Transcriptomic analysis of HepG2 cells treated with BDE-47, BDE-99, BDE-209 and their ternary mixture at 1nM as a dietary relevant concentration
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PROVIDER: PRJNA894472 | ENA |
REPOSITORIES: ENA
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Project description:Polybrominated diphenyl ethers (PBDEs) are persistent organic chemicals implied as flame re-tardants. Humans are mainly exposed to BDE-47, -99 and -209 congeners by diet. PBDEs are metabolic disruptors with liver as main target organ. To investigate their mode of action at a human relevant concentration, we exposed HepG2 cells to these congeners and their mixture at 1 nM for 72h, analyzing their transcriptomic and proteomic profiles. KEGG pathways and GSEA Hallmarks enrichment analyses evidenced that BDE-47 disrupted the glucose metabolism and Hypoxia pathway; all the congeners and the MIX affected lipid metabolism and signaling Hallmarks regulating metabolism as mTORC1 and PI3K/AKT/MTOR. These results were confirmed by glucose secretion depletion and increased lipid accumulation, especially in BDE-47 and -209 treated cells. These congeners also affected the EGFR/MAPK signaling; further, BDE-47 enriched the Estrogen pathway. Interestingly, BDE-209 and the MIX increased ERα gene expression, whereas all the congeners and the MIX induced ERβ and PPARγ. We also found that PBDEs modulated several lncRNAs and that HNRNAP1 represented a central hub in all the four interaction networks. Overall, despite the low concentration used, the PBDEs investigated affected glucose and lipid metabolism with different underlying modes of action, as highlighted by the integrated omics analysis. These results may support the mechanism-based risk assessment of these compounds in relation to liver metabolism disruption.
2022-10-28 | GSE216590 | GEO
Project description:Polychlorinated diphenyl ethers are lipophilic, persistent, and bioaccumulable compounds widely used as flame-retardants. These are chemicals of increasing environmental concern due to their lipophilic, persistent, and bioaccumulable characteristics. The objective of this study was to analyze the potential bioavailability and bioaccumulation of BDE-209 as a source of toxicity. Zebrafish embryos were exposed for 8 days to sediments spiked with an environmentally relevant concentration of BDE-209. We analyzed gene expression changes, thyroid function, and several markers for neurotoxicity. Results of this research highlight the need to consider the capability of BDE-209 to be bioavailable and bioaccumulate, indicating the potential hazardous effects.
2013-01-01 | GSE39169 | GEO
Project description:Polychlorinated diphenyl ethers are lipophilic, persistent, and bioaccumulable compounds widely used as flame-retardants. These are chemicals of increasing environmental concern due to their lipophilic, persistent, and bioaccumulable characteristics. The objective of this study was to analyze the potential bioavailability and bioaccumulation of BDE-209 as a source of toxicity. Zebrafish embryos were exposed for 8 days to sediments spiked with an environmentally relevant concentration of BDE-209. We analyzed gene expression changes, thyroid function, and several markers for neurotoxicity. Results of this research highlight the need to consider the capability of BDE-209 to be bioavailable and bioaccumulate, indicating the potential hazardous effects. Total RNA was isolated using RNeasy kits (Qiagen, Valencia, CA, USA). The RNA quality was assessed with an Agilent 2100 Bioanalyzer (Agilent, Wilmington, DE, USA) and quantity was determined using a NanodropM-BM-. ND-1000 spectrophotometer. Total RNA was stored at -80oC until analyzed with oligonucleotide microarrays. Zebrafish 44,000 gene arrays (Agilent Single Color 19161, Platform number GPL6457) were purchased from Agilent (Sta. Clara, CA, USA). The Agilent one-color microarray hybridization protocol (One-Color Microarray-Based Gene Expression Analysis, version 5.7, Agilent Technologies, Palo Alto, CA) was used for microarray hybridizations following the manufacturerM-bM-^@M-^Ys protocol and recommendations. Four controls and four treated samples were analyzed, each sample consisting of a pool of embryos. One ug of total RNA was used for all hybridizations. cDNA synthesis, cRNA labeling, amplification and hybridization were performed following the manufacturerM-bM-^@M-^Ys kits and protocols (Quick Amp Labeling kit; Agilent, Palo Alto, CA). An Axon GenePixM-BM-. 4000B Microarray Scanner (Molecular Devices Inc., Sunnyvale, CA) was used to scan microarray images at 5 M-NM-<m resolution. Data were resolved from microarray images using Agilent Feature Extraction software and analyzed using GeneSpring (Agilent Technologies, Palo Alto, CA).
2013-01-01 | E-GEOD-39169 | biostudies-arrayexpress
Project description:The batch test of BDE-209 Raw sequence reads
| PRJNA756725 | ENA
Project description:Flame retardants are detected globally in the environment, and pose great risks to human health. The potential effects of these chemicals on the development of nervous system have raise public concerns. In this study, to explore the toxicity profiles of these chemicals in the early developmental stage of human nervous system, we induced neural ectoderm from human embryonic stem cells in the presence of individual or mixture of BDE-47, BDE-209, TBBPA, TBBPS, TCBPA. By analyzing the whole transcriptional changes in the samples treated with 1 μΜ of each chemical, we identified a set of neural development relative biological processes that response to these chemicals. Genes involved in the GO terms relative to neural development were further confirmed by qRT-PCR assay, with samples treated with various concentrations (10 nM, 100 nM, 1 μΜ, 5 μΜ) of these chemicals. We found out that axon guidance and synaptogenesis may be the major target of these chemicals. In addition, these flame retardants may dysregulate the WNT and AHR signaling pathways. BDE-209 showed similar toxicity with BDE-47, whereas TBBPS and TCBPA may not be safe alternatives to TBBPA.
2022-03-01 | GSE128431 | GEO
Project description:Polybrominated diphenyl ethers (PBDEs) are man made chemicals with flame retardant properties which are added to commercial products and materials such as textiles, plastics, electronic devices, household products and furniture to reduce their flammability. In the present study we investigated the differences in the mode of action of three congeners more abundant in the diet yielded relative toxicities scores BDE-209 , 47 , 99 considering their ternary mixture, also, at the mean concentration found in food, which is not cytotoxic, 1nM, by treating the human hepatoma cell line (HepG2) and analyzing correspondent transcriptomic and proteomics profiles. HepG2 cells, treated with 1nM of each congener and also with a mixture containing the three congeners together, were examined with a shotgun proteomic approach in order to analyze the protein differential expression between treated samples, considering also the background proteins coming from control samples represented by untreated HeG2 cells. We consider two biological replicate and two technical replicate for each treated sample, including control samples.
HepG2 cell pellets dedicated to proteomics analysis were homogenized in RIPA buffer (50mM Tris-HCl, pH 7.5; 150mM NaCl; 1% Triton X 100; 1% sodium deoxycholate; 0.1% SDS) added with a protease inhibitor cocktail (Sigma-Aldrich) on ice. Protein lysates were clarified by centrifugation at 14,000 rpm for 15 min at 4 C. Total protein content in each sample was determined by the Pierce BCA Protein Assay Kit (Thermo scientific, Rockford, IL, USA) according to manufacturers instructions, reading absorbance at 562 nm on a NanoDrop spectrophotometer (Thermo). 25 ug of total proteins from each sample were loaded and separated on a 1D gel NuPAGE 4 12% (Novex, Invitrogen, Carlsbad, CA, USA) run in MOPS buffer and stained with the Colloidal Blue Staining kit (Invitrogen, Carlsbad, CA, USA). The entire gel lanes were cut in 12 homogeneous slices which were subjected to trypsin digestion after the reduction and alkylation step, according to an established protocol (Snevechenko et al. 1996). The resulting peptide mixtures were separated by a nanoflow reversed-phase liquid chromatography tandem mass spectrometry using an HPLC Ultimate 3000 (DIONEX, Sunnyvale, CA, USA) connected with a linear ion trap (LTQ XL, ThermoElectron, San Jose, CA) equipped with a nano-electrospray ion source (ESI).
Peptides were at first desalted in a trap column (Acclaim PepMap 100 C18, LC Packings, DIONEX) and then separated in a 10 cm long reverse phase column (Silica Tips FS 360-75-8, New Objective, Woburn, MA, USA) slurry packed in-house with 5 um, 200 A pore size C18 resin (Michrom BioResources, CA). Peptides were eluted using a linear gradient from 96% of buffer A (H2O with 5% acetonitrile and 0.1% formic acid) to 60% of buffer B (acetonitrile with 5% H2O and 0.1% formic acid) for 40 min, at 300 nL/min flow rate.
Peptide ions were analyzed in positive mode, and the HV potential was set up around 1.7 kV. Full MS spectra (m/z 400-2000 mass range) were acquired in a data dependent mode in which each full MS scan was followed by five MS/MS scans, where the five most abundant molecular ions were dynamically selected and fragmented by CID, using a normalized collision energy of 35%.
Database searches were performed using the Sequest algorithm, embedded in Proteome Discoverer 1.4 (PD1.4, Thermo Fisher Scientific). The search criteria for protein identification were set to at least two matching peptides per protein. Tandem mass spectra were analyzed by Sequest HT and matched against the human database (UniProtKB/Swiss Prot protein database, featuring 23.316 entries). Spectra files were searched using Proteome Discoverer 1.4 (ThermoFisher) as search engine with carbamidomethylation on cysteine as static modification, methionine oxidation as variable one and full tryptic peptides with a maximum of two missed cleavages allowed were considered for identification. A mass tolerance of 1.5 Da for precursor ion and 0.8 Da for fragment ions were applied.
The Percolator node of PD1.4 was used for peptide validation based on q-values, choosing high confidence corresponding to a false discovery rate (FDR) inferior to 1% on peptide level. Proteins were identified with a minimum of 2 peptides. Two biological replicas were analyzed and for each replica, two technical replicas were performed.
2021-10-14 | MSV000088230 | MassIVE
Project description:Due to environmental persistence and biotoxicity of polybrominated diphenyl ethers (PBDEs), it is urgent to develop potential technologies to remediate PBDEs. Introducing electrodes for microbial electricity generation to stimulate the anaerobic degradation of organic pollutants is highly promising for bioremediation. However, it is still not clear whether the degradation of PBDEs could be promoted by this strategy. In this study, we hypothesized that the degradation of PBDEs (e.g., BDE-209) would be enhanced under microbial electricity generation condition. The functional compositions and structures of microbial communities in closed-circuit microbial fuel cell (c-MFC) and open-circuit microbial fuel cell (o-MFC) systems for BDE-209 degradation were detected by a comprehensive functional gene array, GeoChip 4.0, and linked with PBDE degradations. The results indicated that distinctly different microbial community structures were formed between c-MFCs and o-MFCs, and that lower concentrations of BDE-209 and the resulting lower brominated PBDE products were detected in c-MFCs after 70-day performance. The diversity and abundance of a variety of functional genes in c-MFCs were significantly higher than those in o-MFCs. Most genes involved in chlorinated solvent reductive dechlorination, hydroxylation, methoxylation and aromatic hydrocarbon degradation were highly enriched in c-MFCs and significantly positively correlated with the removal of PBDEs. Various other microbial functional genes for carbon, nitrogen, phosphorus and sulfur cycling, as well as energy transformation process, were also significantly increased in c-MFCs. Together, these results suggest that PBDE degradation could be enhanced by introducing the electrodes for microbial electricity generation and by specifically stimulating microbial functional genes.
| S-EPMC3734261 | biostudies-literature
Project description:Sinorhizobium meliloti 209 Resequencing
| PRJNA501494 | ENA
Project description:Transcriptomic characterization of BDE-47 exposed cultured primary human cytrophoblasts (2nd trimester) undergoing differentiation in vitro.
2018-09-01 | GSE104896 | GEO
Project description:Spirosoma sp. 209 Genome sequencing and assembly
| PRJNA373991 | ENA