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Genome-wide maps of EWS-FLI1 binding sites and histone modification in murine Ewing sarcoma cells

ABSTRACT: Genome-wide maps of EWS-FLI1 binding sites and histone modification in murine Ewing sarcoma cells

PROVIDER: PRJNA427908 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6430040.fastq.gz	Fastqsanger.gz
	SRR6430041.fastq.gz	Fastqsanger.gz
	SRR6430042.fastq.gz	Fastqsanger.gz
	SRR6430043.fastq.gz	Fastqsanger.gz
	SRR6430039.fastq.gz	Fastqsanger.gz

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Similar Datasets

Genome-wide maps of EWS-FLI1 binding sites and histone modification in murine Ewing sarcoma cells

Project description:We identified global DNA binding properties of EWS-FLI1 in mouse Ewing sarcoma. GGAA microsatellites were found as binding sites of EWS-FLI1 but with less frequency than that in human Ewing sarcoma, and genomic distribution is not conserved between human and mouse.

2018-07-25 | GSE108631 | GEO

USP1 expression driven by EWS-FLI1 transcription factor stabilizes Survivin and promotes Ewing sarcoma cell survival

Project description:Ewing sarcoma (EWS) is a malignant pediatric bone cancer. Most Ewing sarcomas are driven by EWS-FLI1 oncogenic transcription factor that plays roles in transcriptional regulation, DNA damage response, cell cycle checkpoint control, and alternative splicing. USP1, a deubiquitylase which regulates DNA damage and replication stress responses, is overexpressed at both the mRNA and protein levels in EWS cell lines compared to human mesenchymal stem cells, the EWS cell of origin. The functional significance of high USP1 expression in Ewing sarcoma is not known. Here, we identify USP1 as a transcriptional target of EWS-FLI1 and a key regulator of EWS cell survival. We show that EWS-FLI1 knockdown decreases USP1 mRNA and protein levels. ChIP and ChIP-seq analyses show EWS-FLI1 occupancy on the USP1 promoter. Importantly, USP1 knockdown or inhibition arrests EWS cell growth and induces cell death by apoptosis. We observe destabilization of Survivin (also known as BIRC5 or IAP4) and activation of caspases-3 and -7 following USP1 knockdown or inhibition in the absence of external DNA damage stimuli. Notably, EWS cells display hypersensitivity to combinatorial treatment of doxorubicin or etoposide, EWS standard of care drugs, and USP1 inhibitor compared to single agents alone. Together, our study demonstrates that USP1 is regulated by EWS-FLI1, the USP1-Survivin axis promotes EWS cell survival, and USP1 inhibition sensitizes EWS cells to standard of care chemotherapy.

2024-01-26 | PXD041033 | Pride

Identification of genes regulated by knockdown of EWS-FLI1 in Ewing sarcoma cells.

Project description:EWS-FLI1 is the driver oncogene in >85% of Ewing sarcoma tumors. We used siRNA to knock down EWS-FLI1 for 48h hours in two Ewing sarcoma cell lines (EW8, TC71) to identify downstream genes and pathways affected by loss of EWS-FLI1 activity. RNAseq analysis was performed after 48 hours of treatment with a nontargeting siControl or siEWS-FLI1.

2024-09-30 | GSE263504 | GEO

EWS-FLI1 and HOXD13 control tumor cell plasticity in Ewing sarcoma [RNA-seq]

Project description:Posterior homeobox D genes, in particular HOXD13, are over-expressed by Ewing sarcoma, a tumor driven by the oncogenic fusion protein EWS-FLI1. Here, we have found that EWS-FLI1 maintains HOXD13 expression through a GGAA microsatellite enhancer in the developmental posterior HOXD regulatory domain. Activation of this enhancer is EWS-FLI1 dependent and epigenomic silencing of this region leads to loss of HOXD13 expression in Ewing sarcoma cells, but not in unrelated cells. To determine the function of HOXD13 activation in Ewing sarcoma we performed nascent RNA sequencing or RNA sequencing upon HOXD13 knockdown.

2022-06-28 | GSE148494 | GEO

High-throughput RNAi cell viability screen to identify selective targets for EWS-FLI1 positive Ewing sarcoma

Project description:We have performed a high-throughput RNA interference screen to identify targets inhibiting EWS-FLI1 driven cell proliferation in Ewing sarcoma cells. EWS-FLI1 expressing A673 Ewing sarcoma cells were screened both in presence and absence of EWS-FLI1 shRNA induction with druggable siRNA library. Leucine rich repeats and WD repeat Domain containing 1 (LRWD1) targeting siRNA pool was the strongest anti-proliferative hit identified only in presence of EWS-FLI1. Validation experiments confirmed the anti-proliferative effect of LRWD1 depletion especially in EWS-FLI1 expressing cells. Functional analysis of differentially expressed genes in LRWD1 depleted Ewing sarcoma cells showed over-representation of connective tissue development, cell projection morphogenesis and neuronal processes.

2018-09-16 | GSE73092 | GEO

EWS-FLI1 and HOXD13 control tumor cell plasticity in Ewing sarcoma [CITE-seq]

2022-06-28 | GSE165973 | GEO

EWS-FLI1-regulated Core Transcriptional Regulatory Circuit promotes Ewing sarcoma progression

Project description:We identify and validate an Ewing sarcoma-specific CRC, which is under control of EWS-FLI1. Formed by KLF15, TCF4 and NKX2-2, this CRC apparatus coordinates the gene expression programs in Ewing sarcoma cells. These data advance the understanding of the mechanistic basis of transactional dysregulation in Ewing sarcoma, and provide potential novel therapeutic strategies against this malignancy.

2020-09-29 | GSE141493 | GEO

Expression data for analysis of genes regulated by EWS/FLI1 protein levels in Ewing sarcoma cell line A673

Project description:Comparison of gene expression profile of Ewing sarcoma cells which have an exchange of the endogenous EWS/FLI1 to either wild-type or a turnover-deficient mutant EWS/FLI1. Most target genes are saturated as only a few target genes are soly driven by increasing protein amount. The effect of a stable EWS/FLI1 mutant on global gene expression was evaluated in A673 Ewing sarcoma cells.

2016-11-16 | GSE81018 | 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

Reciprocal regulation of extracellular matrix proteins by EWS-FLI1 and AP-1 in Ewing sarcoma cells

Project description:Ribonucleotide reductase (RNR) is the rate limiting enzyme in the synthesis of deoxyribonucleotides and the target of multiple chemotherapy drugs, including gemcitabine and hydroxyurea. In previous work, we identified that inhibition of RNR in Ewing sarcoma tumors upregulates the expression levels of multiple members of the activator protein-1 (AP-1) transcription factor family, including c-Jun and c-Fos, and downregulates the expression of c-Myc. However, the broader functions and downstream targets of AP-1, which are highly context- and cell-dependent, are unknown in Ewing sarcoma tumors. Consequently, in this work, we used genetically defined models, transcriptome profiling, and gene set enrichment analysis to identify that AP-1 and EWS-FLI1, the driver oncogene in most Ewing sarcoma tumors, reciprocally regulate the expression of multiple extracellular matrix proteins, including fibronectins, integrins, and collagens. AP-1 expression in Ewing sarcoma cells also drives, coincident with these perturbations in gene and protein expression, changes in cell morphology and phenotype. Furthermore, we also identified that the EWS-FLI1 oncoprotein dysregulates the expression of multiple AP-1 proteins, aligning with previous reports demonstrating genetic and physical interactions between EWS-FLI1 and AP-1. Overall, these results provide novel insight into the distinct, EWS-FLI1-dependent features of Ewing sarcoma tumors and identify a novel, reciprocal regulation of extracellular matrix components by EWS-FLI1 and AP-1.

2024-09-30 | GSE263503 | GEO

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