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.
Highlights
Bladder cancer (BC) is one of the most common cancers in industrially developed countries
We show that deep sequencing (DS) data correlate with previously published information in 87% of cases, whereas microarray hybridization (MA) and suppression-subtractive hybridization (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
Summary
Bladder cancer (BC) is one of the most common cancers in industrially developed countries. The risk of developing BC is associated with smoking and with exposure to several other carcinogens (Kiriluk et al, 2012). Genetic factors such as chromosomal aberrations (Hoglund, 2012), specific single nucleotide polymorphisms (SNPs) (Golka et al, 2011), mutations (Castillo-Martin et al, 2010), and epigenetic peculiarities (Kim and Kim, 2012) may contribute to tumorigenesis and the progression of BC. 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
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