title: A comparative analysis by SAGE of gene expression profiles of Barrett's esophagus, normal squamous esophagus, and gastric cardia.
abstract: OBJECTIVE
  The metaplastic process in which the normal squamous epithelium of the distal esophagus is replaced by columnar-lined epithelium, known as Barrett's esophagus (BE), is poorly understood. The aim of this study was to define, analyze, and compare transcription profiles of BE, normal cardia epithelium, and squamous epithelium to gain more insight into the process of metaplasia and to identify uniquely expressed genes in these epithelia.
  
  
  METHODS
  Serial analysis of gene expression was applied for obtaining transcription libraries of biopsy specimens taken from a BE-affected patient with intestinal type of metaplasia and from normal squamous and gastric cardia epithelia. Validation of results by reverse-transcription polymerase chain reaction and immunoblotting was performed using tissues of 20 patients with BE.
  
  
  RESULTS
  More than 120,000 tags were sequenced. Between BE and squamous 776, and between BE and gastric cardia 534 tags were significantly differentially expressed (P < .05, pairwise comparison). In contrast, squamous compared with gastric cardia epithelia showed significant differential expression of 1316 tags. The most up-regulated genes in BE compared with squamous epithelium were trefoil factors, annexin A10, and galectin-4. Each of the epithelia showed a unique cytokeratin expression profile.
  
  
  CONCLUSIONS
  This study provides a comparison of the transcriptomes of BE, squamous epithelium, and gastric cardia epithelium. BE proves to be an incompletely differentiated type of epithelium that shows similarities to both normal squamous and gastric cardia epithelia. In addition, several uniquely expressed genes are identified. These results are a major advancement in understanding the process of metaplasia that leads to BE.
authors.affiliation: Laboratory of Experimental Internal Medicine, Academic Medical Center, Amsterdam, The Netherlands. k.k.krishnadath@amc.uva.nl
authors.forename: Jantine W P M
authors.initials: JW
authors.lastname: van Baal
authors.forename: Francesca
authors.initials: F
authors.lastname: Milano
authors.forename: Agnieszka M
authors.initials: AM
authors.lastname: Rygiel
authors.forename: Jacques J G H M
authors.initials: JJ
authors.lastname: Bergman
authors.forename: Wilda D
authors.initials: WD
authors.lastname: Rosmolen
authors.forename: Sander J H
authors.initials: SJ
authors.lastname: van Deventer
authors.forename: Kenneth K
authors.initials: KK
authors.lastname: Wang
authors.forename: Maikel P
authors.initials: MP
authors.lastname: Peppelenbosch
authors.forename: Kausilia K
authors.initials: KK
authors.lastname: Krishnadath
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D001471:Barrett Esophagus / Q000235:genetics* / Q000473:pathology; D001706:Biopsy; D002299:Cardia / Q000166:cytology*; D004947:Esophagus / Q000166:cytology / Q000502:physiology*; D005260:Female; D020869:Gene Expression Profiling; D015723:Gene Library; D006801:Humans; D008297:Male; D008875:Middle Aged; D020411:Oligonucleotide Array Sequence Analysis; D013272:Stomach Diseases / Q000235:genetics* / Q000473:pathology