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Expression data from Zeb1 knockdown NM18 cells

ABSTRACT: Differentiation of epithelial cells is strongly affected by transcription factors related to epithelial to mesenchymal-like progression. We used gene expression profiling to identify genes that are differentially regulated upon repression of the transcription factor Zeb1 (deltaEF1/Areb6). NM18 cells were transfected with non-silencing siRNA (ns-siRNA) or siRNA targeting Zeb1 (Zeb1 siRNA) for 48h. Experiments were performed as independent biological triplicate. Three non-silencing siRNA samples (GSM1322708, GSM1322709, and GSM1322710) were originally deposited in Series GSE54715. The samples were reanalyzed with the Zeb1 siRNA samples and the data is linked at the bottom of the Series record.

ORGANISM(S): Mus musculus

SUBMITTER: Alexander Feuerborn

PROVIDER: E-GEOD-63164 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Zeb1 affects epithelial cell adhesion by diverting glycosphingolipid metabolism.

Mathow Daniel D Chessa Federica F Rabionet Mariona M Kaden Sylvia S Jennemann Richard R Sandhoff Roger R Gröne Hermann-Josef HJ Feuerborn Alexander A

EMBO reports 20150202 3

This study proposes that the transcription factor Zeb1 modulates epithelial cell adhesion by diverting glycosphingolipid metabolism. Zeb1 promotes expression of a-series glycosphingolipids via regulating expression of GM3 synthase (St3gal5), which mechanistically involves Zeb1 binding to the St3gal5 promoter as well as suppressing microRNA-mediated repression of St3gal5. Functionally, the repression of St3gal5 suffices to elevate intercellular adhesion and expression of distinct junction-associa ...[more]

PMID: 25643708

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Gene expression analysis of SW480 colorectal cancer cells with siRNA mediated ZEB1 or control (GFP) knockdown

Project description:Epithelial-to-mesenchymal transition (EMT) is a fundamental process in development and disease. If aberrantly activated it is a trigger for tumour progression and metastasis (Thiery et al, 2009). It is now known that EMT activation is also associated with the maintenance of stem-cell properties (Mani et al, 2008). Since Zinc-finger enhancer binding transcription factor 1 (ZEB1) is a crucial EMT activator, we analyzed the changes in the gene expression profile that accompany siRNA mediated loss of ZEB1 in SW480 colorectal cancer cells. SW480 is a cell line that exhibits mesenchymal characteristics, but reverts to an epithelial phenotype upon ZEB1 knock down (Spaderna et al. 2006 Gastroenterology). SW480 cells were transfected with control (GFP) or ZEB1 siRNA. 72 hours after transfection, cells were harvested, total RNA was isolated and hybridized.

2016-06-15 | E-MTAB-3479 | biostudies-arrayexpress

Basonuclin-1 modulates epithelial plasticity and TGF-?1-induced loss of epithelial cell integrity [BNC1]

Project description:TGF-b1-stimulation induces an epithelial dedifferentiation-process, throughout which epithelial cell sheets disintegrate and gradually switch into fibroblastic-appearing cells (EMT-like transition). Several transcription factors, some of them being TGF-b1-responsive, are functionally involved in such a switch and affect epithelial differentiation and plasticity. We used microarray-based gene expression profiling of mammary epithelial cells that actively undergo TGF-b1-induced epithelial dedifferentiation. Further, we determined gene expression changes in Basonuclin-1 knock-down cells in conjunction with TGF-b1-stimulation in order to determine a possible effect of Bnc1 on TGF-b1-responsive genes. Cells were transfected with non-silencing (control) siRNA or siRNA against Basonuclin-1 (Bnc1) for 24hrs. Subsequently, cells were treated with 5ng/ml TGF-b1 or left untreated for additional 24hrs. The experiments were performed as independent biological triplicate.

2014-03-01 | E-GEOD-54715 | biostudies-arrayexpress

MS-based quantitative proteomic analysis of ribosomal fractions from wild-type and Zeb1-overexpressing human mammary epithelial cell

Project description:Epithelial-mesenchymal transition (EMT) involves profound changes in cell morphology, driven by transcriptional and epigenetic reprogramming. However, it emerges that translation and the ribosome composition play also key role in establishing physio-pathological phenotypes. Using genome-wide analyses, we report significant rearrangement of the translational landscape and machinery during EMT. Specifically, a mesenchymal cell line overexpressing the EMT transcription factor ZEB1 shows alterations in translational reprogramming and fidelity. Considering the change in translational activity of ZEB1-overexpressing mesenchymal cells, including in fidelity activity, we sought for changes in ribosome composition. We thus performed a riboproteome approach, i.e., mass spectrometry (MS)-based quantitative proteomic analysis of purified cytoplasmic ribosomes to highlight any change in relative amount of individual ribosomal proteins between wild-type and ZEB1-overexpressing human mammary epithelial cells.

2024-11-02 | PXD047409 | Pride

ZEB1-regulated inflammatory phenotype in breast cancer cells

Project description:This SuperSeries is composed of the SubSeries listed below. Zinc finger E-box binding protein 1 (ZEB1) and ZEB2 induce epithelial-mesenchymal transition (EMT) and cancer progression. However, little is known about global picture of transcriptional regulation by ZEB1 and ZEB2. Here we identified an inflammatory phenotype regulated by ZEB1 using chromatin immunoprecipitation-sequencing (ChIP-seq) and RNA-sequencing (RNA-seq) in basal type breast cancer cells, followed by gene set enrichment analysis (GSEA) of ZEB1-bound genes.

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Next Generation Sequencing of Wild Type and Zeb1-/- HSCs

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2020-07-02 | GSE153663 | GEO

Next Generation Sequencing of Wild Type and Zeb1-/- CLP

2020-07-02 | GSE153662 | GEO

Next Generation Sequencing of LSK EpCAM+ and EpCAM- of Zeb1-/-

2020-10-01 | GSE154615 | GEO

Expression data from Zeb1 knockdown NM18 cells

Project description:Differentiation of epithelial cells is strongly affected by transcription factors related to epithelial to mesenchymal-like progression. We used gene expression profiling to identify genes that are differentially regulated upon repression of the transcription factor Zeb1 (deltaEF1/Areb6).

2015-02-04 | GSE63164 | GEO

RNA-seq of human colorectal cancer cells in presence and absence of ZEB1

Project description:Characterize the gene expression profile with RNA-seq using Illumina HiSeq2000 of Ls174T and RKO1 CRC cell lines in presence of siRNA against control and ZEB1

2023-07-31 | GSE123416 | GEO

Defining the role of ZEB1 in the pathogenesis of lung cancer

Project description:Using an in vitro model for malignant transformation of human bronchial epithelial cells (HBECs) we have found epithelial-to-mesenchymal transition (EMT) and expression of the EMT-transcription factor ZEB1 are early and critical events. Specifically, we found preexisting oncogenic mutations in TP53 and KRAS were required for HBECs to engage EMT machinery in response to microenvironmental (serum/TGFβ) or specific oncogenetic (MYC) EMT-inducing factors, which induce EMT through distinct TGFβ-dependent and vitamin D receptor (VDR)-dependent pathways, respectively, with both requiring ZEB1. Functional studies demonstrated ZEB1 causally promotes the malignant progression of HBECs and tumorigenicity of NSCLC and small cell lung cancer (SCLC) lines. Mechanistically ZEB1 directly represses ESRP1 leading to increased mesenchymal splicing of CD44, which drives a switch to CD44hi status and defines a highly transformed subpopulation. This was supported by finding ZEB1 is expressed in early-stage primary non-small cell lung cancers (NSCLC), as early as stage IB tumors, and its expression correlates with TNM stage. We conclude that: ZEB1-induced EMT and associated ESRP1 and CD44 molecular changes are important biomarkers for lung cancer pathogenesis; TGFβ and VDR are EMT chemoprevention targets; and as such, ZEB1 represents an important therapeutic target in NSCLC and SCLC.

2016-08-31 | GSE77925 | GEO

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