Dominika Szoke

Genetic Polymorphisms of NOD1 and IL-8, but not Polymorphisms of TLR4 Genes, Are Associated with Helicobacter pylori-Induced Duodenal Ulcer and Gastritis

Background:  Intracellular pathogen receptor NOD1 is involved in the epithelial cell sensing Helicobacter pylori, which results in a considerable interleukin (IL)‐8 production. The aim of this study was to evaluate the relationship between NOD1 and IL‐8 genetic polymorphisms and the development of H. pylori‐induced gastritis and duodenal ulcer (DU), as compared with TLR4 polymorphisms.

Helicobacter pylori and Antrum Erosion‐Specific Gene Expression Patterns: The Discriminative Role of CXCL13 and VCAM1 Transcripts

Background and Aims:  Chronic Helicobacter pylori infection affects approximately half of the world, leads to chronic gastritis and peptic ulceration, and is linked to gastric carcinoma. Our aims were to compare the gene expression profile (GEP) of H. pylori‐positive and H. pylori‐negative gastric erosions and adjacent mucosa to explain the possible role and response to H. pylori infection and to get erosion‐related mRNA expression patterns.

Laser microdissection in translational and clinical research

Laser microdissection (LMD) is now a well established method for isolating individual cells or subcellular structures from a heterogeneous cell population. In recent years, cell, DNA, RNA, and protein based techniques has been successfully coupled to LMD and important information has been gathered through the analysis of the genome, transcriptome, and more recently the proteome of individual microdissected cells.

Evaluation of malignant and benign gastric biopsy specimens by mRNA expression profile and multivariate statistical methods

mRNA expression array and multivariate statistical analysis of gastric biopsies can yield insight into the molecular biology basis of local alterations, supporting expression‐based identification of morphological alterations.

Significantly elevated Helicobacter pylori density and different genotype distribution in erosions as compared with normal gastric biopsy specimen detected by quantitative real-time PCR

Background and aim Determination of the local densities of Helicobacter pylori and its genotypic variations in gastric biopsy specimens by using novel real-time PCR-based methods could support the precise diagnosis and understanding of H. pylori infections. Methods Serial dilutions of H. pylori (0.016–16 μg/μl), control, bacterial, and human DNA samples were prepared. Fresh-frozen gastric biopsy specimens were taken from 103 patients, and the DNA was isolated. Quantitative determination of the ureaseA gene using hybridization probes with parallel evaluation of an internal human control gene (&bgr;-globin) was performed by real-time PCR. CagA and VacA s1 genotypic characterizations were also performed. The data were compared with urea breath test (UBT), histology, and serological testing. Results The presence of H. pylori could be detected by ureaseA–fluorescence energy transfer (53%), UBT (51%), serological testing (48%), and histology (52%) when compared with the gold standard (54%). A significant correlation was found between the quantitative real-time ureaseA/&bgr;-globin ratio-based H. pylori frequency and the UBT results (P<0.01). Significantly increased bacterial density was found in the erosions when compared with the healthy part of the antrum and corpus (P<0.01). Real-time PCR VacA s1 results were in significant correlation (P<0.01) with those of serological tests, but CagA results were not. The genomic profiles (VAC/GAC) were different in 13.7% of the cases, which involved three different locations in the stomach. Conclusion Real-time PCR was the most reliable method for H. pylori diagnosis. Furthermore, quantification and genotyping could also be performed using this technique. The density of H. pylori was significantly increased in macroscopic erosions.

Identification of Consensus Genes and Key Regulatory Elements in 5-Fluorouracil Resistance in Gastric and Colon Cancer

5-fluorouracil (5-FU) is widely used in the treatment of gastric and colorectal cancer. Recent microrarray studies associated different gene lists with 5-FU resistance. A major challenge in the genomic era is to find the most validated genes, and to decipher the regulatory networks responsible for the expression changes in a set of co-regulated transcripts. Our aim was to find genes repeatedly associated with 5-FU resistance, and to identify transcription factors (TFs) having overrepresented binding sites (TFBSs) in the promoter regions of genes associated with 5-FU resistance. Materials and Methods: The analyzed data originated from 5 different publications describing genome-wide gene expression patterns associated with 5- FU resistance in gastric and colorectal cancer. First, a data warehouse containing all genes associated with resistance was set up. 39 genes were identified which were repeatedly associated with resistance. Of these, using the EZ-Retrieve web service, proximal promoter sequences were available for 33 genes. The MotifScanner software was used to detect TFBSs in this set of sequences. Results: A total of 200 different TFBSs were identified. Using the statistics tool of the Java program TOUCAN, 4 binding sites were found to be significantly overrepresented: NFKappaB50 (p = 0.01), EGR2 (p = 0.027), EGR3 (p = 0.007), and NGFIC (or EGR4) (p = 0.001). These genes intercept apoptotic pathways at multiple locations in the tumor cells. Conclusion: We identified a consensus gene list associated with 5-FU resistance, performed an in silico comparative promoter analysis, and highlighted the potential implication of some TFs in the development of chemoresistance.

T-251A polymorphism of IL-8 relating to the development of histological gastritis and G-308A polymorphism of TNF-α relating to the development of macroscopic erosion

Objectives Genetic variations of the inflammatory IL-8 and TNF-&agr; genes can influence the outcome of gastric alterations. Our aims were to determine the prevalence and effect of the T-251A functional polymorphism of IL-8 and the G-308A polymorphism of TNF-&agr; in histological and macroscopic gastric diseases related to Helicobacter pylori infection. Methods Genomic DNA was extracted from biopsy samples from patients with gastritis (n=86, H. pylori positive=41), atrophy (n=32, H. pylori positive=13), intestinal metaplasia (IM) (n=43, H. pylori positive=22) and from histologically negative patients (n=57). The samples were divided by macroscopic diagnosis into erosion and negative groups. The T-251A polymorphism was examined with the amplification refractory mutation system method; the G-308A polymorphism was determined by the polymerase chain reaction-restriction fragment length polymorphism method. For statistical evaluation, Fischers exact test was used. Results In the case of T-251A of IL-8, the frequency of the A/A genotype was significantly increased in gastritis (P=0.049) and IM (P=0.038) groups as compared with the histologically negative ones. No relationship was found between macroscopic erosions and H. pylori infection. In the case of G-308A, the G/G genotype frequency was statistically increased in erosions as compared with negative groups (P=0.035). No difference in the distribution of G-308A genotypes in relation to histological alterations and the H. pylori infection was observed. Conclusions The effect of the polymorphism of IL-8 seems to be relevant in the pathogenesis of histological gastritis and IM, and the effect of the polymorphism of TNF-&agr; is relevant in the pathogenesis of macroscopic erosive gastritis.