A systematic experimental evaluation of microRNA markers of human bladder cancer

• Published in: Frontiers in genetics Vol. 4; p. 247
• Main Authors: Zabolotneva, Anastasia A, Zhavoronkov, Alex A, Shegay, Peter V, Gaifullin, Nurshat M, Alekseev, Boris Y, Roumiantsev, Sergey A, Garazha, Andrew V, Kovalchuk, Olga, Aravin, Alexey, Buzdin, Anton A
• Format: Journal Article
• Language: English
• Published: Switzerland Frontiers Media S.A 01.01.2013
• Subjects: Bladder cancer; Databases, Genetic; Gene Expression Profiling; MicroRNA (miRNA); molecular marker; Oncology; microRNA; intracellular regulatory pathways; transcriptome analysis; molecular markers; bladder cancer
• ISSN: 1664-8021; 1664-8021
• DOI: 10.3389/fgene.2013.00247

MicroRNAs (miRNAs) are a class of small RNAs that regulate gene expression. They are aberrantly expressed in many human cancers and are potential therapeutic targets and molecular biomarkers. In this study, we for the first time validated the reported data on the entire set of published differential miRNAs (102 in total) through a series of transcriptome-wide experiments. We have conducted genome-wide miRNA profiling in 17 urothelial carcinoma bladder tissues and in nine normal urothelial mucosa samples using three methods: (1) An Illumina HT-12 microarray hybridization (MA) analysis (2) a suppression-subtractive hybridization (SSH) assay followed by deep sequencing (DS) and (3) DS alone. We show that DS data correlate with previously published information in 87% of cases, whereas MA and SSH data have far smaller correlations with the published information (6 and 9% of cases, respectively). qRT-PCR tests confirmed reliability of the DS data. Based on our data, MA and SSH data appear to be inadequate for studying differential miRNA expression in the bladder. We report the first comprehensive validated database of miRNA markers of human bladder cancer.