title: Identification of novel long non-coding RNAs in clear cell renal cell carcinoma.
abstract: BACKGROUND
  Long non-coding RNAs (lncRNA) play an important role in carcinogenesis; knowledge on lncRNA expression in renal cell carcinoma is rudimental. As a basis for biomarker development, we aimed to explore the lncRNA expression profile in clear cell renal cell carcinoma (ccRCC) tissue.
  
  
  RESULTS
  Microarray experiments were performed to determine the expression of 32,183 lncRNA transcripts belonging to 17,512 lncRNAs in 15 corresponding normal and malignant renal tissues. Validation was performed using quantitative real-time PCR in 55 ccRCC and 52 normal renal specimens. Computational analysis was performed to determine lncRNA-microRNA (MiRTarget2) and lncRNA-protein (catRAPID omics) interactions. We identified 1,308 dysregulated transcripts (expression change >2-fold; upregulated: 568, downregulated: 740) in ccRCC tissue. Among these, aberrant expression was validated using PCR: lnc-BMP2-2 (mean expression change: 37-fold), lnc-CPN2-1 (13-fold), lnc-FZD1-2 (9-fold), lnc-ITPR2-3 (15-fold), lnc-SLC30A4-1 (15-fold), and lnc-SPAM1-6 (10-fold) were highly overexpressed in ccRCC, whereas lnc-ACACA-1 (135-fold), lnc-FOXG1-2 (19-fold), lnc-LCP2-2 (2-fold), lnc-RP3-368B9 (19-fold), and lnc-TTC34-3 (314-fold) were downregulated. There was no correlation between lncRNA expression with clinical-pathological parameters. Computational analyses revealed that these lncRNAs are involved in RNA-protein networks related to splicing, binding, transport, localization, and processing of RNA. Small interfering RNA (siRNA)-mediated knockdown of lnc-BMP2-2 and lnc-CPN2-1 did not influence cell proliferation.
  
  
  CONCLUSIONS
  We identified many novel lncRNA transcripts dysregulated in ccRCC which may be useful for novel diagnostic biomarkers.
authors: Department of Urology, University Hospital Bonn, Bonn, Germany.
authors: Jasmine Jc
authors: JJ
authors: Blondeau
authors: Institute of Pathology, University Hospital Bonn, Bonn, Germany ; Department of Prostate Cancer Research, University Hospital Bonn, Bonn, Germany ; Center of Integrated Oncology, University Hospital Bonn, Bonn, Germany.
authors: Mario
authors: M
authors: Deng
authors: Department of Urology, University Hospital Bonn, Bonn, Germany ; Department of Prostate Cancer Research, University Hospital Bonn, Bonn, Germany.
authors: Isabella
authors: I
authors: Syring
authors: Department of Urology, University Hospital Bonn, Bonn, Germany.
authors: Sarah
authors: S
authors: Schrödter
authors: Department of Urology, University Hospital Bonn, Bonn, Germany.
authors: Doris
authors: D
authors: Schmidt
authors: Institute of Pathology, University Hospital Bonn, Bonn, Germany ; Department of Prostate Cancer Research, University Hospital Bonn, Bonn, Germany ; Center of Integrated Oncology, University Hospital Bonn, Bonn, Germany.
authors: Sven
authors: S
authors: Perner
authors: Department of Urology, University Hospital Bonn, Bonn, Germany.
authors: Stefan C
authors: SC
authors: Müller
authors: Department of Urology, University Hospital Bonn, Bonn, Germany.
authors: Jörg
authors: J
authors: Ellinger