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Global analysis of the human gastric epithelial transcriptome altered by Helicobacter pylori eradication in vivo
  1. M B Resnick1,
  2. E Sabo1,
  3. P A Meitner1,
  4. S S Kim2,
  5. Y Cho2,
  6. H K Kim2,
  7. R Tavares1,
  8. S F Moss3
  1. 1Department of Pathology, Rhode Island Hospital, Brown University, Providence, Rhode Island, USA
  2. 2Department of Medicine, Uijongbu St Mary Hospital, The Catholic University of Korea, Seoul, South Korea
  3. 3Department of Medicine, Rhode Island Hospital, Brown University, Providence, Rhode Island, USA
  1. Correspondence to:
    M B Resnick
    Department of Pathology, Rhode Island Hospital, 593 Eddy Street, Providence, RI 02903, USA; mresnick{at}


Objective: The transcriptional profile of gastric epithelial cell lines cocultured with Helicobacter pylori and the global gene expression of whole gastric mucosa has been described previously. We aimed to overcome limitations of previous studies by determining the effects of H pylori eradication on the transcriptome of purified human gastric epithelium using each patient as their own control.

Design: Laser capture microdissection (LCM) was used to extract mRNA from paraffin-embedded antral epithelium from 10 patients with peptic ulcer disease, before and after H pylori eradication. mRNA was reverse transcribed and applied on to Affymetrix cDNA microarray chips customised for formalin-fixed tissue. Differentially expressed genes were identified and a subset validated by real-time polymerase chain reaction (PCR).

Results: A total of 13 817 transcripts decreased and 9680 increased after H pylori eradication. Applying cut-off criteria (p<0.02, fold-change threshold 2.5) reduced the sample to 98 differentially expressed genes. Genes detected included those previously implicated in H pylori pathophysiology such as interleukin 8, chemokine ligand 3, β defensin and somatostatin, as well as novel genes such as GDDR (TFIZ1), chemokine receptors 7 and 8, and gastrokine.

Conclusions: LCM of archival specimens has enabled the identification of gastric epithelial genes whose expression is considerably altered after H pylori eradication. This study has confirmed the presence of genes previously implicated in the pathogenesis of H pylori, as well as highlighted novel candidates for further investigation.

  • FFPE, formalin fixed, paraffin embedded
  • LCM, laser capture microdissection
  • PCR, polymerase chain reaction
  • reg 3α, regenerating gene family member 3 α
  • TFF1, trefoil peptide 1

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  • Published Online First: 24 May 2006

  • Funding: Center for Cancer Research Development, National Center for Research Resources, No 5 P20 RR017695-02

  • Competing interests: None.