Whole genome analysis regulation in HepG2 cells exposed to cadmium
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE31286 | GEO | 2012/05/01
SECONDARY ACCESSION(S): PRJNA145865
REPOSITORIES: GEO
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Project description:Cadmium (Cd) is a metal present in working and living environments known to be toxic and carcinogenic, but its mechanism of action remains still unclear. We investigated the gene expression modulation in human hepatoma cell line HepG2 after exposure to 2 M-BM-5m and 10 M-BM-5m cadmium using Agilent Whole human genome expression microarray. HepG2 cells were treated for 24 hours with 2 M-NM-<M and 10 M-NM-<M Cd and normal medium as control. Three independent replicates were used for the each type of stimuli.
2012-04-30 | E-GEOD-31286 | biostudies-arrayexpress
Project description:From the result of comparative the gene expression analyses of human hepatoma cell line, HepG2 following exposures of three heavy metals; arsenic, cadmium and nickel and three carcinogens; N-dimethylnitrosoamine (DMN), 12-O-tetradecanoylphorbol-13-acetate (TPA) and tetrachloroethylene (TCE), 31-55% of the genes altered by As, Cd and Ni exposure were overlapped with those by three model carcinogen exposures in our experiments. In particular, three heavy metals shared certain characteristics with TPA and TCE in remarkable up-regulations of the genes associated with progression of cell cycle, which might play a central role in heavy metal carcinogenesis. In addition, this characteristic of gene expressions alteration was counteracted by intracellular accumulation of vitamine C in As-exposed cells but not in Cd- and Ni-exposed cells. These results suggest that the cell proliferative responses are caused by reactive oxygen species mainly in As exposure, while other mechanisms would be involved in these responses in Cd and Ni exposures. Experiment Overall Design: In this study, we examined the gene expression alteration in human hepatoma cell line, HepG2 following exposures of three heavy metals; arsenic, cadmium and nickel and three carcinogens; N-dimethylnitrosoamine (DMN), 12-O-tetradecanoylphorbol-13-acetate (TPA) and tetrachloroethylene (TCE) using DNA microarray with 8795 human genes. Furthermore, we also performed the DNA microarray analyses for the heavy metal exposed-cells that were loaded with vitamine C beforehand to examine the effects of antioxidant molecule to heavy metal exposures.
2008-06-16 | E-GEOD-8865 | biostudies-arrayexpress
Project description:Heavy metal cadmium (Cd) affects seriously crop growth, quality and yield, and has potential threats to human safety. We found the difference of two ryegrasses (Lolium multiflorum Lam.), a high-Cd tolerance (LmHC) and a low-Cd tolerance (LmLC) cultivars , in response to cadmium stress. The germination rate, plant growth, and fresh weight of LmHC were much better than that of LmLC. So we use RNA sequencing to investigate the differentially expressed genes(DEGs) about cadmium response between LmHC and LmLC. Real-time quantitative PCR analysis showed that the same DEGs of LmLC and LmHC had obviously difference expression level under Cd treatment. It was suggestion that differential expression of DEGs might be involved in regulating Cd tolerance, accumulation and translocation.These results will be helpful for understanding the underlying molecular mechanism in Cd toxicity and provide references for improving the ecological environment through genetic improvement.
2020-01-30 | GSE144460 | GEO
Project description:Thermococcus gammatolerans, the most radioresistant archaeon known to date, is an anaerobic and hyperthermophilic sulfur-reducing organism living in deep-sea hydrothermal vents. Knowledge of mechanisms underlying archaeal metal tolerance in such metal-rich ecosystem is still poorly documented. We showed that T. gammatolerans exhibits high resistance to cadmium (Cd), cobalt (Co) and zinc (Zn), a weaker tolerance to nickel (Ni), copper (Cu) and arsenate (AsO4) and that cells exposed to 1mM Cd exhibit a cellular Cd concentration of 67µM. A time-dependent transcriptomic analysis using microarrays was performed at a non-toxic (100μM) and a toxic (1mM) Cd dose. The reliability of microarray data was strengthened by real time RT-PCR validations. Altogether, 114 Cd responsive genes were revealed and a substantial subset of genes is related to metal homeostasis, drug detoxification, re-oxidization of cofactors and ATP production. This first genome-wide expression profiling study of archaeal cells challenged with Cd showed that T. gammatolerans withstands induced stress through pathways observed in both prokaryotes and eukaryotes but also through new and original strategies. T. gammatolerans cells challenged with 1mM Cd basically promote: 1) the induction of several transporter/permease encoding genes, probably to detoxify the cell; 2) the upregulation of Fe transporters encoding genes to likely compensate Cd damages in iron-containing proteins; 3) the induction of membrane-bound hydrogenase (Mbh) and membrane-bound hydrogenlyase (Mhy2) subunits encoding genes involved in recycling reduced cofactors and/or in proton translocation for energy production. By contrast to other organisms, redox homeostasis genes appear constitutively expressed and only a few genes encoding DNA repair proteins are regulated. We compared the expression of 27 Cd responsive genes in other stress conditions (Zn, Ni, heat shock, γ-rays), and showed that the Cd transcriptional pattern is comparable to other metal stress transcriptional responses (Cd, Zn, Ni) but not to a general stress response.
2012-08-01 | GSE13546 | GEO
Project description:Our main objectives were: 1) to identify transcriptional signatures specific to the exposure to two metals: Ni and Cd; 2) to investigate the mechanisms of toxicity for these two metals; and 3) to develop a predictive tool to identify the sublethal effects of Ni and Cd contaminants in fish sampled from natural environments. The molecular mechanisms underlying nickel (Ni) and cadmium (Cd) toxicity and their specific effects on fish are poorly understood. Documenting gene transcription profiles offers a powerful approach towards identifying the molecular mechanisms affected by these metals and to discover biomarkers of their toxicity. However, confounding environmental factors can complicate the interpretation of the results and the detection of biomarkers for fish captured in their natural environment. In the present study, a 1000 candidate-gene microarray, developed from a previous RNA-seq study on a subset of individual fish from contrasting level of metal contamination, was used to investigate the transcriptional response to metal (Ni and Cd) and non metal (temperature, oxygen, and diet) stressors in yellow perch (Perca flavescens). Specifically, we aimed at 1) identifying transcriptional signatures specific to Ni and Cd exposure, 2) investigating the mechanisms of their toxicity, and 3) developing a predictive tool to identify the sublethal effects of Ni and Cd contaminants in fish sampled from natural environments. A total of 479 genes displayed significantly different transcription levels when temperature varied while 287 and 177 genes were differentially transcribed at different concentrations of Ni and Cd, respectively. These metals were found to mainly affect the transcription level of genes involved in iron metabolism, transcriptional and translational processes, vitamin metabolism, blood coagulation, and calcium transport. In addition, a linear discriminant analysis (LDA) made using gene transcription levels yielded 94% correctly reassigned samples regarding their level of metal contamination, which indicates the potential of the microarray to detect perch response to Cd or Ni effects. Comparison between fish exposed to three temperatures (11, 20, 28M-BM-0C) using a loop design, comparison between control fish and fich exposed to restrictive diet using a pairwise design, comparison between fish exposed to hypoxia and control fish, comparison between fish exposed to two concentrations of cadmium and control fish using a loop design, and comparison between fish exposed to two concentrations of nickel and control fish using a loop design.
2013-09-19 | E-GEOD-50975 | biostudies-arrayexpress
Project description:Plant growth is severely affected by toxic concentrations of the non-essential heavy metal cadmium (Cd). Comprehensive transcriptome analysis by RNA-Seq following cadmium exposure is required to further understand plant responses to Cd and facilitate future systems-based analyses of the underlying regulatory networks. In this study, rice plants were hydroponically treated with 50 µM Cd for 24 hours. In total, ~60,000 transcripts, including transcripts that could not be characterized by microarray-based approaches, were evaluated and ~36,000 transcripts were responsive to Cd exposure. Among multigenic families that may protect cells from generated ROS and reduce Cd toxicity, prominently upregulated antioxidant enzyme genes were identified. Furthermore, 168 different metal ion transporter genes, which might mediate the transport of transition Cd, responded to Cd exposure. qRT-PCR analysis of randomly selected genes indicated that their expression changed obviously after exposure to various heavy metal stresses. The Cd responsive genes included many abiotic stress (drought, high-salinity, low temperature) responsive genes. Based on further investigation into the expression patterns of abiotic stress regulatory genes such as DREB, part of the signal transduction pathway for Cd exposure was determined to cross-talk with abiotic stress signaling pathways. Our results provide useful information for further studies of the molecular mechanisms of plant adaptation to Cd exposure and the improvement of Cd tolerance in crop species.
2014-08-07 | E-MTAB-4306 | biostudies-arrayexpress
Project description:In this study, the metabolic adjustments performed by maize (Zea mays L) seminal roots exposed to 25 µM Cd2+ or 25 µM Cu2+ at pre-emergence are compared, focusing on the proteomic changes after metal exposure. Root width was increased, and root length was decreased after 72 h of metal treatment. Both metals induced H2O2 accumulation and lipid peroxidation in the root tip. These changes were accompanied by increases in lipoxygenase activity and 4-hydroxy-2-nonenal content. NMR spectroscopy revealed that the abundance of 38 water-soluble metabolites was significantly modified by Cd and Cu exposure; this set of metabolites comprised carboxylic acids, amino acids, carbohydrates, and unidentified phenolic compounds. Linoleic acid content significantly decreased in Cu-treated samples. The total amount of proteins detected in maize root apexes was 2,171. Gene ontology enrichment analysis of the differentially accumulated proteins was performed to detect pathways probably affected by metal additions. Both metals altered redox homeostasis, up-regulated oxylipins biosynthetic process, and shifted metabolism towards the oxidative pentose-phosphate in the root apexes. However, the methionine salvage pathway appears as a key metabolic module only under Cd stress. The integrative analysis carried out in this study suggests that most molecular features behind the reprogramming of maize root tips to cope with cadmium and copper toxicity are common, but some are not.
2023-11-22 | PXD043243 | Pride
Project description:Verbena bonariensis is a species with excellent garden plant, good environmental adaptability and great potential for future development.Cadmium has caused serious heavy metal pollution in the soil, which has posed a great threat to plant growth. In this study, Illumina sequencing technology was used to sequence the transcriptome of Verbena bonariensis leaf under normal and Cd stress, respectively. In total, 95,013 transcripts and 63021 genes with an average length of 923 bp and 1,246 bp were constructed from the clean sequence reads, respectively. And 1037 DEGs were found in response to cadmium treatment, of which 10 were selected for qRT-PCR. In conclusion, this study first identified the Verbena bonariensis as a heavy metal tolerant plant and provided the first large-scale transcriptional data set in response to cadmium stress. Our research will help to understand the mechanism of resistance to Cd in the Verbena bonariensis and provide clues for further studies on the relationships between plants and heavy metals in other Verbenaceae plants.
2018-01-18 | GSE101600 | GEO
Project description:Obesity is considered as a major public health concern with strong economic and social burdens. Exposure to pollutants such as heavy metals can contribute to the development of obesity and its associated metabolic disorders, including type 2 diabetes and cardiovascular diseases. Adipose tissue is an endocrine and paracrine organ that plays a key role in the development of these diseases and is one of the main target of heavy metal accumulation. In this study, we determined by inductively coupled plasma mass spectrometry cadmium concentrations in human subcutaneous and visceral adipose tissues, ranging between 2.5 nM and 2.5 µM. We found a positive correlation between cadmium levels and age, sex and smoking status and a negative correlation between cadmium and body mass index. Based on cadmium adipose tissue concentrations found in humans, we investigated the effects of cadmium exposure, at concentrations between 1 nM and 10 µM, on adipose-derived human mesenchymal stem cells differentiated into mature adipocytes in vitro. Transcriptomic analysis highlighted that such exposure altered the expression of genes involved in trace element homeostasis and heavy metal detoxification, such as Solute Carrier Family transporters and metallothioneins. This effect correlated with zinc level alteration in cells and cellular media. Interestingly, dysregulation of zinc homeostasis and transporters has been particularly associated with the development of obesity and type 2 diabetes. Moreover, we found that cadmium exposure induces the pro-inflammatory state of the adipocytes by enhancing the expression of genes such as IL-6, IL-1B and CCL2, cytokines also induced in obesity. Finally, cadmium modulates various adipocyte functions such as the insulin response signaling pathway and lipid homeostasis. Collectively, our data identified some of the cellular mechanisms by which cadmium alters adipocyte functions, thus highlighting new facets of its potential contribution to the progression of metabolic disorders.
2023-06-29 | MTBLS4128 | MetaboLights
Project description:We investigated the impact of cadmium on the global transcriptome of E. coli wild type, ∆gshA and ∆gshB mutant cells to evaluate the molecular basis of cadmium toxicity in the presence or absence of cellular thiols. This global transcriptome analysis were done with cells synthezising GSH (wild type), gamma-glutamyl-cysteine (∆gshB mutant) or neither of the two cellular thiols (∆gshA mutant) under the influence of 100 µM Cd(II).
2008-05-31 | GSE11562 | GEO