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Gene expression profile of NR2E3 in MCF7 cells

ABSTRACT: While the roles of individual nuclear receptor (NR) in human diseases have been well characterized, interplays among NRs have not been extensively characterized due, in part, to technical difficulties in simultaneously monitoring molecular activities of all 48 NR genes. Using systems-level analysis of publically available gene expression data from NCI-60 cell lines, we uncovered novel interaction between ESR1 and orphan receptor NR2E3. Expression of NR2E3 is significantly associated with expression of ESR1 in NCI-60 cell lines as well as in breast cancer patients. To investigate how NR2E3 gene signatures are globally correlated with ESR1 signaling pathway, we performed microarray after knocking down NR2E3 or ESR1 in MCF-7 cells. Keywords: DNA microarray (Illumina human Ht12 V3) 3 shControl, 3 shNR2E3, 3 siLuc, 3 siESR1

ORGANISM(S): Homo sapiens

SUBMITTER: Sangbae Kim

PROVIDER: E-GEOD-18431 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Gene expression profile of NR2E3 in MCF7 cells

Project description:While the roles of individual nuclear receptor (NR) in human diseases have been well characterized, interplays among NRs have not been extensively characterized due, in part, to technical difficulties in simultaneously monitoring molecular activities of all 48 NR genes. Using systems-level analysis of publically available gene expression data from NCI-60 cell lines, we uncovered novel interaction between ESR1 and orphan receptor NR2E3. Expression of NR2E3 is significantly associated with expression of ESR1 in NCI-60 cell lines as well as in breast cancer patients. To investigate how NR2E3 gene signatures are globally correlated with ESR1 signaling pathway, we performed microarray after knocking down NR2E3 or ESR1 in MCF-7 cells. Keywords: DNA microarray (Illumina human Ht12 V3)

2011-12-22 | GSE18431 | GEO

Effect of DC-SCRIPT expression in MCF7 breast cancer cell line

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Effect of DC-SCRIPT expression in MCF7 breast cancer cell line

2015-08-01 | E-GEOD-59995 | biostudies-arrayexpress

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2012-05-14 | E-GEOD-25741 | biostudies-arrayexpress

Comprehensive Study of Nuclear Receptor DNA Binding Provides a Revised Framework for Understanding Receptor Specificity

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Characterization of stem cell-derived liver and intestinal organoids as a model system to study nuclear receptor biology.

Project description:Nuclear receptors (NRs) are ligand-activated transcription factors regulating a large variety of processes involved in reproduction, development, and metabolism. NRs are ideal drug targets. Immortalized cell lines recapitulate NR biology very poorly and primary cultures are laborious and require a constant need for donor material. There is a clear need for development of novel preclinical model systems that better resemble human physiology since technical uncertainty early in drug development is the cause of many preclinical drugs not reaching the clinic. Here, we studied whether organoids, mini-organs derived from the respective tissue’s stem cells, can serve as a novel (preclinical) model system to study NR biology and targeteability. We characterized mRNA expression profiles of the NR superfamily in mouse liver, ileum, and colon organoids. NR mRNA expression patterns were similar to the respective tissues, indicating their suitability for NR research. Metabolic NRs Fxrα, Lxrα, Lxrβ, Pparα, and Pparγ were responsive to ligands in an NR-dependent fashion, as demonstrated by regulation of expression and binding to endogenous target genes. Transcriptome analyses of wildtype colonic organoids stimulated with Rosiglitazone showed that lipid metabolism was the highest significant changed function, greatly mimicking the known function of PPARs and Rosiglitazone in vivo. In conclusion, our results demonstrate that organoids constitutes a versatile and promising in vitro system to study NR biology and targeteability.

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Gene expression profile of TARDBP in hepatocellular carcinoma cell line (SK-Hep1)

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2013-04-22 | E-GEOD-37640 | biostudies-arrayexpress

Gene expression profile of YAP1, TEAD1 and KLF5 in hepatocellular carcinoma cell line (SK-Hep1)

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2013-12-31 | E-GEOD-32597 | biostudies-arrayexpress

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Project description:Determination, using microarrays, of the mouse hepatic global programme of gene expression variations around the clock when animals had ad libitum food access The unique functional versatility of the liver is paramount for the organism homeostasis. Both liver development and adult life are controlled by tightly regulated transcription factor networks, among which nuclear receptors (NRs) regulate essential functions of parenchymal and nonparenchymal cells. Acting as transcription factors sensitive to extracellular cues such as steroidal hormones, lipid metabolites, xenobiotics… and modulated by intracellular signaling pathways, NRs orchestrate many aspects of hepatic physiology. While liver functional zonation and adaptability to fluctuating conditions are known to rely on a sophisticated cellular architecture, the exact functions of NRs in liver cell types remain poorly characterized. As a first step toward the accurate mapping of NR functions in mouse liver, we characterized their levels of expression in whole liver as a function of time and diet, and explored NRs isoform expression in hepatocytes, cholangiocytes, Kupffer cells, hepatic stellate cells and liver sinusoidal cells. In addition, we leveraged liver single cell RNAseq studies to provide here an up-to-date compendium of NR expression in mouse liver in space and time.

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