Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Targeted degradation of BRD9 reverses oncogenic gene expression in synovial sarcoma [ChIP-seq]

ABSTRACT: Targeted degradation of BRD9 reverses oncogenic gene expression in synovial sarcoma [ChIP-seq]

PROVIDER: PRJNA450476 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR7012330.fastq.gz	Fastqsanger.gz
	SRR7012340.fastq.gz	Fastqsanger.gz
	SRR7012331.fastq.gz	Fastqsanger.gz
	SRR7012341.fastq.gz	Fastqsanger.gz
	SRR7012332.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 12

Similar Datasets

Targeted degradation of BRD9 reverses oncogenic gene expression in synovial sarcoma [ChIP-seq]

Project description:We used a CRISPR-based screening approach to identify functional vulnerabilities in pediatric sarcoma cell types, identifying BRD9 as an important dependency in synovial sarcoma cells.

2018-11-01 | GSE113228 | GEO

Targeted degradation of BRD9 reverses oncogenic gene expression in synovial sarcoma [RNA-seq]

2018-11-01 | GSE113227 | GEO

Targeted degradation of BRD9 reverses oncogenic gene expression in synovial sarcoma

Project description:Targeted degradation of BRD9 reverses oncogenic gene expression in synovial sarcoma

| PRJNA450475 | ENA

Targeted degradation of BRD9 reverses oncogenic gene expression in synovial sarcoma [RNA-seq]

Project description:Targeted degradation of BRD9 reverses oncogenic gene expression in synovial sarcoma [RNA-seq]

| PRJNA450466 | ENA

Targeted degradation of BRD9 reverses oncogenic gene expression in synovial sarcoma.

Project description:Synovial sarcoma tumours contain a characteristic fusion protein, SS18-SSX, which drives disease development. Targeting oncogenic fusion proteins presents an attractive therapeutic opportunity. However, SS18-SSX has proven intractable for therapeutic intervention. Using a domain-focused CRISPR screen we identified the bromodomain of BRD9 as a critical functional dependency in synovial sarcoma. BRD9 is a component of SS18-SSX containing BAF complexes in synovial sarcoma cells; and integration of BRD9 into these complexes is critical for cell growth. Moreover BRD9 and SS18-SSX co-localize extensively on the synovial sarcoma genome. Remarkably, synovial sarcoma cells are highly sensitive to a novel small molecule degrader of BRD9, while other sarcoma subtypes are unaffected. Degradation of BRD9 induces downregulation of oncogenic transcriptional programs and inhibits tumour progression in vivo. We demonstrate that BRD9 supports oncogenic mechanisms underlying the SS18-SSX fusion in synovial sarcoma and highlight targeted degradation of BRD9 as a potential therapeutic opportunity in this disease.

| S-EPMC6277197 | biostudies-literature

Targeted degradation of BRD9 reverses oncogenic gene expression in synovial sarcoma

Project description:This SuperSeries is composed of the SubSeries listed below.

2018-11-01 | GSE113229 | GEO

Gene expression analysis of synovial sarcoma, clinical samples

Project description:To identify molecular biomarkers that are useful for diagnosis and its targeting treatment, we analysed expression profile of synovial sarcoma tissue. In the present study, we studied gene expression profiles comparing 11 cases of synovial sarcoma.

2015-07-23 | E-GEOD-65532 | biostudies-arrayexpress

Identification of Altered MicroRNA Expression Patterns in Synovial Sarcoma

Project description:MicroRNAs (miRNAs) are non-coding small RNAs that function as an endogenous regulator of gene expression. Their dysregulation has been implicated in the development of several cancers. However, the status of miRNA in soft tissue sarcomas has not yet been thoroughly investigated. This study examined the global miRNA expression in synovial sarcoma and compared the results to those in another translocation-associated sarcoma, the Ewing family of tumors, and in normal skeletal muscle. The 3D-Gene miRNA microarray platform (Toray, Kamakura, Japan) and unsupervised hierarchical clustering revealed a distinct expression pattern of miRNAs in synovial sarcoma from Ewing tumors and skeletal muscle. Thirty-five of the more than 700 miRNAs analyzed were differentially expressed in synovial sarcomas in comparison to other tissue types. There were 21 significantly up-regulated miRNAs, including some miRNAs, such as let-7e, miR-99b and miR-125a-3p, clustered within the same chromosomal loci. Quantitative reverse transcription-polymerase chain reaction also demonstrated that these miRNAs were over-expressed in synovial sarcomas. The down-regulation of let-7e and miR-99b by anti-miR miRNA inhibitors resulted in the suppression of the proliferation of synovial sarcoma cells, and modulated the expression of their putative targets, HMGA2 and SMARCA5, suggesting that these molecules have a potential oncogenic role. The unique miRNA expression pattern including the over-expressed miRNA clusters in synovial sarcoma warrants further investigation in order to develop a better understanding of the oncogenic mechanisms and future therapeutic strategies for synovial sarcoma. Ten synovial sarcomas, five Ewing tumors and five normal skeletal muscle specimens are analyzed.

2010-10-21 | E-GEOD-18546 | biostudies-arrayexpress

Gene expression profile of poorly differentiated synovial sarcoma

Project description:Poorly differentiated type synovial sarcoma (PDSS) is a variant of synovial sarcoma characterized by predominantly round or short-spindled cells. Although accumulating evidence from clinicopathological studies suggests a strong association between this variant of synovial sarcoma and poor prognosis, little has been reported on the molecular basis of PDSS. To gain insight into the mechanism(s) that underlie the emergence of PDSS, we analyzed the gene expression profiles of 34 synovial sarcoma clinical samples, including 5 cases of PDSS, using an oligonucleotide microarray. In an unsupervised analysis, the 34 samples fell into 3 groups that correlated highly with histological subtype, namely, monophasic, biphasic, and poorly differentiated types. PDSS was characterized by down-regulation of genes associated with neuronal and skeletal development and cell adhesion, and up-regulation of genes on a specific chromosomal locus, 8q21.11. This locus-specific transcriptional activation in PDSS was confirmed by reverse transcriptase (RT)-PCR analysis of 9 additional synovial sarcoma samples. Our results indicate that PDSS tumors constitute a distinct genetic group based on expression profiles. 34 SYT-SSX fusion transcript-positive SS samples, consisting of 21 MSS, 8 BSS and 5 PDSS cases, were analyzed using an oligonucleotide microarray using a GeneChip Human Genome U133 plus 2.0 array (Affymetrix).

2010-09-01 | E-GEOD-20196 | biostudies-arrayexpress

PTEN-deficient synovial sarcoma

Project description:Transcriptome comparisons by RNAseq of genetically engineered mouse models of synovial sarcoma, expressing SS18-SSX1 or SS18-SSX2 and having homozygous conditional genetic silencing of Pten or wildtype Pten.

2016-11-03 | GSE81476 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data