Global analysis of Helicobacter pylori gene expression in human gastric mucosa

Background & Aims: Helicobacter pylori inhabits a highly restricted ecological niche in the human gastric mucosa. Microbial gene expression in the context of persistent infection remains largely uncharacterized. Methods: An RNA analysis method, selective capture of transcribed sequences, was used in conjunction with genomic array hybridization to characterize H. pylori complementary DNAs (cDNAs) obtained from both human and experimentally infected gerbil gastric tissue specimens. Results: Bacterial cDNAs obtained by selective capture of transcribed sequences from tissues hybridized to arrayed DNA fragments representing approximately 70% of open reading frames in the H. pylori genome. RNAs for most of these open reading frames were also detected by array hybridization analyses of total RNA prepared from the isolated H. pylori strains cultured in vitro. However, a subset of H. pylori RNAs detected in gastric tissue specimens was consistently undetectable in bacteria grown in vitro. The majority of these RNAs encode factors unique to H. pylori that are potentially produced in response to interactions with mammalian gastric mucosa. Conclusions: The combination of selective capture of transcribed sequences with array hybridization has allowed a global analysis of bacterial gene expression occurring in human tissues during a natural infection.