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Expression data from NKYS transfected with siRNAs or plasmids

ABSTRACT: The siRNA transfection includes JAK3 and EZH2 siRNAs. The plasmid transfection includes EZH2 WT and its mutants. We used gene expression data from JAK3 siRNA to test whether it affected epigenetic regulation, and used EZH2 mutants to study how it affected EZH2 canonical function. Whole genome microarray comparison of JAK3/EZH2 manipulations and control

ORGANISM(S): Homo sapiens

SUBMITTER: Chong-Lei Bi

PROVIDER: E-GEOD-75680 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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EZH2 phosphorylation by JAK3 mediates a switch to noncanonical function in natural killer/T-cell lymphoma.

Yan Junli J Li Boheng B Lin Baohong B Lee Pei Tsung PT Chung Tae-Hoon TH Tan Joy J Bi Chonglei C Lee Xue Ting XT Selvarajan Viknesvaran V Ng Siok-Bian SB Yang Henry H Yu Qiang Q Yu Qiang Q Chng Wee-Joo WJ

Blood 20160613 7

The best-understood mechanism by which EZH2 exerts its oncogenic function is through polycomb repressive complex 2 (PRC2)-mediated gene repression, which requires its histone methyltransferase activity. However, small-molecule inhibitors of EZH2 that selectively target its enzymatic activity turn out to be potent only for lymphoma cells with EZH2-activating mutation. Intriguingly, recent discoveries, including ours, have placed EZH2 into the category of transcriptional coactivators and thus rais ...[more]

PMID: 27297789

Similar Datasets

Expression data from NKYS transfected with siRNAs or plasmids

Project description:The siRNA transfection includes JAK3 and EZH2 siRNAs. The plasmid transfection includes EZH2 WT and its mutants. We used gene expression data from JAK3 siRNA to test whether it affected epigenetic regulation, and used EZH2 mutants to study how it affected EZH2 canonical function.

2016-07-26 | GSE75680 | GEO

mRNA expression after siRNA-mediated knock down of Enhancer of zeste homolog 2 (Ezh2) in human umbilical vein endothelial cells

Project description:mRNA expression after Ezh2 knock down was analyzed to identify genes regulated by Ezh2. Human umbilical vein endothelial cells (HUVEC) were transfected with 25 nmol/L of control small interfering RNA (siRNA) (Silencer Select Negative Control Ambion, Austin, TX) or siRNA directed against Ezh2 (s4918; Ambion) using Oligofectamine (Invitrogen). Total RNA was harvested 72 hours after transfection.

2012-10-16 | E-GEOD-41610 | biostudies-arrayexpress

Suppression of p53-mediated senescence by non-canonical NF-kappaB pathway mediated regulation of EZH2 expression

Project description:The NF-kappaB and p53 transcription factors control the expression of complex gene regulatory networks in response to many cell stresses and stimuli. This experiment describes gene expression profiling of cells depleted for EZH2, NF-kappaB2, RelB and p53. We find that EZH2 is the major effector of crosstalk between the alternative NF-kappaB and p53 pathways and acts to suppress cellular senescence. Total RNA was obtained from primary juvenile human dermal fibroblasts 48 hours after transfection with siRNA specific for one, or a targeted combination of the transcription factors, or a scrambled siRNA control.

2014-03-31 | E-MTAB-1593 | biostudies-arrayexpress

Effects of plasmids transfection on the RO82_W1 human thyroid cell line

Project description:The goal of this study was to identifiy cellular pathways modified by RO82_W1 cell transfection with PRC, ERRalpha or PRC+ERRalpha plamids relative to transfection with PGl3 plasmid

2012-06-01 | GSE37240 | GEO

Expression data from embryonic stem cells following siRNA transfection of UPS members

Project description:This SuperSeries is composed of the following subset Series: GSE39770: Expression data from embryonic stem cells following siRNA transfection of UPS members [Differentiation_ES] GSE39771: Expression data from embryonic stem cells following siRNA transfection of UPS members [self_renewal] Refer to individual Series

2012-07-31 | E-GEOD-39772 | biostudies-arrayexpress

RNAi profiling of human ezh2 specific siRNA A673 treated cells reveals EZh2 is a mediator of EWS-FLI1 driven tumor growth blocking endothelial and neuro-ectodermal differentiation

Project description:Ewing Tumors (ET) are highly malignant tumors, localized in bone or soft tissue and are molecularly defined by ews/ets translocations. We identified histone methyl-transferase Enhancer of Zeste, Drosophila, Homolog 2 (EZH2) to be increased in ET. EZH2âs suppressive activity maintains stemness in normal and malignant cells. Here we found EZH2 to be upregulated by the pathognomonic fusion oncogene EWS-FLI1 in ET and mesenchymal stem cells. Downregulation of EZH2 by RNA interference in ET suppressed oncogenic transformation by inhibiting clonogenicity in vitro. Similarly, tumor development and metastasis in immunodeficient Rag2-/-Î³C-/- mice was suppressed. EZH2-mediated gene silencing was shown to be dependent on histone deacetylase (HDAC) activity. Subsequent microarray analysis of EZH2 knock down, HDAC-inhibitor treatment and confirmation in independent assays revealed an undifferentiated phenotype maintained by EZH2 in ET. Downregulation of EZH2 decreased histone H3 lysine 27 trimethylation (H3K27me3) at target loci. EZH2 regulated stemness genes such as nerve growth factor receptor (NGFR) as well as genes involved in neuroectodermal differentiation (EMP1, EPHB2, GFAP, GAP43). These data suggest that EZH2 might play a central role in Ewing Tumor pathology shaping the oncogenicity and stem cell phenotype of this tumor presumably by epigenetic regulation. Experiment Overall Design: A673 cells were treated for 24 hours either with 100 nM Trichostatin A (TSA) or 0.01% DMSO. In siRNA experiments with ezh2 specific siRNA A673 cells were resuspended in medium containing 5 nM siRNA and transfection reagent and incubated for 48 hours. RNA from cells under such treatment was isolated with Trizol and subjected to microarray analysis onto human U133A microarray following the Affymetrix protocol.

2008-10-26 | E-GEOD-12692 | biostudies-arrayexpress

Gene expression data at 24hrs post-siRNA transfection for HCT116 cultures transfected with either DDX5si2008, DDX5si2053, or EBNA1si1666 siRNA's or mock transfected.

Project description:HCT116 cells were transfected with two different siRNA's targeting either DDX5, an siRNA targeting EBNA1, or no siRNA (mock). The siRNA targeting EBNA1 is used as a negative control since HCT116 cells do not have the EBNA1 gene. RNA was obtained from cultures at 24hrs post-siRNA transfection using the Qiagen RNeasy Minikit (cat. # 74104) with on-column DNase digestion performed as per the manufacturer's protocol. The RNA samples were isolated at 24hrs post-siRNA transfection since this timepoint precedes an impaired G1-to-S phase cell cycle progression phenotype that is evident at 48hrs post-siRNA transfection and so may reveal gene expression changes occuring before this effect on cell cycle. RNA samples were submitted to the Cold Spring Harbor Laboratory Microarray Faciity where cDNA was prepared, labeled, and hybridized to Affymetrix GeneChip Human Gene 1.0 ST microarrays. Data from the arrays were processed using the RMA method with an up-to-data probe set definition (Biostatistics 4:249-264 and Nucleic Acids Research 33(20):e175. Gene set analysis was performed using generally applicable gene set enrichment (BMC Bioinformatics 10:161). The most differentially regulated gene ontology groups were selected with FDR q-value < 0.1. Expression data from 3 independent HCT116 cutures transfected with either DDX5si2008, DDX5si2053, or EBNA1si1666 and 2 independent cultures transfected with mock conditions (no siRNA) were obtained from RNA samples prepared 24hrs post-siRNA transfection. These cultures were seeded with 200,000 cells per well 24hrs prior to siRNA transfection and were grown in DMEM media supplemented with 10% fetal bovone serum. Transfections were performed using lipofectamine RNAiMAX (Invitrogen 13778-075) and the manufacturer's protocol.

2012-06-01 | E-GEOD-36141 | biostudies-arrayexpress

RNAi knock down using siRNAs targeting PROX1 or Â§-catenin in human colon carcinoma cells

Project description:PROX1 or §-catenin was depleted in SW480 by siRNA transfection and the gene expression profiles were compared to negative controls to study the genes affected.

2018-03-01 | E-MTAB-717 | biostudies-arrayexpress

A novel, druggable casacade links methionine metabolism to epigenomic reprogramming in squamous cancer

Project description:DNA and histone methylation represents perhaps the most significant form of epigenetic regulation in mammalian cells, and their deregulation is most notable and pervasive in cancer. Based on our previous study which demonstrated the interplay between cancer metabolism and epigenetic regulation and the public database showing abnormal expression of LAT1 in upper aerodigestive squamous cell carcinoma (UASCC), we aim to investigate the role of LAT1 as a regulator of epigenomic reprogramming in UASCC. To identify the effect of the blockade of LAT1 on epigenetic regulation, we silenced LAT1 in UASCC cell line and performed RNA-Seq. In addition, we confirmed that Knockdown of LAT1 is associated with the downstream genes of EZH2. Therefore, we performed RNA-Seq after silencing EZH2 by transfection of siRNA and Cut&Tag assays using EZH2 and H3K27me3 antibodies

2024-07-03 | GSE243988 | GEO

Biological significance of EZH2 in uterine cancer

Project description:Change of gene expression profile by EZH2 silencing EZH2 is overexpressed in a number of malignancies, and is an attractive target for cancer treatment. The overexpression of EZH2 was significantly associated with disease free survival and overall survival of patients with ovarian cancer. EZH2 silencing resulted in decreased cell viability and invasion ability, and increased apoptosis. EZH2 silencing significantly enhanced cytotoxicity of paclitaxel, docetaxel and cisplatin in Hec-1A and Ishikawa cells. EZH2 silencing using siRNA incorporated into chitosan nanoparticles (siRNA/CH) resulted in significant inhibition of tumor growth compared to control siRNA/CH. Moreover, EZH2 siRNA/CH in combination with taxanes showed robust anti-tumor effects compared to monotherapy groups. These effects were associated with decreased tumor cell proliferation and angiogenesis, and increased tumor cell apoptosis. Genomic analyses revealed that EZH2 gene silencing resulted in decreased expression of many genes associated with tumor growth.

2019-05-01 | GSE115010 | GEO

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