title: Global analysis of the human gastric epithelial transcriptome altered by Helicobacter pylori eradication in vivo.
abstract: 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.
  
  
  METHODS
  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, beta 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.
authors.affiliation: Department of Pathology, Rhode Island Hospital, 593 Eddy Street, Providence, RI 02903, USA. mresnick@lifespan.org
authors.forename: M B
authors.initials: MB
authors.lastname: Resnick
authors.forename: E
authors.initials: E
authors.lastname: Sabo
authors.forename: P A
authors.initials: PA
authors.lastname: Meitner
authors.forename: S S
authors.initials: SS
authors.lastname: Kim
authors.forename: Y
authors.initials: Y
authors.lastname: Cho
authors.forename: H K
authors.initials: HK
authors.lastname: Kim
authors.forename: R
authors.initials: R
authors.lastname: Tavares
authors.forename: S F
authors.initials: SF
authors.lastname: Moss
mesh_terms: D000328:Adult; D000368:Aged; D004847:Epithelial Cells / Q000382:microbiology / Q000502:physiology*; D005260:Female; D005786:Gene Expression Regulation / Q000235:genetics*; D016481:Helicobacter Infections / Q000188:drug therapy / Q000235:genetics*; D016480:Helicobacter pylori / Q000235:genetics*; D006801:Humans; D008297:Male; D042282:Microdissection / Q000379:methods; D008875:Middle Aged; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D010437:Peptic Ulcer / Q000188:drug therapy / Q000235:genetics; D011706:Pyloric Antrum / Q000473:pathology*; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods; D014158:Transcription, Genetic / Q000235:genetics