Diagnosis of malignancy and benign alterations in gastric biopsy specimen by MRNA expression profiling

Background: The diagnosis of gastric biopsy specimen today is made by histologists and is based on morphological analysis of tissue sections.

Aim: To develop disease specific and low cost mRNA expression arrays, and analysis technology which can contribute to the application of these techniques as a routine procedure.

Materials and methods: After informed consent, gastric biopsy samples were taken from the pathological and healthy part of the stomach. Total RNA was extracted from the biopsies from 11 patients with gastric ulcer (6 H. pylori+), 5 with gastric cancer (1 H. pylori+) and 10 with atrophic gastritis (5 H. pylori+). The mRNA fraction was amplified by T7 RNA amplification method. RNA expression profile was evaluated by Atlas Glass microarrays (1081 genes). Principal component analysis and discriminant analysis were performed. Validation was done by real-time-PCR.

Results: Significantly increased expression was found in oncogenes (v-raf-1, v-erb-b2, v-akt-1, v-mos), growth factor genes (VEGF, PDGF), anti-apoptotic bcl-2 gene and in glutathion-S-transferase resistance-associated protein gene in patients with gastric cancer. Significantly downregulated gene function was found in tumor suppressor genes (DOC, DCC, SIVA, methallothionein-3), metabolic enzyme genes (carbonic anhydrase 2, cytochrome p450, glutathion peroxidase), nitric oxide synthase 2A gene, caspase-2 and -8 apoptosis-related genes, beta-8 integrin and TIMP-2 genes in gastric cancer patients. Using discriminant analysis, based on the application of 5 components all of the cases could be classified correctly.

Conclusions: Based on the present results diagnosis of malignancies in gastric biopsies can be performed by multivariate analysis of mRNA expression patterns. Further studies are needed for further classification of pathological alterations.