Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

10 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Molecular profiling of ovarian cancer from Italian BRCA wild-type patients

ABSTRACT: Objectives. Ovarian cancer (OC) is the eighth most common cancer and the eighth most common cause of cancer-related death in women. Identification of pathogenic variants in OC tissues is important to predict treatment response. This study aim to evaluate the mutational profile of a patient cohort, negative for BRCA1/2 germinal mutations and Mismatch Repair (MMR) defects, using next generation sequencing approach on DNA from formalin-fixed paraffin-embedded (FFPE) samples. We used a custom NGS panel, targeting 34 cancer related-genes, and analyzed NGS data to identify somatic and germline mutations in Italian patients affected by primary epithelia ovarian cancer.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Homo sapiens

SUBMITTER: Domenico Memoli

PROVIDER: E-MTAB-11133 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Interpheron-γ signaling is associated with BRCA-1 loss-of-function mutations in high grade serous ovarian cancer [ChIP-seq]

Project description:Purpose: Loss-of-function mutations of the breast cancer type 1 susceptibility protein (BRCA1) are associated with breast (BC) and ovarian cancer (OC). We assessed responses to histone deacetylase inhibitors (HDACi) and performed genome-wide RNA and chromatin immunoprecipitation (ChIP)-sequencing in isogenic OC cells UWB1.289 (carrying a BRCA1 mutation) and UWB1.289 transduced with wild type BRCA1. Experimental Design: Gene expression profiles of cells harboring mutated vs. functional BRCA1 and treated with the HDACi were integrated with chromatin mapping of histone H3 lysine 9 or 27 acetylation (H3K9ac, H3K27ac) at active promoters and enhancers. Key pathways found deregulated in BRCA1 mutated cells were validated. Results: Gene networks activated in BRCA1-mutated vs. BRCA1+ OC cells relate to Cellular Movement, Cellular Development, Cellular Growth and Proliferation and shared upstream regulators included TGFb1, TNF, and IFN-g. The IFN-g pathway was significantly altered in response to HDACi in BRCA1+ vs. BRCA1-mutated cells and in BRCA1-mutated/or low vs. BRCA1-normal ovarian tumors profiled in the TCGA database. Key IFN-γ-induced genes upregulated at baseline in BRCA1-mutated vs. BRCA1+ OC and BC cells included CXCL10, CXCL11, and IFI16. Increased localization of STAT1 to the promoters of these genes was observed in BRCA1-mutated cells, resulting in diminished cellular responses to IFN-γ or to STAT1 knockdown. The IFN-g signature was associated with improved survival among tumors profiled by the TCGA. Conclusions: Transcriptomic changes affecting IFN-γ response are associated with inactivating BRCA1 mutations in OC. These alterations could contribute to diminished anti-tumor immunity in BRCA1 mutated cells or tumors.

2019-12-31 | GSE131140 | GEO

Interpheron-γ signaling is associated with BRCA-1 loss-of-function mutations in high grade serous ovarian cancer [RNA-seq]

2019-12-31 | GSE131085 | GEO

Methylation profiling of human germ cell cancers of testicular and ovarian origin

Project description:Methylation profiling was performed of human germ cell cancers of testicular and ovarian origin. The main goal of the study was to investigate chromosomal copy numbers and to assess differential methylation patterns.

2019-02-11 | E-MTAB-5842 | biostudies-arrayexpress

Expression data from ovarian cancer cell line OVCAR3 following Knockdown or Knockout of BORIS (CTCFL)

Project description:The identification of prognostic biomarkers is a priority for patients suffering from high-grade serous ovarian cancer (SOC), which accounts for >70% of ovarian cancer (OC) deaths. Meanwhile borderline ovarian cancer (BOC) is a low malignancy tumor and usually patients undergo surgery with low probabilities of recurrence. However, SOC remains the most lethal neoplasm due to the lack of biomarkers for early diagnosis and prognosis. In this regard BORIS (CTCFL), a CTCF paralog, is a promising cancer biomarker that is overexpressed and controls transcription in several cancer types, mainly in OC. Studies suggest that BORIS has an important function in OC by altering gene expression, but the effect and extent to which BORIS influences transcription in OC from a genome-wide perspective is unclear. Here we sought to identify BORIS target genes in an OC cell line (OVCAR3) with potential biomarker use in OC tumor samples. To achieve this, we performed in vitro knockout (KO) and knockdown (KD) experiments of BORIS in OVCAR3 cell line followed by expression microarrays and bioinformatics network enrichment analysis to identify relevant BORIS target genes.

2019-07-31 | GSE130163 | GEO

DNA methylation profile of adipocytes treated with DNMT inhibitor, guadecitabine (100nM, 3X daily).

Project description:Ovarian cancer (OC) cells frequently metastasize to the omentum and adipocytes play a significant role in ovarian tumor progression. Therapeutic interventions targeting aberrant DNA methylation in ovarian tumors have shown promise in the clinic but the effects of epigenetic therapy on the tumor microenvironment are understudied. Here, we examined the effect of adipocytes on OC cell behavior in culture and impact of targeting DNA methylation in adipocytes on OC metastasis. The presence of adipocytes increased OC cell migration and invasion and proximal and direct co-culture of adipocytes . Treatment of adipocytes with hypomethylating agent guadecitabine decreased migration and invasion of OC cells towards adipocytes.

2018-03-10 | GSE111617 | GEO

RNA sequencing of MEX3A knockdown by siRNA in ovarian cancer cells

Project description:RNA-binding proteins can serve as novel potential targets for cancer therapy. We used bioinformatics analysis to screen and identify the key RBPs in ovarian cancer (OC), from which we found that Mex-3 RNA Binding Family Member A (MEX3A) was intimately associated with the clinical prognosis of OC. High expression of MEX3A was involved in the malignant proliferation and aggressiveness of ovarian cancer.

2022-03-31 | GSE189415 | GEO

OCaMIR a non-invasive early diagnostic test for ovarian cancer: A multi-cohort retrospective and prospective analysis

Project description:Owing to the lack of effective screening tools and early detection biomarkers, ovarian cancer (OC) still remains as a deadly disease with highest mortality among other gynecological cancers. So far there have been no attempts to discover biomarkers using early stage OC patients. MicroRNAs (miRNAs) have been recognized as great tool to develop non-invasive biomarkers in various cancers including ovarian cancer.

2020-03-06 | GSE127873 | GEO

Human plasma LC-MSMS for identified protein biomarker for BRCA1/2 positive ovarian cancer

Project description:Ovarian cancer (OC) is the most lethal gynecologic malignancy, attributed by late diagnosis. Genetic alteration of BRCA1/2 was well known risk factors in people who does not occur ovarian cancer. There is a need for convenient and continuous diagnosis of ovarian cancer after genetic testing, and we intend to apply a blood biomarker-based liquid biopsy. In a retrospective study, 20 OC patients and 20 normal controls were used for plasma samples, and BRCA1/2 carriers accounted for half in each group. We applied the bottom-up proteomics approach to depleted plasma samples with a nano-flow LC-MS and analyzed protein data quantitatively.

2021-06-07 | PXD023508 | Pride

Serum miRNA as Potential Biomarkers for ovarian cancer

Project description:Serum samples were obtained from patients with ovarian cancer (OC; n=64) and noncancerous control (n=4) for microarray. We found that four miRNAs were significantly high-expression level in OC relative to the controls.

2023-04-27 | GSE201712 | GEO

Repurposing Live Attenuated Trivalent MMR Vaccine as Cost-effective Cancer ImmunotherapyRepurposing Live Attenuated Trivalent MMR Vaccine as Cost-effective Cancer Immunotherapy

Project description:In this study, we show that intratumoral injections of the trivalent measles, mumps, and rubella (MMR) live attenuated viral vaccine (LAVs) modulate a potent cytotoxic T cells immune response, resulting in tumor growth inhibition and improved survival in syngeneic mouse models of hepatocellular carcinoma (HCC) and colorectal cancer (CRC).

2022-10-27 | PXD031295 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data