Project description:Aim of the study was the distinction of adeoncarcinomas at the gastroesophageal junction by their expression profile. Differential gene expression analysis between tumours of different Siewert type did not reveal relevant results. Stratification into three intrinsic subgroups was done by an diagonal distribution model using the mclust package in R. Clinicopathological and demographic parameters showed a similar distribution within the subgroups. Genes set ernichment analysis revealed different biological features for each subgroup that were also reflected by significant differences in the prognostic outcome for the patients, mainly overall survival and recurrence free survival.
Project description:Aim of the study was the distinction of adeoncarcinomas at the gastroesophageal junction by their expression profile. Differential gene expression analysis between tumours of different Siewert type did not reveal relevant results. Stratification into three intrinsic subgroups was done by an diagonal distribution model using the mclust package in R. Clinicopathological and demographic parameters showed a similar distribution within the subgroups. Genes set ernichment analysis revealed different biological features for each subgroup that were also reflected by significant differences in the prognostic outcome for the patients, mainly overall survival and recurrence free survival.
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.
Project description:Oesophageal TumOesophageal Tumour and Normal Oesophageal and Stomach tissue were analysed with HLA class II Immunopeptidomics using the L243 antibody
Project description:Differential gene expression analysis of oesophageal cells stimulated with a low pH environment. Study designed to identify pathways involved in progression of gastro-oesophageal reflux disease through Barrett's oesophagus to adenocarcinoma. Identified many subsets of genes with involvement in pathogenesis. Keywords = GORD Keywords = Barrett's Oesophagus Keywords = Oesopageal Adenocarcinoma. Keywords: time-course
Project description:Gastro-oesophageal reflux disease is highly prevalent in systemic sclerosis (SSc) and may contribute to oesophageal tissue damage. To investigate the molecular effects of reflux-associated injury, human oesophageal epithelial cells (Het1A) were exposed to bile acids and analysed by RNA sequencing. Chronic bile acid exposure induced transcriptional changes associated with innate immune activation, type I interferon signalling, TGF-β responses, epithelial–mesenchymal transition (EMT), oxidative stress, and mitochondrial dysfunction. Differential gene expression profiles were compared with publicly available SSc oesophageal transcriptomic datasets to identify shared disease-associated pathways. These data provide insight into the molecular mechanisms by which bile acid-induced epithelial injury may contribute to oesophageal pathology in systemic sclerosis.
Project description:The Illumina Infinium HumanMethylation450 BeadChip arrays were performed on a collection of primary oesophageal cancer-associated myofibroblasts (CAM) and their patient-matched adjacent tissue myofibroblasts (ATM). CAM and ATM samples were obtained from patients with oesophageal adenocarcinomas undergoing cancer surgery.