Gene expression profile in laryngeal cancer in vivo by high – density oligonucleotide microarrays analysis
Journal Title: Polski Przegląd Otorynolaryngologiczny - Year 2013, Vol 2, Issue 2
Abstract
Aim of the study: The aim of the project was to analyze the gene expression profile in laryngeal carcinoma, having in mind a search for new molecular markers for that carcinoma. Material and methods: The study comprised a group of 43 patients suffering from squamous cell laryngeal carcinoma. RNA was isolated from frozen tissue fragments. For the examination of gene expression profile, oligonucleotide microarrays of high density were used, provided by Affymetrix (U 133 2.0 PLUS) containing over 54 thousand probes for over 47 thousand transcripts. Genes, selected on the basis of microarray analysis underwent validation by the method of quantitative reaction QPCR. In stage one, unsupervised analysis of a set arrays was carried out, using PCA. In the subsequent stage, analysis using supervised methods was carried out, in order to select differentiating genes. The selected group consisted of 621 genes differentiating samples from neoplastic texture and those from healthy larynx. The hierarchical clustering performed for all analyzed samples, on the basis of 621 selected transcripts revealed that the selected set distinguishes tissue groups well. Results: On the basis of analyses of expression of neoplastic cells and healthy laryngeal cells by the Limma method gene selection was carried out – the potentially new laryngeal carcinoma markers. In order to check the expression of those genes, examination with quantitative reaction PCR was carried out in real time. Conclusions: Four genes, occurred to be good markers of that neoplasm. Those are: metal-proteinase ADAM12, cycline-dependent kinase 2 – CDK2, kinesine 14 – KIF14, suppressor 1 of checkpoint – CHES1.
Authors and Affiliations
Jarosław Markowski, Michał Jarząb, Małgorzata Oczko-Wojciechowska, Tomasz Tyszkiewicz, Dariusz Lange, Barbara Jarząb, Wirginia Likus, Jarosław Paluch
Keywords
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