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MiRNA expression profiling of Human Myeloma Cell Lines Pre- and Post- 5'azacytidine Treatment

ABSTRACT: We performed genome-wide miRNA expression profiling (MEP) of a panel of four human Myeloma cell lines treated with 5'azacytidine compared to control (DMSO treatment), with the objective of unmasking miRNAs silenced by DNA hypermethylation.

ORGANISM(S): Homo sapiens

PROVIDER: GSE53850 | GEO | 2015/08/31

SECONDARY ACCESSION(S): PRJNA233568

REPOSITORIES: GEO

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miRNA expression profiling of Human Myeloma Cell Lines Pre- and Post- 5'azacytidine Treatment

Project description:We performed genome-wide miRNA expression profiling (MEP) of a panel of four human Myeloma cell lines treated with 5'azacytidine compared to control (DMSO treatment), with the objective of unmasking miRNAs silenced by DNA hypermethylation. Total RNA, including miRNA, were extracted using Qiagen miRNeasy kit and profiled using Agilent Human MiRNA Array (Release 16.0, 8X60k)

2015-08-31 | E-GEOD-53850 | biostudies-arrayexpress

Azacytidine time course on MCF7 cells

Project description:MCF7 cells at 80% confluency were treated with 5 micromolar azacytidine with gene expression profiling determined at 0, 1, 2, 3, 4, 6 and 12 hours of exposure to compound. Keywords: time course Approximately 5,000,000 million cells were plated into 10 cm plates from a common pool. Cells were grown in DMEM supplemented with 10% foetal calf serum until 80% confluency was attained. Cells were then exposed to 5 micromolar azacytidine prepared as a 10 millimolar stock in DMSO. Each time point was represented by three biological replicates. Total RNA was extracted from the cells using the trizol method and RNA samples were validated for integrity throughout the isolation and extraction procedure. All gene expression profiles showed similar distributions with similar raw median intensities.

2008-01-11 | E-GEOD-10145 | biostudies-arrayexpress

A comparative analysis of 5-azacytidine and zebularine induced DNA demethylation using whole-genome bisulfite sequencing

Project description:The non-methylable cytosine analogs, 5-azacytidine and zebularine, are widely used to disrupt DNA methyltransferase activity and reduce genomic DNA methylation. In this study, whole-genome bisulfite sequencing is used to construct maps of DNA methylation with single base pair resolution in Arabidopsis thaliana seedlings treated with each demethylating agent. We find that 5-azacytidine and zebularine-treated seedlings have nearly indistinguishable patterns of DNA methylation genome-wide and that 5-azacytidine, despite being more unstable in aqueous solution, has a slightly greater demethylating effect at higher concentrations across the genome. Transcriptome analyses revealed a substantial number of up-regulated genes and transposable element genes, particularly CACTA-like elements, demonstrating that chemical demethylating agents have a disproportionately large effect on loci that are silenced by DNA methylation. Bisulfite-Seq and RNA-Seq

2016-06-24 | E-GEOD-80300 | biostudies-arrayexpress

A comparative analysis of 5-azacytidine and zebularine induced DNA demethylation using whole-genome bisulfite sequencing

2016-06-24 | GSE80300 | GEO

Gene expression profile of OSSL_325096 treated myeloma cells

Project description:OSSL_325096 is a compound that acts as p97/VCP inhibitor and induces apoptosis in myeloma cells. Therefore, we treated KMS12PE and KMS11 myeloma cell lines with OSSL_325096 or DMSO and compare gene expression levels to elucidate the mechanisms of apoptosis.

2019-08-30 | GSE118320 | GEO

Widespread chromatin activation underlies pathogenic mechanisms in multiple myeloma

Project description:RNA-seq analysis comparing the transcriptional landscape of PRDM5 silenced vs mock KMS-11 multiple myeloma cell line

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Gene regulation in Erbb2 transfected NIH3T3 cells after Azacytidine treatment

Project description:5-Azacytidine or 5-aza-2’-deoxycytidine is a chemical analogue of the cytosine nucleoside used in DNA and RNA. Cells in the presence of 5-azacytidine incorporate it into DNA during replication and RNA during transcription. The incorporation of 5-azacytidine into DNA or RNA inhibits methyltransferase thereby causing demethylation in that sequence, affecting the way that cell regulation proteins are able to bind to the DNA/RNA substrate. Inhibition of DNA occurs through the formation of stable complexes between the molecule and with DNA methyltransferases, thereby saturating the cells methylation machinery. 5-azacytidine is mainly used in the treatment of myelodysplastic syndrome. Changes in gene expression levels in Erbb2 transfected murine fibroblast cell line after treatment with Azacytidine in two different concentrations were analysed. Keywords: cDNA microarray, murine fibroblast, azacytidine treatment, carcinogenesis

2009-10-01 | GSE8374 | GEO

RNA-seq of MOLM-13 acute myeloid leukemia cell line treated with single and combination 5-Azacytidine and CB-5083

Project description:MOLM-13 acute myeloid leukemia cells were treated with 7 µM 5-Azacytidine (Cayman Chemical 11164), or 450 nM CB-5083 (Cayman Chemical 19311), or in combination, or 0.1% DMSO as control. Treatments were conducted for 48 hours.

2023-04-22 | E-MTAB-12848 | biostudies-arrayexpress

Gene regulation in Erbb2 transfected NIH3T3 cells after Azacytidine treatment

Project description:5-Azacytidine or 5-aza-2â??-deoxycytidine is a chemical analogue of the cytosine nucleoside used in DNA and RNA. Cells in the presence of 5-azacytidine incorporate it into DNA during replication and RNA during transcription. The incorporation of 5-azacytidine into DNA or RNA inhibits methyltransferase thereby causing demethylation in that sequence, affecting the way that cell regulation proteins are able to bind to the DNA/RNA substrate. Inhibition of DNA occurs through the formation of stable complexes between the molecule and with DNA methyltransferases, thereby saturating the cells methylation machinery. 5-azacytidine is mainly used in the treatment of myelodysplastic syndrome. Changes in gene expression levels in Erbb2 transfected murine fibroblast cell line after treatment with Azacytidine in two different concentrations were analysed. Keywords: cDNA microarray, murine fibroblast, azacytidine treatment, carcinogenesis Gene expression levels of Erbb2 transfected NIH3T3 cell lines treated with 5ÂµM and 10ÂµM Azacytidine were compared to Erbb2 transfected but non-treated NIH3T3 cell line. For each Azacytidine concentration 4-8 experiments were performed including 50% dye swaps. As a controll experiments gene expression levels of NIH3T3 cells with and without Azacytidine treatment were analysed

2009-10-01 | E-GEOD-8374 | biostudies-arrayexpress

RNAseq to investigate transcriptional changes in human MM cell lines due to panobinostat, 5-Azacytidine, panobinostat+5-Azacytidine or n-methyl-2-pyrroldine (NMP) treatments.

Project description:Purpose: We applied RNA sequencing technology for high-throughput analysis of transcriptional changes within human MM cell lines JJN3 and U266 due to individual and combination drug treatment. Methods: JJN3 and U266 cells were treated with pan-HDACi panbobinostat, DNMTi 5-Azacytidine, panobinostat+5-Azacytidine or NMP for 4h or 24h in triplicate and transcriptional changes assessed by RNAseq using Illumina HiSeq platform. Specifically, JJN3 cells were treated with 10nM panobinostat, 2.5µM 5-Azacytidine, panobinostat+5-Azacytidine (at given doses), or 10mM NMP. U266 cells were treated with 10nM panobinostat, 10µM 5-Azacytidine, panobinostat+5-Azacytidine (at given doses), or 10mM NMP. Results: We report unique and overlapping transcriptional signatures that lead to the induction of apoptosis in human MM cell lines in a cell-specific manner due to individual or combination treatments. Conclusions: A detailed analysis of differential transcriptional events in human MM cell lines due to HDACi, DNMTi, HDACi+DNMTi and NMP appear to define the molecular events leading to apoptosis and drug mechanism of action.

2014-04-09 | GSE56623 | GEO

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