title: A systematic experimental evaluation of microRNA markers of human bladder cancer.
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.
  
  
  CONCLUSIONS
  We report the first comprehensive validated database of miRNA markers of human bladder cancer.
authors.affiliation: Group for Genomic Analysis of Cell Signaling Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Moscow, Russia ; Laboratory of Bioinformatics, D. Rogachyov Federal Research Center of Pediatric Hematology, Oncology and Immunology Moscow, Russia ; First Oncology Research and Advisory Center Moscow, Russia.
authors.forename: Anastasia A
authors.initials: AA
authors.lastname: Zabolotneva
authors.forename: Alex A
authors.initials: AA
authors.lastname: Zhavoronkov
authors.forename: Peter V
authors.initials: PV
authors.lastname: Shegay
authors.forename: Nurshat M
authors.initials: NM
authors.lastname: Gaifullin
authors.forename: Boris Y
authors.initials: BY
authors.lastname: Alekseev
authors.forename: Sergey A
authors.initials: SA
authors.lastname: Roumiantsev
authors.forename: Andrew V
authors.initials: AV
authors.lastname: Garazha
authors.forename: Olga
authors.initials: O
authors.lastname: Kovalchuk
authors.forename: Alexey
authors.initials: A
authors.lastname: Aravin
authors.forename: Anton A
authors.initials: AA
authors.lastname: Buzdin
keywords: bladder cancer; intracellular regulatory pathways; microRNA; molecular markers; transcriptome analysis