AUTHOR=Zabolotneva Anastasia , Zhavoronkov Alex A., Shegay Peter V., Gaifullin Nurshat M., Alekseev Boris Y., Roumiantsev Sergey A., Garazha Andrey V., Kovalchuk Olga , Aravin Alexey , Buzdin Anton A.

TITLE=A systematic experimental evaluation of microRNA markers of human bladder cancer

JOURNAL=Frontiers in Genetics

VOLUME=Volume 4 - 2013

YEAR=2013

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2013.00247

DOI=10.3389/fgene.2013.00247

ISSN=1664-8021

ABSTRACT=Background: 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.  
Methods: 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. 
Results: 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.
Conclusions: Based on our data, MA and SSH data appear to be inadequate for studying differential miRNA expression in the bladder. 
Impact: We report the first comprehensive validated database of miRNA markers of human bladder cancer.