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ChIP-chip of BMP2 or control treated human pulmonary artery endothelial cells with anti-beta-catenin or anti-ppar-gamma antibodies on promoter regions

ABSTRACT: Reduced bone morphogenetic protein receptor (BMPR)2 expression in patients with pulmonary arterial (PA) hypertension (PAH), can impair PA endothelial cell (EC) function. We now characterize, in human PAECs, a novel BMPR2-mediated transcriptionally active complex between peroxisome proliferator-activated receptor (PPAR) gamma and beta-catenin (BC), and show that disruption of this complex impairs BMP mediated HPAEC survival. Using whole genome wide ChIP-Chip promoter analysis we delineate PPARG-BC dependent transcription of target genes that include apelin. Comparison of ppar-gamma and beta-catenin occupancy on promoter regions from human pulmonary artery endothelial cells after either treatment with BMP2 or control. A total of 8 samples were created using NimbleGen human HG18 promoter arrays.

ORGANISM(S): Homo sapiens

SUBMITTER: Molong Li

PROVIDER: E-GEOD-29489 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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ChIP-chip of BMP2 or control treated human pulmonary artery endothelial cells with anti-beta-catenin or anti-ppar-gamma antibodies on promoter regions

Project description:Reduced bone morphogenetic protein receptor (BMPR)2 expression in patients with pulmonary arterial (PA) hypertension (PAH), can impair PA endothelial cell (EC) function. We now characterize, in human PAECs, a novel BMPR2-mediated transcriptionally active complex between peroxisome proliferator-activated receptor (PPAR) gamma and beta-catenin (BC), and show that disruption of this complex impairs BMP mediated HPAEC survival. Using whole genome wide ChIP-Chip promoter analysis we delineate PPARG-BC dependent transcription of target genes that include apelin.

2011-05-25 | GSE29489 | GEO

Genome-wide analysis of human pulmonary artery endothelial cells after knockdown of either BMPRII or beta-catenin

Project description:Expression analysis of genes potentially regulated by BMPRII and beta-catenin. BMPRII has been linked as a genetic factor to the disease pulmonary arterial hypertension. Comparison of total mRNA obtained from human pulmonary artery endothelial cells treated with control, bone morphogentic protein receptor II, or beta-catenin siRNA

2010-11-06 | E-GEOD-18956 | biostudies-arrayexpress

Single cell atlas identifies lipid-processing and immunomodulatory endothelial cells in healthy and malignant breast

Project description:Since a detailed inventory of endothelial cell (EC) heterogeneity in breast cancer (BC) is lacking, we perform single cell RNA-sequencing of 26,515 cells (including 8,433 ECs) from 9 BC patients and compare them to published EC taxonomies from lung tumors. Angiogenic ECs are phenotypically similar, while other EC subtypes are different. Predictive interactome analysis reveals known but also previously unreported receptor-ligand interactions between ECs and immune cells, suggesting an involvement of breast EC subtypes in immune responses. We also identify a capillary EC subtype (LIPEC (Lipid Processing EC)), which expresses genes involved in lipid processing that are regulated by PPAR-gamma and is more abundant in peri-tumoral breast tissue. Retrospective analysis of 4,648 BC patients reveals that treatment with metformin (an indirect PPAR-gamma agonist) provides long-lasting clinical benefit and is positively associated with LIPEC abundance. Our findings warrant further exploration of this LIPEC/PPAR-gamma link for BC treatment.

2022-08-02 | GSE155109 | GEO

Effects of Beta Catenin antagonist BC2059 in AML cells

Project description:To determine the global transcriptomic changes induced by treatment with the Beta Catenin antagonist BC2059 in AML cells The canonical WNT-β-catenin pathway is essential for self-renewal, growth and survival of AML stem/blast progenitor cells (BPCs). Deregulated WNT signaling inhibits degradation of β-catenin, causing increased nuclear translocation and co-factor activity of β-catenin with the transcriptional regulator TCF4/LEF1 in AML BPCs. Here, we determined the pre-clinical anti-AML activity of the anthraquinone oxime-analog BC2059 (BC), known to attenuate β-catenin levels. BC treatment disrupted the binding of β-catenin with the scaffold protein TBL1 (transducin β-like 1) and proteasomal degradation and decline in the nuclear levels of β-catenin. This was associated with reduced transcriptional activity of TCF4 and expression of its target genes, cyclin D1, c-Myc and survivin. BC treatment dose-dependently induced apoptosis of cultured and primary AML BPCs. Treatment with BC also significantly improved the median survival of immune-depleted mice engrafted with either cultured or primary AML BPCs exhibiting nuclear expression of β-catenin. Co-treatment with the pan-histone deacetylase inhibitor panobinostat and BC synergistically induced apoptosis of cultured and primary AML BPCs, including those expressing FLT3-ITD, as well as further significantly improved the survival of immune-depleted mice engrafted with primary AML BPCs. These findings underscore the promising pre-clinical activity and warrant further testing of BC against human AML, especially those expressing FLT3-ITD.

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ChIP-chip of siGFP- or siHOTAIR-treated foreskin fibroblasts with anti-LSD1 or anti-SUZ12 antibodies on human HG18 Nimblegen promoter arrays

Project description:Long intergenic noncoding RNAs (lincRNAs) regulate chromatin states and epigenetic inheritance. Here we show that the lincRNA HOTAIR serves as a scaffold for at least two distinct histone modification complexes. A 5’ domain of HOTAIR binds Polycomb Repressive Complex 2 (PRC2) while a 3’ domain of HOTAIR binds the LSD1/CoREST/REST complex. The ability to tether two distinct complexes enables RNA-mediated assembly of PRC2 and LSD1, and coordinates targeting of PRC2 and LSD1 to chromatin for coupled histone H3 lysine 27 methylation and lysine 4 demethylation. Our results suggest that lincRNAs may serve as scaffolds by providing binding surfaces to assemble select histone modification enzymes, and thereby specify the pattern of histone modifications on target genes. LSD1 and SUZ12 co-occupied on 721 genes in human foreskin fibroblasts. Coordinate loss of SUZ12 and LSD1 occupancy was caused by HOTAIR knockdown. Comparison occupancy of LSD1 and SUZ12 of siGFP and siHOTAIR foreskin fibroblasts on human HG18 promoter arrays. Human foreskin fibroblasts were transfected with siGFP or siHOTAIR. The cells were harvested and ChIP analysis with anti-LSD1 and anti-SUZ12 antibodies was performed.

2010-07-07 | E-GEOD-22344 | biostudies-arrayexpress

PLD1 promotes tumor invasion by regulation of MMP-13 expression via phosphorylation of NF-kB in bladder cancer

Project description:Invasion of bladder cancer (BC) cells from the mucosa into the muscle layer is canonical for BC progression while phospholipase D isoform 1 (PLD1) is known to mediate development of cancer through phosphatidic acid (PA) production. We therefore used in silico, in vitro and in vivo approaches to detail the effect of PLD1 on BC invasion. In BC patients, higher levels of PLD1 expression were associated with poor prognosis. PLD1 knockdown significantly suppressed cellular invasion by human BC cells and matrix metalloproteinase-13 (MMP-13) was observed to be an invasion mediator gene. In our mouse bladder carcinogenesis model, the development of invasive BCs was suppressed by PLD1 knockout and a global transcriptomic analysis in this model indicated MMP-13 as a potential tumor invasion gene with NF-kB (nuclear factor-kB) as its transcription regulator. Furthermore, PA administration increased both MMP-13 expression and NF-kB p65 phosphorylation levels. Collectively, we demonstrate that PLD1 promotes tumor invasion of BC by regulation of MMP-13 expression via phosphorylation of NF-kB p65. Our results suggest that PLD1 is a potential therapeutic target to prevent progression in BC patients.

2022-04-05 | GSE166004 | GEO

Histone H3K9 Methyltransferase G9a Represses PPAR? Expression and Adipogenesis [ChIP-Seq and RNA-Seq data]

Project description:PPAR? promotes adipogenesis while Wnt proteins inhibit adipogenesis. However, the mechanisms that control expression of these positive and negative master regulators of adipogenesis remain incompletely understood. By genome-wide histone methylation profiling in preadipocytes, we find that among gene loci encoding adipogenesis regulators, histone methyltransferase (HMT) G9a-mediated repressive epigenetic mark H3K9me2 is enriched on the entire PPAR? locus. H3K9me2 and G9a levels decrease during adipogenesis, which correlates inversely with induction of PPAR?. Removal of H3K9me2 by G9a deletion enhances chromatin opening and binding of adipogenic transcription factor C/EBP-beta to PPAR? promoter, which promotes PPAR? expression. Interestingly, G9a represses PPAR? expression in an HMT activity-dependent manner but facilitates Wnt10a expression independent of its enzymatic activity. Consistently, deletion of G9a or inhibiting G9a HMT activity promotes adipogenesis. Finally, deletion of G9a in mouse adipose tissues increases adipogenic gene expression and tissue weight. Thus, by inhibiting PPAR? expression and facilitating Wnt10a expression, G9a represses adipogenesis. Examination of 3 different histone modification changes in 3T3-L1 preadipocytes

2013-02-01 | E-GEOD-41455 | biostudies-arrayexpress

Chip-chip from Human Pulmonary Fibroblasts with H3K9me2 antibody

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Identification of β-Catenin-Interacting Proteins in Nuclei of Aquaporin-2-Expressing Rat Collecting Duct Cells

Project description:The gene encoding the aquaporin-2 water channel is regulated transcriptionally in response to vasopressin. In the renal collecting duct, vasopressin stimulates the nuclear translocation and phosphorylation (at Ser552) of β-catenin, a multifunctional protein that can act as a transcriptional co-regulator in the nucleus. The purpose of this study was to identify β-catenin interacting proteins in nuclei of rat inner medullary collecting duct (IMCD) cells using both experimental and computational approaches. We used chromatin immunoprecipitation coupled to mass spectrometry (ChIP-MS) in nuclei isolated from rat IMCD suspensions to identify β-catenin interacting proteins. We reproducibly (n=4) identified 43 β-catenin binding proteins, which included a number of known β-catenin binding partners as well as novel interacting proteins. Multiple proteins involved in transcriptional regulation were identified (Taf1, Jup, Tdrd3, Cdh1, Cenpj, and several histones). Many of the identified β-catenin binding partners were found in prior studies to translocate to the nucleus in response to vasopressin. There was one DNA-binding transcription factor (TF), viz. Taf1, part of the RNA-polymerase II pre-initiation complex. To identify sequence-specific TFs that may interact with β-catenin but are expressed at abundance levels too low to be detected by MS, Bayes’ Theorem was used to integrate data from several information sources. The analysis identified several TFs with potential binding sites in the Aqp2 gene promoter that could interact with β-catenin in the regulation of Aqp2 gene transcription viz. Jun, Junb, Jund, Atf1, Atf2, Mef2d, Usf1, Max, Pou2f1, and Rxra. The findings provide information necessary for modeling the transcriptional response to vasopressin.

2018-10-26 | PXD005792 | Pride

Homo sapiens

Project description:ChIP-chip of BMP2 or control treated human pulmonary artery endothelial cells with anti-beta-catenin or anti-ppar-gamma antibodies on promoter regions

| PRJNA141651 | ENA

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