Dataset Information

Expression profile comparison of African American and American Caucasian esophageal squamous epithelium from subjects with and without Barrett's Esophagus

ABSTRACT: Histologically normal biopsies of the esophageal squamous epithelium were collected from consented individuals of either African American (AA) or American Caucasion (Cau) ethnicity. Total RNA was extracted and used to generate Affymetrix expression array profiles. For each racial group collected samples were either controls (no history of BE or EAC) or those with a history of BE (Barrett's Esophagus) and/or EAC (esophageal adenocarcinoma). This allowed us to identify gene with tissue specific expression differences between the two racial groups, as well as those that differed between control and disease groups. Overall design: RNA was extracted from histologically normal squamous mucosa arising within the tubular esophagus above the gastrointestinal junction. Specimens were either collected as biopsies during upper GI endoscopy or as material collected at the time of tumor resection. Samples were processed for hybridization to Affymetrix Human Gene 2.1 ST arrays. Samples were collected from individuals self-identified as either AA or Cau, who had no history of BE or EAC (controls), or those diagnosed with BE and/or EAC. The array data includes 12 AA and 12 Cau controls, as well as 8 AA and 8 Cau diagnosed with BE/EAC.

INSTRUMENT(S): [HuGene-2_1-st] Affymetrix Human Gene 2.1 ST Array [transcript (gene) version]

ORGANISM(S): Homo sapiens

SUBMITTER: Derek John Nancarrow

PROVIDER: GSE77563 | GEO | 2019-02-01

REPOSITORIES: GEO

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	GSE77563_RAW.tar	Raw
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Publications

Constitutively Higher Level of GSTT2 in Esophageal Tissues From African Americans Protects Cells Against DNA Damage.

Ferrer-Torres Daysha D Nancarrow Derek J DJ Steinberg Hannah H Wang Zhuwen Z Kuick Rork R Weh Katherine M KM Mills Ryan E RE Ray Dipankar D Ray Paramita P Lin Jules J Chang Andrew C AC Reddy Rishindra M RM Orringer Mark B MB Canto Marcia I MI Shaheen Nicholas J NJ Kresty Laura A LA Chak Amitabh A Wang Thomas D TD Rubenstein Joel H JH Beer David G DG

Gastroenterology 20181219 5

<h4>Background & aims</h4>African American and European American individuals have a similar prevalence of gastroesophageal reflux disease (GERD), yet esophageal adenocarcinoma (EAC) disproportionately affects European American individuals. We investigated whether the esophageal squamous mucosa of African American individuals has features that protect against GERD-induced damage, compared with European American individuals.<h4>Methods</h4>We performed transcriptional profile analysis of esophagea ...[more]

PMID: 30578782

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Project description:<h4>Background</h4>The incidence of esophageal adenocarcinoma (EAC) has increased nearly five-fold over the last four decades in the United States. Barrett's esophagus, the replacement of the normal squamous epithelial lining with a mucus-secreting columnar epithelium, is the only known precursor to EAC. Like other parts of the gastrointestinal (GI) tract, the esophagus hosts a variety of bacteria and comparisons among published studies suggest bacterial communities in the stomach and esophagus differ. Chronic infection with Helicobacter pylori in the stomach has been inversely associated with development of EAC, but the mechanisms underlying this association remain unclear.<h4>Methodology</h4>The bacterial composition in the upper GI tract was characterized in a subset of participants (n=12) of the Seattle Barrett's Esophagus Research cohort using broad-range 16S PCR and pyrosequencing of biopsy and brush samples collected from squamous esophagus, Barrett's esophagus, stomach corpus and stomach antrum. Three of the individuals were sampled at two separate time points. Prevalence of H. pylori infection and subsequent development of aneuploidy (n=339) and EAC (n=433) was examined in a larger subset of this cohort.<h4>Results/significance</h4>Within individuals, bacterial communities of the stomach and esophagus showed overlapping community membership. Despite closer proximity, the stomach antrum and corpus communities were less similar than the antrum and esophageal samples. Re-sampling of study participants revealed similar upper GI community membership in two of three cases. In this Barrett's esophagus cohort, Streptococcus and Prevotella species dominate the upper GI and the ratio of these two species is associated with waist-to-hip ratio and hiatal hernia length, two known EAC risk factors in Barrett's esophagus. H. pylori-positive individuals had a significantly decreased incidence of aneuploidy and a non-significant trend toward lower incidence of EAC.