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ABSTRACT: Oral Microbiota in Patients with Esophageal adenocarcinoma

PROVIDER: PRJNA974387 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR24676800_1.fastq.gz	Fastqsanger.gz
	SRR24676800_2.fastq.gz	Fastqsanger.gz
	SRR24676801_1.fastq.gz	Fastqsanger.gz
	SRR24676801_2.fastq.gz	Fastqsanger.gz
	SRR24676802_1.fastq.gz	Fastqsanger.gz

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Project description:The aim of this study is to generate and validate biomarkers to stratify patients with Barrett’s esophagus in terms of risk for developing cancer. We studied gene expression profiling in 69 frozen specimens, consisting of esophageal squamous epithelium from 19 healthy subjects, 20 specimens from patients with Barrett’s esophagus and 21 cases of esophageal adenocarcinoma, 9 cased of esophageal squamous cell carcinoma by whole genome microarray analysis. Laser capture microdissection technique was applied to procure cells from defined regions of Barrett’s esophagus metaplasia and esophageal adenocarcinoma. Microarray results were validated by quantitative real-time polymerase chain reaction (qRT-PCR) in an independent cohort consisting of 42 cases. Furthermore, immunohistochemistry was performed using antibodies to two selected target molecules on a third independent cohort of 36 specimens, consisting of 36 cases. A total of 1176 genes were associated significantly with esophageal adenocarcinoma. The expression pattern of a 4 gene signature with the highest discriminant score based on linear discriminant analysis (GeneSpring GX10.2), was identified and validated by qRT-PCR in independent cohort. Gene expression profiling of 20 specimens of Barrett's esophagus patients, 21 specimens of adenocarcinoma patients and 19 biopsies from patients with normal esophageal squamous epithelium, 9 specimens of squamous cell carcinoma were studied.

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Project description:The goal of this experiment is to characterize the copy number changes in esophageal mucosa of patients with Barrett's esophagus (BE) who progress to esophageal dysplasia and adenocarcinoma (BE progressors), as compared to patients with BE who do not progress for at least two years after esophageal mucosal sampling (non-progressors with never dysplastic Barrett's esophagus - NvDBE - samples). We sampled esophageal mucosa from the following groups: 1) non-dysplastic intestinal metaplasia from 16 patients at least 1 year before progression to esophageal dysplasia or adenocarcinoma (PP-BE); 2) non-dysplastic intestinal metaplasia from 21 patients who did not progress to dysplasia or adenocarcinoma for at least 2 years of surveillance after the tested sample (NvDBE) 3) non-dysplastic intestinal metaplasia from 21 patients who had temporally concurrent but spatially separate intestinal metaplasia samples from the same procedure (C-BE). 4) 10 samples of esophageal dysplasia or adenocarcinoma from patients in group 1 and 3. Samples were obtained by endoscopic biopsy, endomucosal resection or surgical resection, processed for clinical purposes by routine histopathologic methods, including formalin fixation and paraffin embedding (FFPE). DNA was extracted from 5 micro tissue sections of FFPE blocks and DNA extracted using QIAamp DNA FFPE Tissue Kit (Qiagen, Germantown, MD). Samples were processed for identification of somatic copy number alterations using the OncoScan FFPE Assay or the OncoScan CNV Assay (Affymetrix, Santa Clara, CA) according to the manufacturer's protocols. After hybridization, the arrays were washed, stained using GeneChip Fluidics Station 450 (Affymetrix) and scanned using GeneChip Scanner 3000 7G (Affymetrix). The CEL files generated are deposited here.

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