Nikotin ve levamisolün SW620 kolon adenokarsinom hücreleri üzerindeki etkilerinin araştırılması ve otomatik mikrodizi analizi için özel R program rutini geliştirilmesi ve uygulanması

Nicotine, the addictive component of tobacco, shows proliferative and antiapoptotic activity in cancer cells. Levamisole, an antihelmintic, on the other hand, has been tested as an additive chemotherapeutic agent and in treatment of nephrotic syndrome. Nicotine and levamisole are both agonists of nicotinic acetylcholine receptors; effects of these two agents have not been studied in colon cancer transcriptome. In this study, nicotine and levamisole exposed SW620 colon cancer cells, at a dose of 1 ?M for 7 days, were studied with respect to changes in expression using microarrays. For data analysis, a custom R-routine which makes extensive use of open source R-BioConductor Project and associated packages has been written; and it is composed of three modules: QualCont module performs quality controls supported with several visual representations and normalization of the raw data; DEGidentifier module performs identification of differentially expressed genes (DEGs) supported with Heatmap and Venn Diagram; and finally FuncAnn module, composed of four main functions, performs functional annotation and analysis of the results in terms of Gene Ontology, pathway analysis, supported with graphics and pathway networksAll arrays passed the quality control criteria. In this study, we show that nicotine and levamisole treatments affect the transcriptome similarly in SW620 cells in terms of both the differential expression and functional analysis. Our findings implicate nicotine and levamisole in steroid biosynthesis, cholesterol biosynthesis and aminoacid degradation metabolisms. Confirmatory analyses have been performed by real time RT-PCR for a selected set of genes.