Human stool exposomics analysis
Ontology highlight
ABSTRACT:
ORGANISM(S): Human Homo Sapiens
TISSUE(S): Feces
SUBMITTER: 
Xin Hu
PROVIDER: ST001804 | MetabolomicsWorkbench | Fri May 07 00:00:00 BST 2021
REPOSITORIES: MetabolomicsWorkbench
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| mwtab | Other |
Items per page: 5 1 - 1 of 1 |
Similar Datasets
Project description:In the small number of thyroids that was analyzed with XLE, 14 environmental chemicals were quantified. The most prevalent was p,p’-DDE, detected in 4 out of 5 thyroid samples, with median concentration (2.20 ng/g). The amounts of individual chemicals were highly variable among the individuals, and the small number of samples precludes any generalization. Nevertheless, HCA of correlation matrix showed high correlation of chemicals measured in the thyroid samples was similar to that in the lung and plasma.
2021-05-07 | ST001803 | MetabolomicsWorkbench
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:We tested the general utility of XLE in a variety of human biological samples by analyzing human lung and thyroid tissues and stool samples. We quantified 32 environmental chemicals in 11 human lungs, with HCB, PCB-28 and PCB-18 being most frequently detected (10 out of 11). The commonly detected chemicals in human plasma were detected less frequently in the lung. For the 11 lungs, p,p’-DDE was detected in eight, PCB-153 in five, PBDE-47 and PCB-138 in four and PCB-180 in three. Although the plasma samples were from non-diseased individuals and the lungs were both diseased and non-diseased individuals, HCA results suggest that environmental chemical profiles in human lung may be very different from plasma.
2021-05-06 | ST001802 | MetabolomicsWorkbench
Project description:Genome wide DNA methylation profiling of cord blood in Faroe Island cohort. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 485,000 CpGs in cord blood samples. Background: Faroe islanders consume marine foods contaminated with methylmercury (MeHg), polychlorinated biphenyls (PCBs), and other toxicants associated with chronic disease risks. Differential DNA methylation at specific CpG sites in cord blood may serve as a surrogate biomarker of health impacts from chemical exposures. Objective: We aimed to identify key environmental chemicals in cord blood associated with DNA methylation changes in a population with elevated exposure to chemical mixtures. Method: We studied 72 participants of a Faroese birth cohort recruited between 1986 and 1987 and followed until adulthood. The cord blood DNA methylome was profiled using Infinium Methylation 450K BeadChips. We determined the associations of CpG site changes with concentrations of MeHg, major PCBs, other organochlorine compounds, (hexachlorobenzene [HCB], p,p’-dichlorodiphenyldichloroethylene [p,p’-DDE] and p,p’-dichlorodiphenyltrichloroethane) and perfluoroalkyl substances. Results: In a combined sex analysis, among the 16 chemicals studied, PCB congener 105 (CB-105) exposure was associated with the majority of differentially methylated CpG sites (214 out of a total of 250). In female-only-analysis, only 73 CB-105 associated CpG sites were detected, 44 of which were mapped to genes in the ELAV1-associated cancer network. In males-only, methylation changes were seen for perfluorooctane sulfonate, HCB, and p,p’-DDE in 10,598; 1,238; and 1,473 CpG sites, respectively, 15% of which were enriched in cytobands of the X chromosome associated with neurological disorders. Conclusion: In this multiple-pollutant and genome-wide study, we identified key epigenetic toxicants. The significant enrichment of specific X-chromosome sites in males implies potentially sex-specific epigenome responses to prenatal chemical exposures.
2018-03-30 | GSE104778 | GEO
Project description:We analyzed 80 archival samples from individuals (57 females, 23 males; aged 41 to 68 y) without known disease or occupational or environmental exposures of concern as a pilot to test the utility of XLE in large-scale human biomonitoring studies. Using a requirement for at least 3 co-eluting accurate mass m/z features ( 5 ppm) within 30 s of database retention time, we identified 49 chemicals belonging to various environmental chemical classes. An unsupervised 2-way hierarchical cluster analysis (HCA) of log transformed intensity showed clustering according to chemical class. In particular, persistent chemicals were highly correlated with each other (all raw P < 0.001), including p,p’-DDE, PCBs 153, 180, 138, 118 and 74, PBDE-47, hexachlorobenzene (HCB) and trans-nonachlor. Results showed a general increase of chemical levels with increasing age quartiles (Q3 and Q4 : 53 to 68 versus Q1 and Q2: 41 to 52) using unsupervised clustering, a trend particularly evident for the cluster of p,p’-DDE, PCBs 153, 180, 138, 118 and 74, PBDE-47, HCB and trans-nonachlor. Examination of data according to body mass index (BMI) showed that individuals with BMI ≥ 40 had lower levels of environmental chemicals, which may be attributed to high lipophilicity and propensity to distribute in adipose tissue versus plasma. Quantification with reference standardization showed that use of two SRM samples with differing environmental chemical concentrations can overcome variable batch effects in quantification for large-scale studies. Examples of the most frequently detected chemicals shows that overall distributions were positively skewed by a small subset of individuals with high concentrations.
2021-05-06 | ST001801 | MetabolomicsWorkbench
Project description:We analyzed 80 archival samples from individuals (57 females, 23 males; aged 41 to 68 y) without known disease or occupational or environmental exposures of concern as a pilot to test the utility of XLE in large-scale human biomonitoring studies. Using a requirement for at least 3 co-eluting accurate mass m/z features ( 5 ppm) within 30 s of database retention time, we identified 49 chemicals belonging to various environmental chemical classes. An unsupervised 2-way hierarchical cluster analysis (HCA) of log transformed intensity showed clustering according to chemical class. In particular, persistent chemicals were highly correlated with each other (all raw P < 0.001), including p,p’-DDE, PCBs 153, 180, 138, 118 and 74, PBDE-47, hexachlorobenzene (HCB) and trans-nonachlor. Results showed a general increase of chemical levels with increasing age quartiles (Q3 and Q4 : 53 to 68 versus Q1 and Q2: 41 to 52) using unsupervised clustering, a trend particularly evident for the cluster of p,p’-DDE, PCBs 153, 180, 138, 118 and 74, PBDE-47, HCB and trans-nonachlor. Examination of data according to body mass index (BMI) showed that individuals with BMI ≥ 40 had lower levels of environmental chemicals, which may be attributed to high lipophilicity and propensity to distribute in adipose tissue versus plasma. Quantification with reference standardization showed that use of two SRM samples with differing environmental chemical concentrations can overcome variable batch effects in quantification for large-scale studies. Examples of the most frequently detected chemicals shows that overall distributions were positively skewed by a small subset of individuals with high concentrations.
2021-05-06 | ST001800 | MetabolomicsWorkbench
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:Hexachlorobenzene (HCB) [CAS:118-74-1; CHEBI:5692] is a persistent environmental pollutant with toxic effects in man and rat. Reported adverse effects are hepatic porphyria, neurotoxicity, and adverse effects on the reproductive and immune system. To obtain more insight into HCB-induced mechanisms of toxicity, we studied gene expression levels using DNA microarrays. For 4 weeks, Brown Norway rats were fed a diet supplemented with 0, 150, or 450 mg HCB/kg. Spleen, mesenteric lymph nodes (MLN), thymus, blood, liver, and kidney were collected and analyzed using the Affymetrix rat RGU-34A GeneChip microarray. Most significant (p < 0.001) changes, compared to the control group, occurred in spleen, followed by liver, kidney, blood, and MLN, but only a few genes were affected in thymus. This was to be expected, as the thymus is not a target organ of HCB. Transcriptome profiles confirmed known effects of HCB such as stimulatory effects on the immune system and induction of enzymes involved in drug metabolism, porphyria, and the reproductive system. In line with previous histopathological findings were increased transcript levels of markers for granulocytes and macrophages. New findings include the upregulation of genes encoding proinflammatory cytokines, antioxidants, acute phase proteins, mast cell markers, complements, chemokines, and cell adhesion molecules. Generally, gene expression data provide evidence that HCB induces a systemic inflammatory response, accompanied by oxidative stress and an acute phase response. In conclusion, this study confirms previously observed (immuno)toxicological effects of HCB but also reveals several new and mechanistically relevant gene products. Thus, transcriptome profiles can be used as markers for several of the processes that occur after HCB exposure.
2011-11-08 | E-TOXM-15 | biostudies-arrayexpress
Project description:Endocrine disruption (ED) can trigger far-reaching effects on environmental populations, justifying a refusal of market approval for chemicals with ED properties. For the assessment of ED effects on the thyroid system, regulatory decisions mostly rely on amphibian studies. Here we present a rapid and reproducible data dependent proteomics approach for identifying comprehensive molecular signatures of interference with the thyroid system in zebrafish (Danio rerio) embryos as an alternative to animal testing. For this, we have analysed the thyroid hormone thyronin (T3) as model substances for thyroidal activity in a modified zebrafish embryo toxicity test (zFET). These fingerprints allow for a definition of solid biomarkers as tools in screening approaches and for integration in chronic toxicity studies for suspect substances, such as the fish early life-stage test (OECD TG 210).
2021-01-14 | PXD019111 | Pride
Project description:Endocrine disruption (ED) can trigger far-reaching effects on environmental populations, justifying a refusal of market approval for chemicals with ED properties. For the assessment of ED effects on the thyroid system, regulatory decisions mostly rely on amphibian studies. Here we present a rapid and reproducible data dependent proteomics approach for identifying comprehensive molecular signatures of interference with the thyroid system in zebrafish (Danio rerio) embryos as an alternative to animal testing. For this, we have analysed the thyroid peroxidase inhibitor 6-propyl-2-thiouracil (6-PTU) as model substances for anti-thyroidal activity in a modified zebrafish embryo toxicity test (zFET). These fingerprints allow for a definition of solid biomarkers as tools in screening approaches and for integration in chronic toxicity studies for suspect substances, such as the fish early life-stage test (OECD TG 210).
2021-01-15 | PXD019079 | Pride