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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Diverse epigenetic strategies interact to control epidermal differentiation [Illumina bead array]

ABSTRACT: It is becoming clear that interconnected functional gene networks, rather than single genes in isolation, govern stem cell self-renewal and differentiation. To identify potential epigenetic networks that impact on human epidermal stem cells we performed siRNA based genetic screens for 332 chromatin modifiers. We developed a Bayesian mixture model to predict putative functional interactions between those epigenetic modifiers that regulated differentiation. This allowed us to discover a network of genetic interactions involving EZH2, UHRF1 (both known to regulate epidermal self-renewal), ING5 (a MORF complex component), BPTF and SMARCA5 (NURF complex components). Genome-wide localisation and global mRNA expression analysis revealed that these factors impact two distinct but functionally related gene sets, including integrin extracellular matrix receptors that mediate anchorage of epidermal stem cells to their niche. Using a competitive epidermal reconstitution assay we confirmed that ING5, BPTF, SMARCA5, EZH2 and UHRF1 control differentiation under physiological conditions. Thus, regulation of distinct gene expression programs through the interplay between diverse epigenetic strategies protects epidermal stem cells from differentiation. Primary human keratinocytes (line Lka, passage 2) were cultured in Keratinocyte Serum Free Medium (KSFM) to 70% confluency in 10 cm dishes. Cells were treated with: vehicle (0.2% DMSO), the EGFR inhibitor AG1478 (10 uM), recombinant human BMP2/7 heterodimer (200 ng/ml) or a combination of AG1478+BMP2/7 (10 uM and 200 ng/ml, respectively) for 48 hours. RNA was extracted directly using a Qiagen RNeasy kit

ORGANISM(S): Homo sapiens

SUBMITTER: Silvia Halim

PROVIDER: E-GEOD-34557 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Diverse epigenetic strategies interact to control epidermal differentiation [ChIP-Seq]

Project description:It is becoming clear that interconnected functional gene networks, rather than single genes in isolation, govern stem cell self-renewal and differentiation. To identify potential epigenetic networks that impact on human epidermal stem cells we performed siRNA based genetic screens for 332 chromatin modifiers. We developed a Bayesian mixture model to predict putative functional interactions between those epigenetic modifiers that regulated differentiation. This allowed us to discover a network of genetic interactions involving EZH2, UHRF1 (both known to regulate epidermal self-renewal), ING5 (a MORF complex component), BPTF and SMARCA5 (NURF complex components). Genome-wide localisation and global mRNA expression analysis revealed that these factors impact two distinct but functionally related gene sets, including integrin extracellular matrix receptors that mediate anchorage of epidermal stem cells to their niche. Using a competitive epidermal reconstitution assay we confirmed that ING5, BPTF, SMARCA5, EZH2 and UHRF1 control differentiation under physiological conditions. Thus, regulation of distinct gene expression programs through the interplay between diverse epigenetic strategies protects epidermal stem cells from differentiation. Examination of genome-wide localisation of ING5 in primary human keratinocytes

2012-06-23 | E-GEOD-34556 | biostudies-arrayexpress

Diverse epigenetic strategies interact to control epidermal differentiation [Illumina bead array]

2012-06-24 | GSE34557 | GEO

Diverse epigenetic strategies interact to control epidermal differentiation [ChIP-Seq]

2012-06-24 | GSE34556 | GEO

Diverse epigenetic strategies interact to control epidermal differentiation

Project description:This SuperSeries is composed of the following subset Series: GSE34556: Diverse epigenetic strategies interact to control epidermal differentiation [ChIP-Seq] GSE34557: Diverse epigenetic strategies interact to control epidermal differentiation [Illumina bead array] Refer to individual Series

2012-06-23 | E-GEOD-34558 | biostudies-arrayexpress

TRANSCRIPTIONAL EFFECTS OF INHIBITING EGFR IN KERATINOCYTES

Project description:EGFR activation is important in human epithelial malignancies, including cutaneous squamous cell carcinoma, lung, colon, pancreatic and other cancers. Therapies targeting EGFR are currently used to treat such cancers, but one significant drawback to EGFR inhibitor therapies is the associated skin toxicity. This toxicity usually presents as papular or pustular folliculitis, dry skin with pruritus and hair and nails abnormalities. The side effects often limit the usefulness of EGFR inhibitors in cancer treatment. The transcriptional changes caused by EGFR inhibition in epidermal keratinocytes have not been extensively explored. To define the transcriptional changes caused by inhibition of EGFR in primary human epidermal keratinocytes, we treated these cells with Tyrphostin and compared treated and control cultures in parallel, using Affymetrix microarrays. Using metaanalysis approaches, we integrated the observed changes with a large set of already existing data on transcriptional profiling in epidermal keratinocytes. We found that EGFR inhibition suppresses expression of genes associated with keratinocyte proliferation, attachment and motility. Apoptosis is facilitated by both induction of proapoptotic and suppression of antiapoptotic genes. Surprisingly, EGFR inhibition induces expression of markers of epidermal differentiation. Time course of human epidermal keratinocytes treated with Tyrphostin (AG1478) and untreated controls

2012-10-19 | E-GEOD-41680 | biostudies-arrayexpress

H3K4me3 ChIP-seq of primary human keratinocytes after 6 hours of differentiation induction

Project description:To determine as a proxy transcriptional activation after induction of differentiation, we performed H3K4me3 ChIP-seq experiment of primary human keratinocytes that were treated with EGFR inhibitor AG1478 and BMP2/7 for 6 hours.

2018-11-28 | GSE115923 | GEO

Genome wide analysis of bivalent domains in two HUES cell lines

Project description:Human embryonic stem (HUES) cells are derived from early individual embryos with unique genetic properties. However, how their epigenetic status might affect their potential to differentiate toward specific lineages remains a puzzling question. Using ChIP-on-chip, the status of bivalent domains on gene promoters (i.e. H3K4 and H3K27 trimethylation) was monitored for both undifferentiated and BMP2 induced cardiac committed cells. A marked difference in the epigenetic profile of HUES cell lines was observed and this was correlated to the pattern of gene expression induced by BMP2 as well as to their potential to generate cardiac progenitors and differentiated myocytes. Thus, the epigenetic H3trimeK4 and H3trimeK27 prints generating bivalent domains on promoters, could be used to predict a preference in their differentiation toward a specific lineage. Using ChIP-on-chip, the status of bivalent domains on gene promoters (i.e. H3K4 and H3K27 trimethylation) was monitored for both undifferentiated and BMP2 induced cardiac committed cells.

2014-10-06 | E-GEOD-59328 | biostudies-arrayexpress

Effect of Mirn378 overexpression on gene expression during C2C12 myogenic and BMP2-induced osteogenic differentiation

Project description:Background: MicroRNAs (miRNAs) are a family of small, non-coding single-stranded RNA molecules involved in post-transcriptional regulation of gene expression. As such, they are believed to play a role in regulating the step-wise changes in gene expression patterns that occur during cell fate specification of multipotent stem cells. Here, we have studied whether terminal differentiation of C2C12 myoblasts is indeed controlled by lineage-specific changes in miRNA expression. Results: Using a previously generated RNA polymerase II (Pol-II) ChIP-on-chip dataset, we show differential Pol-II occupancy at the promoter regions of six miRNAs during C2C12 myogenic versus BMP2-induced osteogenic differentiation. Overexpression of one of these miRNAs, miR-378, enhances Alp activity, calcium deposition and mRNA expression of osteogenic marker genes in the presence of BMP2. Conclusions: Our results demonstrate a previously unknown role for miR-378 in promoting BMP2-induced osteogenic differentiation. Stable C2C12 cell lines C2C12-pMirn0 and C2C12-pMirn378 were generated by lentiviral transduction of C2C12 myoblasts with a Mirn378-overexpression construct and its parent vector, respectively. C2C12-pMirn0 and C2C12-pMirn378 cells were plated at 2.5 x 10^4 cells/cm2 (day -1), cultured for 1 day in DMEM 10%NCS, then (d0) treated with or without 300 ng/ml bone morphogenetic protein 2 (BMP2) for 6 days. RNA was extracted on d0, d3 and d6 and hybridized to GeneChip Mouse Genome 430 2.0 array (Affymetrix).

2014-01-28 | E-GEOD-51883 | biostudies-arrayexpress

Expression data from human dental follicle cells

Project description:We analysed the genexpression of dental follicle cells (DFCs) after 3 days osteogenic differentiation with BMP2 after transfection with a DLX3 plasmid (pDLX3) and after transfection with an empty plasmid (pEV) Total RNAs were isolated from dental follicle cells after transfection with pDLX3 and pEV and osteogenic induction with BMP2 at day 3

2014-08-01 | E-GEOD-59949 | biostudies-arrayexpress

Gene-expression profiles of BMP signaling-affected SK-OV-3 cells

Project description:Bone morphogenetic proteins (BMPs) are extracellular signaling molecules that belong to the transforming growth factor beta (TGF-β) superfamily. By regulating target gene transcription, BMPs control various cellular processes, such as proliferation, differentiation, apoptosis and migration. In addition, rBMP2 was used to observe BMP signaling in treatment of ovarian cancer cell line SK-OV-3. We attempted to address the possible roles of BMP signaling by inhibiting a wide-range of downstream pathways using a small molecule inhibitor of type I BMPRs, dorsomorphin. The potential utility of this molecule as a molecular inhibitor of BMP signaling in treatment of ovarian cancer cell line SK-OV-3 was also evaluated. SK-OV-3 cells were incubated in 12 separate culture dishes, 3 dishes with PBS, 3 dishes with recombinant BMP2 (rBMP2) (100 ng/ml), 3 dishes with DM (5 μM) and 3 dishes with recombinant BMP2 (rBMP2) (100 ng/ml) plus DM (5 μM) in the culture medium for 24 hours prior to the analysis.

2014-08-07 | E-GEOD-60135 | biostudies-arrayexpress

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