Whole genome expression microarray analysis in hepatocellular carcinoma cell line, Huh7 cells, treated with siRNA targeting for nuclear factor 90 (siNF90)
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ABSTRACT: To identify genes regulated by complex of NF90 and nuclear factor 45 (NF45) in hepatocellular carcinoma, we performed comprehensive analyses of mRNA expression in Huh7 cells depleted of NF90. mRNA expression profile in Huh7 cells depleted of NF90.
Project description:Our previous study has showed that complex of NF90 and nuclear factor 45 (NF45) (NF90-NF45) inhibits miRNA biogenesis through negative regulation of primary-miRNA processing step. On the other hand, miRNAs, the biogenesis of which is regulated by NF90-NF45 in hepatocellular carcinoma, are not clear. Thus, to identify the miRNAs, we performed a miRNA array using RNAs extracted from control Huh7 cells and the cells depleted of NF90. Comparison of miRNA expression profile in one non-targeting control siRNA (siNTC)- or two independent siNF90-treated Huh7 cells.
Project description:Our previous study has showed that complex of NF90 and nuclear factor 45 (NF45) (NF90-NF45) inhibits miRNA biogenesis through negative regulation of primary-miRNA processing step. On the other hand, miRNAs, the biogenesis of which is regulated by NF90-NF45 in hepatocellular carcinoma, are not clear. Thus, to identify the miRNAs, we performed a miRNA array using RNAs extracted from control Huh7 cells and the cells depleted of NF90.
Project description:To identify genes regulated by complex of NF90 and nuclear factor 45 (NF45) in hepatocellular carcinoma, we performed comprehensive analyses of mRNA expression in Huh7 cells depleted of NF90.
Project description:The complex of NF90 and NF45 is known to participate in transcriptional regulation, mRNA stabilization and microRNA biogenesis in vitro. However, the physiological function of the NF90-NF45 complex is still unclear. To elucidate its functions, we generated NF90-NF45 double transgenic (dbTg) mice. Robust expression of NF90 and NF45 was detected in skeletal muscle. As mentioned above, NF90-NF45 complex is involved in regulation of genes via transcription and RNA metabolism. To identify genes regulated by NF90-NF45, we performed comprehensive analyses of mRNA expression in quadriceps of wild-type (WT) and NF90-NF45 dbTg mice. mRNA expression profile in quadriceps comparing WT and NF90-NF45 dbTg mice.
Project description:The Wnt signaling pathway is involved in many differentiation events during embryonic development and can lead to tumor formation after aberrant activation of its components. Β-catenin, a cytoplasmic component, plays a major role in the transduction of the canonical wnt/ β-catenin signaling. The aim of this study was to identify novel genes that are regulated by active β-catenin/TCF signaling in hepatocellular carcinoma. We selected and expanded isogenic clones from hepatocellular carcinoma-derived Huh7 cells with high and low β-catenin/TCF activities. We showed that, high TCF activity Huh7 cells lead to bigger and more aggressive tumors when xenografted into nude mice. We used SAGE (Serial Analysis of Gene Expression), genome-wide microarray and in silico promoter analysis in parallel, to compare gene expression between low (basal) and high (transfected) β-catenin/TCF activity clones, those had been xenografted into nude mice. We compared and contrasted SAGE and genome-wide microarray data, in parallel. Finally; after combined analysis, we identified BRI3 and HSF2 as novel targets of Wnt/β-catenin signaling in hepatocellular carcinoma. Experiment Overall Design: High TCF activity Huh7 cell line (Huh7-S33Y) was compared to control Huh7 cell line (Huh7-Vec) by using 10 ug of total RNA isolated from each sample (15 ug of labeled cRNA was hybridized to the arrays). Triplicates are coming from same total RNA extraction.
Project description:This SuperSeries is composed of the following subset Series: GSE11912: Comparison of TCF hyper-activated and control Huh7 cells - SAGE GSE11916: Comparison of TCF hyper-activated and control Huh7 cells - microarray data Refer to individual Series
Project description:The Wnt signaling pathway is involved in many differentiation events during embryonic development and can lead to tumor formation after aberrant activation of its components. ?-catenin, a cytoplasmic component, plays a major role in the transduction of the canonical wnt/ ?-catenin signaling. The aim of this study was to identify novel genes that are regulated by active ?-catenin/TCF signaling in hepatocellular carcinoma. We selected and expanded isogenic clones from hepatocellular carcinoma-derived Huh7 cells with high and low ?-catenin/TCF activities. We showed that, high TCF activity Huh7 cells lead to bigger and more aggressive tumors when xenografted into nude mice. We used SAGE (Serial Analysis of Gene Expression), genome-wide microarray and in silico promoter analysis in parallel, to compare gene expression between low (basal) and high (transfected) ?-catenin/TCF activity clones, those had been xenografted into nude mice. We compared and contrasted SAGE and genome-wide microarray data, in parallel. Finally; after combined analysis, we identified BRI3 and HSF2 as novel targets of Wnt/?-catenin signaling in hepatocellular carcinoma. High TCF activity Huh7 cell line (Huh7-S33Y) was compared to control Huh7 cell line (Huh7-Vec) by using 25 ug of total RNA isolated from each sample
Project description:A powerful approach to study innate antiviral response is to compare the difference between wild type Huh7 cells, which do not support robust replication of hepatitis C virus (HCV)2, versus certain subclones of Huh7 cells that are permissive for HCV replication. We generated two permissive cell lines and two independent non-permissive subclone from Huh7 cells. We compared the global methylation pattern of these different cells and find that Huh7 cells exist as a heterogeneous population of cells with distinct patterns of gene methylation. Comparison of Huh7, HRP1, HRP4, Huh7-pNeo1 and Huh7-pNeo2 cells.
Project description:We used microarray to determine the miRNA whose expression was changed at 12 hours after Y27632 treatment Two-condition experiment; Huh7 control vs Huh7 treated with Y27632 for 12 hours
Project description:To identify candidate genes involved in enhanced tumorigenicity of CD133+ liver tumor-initiating cells Affymetrix Human Genome U133 Plus GeneChip 2.0 HCC cell line Huh7 was sorted into CD133+ and CD133- populations by flow cytometry