Transcriptomic effects of tributyltin (TBT) in zebrafish eleutheroembryos. A functional benchmark dose analysis.
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PROVIDER: PRJNA580463 | ENA |
REPOSITORIES: ENA
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Project description:Purpose: the goal of this project is to study the effects of the TBT (tributyltin) in the transcriptome profiling (RNA-seq) of exposed zebrafish larvae. Methods: Total RNA was isolated from the samples using AllPrep DNA/RNA Mini Kit (Qiagen, CA, USA) as described by the manufacturer. Three high quality sample per condition were chosen to the mRNA enrichment using KAPA Stranded mRNA-Seq Kit Illumina® Platforms (Kapa Biosystems). Transcriptomic profiles were generated by deep sequencing using Illumina TruSeq SBS Kit v3-HS (pair-ended; 2x76bp) on a HiSeq2000 sequencing system. Image analysis, base calling and quality scoring of the run were processed using the manufacturer’s software Real Time Analysis (RTA 1.13.48) and followed by generation of FASTQ sequence files by CASAVA. Statistical analysis: RNA-seq reads were aligned to the D. rerio reference genome (GRCz10) using STAR version 2.5.1b . Genes annotated in GRCz10.84 were quantified using RSEM version 1.2.28 with default parameters. Differential expression analysis between all TBT conditions was performed with the DESeq2 (v.1.10.1) R package with the Likelihood ratio test option. ANOVA-PLS was performed on the normalized data using the lmdme package in R (v. 1.0.136, R Core Team). Results: We generated on average 42 million paired-end reads for each sample and identified aproximatelly 24420 transcripts. 3238 differentially expressed genes (DEGs) were detected which could be divided in 2 clusters including 1703 and 1535 genes, respectively. Affected metabolic pathways were analyzed from the DEGs: DNA-binding, domain transcription factors, transcription, nucleus, regulation of cell proliferation, cell cycle and differentiation, NAD(P)-binding domain, carbon metabolism, transferases, nucleotide binding, catalytic activity, and specially steroid metabolism and biosynthesis, among others, were down or upregulated. Conclusions: The dose-response setup allowed us to determine the most sensitive pathways affected by TBT, mostly related to the steroid biosynthesis, and general cell viability and development. Its covalent binding to RXR receptors seems to be the responsible for their specific disruption but also could be involved in its general toxicity along with an unspecific heavy metal poisoning. Transcriptomic general toxicity was related to a developmental delay which was in agreement with previous morphometric results. Other properties traditionally attributed to TBT as obesogenity only appeared at higher concentrations which were relative close to lethal levels. Other biological levels were also affected at concentrations relative closer to lethality than other endocrine disruptors, suggesting than its mode of action and/or lethality could differ from other EDCs. The present work contributes in the understanding of the environmental hazards associated to TBT.
2020-05-26 | GSE139599 | GEO
Project description:Organotin compounds are highly persistent organic pollutants that bioaccumulate in marine biota, behaving as potent endocrine disruptors. Tributyltin (TBT) has been described as an environmental obesogen, as it contributes in mammals to lipid accumulation in a mechanism mediated by PPARγ and RXR. With the aim of studying the molecular mechanisms that elicit TBT-induced pathogenesis in fish, thicklip grey mullets Chelon labrosus were exposed to low (10 ng/L) and high (500 ng/L) TBT concentrations for 1, 7 and 21 days, and gene transcription and metabolome profiles were studied. With this purpose, the multitissue transcriptome of mullet was sequenced by 454 pyrosequencing obtaining 126 Mb of sequence information. Assembly and annotation allowed spotting 8330 gene signatures on an oligonucleotide microarray that was used to identify hepatic gene transcription profiles specific to each TBT exposure set-up. Functional pathway analysis revealed that early profiles were characterized by genes related to response to organic substances and to oxidative stress and glucose metabolic processes. After 21 days of exposure, enriched GO terms in both concentrations were related to lipid homeostasis with a significant regulation of steroid metabolic and cholesterol biosynthetic processes. Also, the androgen receptor signalling pathway was regulated while PPAR signalling appeared as the most significantly regulated KEGG pathway. Neutral lipid accumulation measured by Oil-Red-O histochemistry did not show any treatment-related effect but hepatic and plasma NMR and GC-MS metabolomic analysis revealed distinctive metabolites. Aqueous profiles were characterised by lactate, glucose and alanine while GC-MS revealed a whole set of discriminating polyunsaturated fatty acids. Thus, TBT pathogenesis involves alterations of lipid metabolism through a mechanism that could involve PPARγ-regulated processes confirming the obesogen hypothesis for TBT in fish. Thicklip grey mullets were exposed to tributyltin (TBT). 3 treatments: control, TBT low dose (10ng/L), TBT high dose (500ng/L); 3 sampling times: 1 day, 1 week, 3 weeks. 6 mullets were dissected in each sampling point and group.
2016-07-31 | E-GEOD-36811 | biostudies-arrayexpress
Project description:Tributyltin (TBT) accumulates at higher levels in the liver than in any other organ, and it acts as a hepatotoxic agent. Most of the available studies on TBT have focused on observations at the cellular level, and studies at the level of genes and proteins have been limited; therefore, the information concerning possible mechanisms of TBT-induced adverse health effects remains scarce and inconclusive. In the present study, we applied a toxicogenomic approach to investigate the effects of TBT on gene expression in the human normal liver cell line HL7702.
2016-09-01 | GSE86259 | GEO
Project description:Obesogens such as tributyltin (TBT) are xenobiotic compounds that promote obesity, in part by distorting the normal balance of lipid metabolism. The obesogenic effects of TBT can be observed in directly exposed (F1 and F2 generations) and also subsequent generations (F3 and beyond) that were never exposed. To address the effects of TBT exposure on germ cells, we exposed pregnant transgenic OG2 mouse dams (F0), which specifically express EGFP in germline cells, to an environmentally relevant dose of TBT throughout gestation through drinking water. When fed with a high fat diet (HFD), F3 male offspring of TBT-exposed F0 dams (TBT-F3) accumulated much more body fat than did Control-F3 males. TBT-F3 males also lost more body fluid and lean compositions than did Control-F3 males. Expression of genes involved in transcriptional regulation or mesenchymal differ-entiation was upregulated in somatic cells of TBT-F1 (but not TBT-F3) E18.5 fetal testes, and promoter-associated CpG islands were hyper-methylated in TBT-F1 somatic cells. Global mRNA expression of protein-coding genes in F1 or F3 fetal testicular cells was unaffected by F0 exposure to TBT; however, expression of a subset of endogenous retroviruses was significantly affected in F1 and F3. We infer that TBT may directly target testicular somatic cells in F1 testes to irreversibly affect epigenetic suppression of endogenous retroviruses in both germline and somatic cells.
2022-03-02 | GSE191199 | GEO
Project description:To identify suitable experimental designsfor toxicology experiments (i.e., sample size, pool size, number of biological replicates, and number of doses), we exposed zebrafish embryos to 0.1% dimethyl sulfoxide for 4-120 hours post fertilization. We then created 96 samples to examine the impact of pool size comprised of 1, 5, 10, and 20 zebrafish embryos each (n = 24). From these, total RNA extraction was extracted and transcriptomic analyses were done using the TempO-Seq S1500+ Surrogate Assay platform. Samples were sequencing on an Illumina NextSeq 2000. The data were simulated to conduct power analyses exploring suitable study designs for identification of differentially expressed genes and for benchmark dose analysis. The aim was to identify a feasible pool size and sample size that would yield an acceptable false discovery rate for these analyses.
2024-04-17 | GSE230213 | GEO
Project description:Obesogenic compounds are chemicals that might have an influence on obesity development through in utero or chronic lifetime exposure. Tributyltin (TBT) is one of the most studied obesogenic compounds, inducing adipogenesis in vitro and increasing body fat after in utero exposure of mice. This study was designed to unravel the molecular mechanisms of TBT, using microarray analysis, and to evaluate the use of toxicogenomics for obesogen screening. The murine 3T3-L1 cell line was used to study TBT induced adipogenesis. Lipid staining as well as gene expression measurements of an adipocyte specific marker gene were performed to select relevant concentrations (10 nM, 50 nM) and time points (day1, day10) for microarray analysis. Additionally, solvent control and positive control (MDI) treated 3T3-L1 cells were included in the analysis. The microarray results were analysed using GO enrichment and Pathway analysis tools, which revealed enrichment of several GO terms involved in energy and fat metabolism after 10 days of TBT exposure. Pathway analysis unveiled PPAR signalling pathway as the sole pathway significantly enriched after 1 day and the most significantly enriched pathway after 10 days of exposure. By examination of effects on both cell physiological and gene expression level we provide a detailed overview of TBT induced obesogenic mechanisms. To our knowledge, this is the first study delivering an in depth mechanistic outline of the mode of action of TBT as an obesogen. Furthermore, our results show that combining omics with 3T3-L1 cells is promising for screening of potential obesogenic compounds. A separate v+2 A-optimal hybridization design was used for each time-point. Using this design each exposure condition is represented by three biological replicates, with each biological replicate analysed in technical duplicate while applying the dye swap principle to correct for dye bias. Two concentrations of TBT (10 nM, 50 nM), DMSO and MDI (positive control, adipogenic hormone cocktail) were the conditions tested, at two time-points (day 1 and day10).
2013-02-25 | E-GEOD-41340 | biostudies-arrayexpress
Project description:Environmental obesogens are being studied for their potential role in the increasing prevalence of obesity globally. A major area of focus in this field of research has been on the mechanism by which these agents act. In this study we focused on the organotin tributyltin (TBT), a water pollutant exposed to humans through diet. The mechanism by which TBT is believed to act is by binding to the PPAR nuclear receptor which heterodimerizes with RXR to alter gene regulation. To test whether this was the dominant mechanism for TBT activity, we performed time-course studies of transcription and chromatin accessibility in mesenchymal stem cells differentiating to adipocytes. We found limited evidence for PPAR effects by TBT, but a strong response by Ras-related GTPases and evidence for the loss of TEAD transcription factor activity during differentiation. These observations combine to implicate a known property of organotins, to cause cytoskeletal depolymerization. We propose a model for TBT activity involving a primary effect of cytoskeletal damage, leading to the loss of YAP co-regulator activity and the consequent failure of TEAD repression of adipogenesis.
2024-01-01 | GSE207038 | GEO
Project description:Environmental obesogens are being studied for their potential role in the increasing prevalence of obesity globally. A major area of focus in this field of research has been on the mechanism by which these agents act. In this study we focused on the organotin tributyltin (TBT), a water pollutant exposed to humans through diet. The mechanism by which TBT is believed to act is by binding to the PPAR nuclear receptor which heterodimerizes with RXR to alter gene regulation. To test whether this was the dominant mechanism for TBT activity, we performed time-course studies of transcription and chromatin accessibility in mesenchymal stem cells differentiating to adipocytes. We found limited evidence for PPAR effects by TBT, but a strong response by Ras-related GTPases and evidence for the loss of TEAD transcription factor activity during differentiation. These observations combine to implicate a known property of organotins, to cause cytoskeletal depolymerization. We propose a model for TBT activity involving a primary effect of cytoskeletal damage, leading to the loss of YAP co-regulator activity and the consequent failure of TEAD repression of adipogenesis.
2024-01-01 | GSE207039 | GEO
Project description:Obesogenic compounds are chemicals that might have an influence on obesity development through in utero or chronic lifetime exposure. Tributyltin (TBT) is one of the most studied obesogenic compounds, inducing adipogenesis in vitro and increasing body fat after in utero exposure of mice. This study was designed to unravel the molecular mechanisms of TBT, using microarray analysis, and to evaluate the use of toxicogenomics for obesogen screening. The murine 3T3-L1 cell line was used to study TBT induced adipogenesis. Lipid staining as well as gene expression measurements of an adipocyte specific marker gene were performed to select relevant concentrations (10 nM, 50 nM) and time points (day1, day10) for microarray analysis. Additionally, solvent control and positive control (MDI) treated 3T3-L1 cells were included in the analysis. The microarray results were analysed using GO enrichment and Pathway analysis tools, which revealed enrichment of several GO terms involved in energy and fat metabolism after 10 days of TBT exposure. Pathway analysis unveiled PPAR signalling pathway as the sole pathway significantly enriched after 1 day and the most significantly enriched pathway after 10 days of exposure. By examination of effects on both cell physiological and gene expression level we provide a detailed overview of TBT induced obesogenic mechanisms. To our knowledge, this is the first study delivering an in depth mechanistic outline of the mode of action of TBT as an obesogen. Furthermore, our results show that combining omics with 3T3-L1 cells is promising for screening of potential obesogenic compounds.
2013-02-25 | GSE41340 | GEO
Project description:Organotin compounds are highly persistent organic pollutants that bioaccumulate in marine biota, behaving as potent endocrine disruptors. Tributyltin (TBT) has been described as an environmental obesogen, as it contributes in mammals to lipid accumulation in a mechanism mediated by PPARγ and RXR. With the aim of studying the molecular mechanisms that elicit TBT-induced pathogenesis in fish, thicklip grey mullets Chelon labrosus were exposed to low (10 ng/L) and high (500 ng/L) TBT concentrations for 1, 7 and 21 days, and gene transcription and metabolome profiles were studied. With this purpose, the multitissue transcriptome of mullet was sequenced by 454 pyrosequencing obtaining 126 Mb of sequence information. Assembly and annotation allowed spotting 8330 gene signatures on an oligonucleotide microarray that was used to identify hepatic gene transcription profiles specific to each TBT exposure set-up. Functional pathway analysis revealed that early profiles were characterized by genes related to response to organic substances and to oxidative stress and glucose metabolic processes. After 21 days of exposure, enriched GO terms in both concentrations were related to lipid homeostasis with a significant regulation of steroid metabolic and cholesterol biosynthetic processes. Also, the androgen receptor signalling pathway was regulated while PPAR signalling appeared as the most significantly regulated KEGG pathway. Neutral lipid accumulation measured by Oil-Red-O histochemistry did not show any treatment-related effect but hepatic and plasma NMR and GC-MS metabolomic analysis revealed distinctive metabolites. Aqueous profiles were characterised by lactate, glucose and alanine while GC-MS revealed a whole set of discriminating polyunsaturated fatty acids. Thus, TBT pathogenesis involves alterations of lipid metabolism through a mechanism that could involve PPARγ-regulated processes confirming the obesogen hypothesis for TBT in fish.
2016-07-31 | GSE36811 | GEO