Research with bioinformatic and molecular analysis methods of RNA based biomarkers in clear cell renal cell carcinoma


Thesis Type: Postgraduate

Institution Of The Thesis: Bursa Uludağ University, Tıp Fakültesi, Temel Tıp Bilimleri, Turkey

Approval Date: 2020

Thesis Language: Turkish

Student: UFUK ÜNAL

Supervisor: Gülşah Çeçener

Abstract:

Clear cell type renal cell carcinoma (CCRCC) causes more than 75,000 deaths per year worldwide. In recent years, understanding the functions of genes and microRNA (miRNA) that play a role in the formation of CCRCC enables the elucidation of its molecular pathology and the development of new molecular targeted therapies. In the thesis study, in silico analysis of 6.056 CCRCC patient data obtained from global data banks; Determined among candidate genes that have a potential role in CCRCC development and miRNAs targeting these genes; Expression analyzes of VHL, KAT5 and HIF1A and miR-22, miR-138 and miR-223 were performed in paraffinised tumor and normal tissues of 100 CCRCC patients. Quantitative data of in silico analysis obtained; Normality test, t-test, X2, correlation test and ROC analysis. When the gene and miRNA expression differences of the patients' tumor and normal tissues were compared; -0.39-fold decrease in VHL (p = 0.4419), 1.23-fold increase in HIF1A (p = 0.0402), 1.88-fold increase in KAT5 (p = 0.001), miR-223 0.97-fold increase in (p = 0.0458), -3.84-fold decrease in miR-138 (p <0.0001) and -1.17-fold decrease in miR-22 (p = 0.0309) Determined. In addition, as a result of the DNA sequence analysis performed in the VHL gene, 26% of the patients have changed. As a result of the Western blot analysis, while there was no change in VHL, an increase in the amount of KAT5 protein was determined (p = 0.048). When the obtained findings are compared with the clinicopathological data of the patients; VHL gene expression showed statistical significance with diagnostic value of CD10 (p = 0.047), LMWCK (p = 0.004), CK19 (p = 0.025) and PAS (p = 0.034) values. HIF1A and KAT5 expressions are correlated with LMWCK (p = 0.018, p = 0.018). Differences in expression of miR-22 among miRNAs targeting related genes, differ in expression of miR-138 by perirenal adipose tissue invasion (p = 0.003), degree of prostitution (p = 0.037), and pathology tumor stage (p = 0.038). Showed a statistically significant correlation with perirenal adipose tissue invasion (p = 0.05). Within the scope of the thesis study, in the light of the findings obtained by investigating potential genetic and epigenetic changes in the development of CCRCC, the differences in expression levels of mir-22 and mir-138 have the potential to be biomarkers in order to determine the poor prognosis in CCRCC. In addition, obtaining preliminary data on the usability of mir-22 and mir-138 as potential therapeutic targets forms the basis for further studies involving the development of targeted therapies. The present thesis study contributes to the development of individual-specific effective treatment models by distinguishing patients with CCRCC with poor prognosis by molecular biomarkers.