group), i.e., 6-d control, 6-d exposed, 13-d control and 6-d exposed with 7-d recovery, were analyzed using the new 15K oligo array. Bioinformatics and statistical analyses have identified specific neurological pathways affected by CL-20 and recovery of these pathways after CL-20 removal. These results provide significant insights on the CL-20 toxic mode of action and how earthworms can recover from chemical stressors. Adult earthworms (E. fetida) were exposed on filter paper to CL-20 (0.2 ug/cm2) for 6 days with or without 7-day recovery (4 treatment groups in total). Each treatment group had 9 replicate worms, six of which were used for gene expression analysis. Worms were measured for their medial giant nerve fiber conduction velocity using a non-invasive electrophysiological technique immediately before takedown. At the termination of the 6-d or 13-d experiment, worms were snap-frozen and fixed in RNAlater-ICE. Total RNA was isolated from the fixed worms. A total of 24 worm RNA samples were hybridized to three 8x15K custom-designed Agilent oligo arrays using Agilentâs one-color Low RNA Input Linear Amplification Kit. The array contains 15,208 non-redundant 60-mer probes, each targeting a unique E. fetida transcript. After hybridization and scanning, gene expression data were acquired using GenePix Pro 6.0.
2009-10-14 | E-GEOD-18536 | biostudies-arrayexpress