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The Ewing sarcoma cell line atlas (ESCLA) - The relevance of the transcription factors GATA2 and E2F2 in a Ewing sarcoma cell line model

ABSTRACT: The Ewing sarcoma cell line atlas (ESCLA) - The relevance of the transcription factors GATA2 and E2F2 in a Ewing sarcoma cell line model

PROVIDER: PRJNA873721 | ENA |

REPOSITORIES: ENA

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The Ewing sarcoma cell line atlas (ESCLA) - The relevance of the transcription factors GATA2 and E2F2 in a Ewing sarcoma cell line model

Project description:Cell lines have been essential for major discoveries in cancer including Ewing sarcoma (EwS). EwS is a highly aggressive pediatric bone or soft-tissue cancer characterized by oncogenic EWSR1-ETS fusion transcription factors converting polymorphic GGAA-microsatellites (mSats) into neo-enhancers. However, further detailed mechanistic evaluation of gene regulation in EwS have been hindered by the limited number of well-characterized cell line models. Here, we present the Ewing Sarcoma Cell Line Atlas (ESCLA) comprising 18 EwS cell lines with inducible EWSR1-ETS knockdown that were profiled by whole-genome-sequencing, DNA methylation arrays, gene expression and splicing arrays, mass spectrometry, and ChIP-seq for EWSR1-ETS and histone marks. Systematic analysis of these multi-dimensional data identified GATA2 and E2F2 as EWSR1-ETS-driven putative co-regulatory transcription factors. To evaluate the relevance of these transcrition factors, RNA interference in a Ewing sarcoma cell line was employed with subsequent Affymetrix Exon array profiling. The expression data were analysed in synopsis with the effects of EWSR1-FLI1 in the same cell line.

2022-08-26 | GSE212063 | GEO

ETS family proteins bind glucocorticoid receptor: relevance for treatment of Ewing sarcoma

Project description:Differential expression of gene was analyzed after FLI1 silencing in Ewing Sarcoma cell line A673.

2019-10-01 | GSE135229 | GEO

The Ewing Sarcoma Cell Line Atlas (ESCLA)

Project description:The Ewing Sarcoma Cell Line Atlas (ESCLA)

| PRJNA735784 | ENA

RUNX3 Facilitates Growth of Ewing Sarcoma Cells

Project description:Ewing sarcoma is an aggressive pediatric small round cell tumor that predominantly occurs in bone. Approximately 85% of Ewing sarcomas harbor the EWS/FLI fusion protein, which arises from a chromosomal translocation, t(11:22)(q24:q12). EWS/FLI interacts with numerous lineage-essential transcription factors to maintain mesenchymal progenitors in an undifferentiated state. We previously showed that EWS/FLI binds the osteogenic transcription factor RUNX2 and prevents osteoblast differentiation. In this study, we investigated the role of another Runt-domain protein, RUNX3, in Ewing sarcoma. RUNX3 participates in mesenchymal-derived bone formation and is a context dependent tumor suppressor and oncogene. RUNX3 was detected in all Ewing sarcoma cells examined, whereas RUNX2 was detected in only 73% of specimens. Like RUNX2, RUNX3 binds to EWS/FLI via its Runt domain. EWS/FLI prevented RUNX3 from activating the transcription of a RUNX-responsive reporter, p6OSE2. Stable suppression of RUNX3 expression in the Ewing sarcoma cell line A673 delayed colony growth in anchorage independent soft agar assays and reversed expression of EWS/FLI-responsive genes. These results demonstrate an important role for RUNX3 in Ewing sarcoma. RNA-seq to compare transcriptiome of control A673 ewing sarcoma cells stably expression a non-target or RUNX3 shRNA

2014-05-01 | E-GEOD-56900 | biostudies-arrayexpress

HDGF ChIP-Seq in Ewing sarcoma cell line RD-ES

Project description:HDGF is implicated in Ewing sarcoma. We used HDGF ChIP-Seq in combination with gene expression profiling to identify genes and pathways it regulates in Ewing sarcoma.

2024-07-01 | GSE155456 | GEO

Genome-wide profiling of siRNA targeting EWS-FLI1 in TC32 Ewing sarcoma cell line

Project description:Identification of genes and pathways that were influenced by knock-down EWS-FLI1 in TC32 Ewing sarcoma cell line.

2018-09-05 | GSE103843 | GEO

ETS family proteins bind glucocorticoid receptor: relevance for treatment of Ewing sarcoma

Project description:ETS family proteins bind glucocorticoid receptor: relevance for treatment of Ewing sarcoma

| PRJNA558012 | ENA

Systematic multi-omics cell line profiling uncovers principles of Ewing sarcoma fusion oncogene-mediated gene regulation

Project description:Ewing sarcoma (EwS) is characterized by EWSR1-ETS fusion transcription factors converting polymorphic GGAA microsatellites (mSats) into potent neo-enhancers. Although the paucity of additional mutations makes EwS a genuine model to study principles of cooperation between dominant fusion oncogenes and neo-enhancers, this is impeded by the limited number of well-characterized models. Here we present the Ewing Sarcoma Cell Line Atlas (ESCLA), comprising whole-genome, DNA methylation, transcriptome, proteome, and chromatin immunoprecipitation sequencing (ChIP-seq) data of 18 cell lines with inducible EWSR1-ETS knockdown. The ESCLA shows hundreds of EWSR1-ETS-targets, the nature of EWSR1-ETS-preferred GGAA mSats, and putative indirect modes of EWSR1-ETS-mediated gene regulation, converging in the duality of a specific but plastic EwS signature. We identify heterogeneously regulated EWSR1-ETS-targets as potential prognostic EwS biomarkers. Our freely available ESCLA (http://r2platform.com/escla/) is a rich resource for EwS research and highlights the power of comprehensive datasets to unravel principles of heterogeneous gene regulation by chimeric transcription factors.

2024-06-18 | PXD052856 | Pride

Ewing Sarcoma

Project description:This SuperSeries is composed of the following subset Series: GSE36857: Goldengate Methylation analysis: Ewing Sarcoma GSE36858: 5- AZA treatment of EWS cell lines Refer to individual Series

2012-09-01 | E-GEOD-36859 | biostudies-arrayexpress

In Vitro Characterization of A4573 Preclinical Radiation-Adapted Model for Ewing Sarcoma

Project description:Analysis of differentially expressed genes in wild type A4573 Ewing Sarcoma cells when compared to A4573 Ewing Sarcoma cells that received six 4 Gy fractions (cumulative dose of 24 Gy) of ionizing radiation (radiation-adapted cell line). The hypothesis tested being that repeated ionizing radiation exposure of modifies radiation therapy response in Ewing Sarcoma.

2017-05-10 | GSE98706 | GEO

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