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A genome-wide CRISPR/Cas9 screen identifies therapeutic targets required for the tumorigenesis of ovarian clear cell carcinoma (OCCC).

ABSTRACT: A genome-wide CRISPR/Cas9 screen identifies therapeutic targets required for the tumorigenesis of ovarian clear cell carcinoma (OCCC).

PROVIDER: PRJNA782904 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17017200.fastq.gz	Fastqsanger.gz
	SRR17017201.fastq.gz	Fastqsanger.gz
	SRR17017202.fastq.gz	Fastqsanger.gz
	SRR17017203.fastq.gz	Fastqsanger.gz
	SRR17017204.fastq.gz	Fastqsanger.gz

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A genome-wide CRISPR/Cas9 screen identifies therapeutic targets required for the tumorigenesis of ovarian clear cell carcinoma (OCCC).

Project description:To identify genes critical for the proliferation of ovarian clear cell carcinoma (OCCC), we performed CRISPR/CAS9 screens against the OCCC cell lines OVICE, ES2, TOV21G and JHOC5 using the TKOv3 sgRNA library.

2022-06-08 | GSE189405 | GEO

The splicing factor DHX38/PRP16 is required for ovarian clear cell carcinoma tumorigenesis, as revealed by a CRISPR-Cas9 screen

Project description:Certain cancers, such as ovarian clear cell carcinoma (OCCC), display high levels of genetic variation between patients, confounding the development of effective therapies. In order to identify novel genes critical to OCCC growth, we employed the pooled genome-scale CRISPR Knock-Out (GeCKO) v2 CRISPR-Cas9 knockout screening system using the OCCC cell line JHOC5, as well as the T-antigen immortalized normal ovarian surface epithelium cell line OSE3 as a negative control. We identified the gene encoding DHX38/PRP16, an ATP-dependent RNA helicase involved in splicing, as critical for the growth and tumorigenesis of OCCC; DHX38 knockdown in OCCC cells, but not normal cells, induces apoptosis and impairs OCCC tumorigenesis in a mouse model. Our results suggest that DHX38/PRP16 may play a role in OCCC tumorigenesis, and can be regarded as a promising therapeutic target.

2022-01-19 | GSE188485 | GEO

Gene expression profile at single cell level of ovarian clear cell carcinoma (OCCC) [snRNA-seq OCCC]

Project description:The diversity of chemoresistant OCCC is unknown. We performed single nucleus RNA sequencing (snRNA-seq) to analyze the diversity of OCCC.

2024-03-30 | GSE224334 | GEO

Profiling of circRNA Expression in Human Ovarian Clear Cell Carcinoma (OCCC)

Project description:To identify highly expressed circular RNAs (circRNAs) in OCCC and elucidate their function, we performed a circRNA microarray analysis using two OCCC clinical samples and their corresponding normal ovarian tissues from the opposite side, screening 13,617 circRNAs.

2024-05-17 | GSE266248 | GEO

Visium spatial gene expression analyses of ovarian clear cell carcinoma (OCCC) [visium OCCC]

Project description:Visium spatial gene expression analyses of ovarian clear cell carcinoma (OCCC) [visium OCCC]

| PRJNA930670 | ENA

Coexistent ARID1A-PIK3CA mutations promote ovarian clear cell tumorigenesis through pro-tumorigenic inflammatory cytokine signaling

Project description:Ovarian clear cell carcinoma (OCCC) is an aggressive form of ovarian cancer with high ARID1A mutation rates. Here we present a genetically engineered mouse model of OCCC. We find that ARID1A inactivation is not sufficient for tumor formation, but requires concurrent activation of the phosphoinositide 3-kinase catalytic subunit, PIK3CA. Remarkably, the mice develop highly penetrant tumors with OCCC-like histopathology, culminating in hemorrhagic ascites and a median survival period of 7.5 weeks. Therapeutic treatment with the pan-PI3K inhibitor, BKM120, prolonged mouse survival by inhibiting tumor cell growth. Cross-species gene expression comparisons support a role for IL-6 inflammatory cytokine signaling in OCCC pathogenesis. We further show that ARID1A-PIK3CA mutations cooperate to promote tumor growth through sustained IL-6 overproduction. Our findings establish an epistatic relationship between SWI/SNF chromatin remodeling and PI3K pathway mutations in OCCC and demonstrate that these pathways converge on pro-tumorigenic cytokine signaling. We propose that ARID1A protects against inflammation-driven tumorigenesis.

2014-12-31 | GSE57380 | GEO

The phosphate exporter XPR1/SLC53A1 is required for the tumorigenicity of ovarian cancer.

Project description:Ovarian cancer is the fifth cause of cancer-related death in women. Ovarian clear cell carcinoma (OCCC) is a chemotherapy-resistant epithelial ovarian cancer with poor prognosis. As a basis for the development of therapeutic agents that may improve the prognosis of OCCC, we performed a screen for proteins critical for the tumorigenicity of OCCC using the CRISPR/Cas9 system. Here we show that knockdown of the phosphate exporter XPR1/SLC53A1 induces the growth arrest and apoptosis of OCCC cells in vitro. Moreover, we demonstrate that knockdown of XPR1/SLC53A1 inhibits the proliferation of OCCC cells xenografted into immunocompromised mice. These results suggest that XPR1/SLC53A1 plays a critical role in the tumorigenesis of OCCC cells. We speculate that XPR1/SLC53A1 might be a promising molecular target for the therapeutic treatment of OCCC.

2022-07-07 | GSE189552 | GEO

PPP2R1A mutations cause ATR inhibitor synthetic lethality in ARID1A deficient ovarian clear cell carcinoma

Project description:Ovarian clear cell carcinoma (OCCC) is a cancer of unmet need characterized by ARID1A mutation. Prior work identified an ARID1A/ATR synthetic lethality, information that led to phase II clinical trials. Using genome-wide CRISPR-Cas9 mutagenesis and interference screens, we identified protein phosphatase 2A (PP2A) subunits, including PPP2R1A, as determinants of ATRi sensitivity in ARID1A mutant OCCC. Analysis of an OCCCs cohort indicated that >1/3 possessed both PPP2R1A and ARID1A loss-of-function mutations. CRISPR-prime editing demonstrated that oncogenic PPP2R1A p.R183 missense mutations enhance in vitro and in vivo ATRi sensitivity in ARID1A mutant OCCC. OCCC patients with both ARID1A and PPP2R1A mutations also showed clinical responses to ATRi in a phase II trial. Mechanistically, this synthetic lethal effect is dependent upon WNK1 kinase, which opposes PP2A function. This data suggests that co-occurrence of PPP2R1A and ARID1A mutations in OCCC should be assessed as a biomarker of ATRi response in on-going clinical trials.

2023-05-10 | PXD040422 | Pride

Gene expression profile at single cell level of ovarian clear cell carcinoma (OCCC) [snRNA-seq OCCC]

Project description:Gene expression profile at single cell level of ovarian clear cell carcinoma (OCCC) [snRNA-seq OCCC]

| PRJNA930669 | ENA

CRISPR-Cas9 RBM10 synthetic lethality screen

Project description:Genome-wide CRISPR-Cas9 knockout screen using TKOv1 sgRNA library was performed in isogenic RBM10-proficient and RBM10-deficient HCC827 cells.

2023-03-04 | E-MTAB-12724 | biostudies-arrayexpress

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