MiRNA expression profile of pre-transfected HEY cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Shubin Shahab
PROVIDER: E-GEOD-29126 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:MicroRNAs (miRNAs) are a class of regulatory RNAs that control the expression of genes critical to cell function. Ectopic expression of miRNAs has been shown to result in genome-wide changes in patterns of gene expression. While the reasons for these global alterations in gene expression patterns have been attributed to the ability of miRNAs to target multiple genes, and/or to induce indirect effects downstream of target genes, the molecular basis of indirect effects of miRNA regulation remains poorly understood. In this study, we demonstrate the potential of miRNAs to regulate other miRNAs. Using miRNA microarray analysis, we show that over 70 different miRNAs are differentially expressed ( M-bM-^IM-%1.4 fold, FDR M-bM-^IM-$ 5%) in human ovarian cancer cells after transfection with a single miRNA (miR-7). We present evidence that a major component of miR-7-induced changes in levels of miRNAs is the indirect consequence of miR-7-mediated alterations in levels of protein-coding genes (e.g., transcription and splicing factors) that exert trans-regulatory control on miRNAs. HEY cells were transfected with either hsa-miR-7 (2 biological replicates) or a negative control miRNA, miR-NC (2 biological replicates), and then grown in 6-well plates for ~48 hours. The difference in miRNA expression pattern between the miR-7-transfected cells and the miR-NC-transfected cells was determined using an Affymetrix GeneChip miRNA Array.
2012-04-08 | E-GEOD-29129 | biostudies-arrayexpress
Project description:MicroRNAs (miRNAs) are short (~22 nucleotides) regulatory RNAs that can modulate gene expression and are aberrantly expressed in many diseases including cancer. We wanted to quantify the levels of endogenous miRNAs in pre-transfected HEY ovarian cancer cells to identify the highly expressed miRNAs. It was previously established that transfection of small RNAs can globally perturb gene expression, and one mechanism responsible for such alterations may involve de-repression of targets of endogenous miRNAs because of the saturation of the RISC complexes by the exogenously administered small RNA (Khan et al., 2009. Nat Biotechnol 27, 549-555). By measuring the levels of miRNAs in the pre-transfected HEY cells, we wanted to determine the miRNAs most highly expressed in HEY cells, and therefore, most likely to experience the effects of such competition.
2012-04-09 | GSE29126 | GEO
Project description:The innate immune system is vital to rapidly responding to pathogens and Toll-like receptors (TLRs) are a critical component of this response. Nanovesicular exosomes play a role in immunity, but to date their exact contribution to the dissemination of the TLR response is unknown. To understand the effect of exosomal cargo released from locally stimulated cells on distal cell expression, we collected exosomes from local ovarian adenocarcinoma (HEY) cells that were either unstimulated (control-exosomes), stimulated with pIC (pIC-exosomes), or lipopolysaccharide (LPS-exosomes) for 48 hours. The three groups of exosomes were added to naïve (distal) cells and the gene expression profiles were compared between local TLR stimulation (for 6 hours) and distal stimulation mediated by exosomes at the 48-hour time point The goal of the study was to delineate the differential effector function of TLR-exosomes based on the innate immune activation state (control-, LPS-, pIC-stimulation) of the cell of origin in vitro. We used microarrays to understand the changes in gene expression in 2 samples of local hey cells either unstimulated(control) or stimulated with poly(I:C) or LPS each. We also profiled 2 samples of distal naïve cells that were exposed to either control, LPS or poly(I:C) exosomes from local cells. Here we show that exosomes from TLR stimulated cells (TLR-exosomes) can largely recapitulate TLR activation in distal cells in vitro. We can abrogate the action-at-a-distance signaling of exosomes by UV irradiation, demonstrating that RNA is crucial for their effector function. This work definitively establishes the differential effector function for TLR-exosomes in communicating the activation state of the cell of origin. HEY cells were either unstimulated (Local control) or stimulated with LPS or poly (I:C) for 6 hours and the RNA from these cells was profiled using a microarray. Exosomes were collected from local cells that were unstimulated or stimulated for 48 hours and added to distal (naive) HEY cells that were exposed to control exosomes, LPS exosomes or pIC exosomes and then the RNA was collected for analysis by microarray. mRNA expression was captured on Affymetrix U133 Plus 2 chips. mRNA microarray data were analyzed using the Expression Console software (Affymetrix) and Bioconductor tools written in the R statistical programming language. Pre-processing of raw signal intensities and normalization was performed using GCRMA (R). Linear modelling of the transformed data was determined by using Limma in R with the Benjamini and Hochberg correction. Differentially expressed probesets were identified using a threshold 5% FDR correction and a fold change ⥠1.4 was applied
2016-05-17 | E-GEOD-81248 | biostudies-arrayexpress
Project description:MicroRNAs (miRNAs) are short (~22 nucleotides) regulatory RNAs that can modulate gene expression and are aberrantly expressed in many diseases including cancer. Previous studies have shown that miRNAs inhibit the translation and facilitate the degradation of their targeted mRNAs making them attractive candidates for use in cancer therapy. However, the potential clinical utility of miRNAs in cancer therapy rests heavily upon our ability to understand and accurately predict the consequences of fluctuations in levels of miRNAs within the context of complex tumor cells. To evaluate the predictive power of current models, levels of miRNAs and their targeted messenger RNAs (mRNAs) were measured in laser captured micro-dissected (LCM) ovarian cancer epithelial cells (CEPI) and compared with levels present in ovarian surface epithelial cells (OSE). We found that the predicted inverse correlation between changes in levels of miRNAs and levels of their mRNA targets held for only ~6-11% of predicted target mRNAs. Our results underscore the complexities of miRNA-mediated regulation in vivo and caution against the widespread clinical application of miRNAs and miRNA inhibitors until the basis of these complexities is more fully understood. mRNAs were collected from 3 miR-7 treated, 2 miR-128 treated , and 3 negative control miRNA treated HEY ovarian cancer cell samples. The mRNA expression pattern was compared between the miR-7 treated cells and the negative control treated cells, and separately between the miR-128 treated cells and the negative control treated cells using the Affymetrix U133 Plus 2.0 3' expression array.
2011-07-28 | E-GEOD-27431 | biostudies-arrayexpress
Project description:We used an in vitro cardiomyocyte differentiation system with inducible Hey1 or Hey2 expression to study target gene regulation in cardiomyocytes (CM) generated from murine embryonic stem cells (ESC). The effects of Hey1 and Hey2 are largely redundant, but cell type specific. The number of regulated genes is comparable between ESC and CM, but the total number of binding sites is much higher, especially in ESC, targeting mainly genes involved in transcriptional regulation and developmental processes. Repression by Hey generally correlates with the extent of Hey-binding to target promoters, subsequent Hdac recruitment and lower histone acetylation. Functionally, treatment with the Hdac inhibitor TSA abolished Hey target gene regulation. However, in CM the repressive effect of Hey-binding is lost for a subset of genes. These lack Hey-dependent histone deacetylation in CM and are enriched for binding sites of cardiac specific activators like Srf, Nkx2-5, and Gata4.
2016-01-01 | GSE60746 | GEO
Project description:HEY cells display a mesenchymal phenotype (elongated). After a 48hr transfection with mir-429 their phenotype changes to an epithelial-like (cuboidal)
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Project description:We used an in vitro cardiomyocyte differentiation system with inducible Hey1 or Hey2 expression to study target gene regulation in cardiomyocytes (CM) generated from murine embryonic stem cells (ESC). The effects of Hey1 and Hey2 are largely redundant, but cell type specific. The number of regulated genes is comparable between ESC and CM, but the total number of binding sites is much higher, especially in ESC, targeting mainly genes involved in transcriptional regulation and developmental processes. Repression by Hey generally correlates with the extent of Hey-binding to target promoters, subsequent Hdac recruitment and lower histone acetylation. Functionally, treatment with the Hdac inhibitor TSA abolished Hey target gene regulation. However, in CM the repressive effect of Hey-binding is lost for a subset of genes. These lack Hey-dependent histone deacetylation in CM and are enriched for binding sites of cardiac specific activators like Srf, Nkx2-5, and Gata4.
2016-01-01 | GSE60699 | GEO
Project description:We used an in vitro cardiomyocyte differentiation system with inducible Hey1 or Hey2 expression to study target gene regulation in cardiomyocytes (CM) generated from murine embryonic stem cells (ESC). The effects of Hey1 and Hey2 are largely redundant, but cell type specific. The number of regulated genes is comparable between ESC and CM, but the total number of binding sites is much higher, especially in ESC, targeting mainly genes involved in transcriptional regulation and developmental processes. Repression by Hey generally correlates with the extent of Hey-binding to target promoters, subsequent Hdac recruitment and lower histone acetylation. Functionally, treatment with the Hdac inhibitor TSA abolished Hey target gene regulation. However, in CM the repressive effect of Hey-binding is lost for a subset of genes. These lack Hey-dependent histone deacetylation in CM and are enriched for binding sites of cardiac specific activators like Srf, Nkx2-5, and Gata4. Control cells and cells with Hey1 or Hey2 overexpression, no replicates
2016-07-03 | E-GEOD-60746 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE28487: miRNA expression profiling of human immune cell subsets (Roche) GSE28489: miRNA expression profiling of human immune cell subsets (HUG) GSE28490: mRNA expression profiling of human immune cell subset (Roche) GSE28491: mRNA expression profiling of human immune cell subsets (HUG) Blood consists of different cell populations with distinct functions and correspondingly, distinct gene expression profiles. In this study, global miRNA expression profiling was performed across a panel of nine human immune cell subsets (neutrophils, eosinophils, monocytes, B cells, NK cells, CD4 T cells, CD8 T cells, mDCs and pDCs) to identify cell-type specific miRNAs. mRNA expression profiling was performed on the same samples, to determine if miRNAs specific to certain cell types down-regulated expression levels of their target genes. Six cell-type specific miRNAs (miR-143; neutrophil specific, miR-125; T cells and neutrophil specific, miR-500; monocytes and pDC specific, miR-150; lymphoid cells specific, miR-652 and miR-223; both myeloid cells specific) were negatively correlated with expression of their predicted target genes. These results were further validated using an independent cohort where similar immune cell subsets were isolated and profiled for both miRNA and mRNA expression. miRNAs negatively correlated with target gene expression in both cohorts were identified as candidates for miRNA-mRNA regulatory pairs and were used to construct a cell-type specific regulatory network. miRNA-mRNA pairs formed two distinct clusters in the network corresponding to myeloid (nine miRNAs) and lymphoid lineages (two miRNAs). Several myeloid specific miRNAs targeted common genes including ABL2, EIF4A2, EPC1 and INO80D; these common targets were enriched for genes involved in the regulation of gene expression (p < 9.0E-7). Those miRNA might therefore have significant further effect on gene expression by repressing the expression of genes involved in transcriptional regulation. The miRNA and mRNA expression profiles reported in this study form a comprehensive transcriptome database of various human blood cells and serve as a valuable resource for elucidating the role of miRNA mediated regulation in the establishment of immune cell identity. Refer to individual Series
2012-01-23 | E-GEOD-28492 | biostudies-arrayexpress
Project description:We used an in vitro cardiomyocyte differentiation system with inducible Hey1 or Hey2 expression to study target gene regulation in cardiomyocytes (CM) generated from murine embryonic stem cells (ESC). The effects of Hey1 and Hey2 are largely redundant, but cell type specific. The number of regulated genes is comparable between ESC and CM, but the total number of binding sites is much higher, especially in ESC, targeting mainly genes involved in transcriptional regulation and developmental processes. Repression by Hey generally correlates with the extent of Hey-binding to target promoters, subsequent Hdac recruitment and lower histone acetylation. Functionally, treatment with the Hdac inhibitor TSA abolished Hey target gene regulation. However, in CM the repressive effect of Hey-binding is lost for a subset of genes. These lack Hey-dependent histone deacetylation in CM and are enriched for binding sites of cardiac specific activators like Srf, Nkx2-5, and Gata4. ES cells and cardiomyocytes with Hey1 or Hey2 overexpression were compared to control cells
2016-07-03 | E-GEOD-60699 | biostudies-arrayexpress