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Isoform switching events in Barrett's Esophagus and esophageal adenocarcinoma

ABSTRACT: Isoform switching events in Barrett's Esophagus and esophageal adenocarcinoma

PROVIDER: PRJNA798444 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17658200_1.fastq.gz	Fastqsanger.gz
	SRR17658200_2.fastq.gz	Fastqsanger.gz
	SRR17658201_1.fastq.gz	Fastqsanger.gz
	SRR17658201_2.fastq.gz	Fastqsanger.gz
	SRR17658202_1.fastq.gz	Fastqsanger.gz

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Isoform switching events in Barrett's Esophagus and esophageal adenocarcinoma

Project description:Global isoform switching in esophageal adenocarcinoma (EAC) has not been previously characterized. This form of alternative splicing has recently been recognized as highly prevalent in multiple other cancers. In this study, isoform switch analysis was performed using next generation sequencing of RNA isolated from patient tissues across a continuum of histopathologies, ranging from low risk Barrett’s esophagus (BE) to BE with dysplasia and EAC. Patients were stratified based on histopathology.

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Project description:Samples were obtained from 8 patients with Barrett's associated adenocarcinomas after transhiatal esophagectomy. Samples representative of the normal esophageal epithelium (N), Barrett’s esophagus (B) and esophageal adenocarcinomas (ADC) were obtained from every patient by experienced GI pathologists. RNA were extracted and samples were profiled for detection of genes differentially expressed in B and ADC relative to N and in ADC relative to B. Keywords: other

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Gene expression profiling reveals stromal genes expressed in common between Barrett's esophagus and adenocarcinoma.

Project description:samples contain normal, Barrett and duodenum and adenocarcinoma BACKGROUND & AIMS: Barrett's esophagus is a precursor of esophageal adenocarcinoma. DNA microarrays that enable a genome-wide assessment of gene expression enhance the identification of specific genes as well as gene expression patterns that are expressed by Barrett's esophagus and adenocarcinoma compared with normal tissues. Barrett's esophagus length has also been identified as a risk factor for progression to adenocarcinoma, but whether there are intrinsic biological differences between short-segment and long-segment Barrett's esophagus can be explored with microarrays. METHODS: Gene expression profiles for endoscopically obtained biopsy specimens of Barrett's esophagus or esophageal adenocarcinoma and associated normal esophagus and duodenum were identified for 17 patients using DNA microarrays. Unsupervised and supervised approaches for data analysis defined similarities and differences between the tissues as well as correlations with clinical phenotypes. RESULTS: Each tissue displays a unique expression profile that distinguishes it from others. Barrett's esophagus and esophageal adenocarcinoma express a unique set of stromal genes that is distinct from normal tissues but similar to other cancers. Adenocarcinoma also showed lower and higher expression for many genes compared with Barrett's esophagus. No difference in gene expression was found between short-segment and long-segment Barrett's esophagus. CONCLUSIONS: The genome-wide assessment provided by current DNA microarrays reveals many candidate genes and patterns not previously identified. Stromal gene expression in Barrett's esophagus and adenocarcinoma is similar, indicating that these changes precede malignant transformation. A disease state experiment design type is where the state of some disease such as infection, pathology, syndrome, etc is studied. Keywords: disease_state_design

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