Project description:This SuperSeries is composed of the following subset Series: GSE36839: Expression data from OE33 oesophageal adenocarcinoma tumour cells following 24 hour co-culture with human adipose tissue explants or control M199 medium. GSE36840: Expression data from OE33 oesophageal adenocarcinoma tumour cells following 24 hour co-culture with human adipocytes or control M199 medium. Refer to individual Series
2012-07-31 | E-GEOD-36841 | ArrayExpress
Project description:Expression data from OE33 oesophageal adenocarcinoma tumour cells following 24 hour co-culture with human adipocytes, adipose tissue explants or control M199 medium
Project description:Obesity is linked to increased mortality from many cancer types, and oesophageal adenocarcinoma displays one of the strongest epidemiological associations. The aim of this study was to dissect molecular pathways linking obesity with oesophageal adenocarcinoma and to determine if obesity is linked to increased aggressiveness of this disease. Affymetrix microarrays were used to identify altered signaling pathways in an oesophageal adenocarcinoma cell line following co-culture with isolated adipocytes from viscerally obese oesophageal adenocarcinoma patients (n=6).
Project description:Obesity is linked to increased mortality from many cancer types, and oesophageal adenocarcinoma displays one of the strongest epidemiological associations. The aim of this study was to dissect molecular pathways linking obesity with oesophageal adenocarcinoma and to determine if obesity is linked to increased aggressiveness of this disease. Affymetrix microarrays were used to identify altered signaling pathways in an oesophageal adenocarcinoma cell line following co-culture with visceral adipose tissue from viscerally obese oesophageal adenocarcinoma patients (n=6).
Project description:Three oesophageal tissue derived cell lines, one from a normal tissue (HET1A) and two from tumour tissues (OE33 and OE199) were mixed with same number of each cell type in the same tube to get a mixed population. The C1 platform (Fluidigm) was used to capture single-cells and scATAC-seq protocols from Fluidigm ScriptHub is then used to generate the sequencing library. A single-cell ATAC-seq Bioinformatics pipeline is then developed to deconvolute the cells into their respective cell types.
Project description:Background: Successful treatment of oesophageal cancer is hampered by recurrent drug resistant disease. We have previously demonstrated the importance of apoptosis and autophagy for the recovery of oesophageal cancer cells following drug treatment. When apoptosis (with autophagy) is induced, these cells are chemosensitive and will not recover following chemotherapy treatment. In contrast, when cancer cells exhibit only autophagy and limited Type II cell death, they are chemoresistant and recover following drug withdrawal. Methods: MicroRNA (miRNA) expression profiling of an oesophageal cancer cell line panel was used to identify miRNAs that were important in the regulation of apoptosis and autophagy. The effects of miRNA overexpression on cell death mechanisms and recovery were assessed in the chemoresistant (autophagy inducing) KYSE450 oesophageal cancer cells. Results: MiR-193b was the most differentially expressed miRNA between the chemosensitive and chemoresistant cell lines with higher expression in chemosensitive apoptosis inducing cell lines. Colony formation assays showed that overexpression of miR-193b significantly impedes the ability of KYSE450 cells to recover following 5-fluorouracil (5-FU) treatment. The critical mRNA targets of miR-193b are unknown but target prediction and siRNA data analysis suggest that it may mediate some of its effects through stathmin 1 regulation. Apoptosis was not involved in the enhanced cytotoxicity. Overexpression of miR- 193b in these cells induced autophagic flux and non-apoptotic cell death. Conclusion: These results highlight the importance of miR-193b in determining oesophageal cancer cell viability and demonstrate an enhancement of chemotoxicity that is independent of apoptosis induction. Overall design: The miRNA expression profile was determined of four human oesophageal cancer cell lines OE19, OE21, OE33 and KYSE450. The miRNA expression of each cell line was analyzed in triplicate.
Project description:Exosomes were purified from 250 ul serum using ExoQuickTm. The presence of particles consistent in size with exosomes (60-150nm) was confirmed using a Nanosight LM10. miRNA was extracted from exosomes using an miRNeasy Serum/Plasma kit (Qiagen, #217184). miRNA was reversed transcribed using a TaqMan® microRNA Reverse Transcription Kit (Life technologies, #4366596). miRNA profiling was performed with a high throughput TaqMan® OpenArray® Human microRNA panel (Life technologies, #4461104). The panel consisted of probes for 754 human miRNAs that are based on miRNA sequences derived from Sanger miRBase v14. MegaplexTM Primer Human Pool A v2.1 and Human Pool B v2.0 or v3.0 The poor prognosis and rising incidence of oesophageal adenocarcinoma highlight the need for improved methods for detection of this cancer. Molecular biomarkers offer potential for this. The potential for circulating miRNAs as biomarkers in some other cancers has been shown, but circulating miRNAs have not been well characterized in oesophageal adenocarcinoma. This study investigated whether circulating miRNAs could be used to detect oesophageal adenocarcinoma. Overall design: OpenArray high throughput real time PCR of microRNAs -- 19 patients without oesophageal disease, 10 patients with non-dysplastic Barrett's Oesophagus, 18 patients with locally advanced Oesophageal Adenocarcinoma
Project description:A cell line (MFD-1) was derived from a 55-year old male with oesophageal adenocarcinoma. Using different sources of genetic material from normal and tumour tissue surgically resected, peripheral blood and the derived cell line a high concordance of genotypes calls across the whole genome confirms MFD-1 was derived from parent tumour. The SNP6 array contained 906,000 probes for the genotyping of SNPs and 946,000 probes for the genotyping of non-polymorphic copy number. Affymetrix CEL files were analysed using the tool PICNIC2 (predicting absolute allele copy number variation with microarray cancer data).