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

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. 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.本研究从签署知情同意的自我认定为非裔美国人（African American, AA）或美国白人（American Caucasian, Cau）的个体中，采集了食管鳞状上皮组织学正常的活检样本。提取总RNA后，制备Affymetrix基因表达芯片图谱。按种族分组后，采集的样本分为两类：对照组（无巴雷特食管（Barrett's Esophagus, BE）或食管腺癌（esophageal adenocarcinoma, EAC）病史者），以及存在BE和/或EAC病史者。借此可鉴定出两种族群体间存在组织特异性表达差异的基因，以及对照组与疾病组间存在表达差异的基因。所有用于实验的RNA均提取自胃肠交界上方管状食管内的组织学正常鳞状黏膜。标本可通过上消化道内镜活检获取，或在肿瘤切除术中采集。样本经预处理后与Affymetrix Human Gene 2.1 ST基因芯片进行杂交。本次研究的样本均来自自我认定为非裔美国人或美国白人的个体，涵盖无BE/EAC病史的对照个体与确诊BE和/或EAC的个体。本芯片数据集共包含12例非裔美国人对照样本、12例美国白人对照样本，以及8例确诊BE/EAC的非裔美国人样本与8例确诊BE/EAC的美国白人样本。