Next Generation Sequencing Analysis of Clear Cell Renal Cell Carcinoma and its Comparison with Meta-Analysis of Microarray

Abstract

Clear cell renal cell carcinoma (ccRCC) is the most predominant sub type of Renal cell carcinoma and accounts for about 75-80% of all kidney malignancies. Although extensive studies have been carried out for identifying the therapeutic targets of ccRCC. Yet, patients that undergo targeted therapies eventually exhibit continued disease progression or are resistant to the approved targeted drugs. Therefore, there is an urge to discover novel biomarkers and therapeutic targets for ccRCC. The integration of powerful approaches like meta-analysis of microarrays and next generation sequencing provides an opportunity to get better insights into pathogenesis of ccRCC and to predict more reliable potential biomarkers and therapeutic targets for ccRCC . The unavailability of a stand-alone Graphical user Interface(GUI) for meta-analysis of microarrays limits the research of a biologist having little knowledge over programming and linux commands. Identifying molecular biomarkers and therapeutic target and designing an interactive interface for meta-analysis of microarrays has been at the forefront of current study. In order to achieve the goals and objectives of the study, an interface was designed for meta-analysis of microarrays and meta-analysis using the developed interface and miRNA-seq data analysis have been performed. The data analysis has revealed SLC25A3, HNRNP, ZPR1, ABCF1, CBX3, ELOB, STARD7,RPS24, CFL1, SMNDC1 and EIF4G2 as significant differentially expressed genes for disease. The effect of differential expression of ZPR1, ABCF1, CBX3, STARD7 and SMNDC1 genes in ccRCC patients is not stated in the literature therefore these genes can be considered as novel discovery. The genes CBX3 and SMNDC1 already serves as therapeutic targets for different carcinomas. Hence, these two genes could be taken as therapeutic targets for ccRCC. Rational drug designing should be performed while considering CBX3 and SMNDC1 as targets to pave a path towards improved and effective therapy for ccRCC