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Determine the effects on the transcriptome of depleting STAG2 in RT112, a bladder cancer cell line.

ABSTRACT: Determine the effects on the transcriptome of depleting STAG2 in RT112, a bladder cancer cell line.

PROVIDER: PRJNA647617 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12283538.fastq.gz	Fastqsanger.gz
	SRR12283539.fastq.gz	Fastqsanger.gz
	SRR12283540.fastq.gz	Fastqsanger.gz
	SRR12283541.fastq.gz	Fastqsanger.gz
	SRR12283542.fastq.gz	Fastqsanger.gz

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Determine the effects on the transcriptome of depleting STAG2 in RT112, a bladder cancer cell line.

Project description:Determine the effects on the transcriptome of depleting STAG2 in RT112, a bladder cancer cell line.

2020-07-23 | GSE154878 | GEO

STAG2 loss-of-function affects short-range genomic contacts and modulates urothelial differentiation in bladder cancer cells

Project description:Cohesin exists in two variants, containing either STAG1 or STAG2. STAG2 is one of the most commonly mutated genes in human cancer, and a major bladder cancer tumor suppressor. Little is known about how its inactivation contributes to tumor development. Here, we analyze the genomic distribution of STAG1 and STAG2 and perform STAG2 loss-of-function experiments using RT112 bladder cancer cells; we then analyze the resulting genomic effects by integrating gene expression and chromatin interaction data.

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Recurrent inactivation of STAG2 in bladder cancer is not associated with aneuploidy [GPL6984]

Project description:STAG2 is a novel UBC tumor suppressor acting through mechanisms that are different from its role to prevent aneuploidy Gene copy number analyses of STAG2 in urinary bladder tumors. R values were extracted from beadstudio and normalised using the pounds method. Log R Ratios were calculated using an average value of R from 200 cases and controls from the Epicuro study. WaviCGH was used to generate copy number calls and log R ratios in the region of STAG2 on the X chromosome were also visualised manually to determine STAG2 loss.

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Recurrent inactivation of STAG2 in bladder cancer is not associated with aneuploidy [GPL6983]

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Project description:Aneuploidy is among the most common hallmarks of cancer, yet the underlying genetic mechanisms are still poorly defined. We have recently identified STAG2 as a gene that is mutated in human cancer and whose inactivation leads directly to chromosomal instability and aneuploidy. However, no single tumor type has yet been identified in which inactivation of a cohesin subunit represents a predominant mutational event. Here we used immunohistochemistry to screen a panel of 2,214 tumors from each of the major human tumor types to identify additional tumor types harboring somatic loss of STAG2. Strikingly, STAG2 expression was completely absent in 18% of urothelial carcinomas, the most common type of bladder cancer and the fifth most common cancer in the United States. DNA sequencing revealed that somatic mutations of STAG2 were present in 21% of urothelial carcinomas, which were found to be a group of highly aneuploid tumors. The acquisition of STAG2 mutations was shown to be an early event in the pathogenesis of urothelial carcinoma. STAG2 loss was significantly associated with lymph node invasion, increased disease recurrence, and reduced cancer-specific survival. These results identify STAG2 as one of the most commonly mutated genes in bladder cancer discovered to date, and demonstrate that STAG2 inactivation defines an aggressive subtype of bladder cancer with particularly poor prognosis. Affymetrix CytoScan HD Arrays were performed according to the manufacturer's directions on genomic DNA extracted directly from snap-frozen human urothelial carcinoma primary tumors. Copy number analysis using Affymetrix CytoScan HD Arrays was performed for 12 human urothelial carcinomas of the bladder with truncating mutations of the STAG2 gene.

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Gene Expression of human bladder cancer cell line RT112 and Gemcitabine Resistant Bladder Cancer cell line RT112-Gr

Project description:In this research, Human OneArray Microarray analysis was performed to obtain broad spectrum information about the genes differentially expressed in human bladder cancer cell line RT112 and Gemcitabine Resistant Bladder Cancer cell line RT112-Gr.

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Frequent truncating mutations of STAG2 in bladder cancer

Project description:Here we report the discovery of truncating mutations of the gene encoding the cohesin subunit STAG2, which regulates sister chromatid cohesion and segregation, in 36% of papillary non-invasive urothelial carcinomas and 16% of invasive urothelial carcinomas of the bladder. Our studies suggest that STAG2 has a role in controlling chromosome number but not the proliferation of bladder cancer cells. These findings identify STAG2 as one of the most commonly mutated genes in bladder cancer. Affymetrix CytoScan HD Arrays were performed according to the manufacturer's directions on genomic DNA extracted directly from 12 snap-frozen human urothelial carcinoma primary tumors with somatic mutations of the STAG2 gene.

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Chromatin Profiling of RT112 bladder cancer cell line

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Project description:Chromatin Profiling of RT112 bladder cancer cell line

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