Identification of Helicobacter pylori and antrum erosion specific gene expression patterns in gastric biopsy samples by whole genomic microarray analysis

Background: The high-density oligonucleotide microarray analysis gives an opportunity for studying the genetic and gene expression background of the diseases, even in small biopsy specimen.

Aims: our aims were to identify Helicobacter pylori (HP) infection and antrum erosion associated gene expression patterns (GEP) and to compare the gene expression profile of HP+ and HP- gastric erosions to explain the possible role and effect of HP infection.

Materials and Methods: Total RNA was extracted from frozen gastric biopsy specimens of 8 patients with HP+ antrum erosion and from 8 adjacent normal mucosa, from 8 patients with HP- antrum erosion and from 8 adjacent normal mucosa. The mRNA fraction from the extracted total RNA was amplified by T7 RNA amplification method. Biotin-labeled cRNA probes were synthesized and fragmented. The genome-wide mRNA expression profile was evaluated by GeneChip U133 Plus 2.0 microarrays. Two independent normalization methods (MAS5.0, RMA), PAM feature selection and hierarchical cluster analysis were done. The microarray results were confirmed by real-time RT-PCR.

Results: Significant overexpression of HLA-DMA, HLA-DQA1, HLA-DQB1 antigen presentation genes, IL7R, ubiquitin D, KLRB1, lactoferrin antimicrobial immune response-related genes, CXCL2, CXCL5, CXCL13 and CCL20 chemokine ligand genes were established in HP+ patients compared to HP- patients. In erosive antrum gastritis increased proliferation (MET) and transport processes (SCFD1, KPNA4) were found, while genes associated with adhesion (SIGLEC11), transcription regulation (SMARCA4) and electron- and iontransport (ACADM, CLIC6) were downregulated.

Conclusions: The presented GEP can be used for multifunctional mRNA-based classification of routine gastric biopsies. These genes can be the targets of further DNA sequence.