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Identification of genes regulated by loss of RRM1 in Ewing sarcoma cells.

ABSTRACT: Identification of genes regulated by loss of RRM1 in Ewing sarcoma cells.

PROVIDER: PRJNA891230 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR21930262_1.fastq.gz	Fastqsanger.gz
	SRR21930262_2.fastq.gz	Fastqsanger.gz
	SRR21930263_1.fastq.gz	Fastqsanger.gz
	SRR21930263_2.fastq.gz	Fastqsanger.gz
	SRR21930264_1.fastq.gz	Fastqsanger.gz

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Identification of genes regulated by loss of RRM1 in Ewing sarcoma cells.

Project description:Ribonucleotide reductase (RNR), which is composed of RRM1 and RRM2 subunits, is the rate limiting enzyme in the synthesis of deoxyribonucleotides and required for DNA replication and DNA damage repair. We used a conditional knockout (CRISPR/Cas9) and rescue approach to target RRM1 in Ewing sarcoma cells and identify downstream pathways impacted by the loss of RNR activity. RNA-seq analysis was performed at times 0 and 48 hours after removal of doxycycline from cell culture media, which results in loss of the RRM1 protein.

2023-08-23 | GSE215881 | GEO

The effect of STAG2 loss in Ewing sarcoma [HiChIP]

Project description:Ewing sarcoma is an aggressive malignancy characterized by oncogenic rearrangements of the EWS gene with an ETS-family transcription factor, most commonly FLI. Recent comprehensive next-generation sequencing efforts have revealed few other highly recurrent mutations in this disease apart from loss-of-function mutations in STAG2 which occur in 15-20% of tumors. STAG2 is a member of the cohesin complex, which regulates sister chromatid alignment during mitosis and epigenetic regulation of gene expression. While some studies suggest that loss of STAG2 is associated with the development of aneuploidy, this is not the case in Ewing sarcoma. To investigate whether STAG2 loss affects epigenetic regulation of gene expression in Ewing sarcoma, we developed isogenic Ewing sarcoma cell lines with STAG2 knockout. We found that Ewing sarcoma cells engineered for loss of STAG2 maintain an intact cohesion complex that alternately incorporates STAG1.

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The effect of STAG2 loss in Ewing sarcoma [RNA-Seq]

Project description:Ewing sarcoma is an aggressive malignancy characterized by oncogenic rearrangements of the EWS gene with an ETS-family transcription factor, most commonly FLI. Recent comprehensive next-generation sequencing efforts have revealed few other highly recurrent mutations in this disease apart from loss-of-function mutations in STAG2 which occur in 15-20% of tumors. STAG2 is a member of the cohesin complex, which regulates sister chromatid alignment during mitosis and epigenetic regulation of gene expression. While some studies suggest that loss of STAG2 is associated with the development of aneuploidy, this is not the case in Ewing sarcoma. To investigate whether STAG2 loss effects epigenetic regulation of gene expression in Ewing sarcoma, we developed isogenic Ewing sarcoma cell lines with STAG2 knockout. We found that Ewing sarcoma cells engineered for loss of STAG2 maintain an intact cohesion complex that alternately incorporates STAG1.

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The effect of STAG2 loss in Ewing sarcoma [ChIP-seq]

Project description:Ewing sarcoma is an aggressive malignancy characterized by oncogenic rearrangements of the EWS gene with an ETS-family transcription factor, most commonly FLI. Recent comprehensive next-generation sequencing efforts have revealed few other highly recurrent mutations in this disease apart from loss-of-function mutations in STAG2 which occur in 15-20% of tumors. STAG2 is a member of the cohesin complex, which regulates sister chromatid alignment during mitosis and epigenetic regulation of gene expression. While some studies suggest that loss of STAG2 is associated with the development of aneuploidy, this is not the case in Ewing sarcoma. To investigate whether STAG2 loss effects epigenetic regulation of gene expression in Ewing sarcoma, we developed isogenic Ewing sarcoma cell lines with STAG2 knockout. We found that Ewing sarcoma cells engineered for loss of STAG2 maintain an intact cohesion complex that alternately incorporates STAG1.

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Project description:Ewing sarcoma is an aggressive malignancy characterized by oncogenic rearrangements of the EWS gene with an ETS-family transcription factor, most commonly FLI. Recent comprehensive next-generation sequencing efforts have revealed few other highly recurrent mutations in this disease apart from loss-of-function mutations in STAG2 which occur in 15-20% of tumors. STAG2 is a member of the cohesin complex, which regulates sister chromatid alignment during mitosis and epigenetic regulation of gene expression. While some studies suggest that loss of STAG2 is associated with the development of aneuploidy, this is not the case in Ewing sarcoma. To investigate whether STAG2 loss effects epigenetic regulation of gene expression in Ewing sarcoma, we developed isogenic Ewing sarcoma cell lines with STAG2 knockout. We found that Ewing sarcoma cells engineered for loss of STAG2 maintain an intact cohesion complex that alternately incorporates STAG1.

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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

Identification of genes regulated by ID2 in Ewing sarcoma cells.

Project description:Identification of genes regulated by ID2 in Ewing sarcoma cells.

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The effect of STAG2 loss in Ewing sarcoma

Project description:The effect of STAG2 loss in Ewing sarcoma

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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

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