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.
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.
Project description:Endometriosis, a benign inflammatory disease whereby endometrial-like tissue grows outside the uterus, is a risk factor for endometriosis-associated ovarian cancers. In particular, ovarian endometriomas, cystic lesions of deeply invasive endometriosis, are considered the precursor lesion for ovarian clear-cell carcinoma (OCCC). To explore the transcriptomic landscape, OCCC from women with pathology-proven concurrent endometriosis (n = 4) were compared to benign endometriomas (n = 4) by bulk RNA and small-RNA sequencing.
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.
Project description:Ovarian clear cell carcinoma (OCCC) is an epithelial ovarian cancer (EOC) histology having distinct pathology, biology, and molecular footprints. OCCC is chemo-resistant and has the worst stage-adjusted prognosis amongst EOC. Yet, treatment for OCCC patients is no different than other EOC. As OCCC incidence rate has significantly increase in recent decades, it is critical to find OCCC-tailored therapeutic. However, majority of EOC gene expression molecular subtypes (GEMS) studies for personalized medicine focused on the high grade serous histology, and studies in OCCC GEMS were of small sample size. Using more than 200 OCCC gene expression profiles, we identified two OCCC subtypes: EpiCC—epithelial-like, early stage, good prognosis, relative higher rate of gene mutations in SWI/SNF complex; and MesCC—mesenchymal-like, late stage, and poor prognosis. The differential prognosis between EpiCC and MesCC could be observed as early as stage IC. Genetic, copy number and transcriptome profiling showed that both EpiCC and MesCC carried OCCC-associated aberrations. The EpiCC and MesCC are reproducible in validation cohorts and OCCC cell lines. Cell lines assays showed that MesCC is more proliferative and more anoikis resistant than EpiCC. Both EpiCC and MesCC are resistant to cisplatin. Applying the OCCC subtypes to TCGA 534 renal clear cell carcinoma indicated interoperability of the subtyping scheme, and revealed preferential response of EpiCC to sorafenib, and MesCC to bevacizumab. The EpiCC and MesCC classification shows promise in prognostication utility especially for stage IC OCCC patients, and warrants further investigation for subtype-tailored treatment regimen.
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.
Project description:The diversity of chemoresistant OCCC is unknown. We performed single nucleus RNA sequencing (snRNA-seq) to analyze the diversity of OCCC.
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.