Journal of Gastroenterology

, Volume 44, Issue 9, pp 897–911

Differential gene expression in normal esophagus and Barrett’s esophagus

  • Jacob Wang
  • Rong Qin
  • Yan Ma
  • Huiyun Wu
  • Heiko Peters
  • Matthew Tyska
  • Nicholas J. Shaheen
  • Xiaoxin Chen
Original Article—Alimentary Tract

DOI: 10.1007/s00535-009-0082-2

Cite this article as:
Wang, J., Qin, R., Ma, Y. et al. J Gastroenterol (2009) 44: 897. doi:10.1007/s00535-009-0082-2



As the premalignant lesion of human esophageal adenocarcinoma (EAC), Barrett’s esophagus (BE) is characterized by intestinal metaplasia in the normal esophagus (NE). Gene expression profiling with microarray and serial analysis of gene expression (SAGE) may help us understand the potential molecular mechanism of human BE.


We analyzed three microarray datasets (two cDNA arrays and one oligonucleotide array) and one SAGE dataset with statistical tools, significance analysis of microarrays (SAM) and SAGE(Poisson), to identify individual genes differentially expressed in BE. Gene set enrichment analysis (GSEA) was used to identify a priori defined sets of genes that were differentially expressed. These gene sets were grouped according to either certain signaling pathways (GSEA curated), or the presence of consensus binding sequences of known transcription factors (GSEA motif). Immunohistochemical staining (IHC) was used to validate differential gene expression.


Both SAM and SAGE(Poisson) identified 68 differentially expressed genes (55 BE genes and 13 NE genes) with an arbitrary cutoff ratio (≥4-fold). With IHC on matched pairs of NE and BE tissues from 6 patients, these genes were grouped into 6 categories: category I (25 genes only expressed in BE), category II (5 genes only expressed in NE), category III (8 genes expressed more in BE than in NE), and category IV (2 genes expressed more in NE than in BE). Differential expression of the remaining genes was not confirmed by IHC either due to false discovery (category V), or lack of proper antibodies (category VI). Besides individual genes, the TGFβ pathway and several transcription factors (CDX2, HNF1, and HNF4) were identified by GSEA as enriched pathways and motifs in BE. Apart from 9 target genes known to be up-regulated in BE, IHC staining confirmed up-regulation of 19 additional CDX1 and CDX2 target genes in BE.


Our data suggested an important role of CDX1 and CDX2 in the development of BE. The IHC-confirmed gene list will lead to future studies on the molecular mechanism of BE.


Barrett’s esophagus Intestinal metaplasia Expression profile SAM GSEA 



Barrett’s esophagus


Esophageal adenocarcinoma


False discovery rate


Gene Map Annotator and Pathway Profiler


Gene ontology


Gene set enrichment analysis


Immunohistochemical staining


Intestinal metaplasia


Normal esophagus


Serial analysis of gene expression


Significance analysis of microarrays

Supplementary material

535_2009_82_MOESM1_ESM.doc (496 kb)
Supplementary material (DOC 495 kb)
535_2009_82_MOESM2_ESM.xls (9.9 mb)
Supplementary files (XLS 10110 kb)
535_2009_82_MOESM3_ESM.ppt (260 kb)
Supplementary figures (PPT 260 kb)

Copyright information

© Springer 2009

Authors and Affiliations

  • Jacob Wang
    • 1
    • 2
  • Rong Qin
    • 1
  • Yan Ma
    • 1
  • Huiyun Wu
    • 3
  • Heiko Peters
    • 4
  • Matthew Tyska
    • 5
  • Nicholas J. Shaheen
    • 2
  • Xiaoxin Chen
    • 1
    • 2
  1. 1.Cancer Research Program, Julius L. Chambers Biomedical/Biotechnology Research InstituteNorth Carolina Central UniversityDurhamUSA
  2. 2.Division of Gastroenterology and Hepatology, Department of Medicine, Center for Gastrointestinal Biology and DiseaseUniversity of North Carolina at Chapel HillChapel HillUSA
  3. 3.Department of Biostatistics, Vanderbilt University School of MedicineVanderbilt-Ingram Cancer Center/Biostatistics Shared ResourceNashvilleUSA
  4. 4.Institute of Human Genetics, International Centre for LifeUniversity of Newcastle upon TyneNewcastle upon TyneUK
  5. 5.Department of Cell and Developmental BiologyVanderbilt University Medical CenterNashvilleUSA

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