Chromatin reprogramming and differential gene expression in a model of EMT (spheroid A549 treated with TGF/TNF)
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Marcin Cieslik
PROVIDER: E-GEOD-42375 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
Epigenetic coordination of signaling pathways during the epithelial-mesenchymal transition.
Cieślik Marcin M Hoang Stephen A SA Baranova Natalya N Chodaparambil Sanjay S Kumar Manish M Allison David F DF Xu Xiaojiang X Wamsley J Jacob JJ Gray Lisa L Jones David R DR Mayo Marty W MW Bekiranov Stefan S
Epigenetics & chromatin 20130902 1
<h4>Background</h4>The epithelial-mesenchymal transition (EMT) is a de-differentiation process required for wound healing and development. In tumors of epithelial origin aberrant induction of EMT contributes to cancer progression and metastasis. Studies have begun to implicate epigenetic reprogramming in EMT; however, the relationship between reprogramming and the coordination of cellular processes is largely unexplored. We have previously developed a system to study EMT in a canonical non-small ...[more]
Similar Datasets
Project description:TGFbeta/TNFalpha treated spheroid A549 cultures are a model of the epithelial-mesenchymal transition (EMT). These experiments capture the changes in global gene expression that result from cells being induced to undergo EMT (3D control vs 3D treated), but also the differences in gene expression when A549 is grown in spheroid cultures (2D control vs 3D untreated). EMT is efficiently induced only in the spheroid culture model. A total of 8 samples are analyzed, corresponding to 4 conditions (2D control, 2D treated, 3D control, 3D treated) and 2 biological replicates.
2013-09-12 | E-GEOD-42373 | biostudies-arrayexpress
Project description:Bacterial pathogens must be able to both recognize suitable niches within the host for colonization and successfully compete with commensal flora for nutrients in order to establish infection. Ethanolamine (EA) is a major component of mammalian and bacterial membranes and may be used by pathogens as a carbon and/or nitrogen source in the gastrointestinal tract. We examined how EA influences gene expression in the human pathogen enterohemorrhagic Escherichia coli O157:H7 (EHEC). Our results indicate EA is not only important for nitrogen metabolism, but that EA is used in cell-to-cell signaling to activate virulence gene expression. Genes encoding for the global regulatory proteins QseC, QseE, and QseA, as well as for attaching and effacement (AE) lesion formation and Shiga toxin are differentially regulated when EHEC is grown with micromolar concentrations of EA. We also constructed a deletion of eutR that encodes the regulator of the eut (EA utilization) operon and examined virulence gene expression. These results suggest that EutR is important in regulating gene expression in response to EA, but that EA signaling does not occur solely through EutR. This is the first report linking EA to cell-to-cell signaling and pathogenesis. Design of the study was to compare the transcriptional response of WT cells grown with ethanolamine to that of wild type cells grown without ethanolamine.
2012-06-17 | E-GEOD-34046 | biostudies-arrayexpress
Project description:We studied the extent of chromatin remodeling in an in-vitro model of the epithelial-mesenchymal transition (EMT). EMT is induced in spheroid cultures (3D) using simultaneously two cytokines: TGFbeta and TNFalpha. The epithelial-mesenchymal transition (EMT) is a cellular de-differentiation process that has been implicated in cancer progression and metastasis. Increasing evidence suggests that EMT is regulated and established by epigenetic reprogramming, however a systems-level mechanism describing how chromatin remodeling contributes to the phenotypic switch is not known. We have generated genome-wide maps of 18 histone modifications/variants and variants in both the epithelial and mesenchymal states and quantified patterns of epigenetic changes at gene and enhancer loci. Clusters of these patterns reveal that EMT-related genes and their proximal enhancers are regulated through coordinated patterns of chromatin activation and repression at both gene and enhancer loci. At the cellular level, the remodeling of gene loci translates into a modular protein interaction network that recapitulates EMT-related signaling. Moreover, differentially activated or repressed enhancers are associated with two non-overlapping sets of transcription factors. We propose a chromatin-mediated regulatory feedback loop model where the NFkappaB and AP-1 transcription factors (TFs) bind activated enhancers, that regulate EMT-related genes, which in turn activate signaling pathways upstream of these TFs.
2013-09-12 | E-GEOD-42374 | biostudies-arrayexpress
Project description:Recent studies have characterized the genomic structures of many eukaryotic cells, often with a focus on their relation to gene expression. So far, these studies have largely only investigated cells grown in 2D culture, although the transcriptomes of 3D cultured cells are generally closer to their in vivo phenotype. To examine the effects of spatial constraints on chromosome conformation, we investigated the genomic architecture of mouse hepatocytes grown in 2D and 3D cultures using in situ Hi-C. Our results reveal significant differences in long-range genomic interactions, notably in compartment identity and strength as well as in TAD-TAD interactions, but only minor differences at the TAD level. RNA-seq analysis reveals an up-regulation in the 3D cultured cells of those genes involved in physiological hepatocyte functions. We find that these genes are associated with only a subset of the structural changes, suggesting that the differences in genomic structure are indeed critically important for transcriptional regulation but also that there are major structural differences owing to other functions than gene expression. Overall, our results indicate that growth in 3D significantly alters longer-range genomic interactions, which may be consequential for a subset of genes that are important for the physiological functioning of the cell.
2020-09-30 | E-MTAB-8303 | biostudies-arrayexpress
Project description:The use of induced pluripotent stem cells (iPSC) derived from independent patients and sources holds considerable promise to improve the understanding of development and disease. However, optimized use of iPSC depends on our ability to develop methods to efficiently qualify cell lines and protocols, monitor genetic stability, and evaluate self-renewal and differentiation potential. To accomplish these goals, 57 stem cell lines from 10 laboratories were differentiated to 7 different states, resulting in 248 analyzed samples. Cell lines were differentiated and characterized at a central laboratory using standardized cell culture methodologies, protocols, and metadata descriptors. Stem cell and derived differentiated lines were characterized using RNA-seq, miRNA-seq, copy number arrays, DNA methylation arrays, flow cytometry, and molecular histology. All materials, including raw data, metadata, analysis and processing code, and methodological and provenance documentation are publicly available for re-use and interactive exploration at https://www.synapse.org/pcbc . The goal is to provide data that can improve our ability to robustly and reproducibly use human pluripotent stem cells to understand development and disease. 114 samples This submission represents DNA methylation component of study.
2016-08-20 | E-GEOD-85828 | biostudies-arrayexpress
Project description:SMCs must undergo specialzed patterning during blood vessel stabilization. We used microarray analysis to identify differentially expressed genes as smooth muscle cells were induced to assemble into a network of elongated cords. Two time points (Day 0 and Day 8) and three biological replicates for each, using Affymetrix HGU133A and HGU133B arrays for each sample.
2011-04-17 | E-GEOD-21363 | biostudies-arrayexpress
Project description:The development of more complex but reliable systems for compound testing in a pharmaceutical context is a challenging task to date. Three-dimensional (3D), organ mimetic cell culture is aiming to become an alternative to common two-dimensional (2D) cell culture or animal testing in that field. We developed a biocompatible 3D cell culture environment for a hepatocellular carcinoma (HCC) model that enables cellular maintenance in a polycarbonate scaffold structure. Albumin, regarded as a differentiation marker, was elevated in statically 3D cultivated HepG2 cells. Expression of HCC tumor marker alpha-fetoprotein (AFP) was reduced compared to immunofluorescence stainings of 2D cultivated cells. Remarkably, expression of cytokeratin and pathophysiologically relevant beta-1 integrin (ITGB1) was found enhanced in nonperfused 3D cell culture. Changes in gene expression induced by the 3D cultivation environment were investigated using Ingenuity Pathway Analysis (IPA). Our findings revealed involvement of the insulin growth factor (IGF) signaling pathway in upregulation of matrix metalloproteinases (MMP) and ITGB1. The experimental data indicate a more differentiated state in 3D cultivated HepG2 cells than in the respective 2D experiments. Hence, scaffold-supported 3D cultivation of HepG2 cells may lead to a gain of information valuable for both drug testing and cancer research. HepG2 cells were cultivated for five days under 2D and 3D statical and perfused conditions. Cultivation was started with 0.25x10^6 cells in 2D and with 1x10^6 vital cells for the 3D experiments. The day of seeding was defined as d0. The groups were classified as follows: 2D, i.e., monolayer cultures, 3D, i.e., statical 3D cultures and BR, which denotes perfused 3D culture of HepG2 cells. The perfusable bioreactor system was operated using a peristaltic pump. It houses the MatriGrid, a polycarbonate-based microporous cellular support. For 3D static cultivation, cell-inoculated MatriGrids were placed in wells of a 24-well plate. Microarray experiments of three 2D (i.e., control), three 3D statically and three actively perfused 3D cultivations were performed at SIRS-Lab GmbH (SIRS-Lab GmbH, Jena, Germany) according to the manufacturer's instructions (Illumina, San Diego, CA). Altogether, 9 RNA samples of hepatocyte cultures and an internal control RNA were hybridized on two HumanHT-12 v4 Expression BeadChips.
2012-11-01 | E-GEOD-41962 | biostudies-arrayexpress
Project description:The development of more complex but reliable systems for compound testing in a pharmaceutical context is a challenging task to date. Three dimensional (3D), organ mimetic cell culture is aiming to become an alternative to common two dimensional (2D) cell culture or animal testing in that field. We developed a biocompatible 3D cell culture environment for a 3D hepatocyte cell culture that enables cellular maintenance in a polycarbonate scaffold structure. Our data indicate that an actively perfused three dimensional cell culture displays a more pronounced metabolic genotype than statically cultivated hepatocytes. Human hepatocytes of three donors were cultivated for five days under 2D and 3D statical and perfused conditions. Cultivation was started with 0.25 x106 in 2D and with 1x 106 vital cells for the 3D experiments. The day of seeding was defined as d0. The groups were classified as follows: 2D i.e.monolayer cultures, 3D i.e. statical 3D culture and BR denotes perfused 3D culture of hepatocytes. The perfusable bioreactor system was operated using a peristaltic pump. It houses the MatriGrid, a polycarbonate based microporous cellular support. For 3Dstatic cultivation, cell- inoculated MatriGrids were placed in wells of a 24 wells plate. Microarray experiments of three 2D (i.e. control), three 3D statically and three actively perfused 3D cultivations, respectively, were performed at SIRS-Lab GmbH (SIRS-Lab GmbH, Jena, Germany) according to the manufacturerM-bM-^@M-^Ys instructions (Illumina, San Diego, CA). Altogether, 8 RNA samples of hepatocyte cultures and an internal control RNA were hybridized on two HumanHT-12 v4 Expression BeadChips.
2013-03-31 | E-GEOD-44580 | biostudies-arrayexpress
Project description:Comparison of gene expression profile of human pluripotent stem cells (hHSC_F1285T_iPS2) expanded in perfused stirred tank bioreactors after 3 and 7 days compared to 2D precultures (day 0)
2016-06-27 | E-MTAB-4149 | biostudies-arrayexpress
Project description:B-cell lymphoma/leukemia (BCL) 11B represents a major regulator of vital processes in post-thymic lymphocytes as well as of lymphocyte differentiation by blocking NK cell and promoting T cell development and is thus considered a \\"guardian of T cell fate\\". Interestingly, on the one hand, NK cell maturation correlates with increased expression of BCL11B, on the other hand, native or induced T cell populations characterized by multiple NK cell features showed reduced BCL11B expression. Both NK cells or T cells display unique and desired features for cellular therapies. NK cells are able to efficiently lyse cancerous or virally infected cells but can only be poorly expanded in vitro. In contrast, T cell cytotoxic activity is limited by T cell receptor (TCR) but in vitro expansion is easily achievable. We show that from buffy coats of healthy donors isolated and CRISPR/Cas9-mediated BCL11B knock-out CD8+ T cells stimulated with IL-15 acquired remarkable innate characteristics and combine spontaneous and antibody-dependent NK cell cytotoxicity with T cell capability for rapid in vitro expansion. The observed features of the induced innate CD8+ (iiT8) cells make them an interesting and promising tool for cellular therapy.
2022-12-07 | E-MTAB-12064 | biostudies-arrayexpress