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MiRNA expression profile in HOS cells exposed to sodium fluoride

ABSTRACT: Fluorosis is caused due to excess of fluoride intake over a long period of time. Aberrant change in RUNX2-mediated signaling cascade is one of the decisive steps during the pathogenesis of fluorosis. Till date, role of fluoride on the epigenetic alterations is not studied. In the present study, global expression profiling ofshort non-coding RNAs, in particular miRNAs and snoRNAs was carried out in NaF treated HOS cells to understand their possible role in the development of fluorosis. RT-PCR and insilico hybridization revealed that miR-124 and miR-155 can be directly involved in the transcriptional regulation of RUNX2 and RANKL genes. Compare to control, C/D box analysis revealed mark elevation in the number of UG dinucleotides and D-box sequences in NaF exposed HOS cells. Herein, we report miR-124 and miR-155 as the new possible players involved in the development of fluorosis. We also state that the alterations in UG dinucleotides and D-box sequences of snoRNAs could be due to NaF exposure.

ORGANISM(S): synthetic construct Homo sapiens

PROVIDER: GSE57550 | GEO | 2015/01/01

SECONDARY ACCESSION(S): PRJNA246687

REPOSITORIES: GEO

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miRNA expression profile in HOS cells exposed to sodium fluoride

Project description:Fluorosis is caused due to excess of fluoride intake over a long period of time. Aberrant change in RUNX2-mediated signaling cascade is one of the decisive steps during the pathogenesis of fluorosis. Till date, role of fluoride on the epigenetic alterations is not studied. In the present study, global expression profiling ofshort non-coding RNAs, in particular miRNAs and snoRNAs was carried out in NaF treated HOS cells to understand their possible role in the development of fluorosis. RT-PCR and insilico hybridization revealed that miR-124 and miR-155 can be directly involved in the transcriptional regulation of RUNX2 and RANKL genes. Compare to control, C/D box analysis revealed mark elevation in the number of UG dinucleotides and D-box sequences in NaF exposed HOS cells. Herein, we report miR-124 and miR-155 as the new possible players involved in the development of fluorosis. We also state that the alterations in UG dinucleotides and D-box sequences of snoRNAs could be due to NaF exposure. HOS cells grown on MEM media were treated with sodium fluoride and total RNA was isolated from cells after one month of chronic exposure; Cells grown on six 25mm flask. two replicates of control and two different concentration of exposed samples; two replicate are served as control

2015-01-01 | E-GEOD-57550 | biostudies-arrayexpress

Gene expression profiling of HOS (human osteosarcoma) cells exposed to fluoride

Project description:Though fluoride is considered an essential trace element, chronic exposure to fluoride is known to cause toxic effects. Chronic exposure of high concentration of fluoride may leads to fluorosis. To understand the molecular mechanism of fluoride induced toxicity gene expression profiling was performed on osteosarcoma cells (HOS). Cells were exposed to sub-lethal concentration of fluoride (8 ppm) for 30 days. Our result demonstrates that fluoride alters multiple biological pathways including bone development, osteoblast differentiation and apoptotic pathways. HOS cells grown in MEM were treated with fluoride and total RNA was isolated from cells after 30 days exposure. Three replicates per group were used for the experiment.

2016-06-30 | E-GEOD-70719 | biostudies-arrayexpress

Identification of genes involved in apoptosis induced by sodium fluoride in rat oral epithelial cells

Project description:Although an appropriate range of fluoride is thought to be safe and effective, excessive fluoride intake results in toxic effects in either hard tissues of teeth and skeleton or soft tissues of kidney, lung and brain. It is also well known that fluoride at a millimolar range elicits the complex cellular responses such as enzyme activity, signal transduction and apoptosis in many kinds of cells. However, its toxic effects are still unclear. In this study, to identify genes involved in apoptosis induced by sodium fluoride (NaF) in rat oral epithelial ROE2 cells, global-scale gene expression analysis was carried out using a GeneChipM-BM-. system. NaF (2 mM) significantly induced apoptosis accompaning chromatin condensation and caspase-3 activation. Total RNA samples were prepared from the NaF-treated cells, and quality of the RNA was analyzed using a Bioanalyzer 2100. Gene expression was monitored by an Affymetrix GeneChipM-BM-. system with a Rat Genome 230 2.0 array. Sample preparation for array hybridization was carried out as described in the manufacturerM-bM-^@M-^Ys instructions.

2014-01-09 | E-GEOD-53937 | biostudies-arrayexpress

Gene expression profiling of HOS (human osteosarcoma) cells exposed to fluoride

2016-06-30 | GSE70719 | GEO

Sodium fluoride exposure leads to ATP depletion and altered RNA decay in Escherichia coli under anaerobic conditions

Project description:We report genome-wide transcriptome profiles of E. coli obtained in the absence (control) and presence of 20 mM and 70 mM sodium fluoride (NaF) under anaerobic conditions, and assess the impact of fluoride-dependent ATP depletion on RNA turnover. We found that transcripts with increased abundance in response to NaF treatment correspond to genes that control cell envelope and osmotic stress adaptation, signal transduction systems, lipid biosynthesis, amine and polyamine degradation as well as acquisition of iron and iron homeostasis. In contrast, downregulated genes are involved in glycolysis, fatty acid metabolism, amino acid biosynthesis, energy production, cytochrome c biogenesis, protein translocation, translation, translation factors, protein folding/processing factors, transport for amino acid, sugar, or ion, and RNA metabolism. By using a quantile-based K-means clustering approach to identify gene clusters with similar expression profiles, we identified subset (100 genes) of transcriptome whose gene expression was up- and down-regulated under fluoride and diluted fluoride conditions, respectively. In addition, we found that about 40% of the highly abundant transcripts carry repetitive extragenic palindromes (REPs). By determining the mRNA stability of osmC as well as yghA, and addressing their ribonucleases/enzymes required for RNA degradation under anaerobic conditions, we found that fluoride ions slow down RNA degradation by increasing RNA stability, in turn increasing the steady-state level of RNA. Furthermore, our results show that turnover of these REP-containing transcripts is dependent on RNase E. Collectively, our study not only reveal the effects of NaF at the whole transcriptome level under hypoxic growth conditions, but also shows that fluoride can affect gene expression post-transcriptionally by slowing down the ATP-dependent degradation of structured RNAs.

2023-03-10 | GSE211579 | GEO

Identification of genes involved in cell death induced by sodium fluoride in rat oral epithelial cells

2014-01-09 | GSE53937 | GEO

Unamplified mRNA abundance in miR-124 and mock-transfected cells

Project description:To compare total RNA levels in miR-124 and mock-transfected cells (Figure S3), 5-10 ug of total RNA from miR-124-transfected cells or mock-transfected cells or universal reference RNA (Stratagene Cat# 740000) was reverse transcribed with Superscript III (Invitrogen Cat# 18080085) in the presence of aminoallul-dUTP 5-(3-aminoallyl)-dUTP (Ambion Cat# AM8439) and natural dNTPs (GE Healthsciences Cat# US77212) with 10 ug of N9 primer (Invitrogen). Subsequently, amino-allyl-containing cDNAs from miR-124 and mock-transfected cells were covalently linked to Cy5 NHS-monoesters, and universal reference cDNA was covalently linked to Cy3 NHS-monoesters (GE HealthSciences Cat# RPN5661). Cy5- and Cy3-labeled cDNAs were mixed and diluted into 50 ul of solution containing 3x SSC, 25 mM Hepes-NaOH (pH 7.0), 20 ug human Cot-1 DNA (Invitrogen Cat# 15279011), 20 ug of poly(A) RNA (Sigma Cat# P9403), 25 ug of yeast tRNA (Invitrogen Cat# 15401029), and 0.3% SDS. The sample was incubated at 95 C for 2 min, spun at 14,000 rpm for 10 mins in a microcentrifuge, then hybridized at 65 C

2009-11-10 | GSE18837 | GEO

RNA-Seq of FEX1, FEX2 deleted S. cerevisiae (yeast) treated with sodium fluoride against untreated control

Project description:Fluoride is a highly abundant, naturally occurring toxicant that causes oxidative stress, cell cycle arrest, and apoptosis at high concentrations. Our lab has created a fluoride-sensitized yeast model lacking fluoride exporters, FEX1 and FEX2. These yeast undergo cell cycle arrest and apoptosis at over 1000-fold less fluoride concentration than in wild type, and oxidative stress within four hours. To determine the mechanism by which fluoride triggers oxidative stress, we grew cells in 25 mL YPD media at starting O.D. 0.1 in +/- 50 uM NaF. After four hours, the cells were washed twice with sterile water, and RNA was harvested and treated with DNAse. RNA was then sent to the the Yale Center for Genome Analysis for quality analysis with a Bioanalyzer and subsequent poly-A sequencing.

2021-12-02 | E-MTAB-8061 | biostudies-arrayexpress

Unamplified mRNA abundance in miR-124 and mock-transfected cells

2010-06-20 | E-GEOD-18837 | biostudies-arrayexpress

Micromolar fluoride alters ameloblast lineage cells in vitro

Project description:Previously characterized ameloblast-lineage cells were used in this study to determine whether micromolar levels of fluoride could be directly affect these cells. Six samples altogether were analyzed in this study. Every two of them were from a same biological souce and subject to with or without the treatment of 10uM NaF (the only difference between the two samples.) The experiment was repeated 3 times.

2010-06-30 | E-GEOD-5365 | biostudies-arrayexpress

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