You have accessJournal of UrologyBladder Cancer: Basic Research II1 Apr 2014MP28-13 EXPRESSION ANALYSIS OF LOW AND HIGH-GRADE HUMAN BLADDER CANCER TUMOUR SAMPLES AND BLADDER CANCER CELL LINES WITH RNA-SEQ IDENTIFIES A NEW GROUP OF ENHANCER RNAS WITH POTENTIAL REGULATORY FUNCTION Aidan P. Noon, Yu Liu, Thomas Hermanns, Girish S. Kulkarni, Theodorus H. van der Kwast, Azar Azad, Alexandre R. Zlotta, and Jeffrey L. Wrana Aidan P. NoonAidan P. Noon More articles by this author , Yu LiuYu Liu More articles by this author , Thomas HermannsThomas Hermanns More articles by this author , Girish S. KulkarniGirish S. Kulkarni More articles by this author , Theodorus H. van der KwastTheodorus H. van der Kwast More articles by this author , Azar AzadAzar Azad More articles by this author , Alexandre R. ZlottaAlexandre R. Zlotta More articles by this author , and Jeffrey L. WranaJeffrey L. Wrana More articles by this author View All Author Informationhttps://doi.org/10.1016/j.juro.2014.02.662AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookTwitterLinked InEmail INTRODUCTION AND OBJECTIVES Despite continuing improvement in our understanding of urothelial bladder cancer (UBC), the molecular traits that underpin indolent low grade (LG) versus aggressive high grade (HG) UBC remain to be fully elucidated. High-throughput RNA sequencing (RNA-Seq) provides new insights into transcriptome complexity in cancer, enabling the detection of novel transcripts in both coding and non-coding RNA. One new family member of non-coding RNAs is enhancer RNAs (eRNAs), which have tissue specific expression patterns and regulatory functions. Although many eRNAs may represent transcriptional noise, some of them are thought to exert regulatory functions on nearby genes on the same chromosome (cis) or at distance on other chromosomes (trans). We set out to identify eRNAs that might have a regulatory role in UBC, possibly driving a HG phenotype. METHODS We performed whole transcriptome RNA sequencing (Illumina HiSeq 2000) on a cohort of 49 archival, formalin fixed paraffin embedded (FFPE) LG (n = 27) and HG (n = 22) UBC samples. The predicted eRNA annotations from ENCODE were used in our analyses. Our wRNAseq platform is not strand specific; therefore, we only characterized intergenic eRNAs within 5 – 100kb of the transcription sites of differentially expressed genes (DEGs) between the LG and HG samples (false discovery rate <0.05, fold change >2). To validate these in-silica analyses and provide a model for functional study, the differentiated expression of candidate eRNAs were investigated in UBC cell lines of different grades and a non-UBC cell line using qPCR. RESULTS RNA-Seq revealed 9049 intergenic eRNAs in the whole UBC cohort and 369 strongly differentially expressed between the LG and HG tumours. Among these 369, 147 were identified associated with coding DEGs and we named them as intergenic bladder cancer – eRNAS (iBC-eRNAs). Network analysis of iBC-eRNAs and their associated DEGs identified three major functional clusters including cell cycle, histone complexes and morphogenic regulators. Analysis of BC cell lines confirmed expression of eRNAs (qPCR) and their associated DEGs (RNA-Seq & qPCR). CONCLUSIONS Our results identify for the first time a functional network of eRNAs in human UBC. Some eRNAs are adjacent to genes that are also differentially expressed between LG and HG tumours suggesting possible eRNA-dependent regulation. Analysis of iBC-eRNA in human BC cell lines has enabled us to validate and explore the functional role of iBC-eRNAs and their associated DEGs. Ontario Premier Summit Award - (JLW) © 2014FiguresReferencesRelatedDetails Volume 191Issue 4SApril 2014Page: e301 Advertisement Copyright & Permissions© 2014MetricsAuthor Information Aidan P. Noon More articles by this author Yu Liu More articles by this author Thomas Hermanns More articles by this author Girish S. Kulkarni More articles by this author Theodorus H. van der Kwast More articles by this author Azar Azad More articles by this author Alexandre R. Zlotta More articles by this author Jeffrey L. Wrana More articles by this author Expand All Advertisement Advertisement PDF downloadLoading ...