DNA Methylation Profiles of Ovarian Clear Cell Carcinoma
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ABSTRACT:
PROVIDER: PRJNA767374 | ENA |
REPOSITORIES: ENA
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Project description:The microRNA profiles of ovarian clear cell carcinoma
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Project description:To investigate the microRNA profiles of ovarian clear cell carcinoma (OCCC), microRNA sequencing was performed using formalin-fixed, paraffin-embedded (FFPE) and fresh-frozen clinical samples. Moreover, patient-derived xenograft (PDX) tumors and cell lines were also investigated.
2022-04-16 | GSE200852 | GEO
Project description:Clear cell ovarian carcinoma (CCOC) is the second most common subtype of epithelial ovarian carcinoma. Late stage CCOC is not responsive to gold-standard chemotherapy and result in suboptimal outcome for patients. In-depth molecular insight is urgently needed to stratify the disease and drive therapeutic development. We conducted global proteomics in 192 cases of CCOC comparing to other epithelial ovarian carcinoma subtypes.
2022-09-02 | PXD032355 | Pride
Project description:Background. Ovarian clear cell carcinoma (OCCC) is a rare ovarian cancer histotype that tends to be resistant to standard platinum-based chemotherapeutics. We sought to better understand the role of DNA methylation in clinical and biological subclassification of OCCC. Methods. We interrogated genome-wide methylation using DNA from fresh frozen tumors from 271 cases, applied non-smooth non-negative matrix factorization (nsNMF) clustering, and evaluated clinical associations and biological pathways. Results. Two approximately equally sized clusters that associated with several clinical features were identified. Compared to Cluster 2 (N=137), Cluster 1 cases (N=134) presented at a more advanced stage, were less likely to be of Asian ancestry, and tended to have poorer outcomes including macroscopic residual disease following primary debulking surgery (p-values <0.10). Subset analyses of targeted tumor sequencing and immunohistochemical data revealed that Cluster 1 tumors showed TP53 mutation and abnormal p53 expression, and Cluster 2 tumors showed aneuploidy and ARID1A/PIK3CA mutation (p-values <0.05). Cluster-defining CpGs included 1,388 CpGs residing within 200 bp of the transcription start sites of 977 genes; 38% of these genes (N=369 genes) were differentially expressed across cluster in transcriptomic subset analysis (p-values <10-4). Differentially expressed genes were enriched for six immune-related pathways, including interferon alpha and gamma responses (p-values < 10-6). Conclusions. DNA methylation clusters in OCCC correlate with disease features and gene expression patterns among immune pathways. Impact. This work serves as a foundation for integrative analyses that better understand the complex biology of OCCC in an effort to improve potential for development of targeted therapeutics.
2021-12-10 | GSE185008 | GEO
Project description:12 ovarian clear cell carcinoma cell lines were transcriptomically profiles using the illumina human v6 chip
2008-11-13 | E-TABM-540 | biostudies-arrayexpress
Project description:ARID1A, which encodes a component of the SWI/SNF chromatin-remodeling complex, is commonly mutated in ovarian clear cell carcinoma and many other cancer types. We used label-free LC-MS/MS to identify ARID1A-dependent proteome changes in ovarian clear cell carcinoma cell lines. In our first analysis, we compared ARID1A-wildtype ovarian clear cell carcinoma cell line OVCA429 with or without ARID1A CRISPR knockout. In a complementary analysis, we compared ARID1A-mutated ovarian clear cell carcinoma cell line OVISE with or without ARID1A overexpression using a tet-inducible promoter.
2016-07-13 | MSV000079904 | MassIVE
Project description:Exploring the expression profile of ovarian clear cell carcinoma cancer cell subpopulations- derived tumors grown within a murine and a human cellular tissues.
2013-01-07 | GSE43208 | GEO
Project description:Immune subtype of ovarian clear cell carcinoma
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Project description:Ovarian cancer (OC) is a highly fatal and refractory malignancy affecting women, with platinum resistance remaining a major clinical dilemma. Ovarian clear cell carcinoma (OCCC) frequently exhibits increased platinum refractoriness than the other OC subtypes, accompanied by heightened glycogen that engenders clear-cell morphology and wild-type p53. However, their roles in platinum resistance are unclear. Here, we investigated whether glycogen promotes OCCC platinum resistance, and found that GYS1 as a rate-limiting enzyme in glycogen synthesis is clinically associated with poor prognosis and chemoresistance in OCCC. GYS1 is a rate-limiting enzyme in glycogen synthesis, which is clinically associated with poor prognosis and chemoresistance in OCCC. Mechanistically, p53 promotes GYS1 breakdown via upregulating RNF144a, while GYS1 enhances reversed ubiquitination and degradation toward p53 by competitively bound to the USP14, forming a positive feedback circuit. Under platinum stress the accumulated glycogen is mobilized by p53/GYS1 feedback circuit, which fueling energetic NADPH production, hence gaining disulfidptosis invulnerability and increased platinum resistance in OCCC. Collectively, our study identifies glycogen as a contributor to OCCC platinum resistance and elucidates the underlying mechanisms, highlighting a crucial p53/GYS1 positive feedback loop. In this project, we utilized IP-MS for identification of p53 binding proteins in six pairs of ovarian clear cell carcinoma.
2026-09-14 | PXD057846 | Pride
Project description:We performed RNA Sequencing on eleven ovarian clear cell carcinoma and five uterine clear cell carcinoma patients to identify the unique transcriptional expression profiles of clear cell uterine and ovarian cancer, and investigates correlations with demographic factors and tumor characteristics, such as stage and PD-L1 immunohistochemical expression.
2020-12-22 | GSE160692 | GEO