title: Gene expression in Barrett's esophagus: laser capture versus whole tissue.
abstract: OBJECTIVE
  Diagnosis of Barrett's esophagus (BE) is typically done through morphologic analysis of esophageal tissue biopsy. Such samples contain several cell types. Laser capture microdissection (LCM) allows the isolation of specific cells from heterogeneous cell populations. The purpose of this study was to determine the degree of overlap of the two sample types and to define a set of genes that might serve as biochemical markers for BE.
  
  
  METHODS
  Biopsies were obtained from regions of the glandular tissue of BE and normal esophagus from 9 subjects with BE. Samples from 5 subjects were examined as whole tissue (BE [whole]; E [whole]), and in 4 subjects the glandular epithelium of BE was isolated using LCM (BE [LCM]) and compared with the averaged values (E [LCM]) for both basal cell (B [LCM]) and squamous cell (S [LCM]) epithelium.
  
  
  RESULTS
  Gene expression revealed 1797 probe sets between BE [whole] and E [whole] (fold change > 2.0; p<0.001). Most of these genes (74%) were also differentially expressed between BE [LCM] and E [LCM], showing that there was high concordance between the two sampling methods. LCM provided a great deal of additional information (2113 genes) about the alterations in gene expression that may represent the BE phenotype.
  
  
  CONCLUSIONS
  There are differences in gene expression profiles depending on whether specimens are whole tissue biopsies or LCM dissected. Whole tissue biopsies should prove satisfactory for diagnostic purposes. Because the data from LCM samples delineated many more Barrett's-specific genes, this procedure might provide more information regarding pathogenesis than would whole tissue material.
authors.affiliation: Michael E. DeBakey Veterans Administration Medical Center and Baylor College of Medicine, Houston, Texas, USA. hasheme@bcm.tmc.edu
authors.forename: Hashem B
authors.initials: HB
authors.lastname: El-Serag
authors.forename: Zhannat Z
authors.initials: ZZ
authors.lastname: Nurgalieva
authors.forename: Toni-Ann
authors.initials: TA
authors.lastname: Mistretta
authors.forename: Milton J
authors.initials: MJ
authors.lastname: Finegold
authors.forename: Rhonda
authors.initials: R
authors.lastname: Souza
authors.forename: Susan
authors.initials: S
authors.lastname: Hilsenbeck
authors.forename: Chad
authors.initials: C
authors.lastname: Shaw
authors.forename: Gretchen
authors.initials: G
authors.lastname: Darlington
mesh_terms: D000704:Analysis of Variance; D001471:Barrett Esophagus / Q000235:genetics* / Q000473:pathology; D015415:Biomarkers / Q000032:analysis; D001706:Biopsy; D004945:Esophagoscopy; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D007834:Lasers; D042282:Microdissection / Q000379:methods*
chemical_list: D015415:Biomarkers