DNA methylation anaylsis of placenta samples exposed to variable levels of arsenic during pregnancy
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE71678 | GEO | 2016/07/01
SECONDARY ACCESSION(S): PRJNA291784
REPOSITORIES: GEO
Similar Datasets
Project description:Genome-wide profiling of placental DNA methylation in relation to arsenic exposure. The Illumina 450k methylation array was used to profile 343 samples for which 3 different measurements of arsenic exposure were available during gestation. These samples have been collected from the New Hampshire Birth Cohort Study (NHBCS). Bisulfite converted DNA was hybridized to the 450k platform and processed at the University of Minnesota Genomic Core
2016-07-01 | E-GEOD-71678 | biostudies-arrayexpress
Project description:Genome wide DNA methylation profiling of arsenic exposure and non-exposure population and patients with skin leisons. The Illumina Infinium HumanMethylation450 BeadChip (HM450K) was used to obtain DNA methylation profiles across approximately 450,000 CpGs in genomic DNA extracted from blood buffy coat samples. Samples included 66 arsenic exposure individuals, 35 non-exposure individuals and 18 arsenical skin lesion patients.
2018-07-10 | GSE109914 | GEO
Project description:Arsenic is environmental risk factor and has been linked to urothelial carcinoma incidence. Arsenic exposure-induced malignant transformed cells was established from normal urothelial cells by chronic arsenic exposure for 10 months. The purpose of the present study is to elucidate the relevant molecular alterationon on arsenic-induced malignant transformation.
2016-11-19 | GSE90023 | GEO
Project description:We are investigating the transcriptional response of newborns in response to prenatal arsenic exposure We used microarrays to detail the global programme of gene expression response due to prenatal arsenic exposure Keywords: dose (arsenic)
2007-11-01 | GSE7967 | GEO
Project description:We describe the alterations in DNA methylation around the promoter region and the impact on gene expression in HaCaT cells during the transformation process caused by chronic exposure to arsenic. Nucleic acids were extracted at the beginning of treatment and at weeks 0, 5, 15, and 25. Cell cultures with the same passage (week 25) and no arsenic treatment served as controls.
2019-11-02 | E-MTAB-7972 | biostudies-arrayexpress
Project description:We describe the alterations in DNA methylation around the promoter region and the impact on gene expression in HaCaT cells during the transformation process caused by chronic exposure to arsenic. Nucleic acids were extracted at the beginning of treatment and at weeks 0, 5, 15, and 25. Cell cultures with the same passage (week 25) and no arsenic treatment served as controls.
2019-11-02 | E-MTAB-7973 | biostudies-arrayexpress
Project description:Talemi2014 - Arsenic toxicity and
detoxification mechanisms in yeast
The model implements arsenite (AsIII)
transport regulation, its distribution within main cellular AsIII
pools and detoxification. The intracellular As pools considered are
free AsIII (AsIIIin), protein-bound AsIII (AsIIIprot), glutathione
conjugated AsIII (AsGS3) and vacuolar sequestered AsIII (vAsGS3).
This model is described in the article:
Mathematical modelling of
arsenic transport, distribution and detoxification processes in
yeast.
Talemi SR, Jacobson T, Garla V,
Navarrete C, Wagner A, Tamás MJ, Schaber J.
Mol. Microbiol. 2014 Jun; 92(6):
1343-1356
Abstract:
Arsenic has a dual role as causative and curative agent of
human disease. Therefore, there is considerable interest in
elucidating arsenic toxicity and detoxification mechanisms. By
an ensemble modelling approach, we identified a best
parsimonious mathematical model which recapitulates and
predicts intracellular arsenic dynamics for different
conditions and mutants, thereby providing novel insights into
arsenic toxicity and detoxification mechanisms in yeast, which
could partly be confirmed experimentally by dedicated
experiments. Specifically, our analyses suggest that: (i)
arsenic is mainly protein-bound during short-term (acute)
exposure, whereas glutathione-conjugated arsenic dominates
during long-term (chronic) exposure, (ii) arsenic is not stably
retained, but can leave the vacuole via an export mechanism,
and (iii) Fps1 is controlled by Hog1-dependent and
Hog1-independent mechanisms during arsenite stress. Our results
challenge glutathione depletion as a key mechanism for arsenic
toxicity and instead suggest that (iv) increased glutathione
biosynthesis protects the proteome against the damaging effects
of arsenic and that (v) widespread protein inactivation
contributes to the toxicity of this metalloid. Our work in
yeast may prove useful to elucidate similar mechanisms in
higher eukaryotes and have implications for the use of arsenic
in medical therapy.
This model is hosted on
BioModels Database
and identified by:
BIOMD0000000547.
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To the extent possible under law, all copyright and related or
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Public Domain Dedication for more information.
2014-09-04 | BIOMD0000000547 | BioModels
Project description:In the present study, we employed the RNA sequencing platform to examine the molecular response of zebrafish liver to arsenic exposure and carry out detailed transcriptomic analyses for further understanding of molecular toxicity. We found that several important biological processes were perturbed by arsenic exposure, including oxidation reduction, translation, iron ion transport, cell redox and homeostasis, as well as related pathways in metabolism and diseases. Furthermore, as there are currently no biomarker genes available for predicting arsenic exposure, we took the advantage of RNA sequencing platform to identify most suitable biomarker genes from top responsive genes to arsenic exposure. We first validated these top responsive genes by RT-qPCR in zebrafish and then in Japanese medaka (Oryzias latipes) at individual fish level for more robustly responsive genes across different fish species. Transcriptome profiling of arsenic-treated sample and control sample were generated by deep sequencing using 3' RNA-SAGE on the SOLiD system.
2013-09-04 | E-GEOD-48427 | biostudies-arrayexpress
Project description:The present study used microarray expression profiling to determine the effects of embryonic arsenic exposure. Fertilized killifish (Fundulus heteroclitus) eggs were exposed to 0, 5, 15, or 25ppm arsenic as sodium arsenite. To examine differentially expressed genes, the microarrays were probed using RNA obtained from the control and 25ppm-exposed killifish just after hatching. No differences were noted in survival or hatching success between any of the groups. After analysis, a set of 332 genes was found to accurately distinguish between the control and 25ppm exposure groups. Expression of several of the genes (CDBP1, Arts1, FetB, and Fbp7) was quantified by qPCR in the lower exposure groups and at earlier time points to examine temporal and dose-responsive expression patterns. These results will enable us to better understand how arsenic impacts development.
2011-08-01 | GSE29976 | GEO
Project description:The present study used microarray expression profiling to determine the effects of embryonic arsenic exposure. Fertilized killifish (Fundulus heteroclitus) eggs were exposed to 0, 5, 15, or 25ppm arsenic as sodium arsenite. To examine differentially expressed genes, the microarrays were probed using RNA obtained from the control and 25ppm-exposed killifish just after hatching. No differences were noted in survival or hatching success between any of the groups. After analysis, a set of 332 genes was found to accurately distinguish between the control and 25ppm exposure groups. Expression of several of the genes (CDBP1, Arts1, FetB, and Fbp7) was quantified by qPCR in the lower exposure groups and at earlier time points to examine temporal and dose-responsive expression patterns. These results will enable us to better understand how arsenic impacts development. Killifish eggs were fertilized, divided into petri dishes containing 40 eggs (n=10 replicate petri dishes), and cultured until hatch in 0 or 25 ppm arsenic as sodium arsenite. Four to five hatchlings within each petri dish were pooled to obtain RNA. A total of 20 arrays were probed, 10 with RNA from control fish and 10 with RNA from the arsenic-exposed fish.
2011-07-31 | E-GEOD-29976 | biostudies-arrayexpress