INTESTINAL FILTER FOR USE IN OESOPHAGEAL CANCER RESEARCH
Ontology highlight
ABSTRACT: This study utilise the examination of normal gastro-intestinal tissues to determine a tissue specific signal for use in deriving the intestinal signature of intestinal metaplasias of the oesophagus. Normal oesophageal, colonic and duodenal tissue biopsies were taken after informed consent and RNA was extracted following histological examination of adjacent tissues for normal aperaing mucosa.
Project description:This study utilise the examination of normal gastro-intestinal tissues to determine a tissue specific signal for use in deriving the intestinal signature of intestinal metaplasias of the oesophagus. Normal oesophageal, colonic and duodenal tissue biopsies were taken after informed consent and RNA was extracted following histological examination of adjacent tissues for normal aperaing mucosa. Three of each tissue type
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: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.<br><br>Missing data files: GSM38763.CEL (Time 0 mins rep 1), GSM38764.CEL (Time 0 mins rep 2), GSM38771.CEL (Time 240 mins rep 1), and GSM38772.CEL (Time 240 mins rep 2).
Project description:Selective markers are needed for earlier diagnosis, optimal staging and treatment of oesophageal adenocarcinoma. This quantitative shotgun proteomic study used patient-matched fresh frozen tissue samples of OAC, normal oesophagus and normal stomach.
Project description:mucosal biopsies were taken from patients at pre and post-argon plasma coagulation (APC) ablation of Barrett's oesophagus, and from healthy controls. Total RNA was extracted using Trizol. 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. Endoscopic surveillance remains the mainstay of cancer prevention in individuals with Barrett’s oesophagus, and definitive management by surgery or endoscopy is reserved for high grade dysplasia or cancer. There are several endoscopic treatments that are widely used for Barrett’s oesophagus, including argon plasma coagulation (APC). The normality of the regenerated neosquamous epithelium after ablation has been called into question. In the current study we profiled global microRNA expression in oesophageal mucosa before and after ablation of Barrett’s oesophagus using Argon plasma coagulation. Our aim was to investigate differences in microRNA expression between neosquamous and normal squamous tissues.
Project description:To investigate gene expression profiles of Barrett's oesophagus and oesophageal adenocarcinoma samples, we carried out RNA-seq to identify differentially expressed genes in each disease state.
Project description:Regionalized disease prevalence is a common feature of the gastrointestinal tract. Herein, we employed regionally resolved Smart-seq3 single-cell sequencing, generating a comprehensive cell atlas of the adult oesophagus. Characterizing the oesophageal axis, we unveil non-uniform distribution of epithelial basal cells, fibroblasts and immune cells. In addition, we reveal a position-dependent, but cell subpopulation-independent, transcriptional signature, collectively generating a regionalized landscape. Combining in vivo models with organoid co-cultures, we demonstrate that proximal and distal basal progenitor cell states are functionally distinct. We find that proximal fibroblasts are more permissive for organoid growth compared to distal fibroblasts and that the immune cell profile is regionalized in two dimensions, where proximal-distal and epithelial-stromal gradients impact epithelial maintenance. Finally, we predict and verify how WNT-, BMP-, IGF- and NRG-signalling are differentially engaged along the oesophageal axis. We establish a cellular and transcriptional framework for understanding oesophageal regionalization, providing a functional basis for epithelial disease susceptibility.
Project description:Profiling open chromatin in different tissue types around the gastro-oesophageal junction to allow for clustering of samples and investigation of transcription factor binding site motif enrichment.