Gergely Tölgyesi

Integrative molecular bioinformatics study of human adrenocortical tumors: microRNA, tissue-specific target prediction, and pathway analysis

MicroRNAs (miRs) are involved in the pathogenesis of several neoplasms; however, there are no data on their expression patterns and possible roles in adrenocortical tumors. Our objective was to study adrenocortical tumors by an integrative bioinformatics analysis involving miR and transcriptomics profiling, pathway analysis, and a novel, tissue-specific miR target prediction approach. Thirty-six tissue samples including normal adrenocortical tissues, benign adenomas, and adrenocortical carcinomas (ACC) were studied by simultaneous miR and mRNA profiling. A novel data-processing software was used to identify all predicted miR-mRNA interactions retrieved from PicTar, TargetScan, and miRBase. Tissue-specific target prediction was achieved by filtering out mRNAs with undetectable expression and searching for mRNA targets with inverse expression alterations as their regulatory miRs. Target sets and significant microarray data were subjected to Ingenuity Pathway Analysis. Six miRs with significantly different expression were found. miR-184 and miR-503 showed significantly higher, whereas miR-511 and miR-214 showed significantly lower expression in ACCs than in other groups. Expression of miR-210 was significantly lower in cortisol-secreting adenomas than in ACCs. By calculating the difference between dCT(miR-511) and dCT(miR-503) (delta cycle threshold), ACCs could be distinguished from benign adenomas with high sensitivity and specificity. Pathway analysis revealed the possible involvement of G2/M checkpoint damage in ACC pathogenesis. To our knowledge, this is the first report describing miR expression patterns and pathway analysis in sporadic adrenocortical tumors. miR biomarkers may be helpful for the diagnosis of adrenocortical malignancy. This tissue-specific target prediction approach may be used in other tumors too.

Gene expression profiling of experimental asthma reveals a possible role of paraoxonase-1 in the disease

In this study, we aimed to identify novel genes involved in experimental and human asthma, importance of which has not yet been recognized. In an ovalbumin-induced murine model of asthma, we applied microarray gene expression analysis at different time points after allergen challenges. Advanced statistical methods were used to relate gene expression changes to cellular processes and to integrate our results into multiple levels of information available in public databases. At 4 h after the first allergen challenge, gene expression pattern reflected mainly an acute, but non-atopic, inflammatory response and strong chemotactic activity. At 24 h after the third allergen challenge, gene set enrichment analysis revealed significant over-representation of gene sets corresponding to T(h)2-type inflammation models. Among the top down-regulated transcripts, an anti-oxidant enzyme, paraoxonase-1 (PON1), was identified. In human asthmatic patients, we found that serum PON1 activity was reduced at exacerbation, but increased parallel with improving asthma symptoms. PON1 gene polymorphisms did not influence the susceptibility to the disease. Our observations suggest that an altered PON1 activity might be involved in the pathogenesis of asthma, and serum PON1 level might be used for following up the effect of therapy.

IL-18 induces a marked gene expression profile change and increased Ccl1 (I-309) production in mouse mucosal mast cell homologs.

Helminthic infections, which are particularly common in the developing world, are associated with the accumulation of mucosal mast cells (MMCs) in the epithelial layer of the gut. Although intestinal parasite infection models argue that IL-18 plays a role in MMC differentiation and function, the direct effect of IL-18 on MMCs is still not well understood. To clarify the role of IL-18 in mast cell biology, we analyzed gene expression changes in MMCs in vitro. DNA microarray technology uncovered a group of chemokines regulated by IL-18, among which Ccl1 (I-309, TCA-3) showed the highest up-regulation. Ccl1 induction was only transient in mast cells and was characteristic for both immature and mature MMCs, but not for connective tissue-type mast cells. IL-18 exerts its Ccl1-inducing effect in MMCs primarily via the activation of NFkappaB. Moreover, IL-18 was effective both in the absence and the presence of IgE-antigen complex. The Ccl1 receptor (CCR8) is known to be expressed by T(h)2 cells and is involved in their recruitment. Our present findings suggest that IL-18 may contribute to mast cell-influenced Th2 responses by inducing Ccl1 production.

Involvement of TNFα –308A Promoter Polymorphism in the Development of Asthma in Children Infected With Chlamydophila pneumoniae

Several data indicate a connection between Chlamydophila pneumoniae infection and asthma. Although C. pneumoniae is a common cause of infection, not all infected patients develop asthma. This suggests that certain individuals may be genetically predisposed to the chronic effects of C. pneumoniae infection on airway functions. We investigated the possible modifying effect of different polymorphisms on C. pneumoniae infection and on the susceptibility to asthma in 318 children, among those 144 had asthma and 174 had no asthmatic symptoms. C. pneumoniae–specific antibodies were measured by ELISA. Tumor necrosis factor-α (TNFα), monocyte chemoattractant protein-1 (MCP-1), and RANTES (regulated on activation normal T cell expressed and secreted) genotypes were determined by PCR–restriction fragment length polymorphism (RFLP). There were no significant differences in the percentage of children positive for C. pneumoniae–specific antibodies between cases and controls. None of the genotypes was associated with altered susceptibility to C. pneumoniae infection. Among asthmatic children carrying the TNFα –308A allele, there were significantly more patients positive for C. pneumoniae–specific IgG, than among control children carrying the same allele (20.1% versus 9.2% of asthmatic versus control children, respectively; p = 0.002; odds ratio = 3.52 (1.52–7.53); p = 0.005). This study indicates the possible roles of polymorphisms in the immune system in the susceptibility to asthma in children infected with C. pneumoniae.

Pediatric Asthmatic Patients Have Low Serum Levels of Monocyte Chemoattractant Protein-1

Serum levels of MCP-1 were measured in children with and without asthma in order to determine a possible correlation between the MCP-1-2518A/G polymorphism, serum levels of MCP-1 and asthma. Two groups of subjects −160 children with asthma and 158 healthy children were screened with a PCR-based genotyping assay. Serum MCP-1 level was measured by ELISA. The -2518G allele occurred at a significantly higher frequency in asthmatic children than in controls. The mean serum MCP-1 level was significantly lower in the asthmatic than in the control children. There was no significant association between the MCP-1 genotypes and the serum MCP-1 levels.