Mutation profiling of EOC biopsies from synchronous diseases
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB12935 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR1300850.fastq.gz | Fastqsanger.gz | |||
| ERR1300850_1.fastq.gz | Fastqsanger.gz | |||
| ERR1300850_2.fastq.gz | Fastqsanger.gz | |||
| ERR1300860.fastq.gz | Fastqsanger.gz | |||
| ERR1300860_1.fastq.gz | Fastqsanger.gz |
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Project description:We optimized a method previously developed to extract EVs from epithelial ovarian cancer (EOC) tissues and investigated whether cryopreservation of EOC tissues in clinical practice affects the phenotypes, contents, and biological functions of subsequently extracted EVs.
2023-05-10 | PXD039422 | Pride
Project description:Epithelial ovarian cancer (EOC) is the most lethal gynecological malignancy. On the basis of its histopathology and molecular-genomic changes ovarian cancer has been divided into subtypes, each with distinct biology and outcome. The aim of this study was to develop a panel of patient-derived EOC-xenografts that recapitulate the molecular and biological heterogeneity of human ovarian cancer. Thirty-four EOC-xenografts were successfully established, either subcutaneously or intraperitoneally, in nude mice. The xenografts were histologically similar to the corresponding patient tumor and comprised all the major ovarian cancer subtypes. After orthotopic transplantation in the bursa of the mouse ovary, they disseminate into the organs of the peritoneal cavity and produce ascites, typical of ovarian cancer. Gene expression analysis and mutation status indicated a high degree of similarity with the original patient and discriminate different subsets of xenografts. They were very responsive, responsive and resistant to cisplatin, resembling the clinical situation in ovarian cancer. This panel of patient-derived EOC-xenografts that recapitulate the recently type I and type II classification serves to study the biology of ovarian cancer, identify tumor-specific molecular markers and develop novel treatment modalities.
2015-01-07 | GSE56920 | GEO
Project description:Epithelial ovarian cancer (EOC) is the most lethal gynecological malignancy. On the basis of its histopathology and molecular-genomic changes ovarian cancer has been divided into subtypes, each with distinct biology and outcome. The aim of this study was to develop a panel of patient-derived EOC-xenografts that recapitulate the molecular and biological heterogeneity of human ovarian cancer. Thirty-four EOC-xenografts were successfully established, either subcutaneously or intraperitoneally, in nude mice. The xenografts were histologically similar to the corresponding patient tumor and comprised all the major ovarian cancer subtypes. After orthotopic transplantation in the bursa of the mouse ovary, they disseminate into the organs of the peritoneal cavity and produce ascites, typical of ovarian cancer. Gene expression analysis and mutation status indicated a high degree of similarity with the original patient and discriminate different subsets of xenografts. They were very responsive, responsive and resistant to cisplatin, resembling the clinical situation in ovarian cancer. This panel of patient-derived EOC-xenografts that recapitulate the recently type I and type II classification serves to study the biology of ovarian cancer, identify tumor-specific molecular markers and develop novel treatment modalities. EOC-xenografts collected from subcutis, abdominal masses and ascitic fluid of mice engrafted with tumors at different passages (from 1 to 6) and from patient specimens, underwent one-color microarray-based gene expression profiling. To assess the amount of human- and mouse-derived cells in the xenograft tumors, total RNA was evaluated by species specific qPCR assays for beta actin. Only samples with a human RNA content > 75% were analyzed. Nine patient specimens and 62 xenograft samples (representing 29 EOC-xenograft models) underwent gene expression analysis with SurePrint G3 Human GE V2 8x60K microarrays.
2015-01-07 | E-GEOD-56920 | biostudies-arrayexpress
Project description:We performed Array CGH on 25 patients with high grade serous epithelial ovarian cancer (HGS-EOC): each of this had multiple biopsies taken at the moment of the surgery in different anatomical sites, and 18 had also temporal biopsies taken after several cycles of chemotherapy. Blood was used as control. The experiment was performed to identify genomic alterations that can be used to classify the disease, going beyond the individual tumor heterogeneity.
2019-12-19 | E-MTAB-6900 | biostudies-arrayexpress
Project description:In epithelial ovarian cancer (EOC), acquisition of invasiveness is accompanied by the loss of the epithelial features and the gain of a mesenchymal phenotype, a process known as epithelial-mesenchymal transition (EMT). Understanding the regulation of cell behavior during EMT is crucial for identifying the molecular mechanisms of EOC dissemination. Previously we identified the mannose receptor LY75 as the cellular phenotype modulator. LY75 suppression induces the mesenchymal to epithelial transition (MET) in EOC cell lines with mesenchymal phenotype. In this study, we used the Reduced Representation Bisulfite Sequencing (RRBS) technology for a comprehensive analysis of DNA methylation alterations during LY75-mediated EMT in EOC cells. Three different comparison (M vs E) combinations were used for RRBS analysis, as further analysis of the sequencing data based on differentially methylated regions (DMRs) covering genes’ exons and promoter regions was indicative for about 10,000 genes displaying DMRs for each of the three experimental combinations. Consecutive Venn diagram analysis of the DMRs data from the of the three experimental combinations revealed 6666 genes, displaying common altered DMRs in their exons/promoter regions, following LY75-mediated EMT alterations in EOC cells. Based on the 6666 gene list, we further proceeded with a more stringent selection of genes displaying rather high degree (>70%) of methylation in their promoter regions and previously shown to be implicated in cancer-related EMT signaling. Our stringent selection retained 45 genes (see Supplemental Table 1E), as the DNA methylation status of the promoter regions of most of these genes was further validated by an alternative approach (BSP sequencing). Ten genes were finally selected, whose promoter DNA methylation pattern coincided with their mRNA and protein expression levels. Further in vitro and in vivo studies are warranted to more completely elucidate the functional implications of these 10 genes in ovarian tumorigenesis.
2020-03-30 | GSE142310 | GEO
Project description:Most (70%) epithelial ovarian cancers (EOCs) are diagnosed late. Non-invasive biomarkers that facilitate disease detection and predict outcome are needed. The microRNAs (miRNAs) represent a new class of biomarkers. This study was to identify and validate plasma miRNAs as biomarkers in EOC. We evaluated plasma samples of 360 EOC patients and 200 healthy controls from two institutions. All samples were grouped into screening, training and validation sets. We scanned the circulating plasma miRNAs by TaqMan low-density array in the screening set and identified/validated miRNA markers by real-time polymerase chain reaction assay in the training set. Receiver operating characteristic and logistic regression analyses established the diagnostic miRNA panel, which were confirmed in the validationsets. We found higher plasma miR-205 and lower let-7f expression in cases than in controls. MiR-205 and let-7f together provided high diagnostic accuracy for EOC, especially in patients with stage I disease. The combination of these two miRNAs and carbohydrate antigen-125 (CA-125) further improved the accuracy of detection. MiR-483-5p expression was elevated in stages III and IV compared with in stages I and II, which was consistent with its expression pattern in tumor tissues. Furthermore, lower levels of let-7f were predictive of poor prognosis in EOC patients. Our findings indicate that plasma miR-205 and let-7f are biomarkers for ovarian cancer detection that complement CA-125; let-7f may be predictive of ovarian cancer prognosis.
2013-08-30 | GSE50472 | GEO
Project description:Profiling cancer gene mutations in longitudinal epithelial ovarian cancer biopsies by targeted next-generation sequencing: a retrospective study
| PRJEB6773 | ENA
Project description:Most (70%) epithelial ovarian cancers (EOCs) are diagnosed late. Non-invasive biomarkers that facilitate disease detection and predict outcome are needed. The microRNAs (miRNAs) represent a new class of biomarkers. This study was to identify and validate plasma miRNAs as biomarkers in EOC. We evaluated plasma samples of 360 EOC patients and 200 healthy controls from two institutions. All samples were grouped into screening, training and validation sets. We scanned the circulating plasma miRNAs by TaqMan low-density array in the screening set and identified/validated miRNA markers by real-time polymerase chain reaction assay in the training set. Receiver operating characteristic and logistic regression analyses established the diagnostic miRNA panel, which were confirmed in the validationsets. We found higher plasma miR-205 and lower let-7f expression in cases than in controls. MiR-205 and let-7f together provided high diagnostic accuracy for EOC, especially in patients with stage I disease. The combination of these two miRNAs and carbohydrate antigen-125 (CA-125) further improved the accuracy of detection. MiR-483-5p expression was elevated in stages III and IV compared with in stages I and II, which was consistent with its expression pattern in tumor tissues. Furthermore, lower levels of let-7f were predictive of poor prognosis in EOC patients. Our findings indicate that plasma miR-205 and let-7f are biomarkers for ovarian cancer detection that complement CA-125; let-7f may be predictive of ovarian cancer prognosis. We designed a multi-stage, retrospective, nested case-control study to determine whether serum miRNA profiles can be used to predict EOC development. All samples were grouped into screening, training, and validation sets. A total of 560 plasma samples (360 cases and 200 controls) were obtained from Tianjin Medical University Cancer Institute and Hospital (TCIH) and Cancer Center of Nanjing Medical University. The cases and controls were well matched for age. The International Federation of Gynaecology and Obstetrics (FIGO) staging system was used to stage cases. All patients and controls were genetically unrelated, ethnic Han Chinese women who were permanent residents of the urban area of Tianjin and Nanjing. Controls with cardiovascular, respiratory, digestive, urinary, reproductive, and endocrine diseases were excluded. The study protocols were approved by the Tianjin and Nanjing Center review committees. In screening set, to detect generalizable miRNA signatures, we pooled serum samples of 10 early-stage cases (stage I), 10 late-stage cases (stage IIIc-IV), and 10 healthy controls, respectively, and analyzed these three pool samples using a TaqMan low-density array (TLDA set 2.0, Applied Biosystems) chip screening in the discovery stage. In training set, the miRNAs identified in the screening set were validated using quantitative reverse transcription-polymerase chain reaction (qRT-PCR) on individual plasma samples of 76 EOC patients and 30 normal controls. In validation set, the validation set comprised a two-phase process. Promising associations from the screening and training set were evaluated in the validation phase I set, comprising 134 cases and 70 controls from Tianjin Center. The validation phase II set included samples of 77 EOC cases and 50 normal controls were from Tianjin Center and 73 EOC cases and 50 normal controls were from Nanjing Center.
2013-08-30 | E-GEOD-50472 | biostudies-arrayexpress
Project description:Purpose: The majority of patients with epithelial ovarian cancer (EOC) is diagnosed at advanced stage and has a poor prognosis. A proportion of these patients though will fare well, with a prognosis similar to patients with early stage disease while others die very quickly. Clinicopathological prognostic factors do not allow precise identification of these subgroups. Thus we have validated a molecular subclassification as prognostic factor in EOC. Experimental Design: One hundred ninety-four patients with EOC stage II to IV were characterized by whole-genome expression profiling of tumor tissues and classified using a published 112 gene-set, derived from a FIGO stage directed supervised classification approach. Results: The 194 tumor samples were classified into two subclasses of 95 (subclass 1) and 99 (subclass 2) tumors, grouping all 9 FIGO II tumors in subclass 1 (p=0.001). Subclass 2 (54% of advanced stage tumors) correlated significantly with peritoneal carcinomatosis and non-optimal debulking. Patients with subclass 2 tumors had a worse progression free survival (HR 1.67, p=0.005) by univariate analysis, but it was not an independent factor in multiple analysis. However, overall survival was impaired both, univariate (HR 3.68, p<0.001) and in models corrected for relevant clinicopathologic parameters (HR 3.13, p<0.001). Significance analysis of microarrays revealed 2,115 genes differentially expressed in both subclasses (FDR 5%). Conclusion: In this validation study we showed that in advanced-stage epithelial ovarian cancer two approximately equally large molecular subtypes exist, independent from classical clinocopathological parameters presenting with highly different whole genome expression profiles and an impressively different overall survival. Purpose: The majority of patients with epithelial ovarian cancer (EOC) is diagnosed at advanced stage and has a poor prognosis. A proportion of these patients though will fare well, with a prognosis similar to patients with early stage disease while others die very quickly. Clinicopathological prognostic factors do not allow precise identification of these subgroups. Thus we have validated a molecular subclassification as prognostic factor in EOC. Experimental Design: One hundred ninety-four patients with EOC stage II to IV were characterized by whole-genome expression profiling of tumor tissues and classified using a published 112 gene-set, derived from a FIGO stage directed supervised classification approach. Results: The 194 tumor samples were classified into two subclasses of 95 (subclass 1) and 99 (subclass 2) tumors, grouping all 9 FIGO II tumors in subclass 1 (p=0.001). Subclass 2 (54% of advanced stage tumors) correlated significantly with peritoneal carcinomatosis and non-optimal debulking. Patients with subclass 2 tumors had a worse progression free survival (HR 1.67, p=0.005) by univariate analysis, but it was not an independent factor in multiple analysis. However, overall survival was impaired both, univariate (HR 3.68, p<0.001) and in models corrected for relevant clinicopathologic parameters (HR 3.13, p<0.001). Significance analysis of microarrays revealed 2,115 genes differentially expressed in both subclasses (FDR 5%). Conclusion: In this validation study we showed that in advanced-stage epithelial ovarian cancer two approximately equally large molecular subtypes exist, independent from classical clinocopathological parameters presenting with highly different whole genome expression profiles and an impressively different overall survival. Targeted therapies in second line treatment gain more and more importance in managing recurrent or progressive carcinomas, particularly in ovarian cancer, a cancer entity characterized by a very high recurrence rate. One step ahead, it is necessary to define new therapeutic targets and to select patients who might benefit from these therapies already in first line settings. A robust molecular subclassification could provide both, an adequate patient selection and potential new targets. Notably, the validation of such a subclassification is of outstanding importance to obtain a reliable basis for a specific clinical decision and a rational for the expensive development of new targeted therapies. This work provides a comprehensive basis for both. The expression values of 204 epithelial ovarian cancer tissues are determined and used for the validation of a subclassification approach (Cancer Sci. 2009 Aug;100(8):1421-8.)
2014-01-01 | E-GEOD-49997 | biostudies-arrayexpress
Project description:The study aims at dissecting the heterogeneity across multiple biopsies of high grade serous epithelial ovarian cancer (HGS-EOC) through a comprehensive characterization of variants and structural changes at the whole exome level. To this aim, the study uses samples from multiple bioptic sites taken from eight HGS-EOC patients.
| EGAS00001003048 | EGA