Long Noncoding RNA in Prostate, Bladder, and Kidney Cancer Elena S. Martens-Uzunova, René Böttcher, Carlo M. Croce, Guido Jenster, Tapio Visakorpi, George A. Calin  European Urology  Volume 65, Issue 6, Pages 1140-1151 (June 2014) DOI: 10.1016/j.eururo.2013.12.003 Copyright © 2013 European Association of Urology Terms and Conditions

Fig. 1 Genomic organisation of different long noncoding RNA (lncRNA) classes. A grey and black line represents DNA strands. Grey boxes represent protein- or lncRNA-coding genomic exons. Thin black lines represent spliced introns. Arrows indicate direction of transcription. Protein-coding transcripts (messenger RNAs) are orange. Noncoding transcripts (lncRNAs) are green. Pseudogenes have a diagonal stripe pattern. Intron boundaries of circular RNA precursors are shown in red (-5′) and yellow (-3′). European Urology 2014 65, 1140-1151DOI: (10.1016/j.eururo.2013.12.003) Copyright © 2013 European Association of Urology Terms and Conditions

Fig. 2 The expression of tumour suppressor phosphatase and tensin homolog (PTEN) is regulated by a complex noncoding RNA (ncRNA) network representing many long ncRNA (lncRNA) functions. (1) The PTEN gene encoded at chromosome 10 is transcribed to PTEN messenger RNA (mRNA; in brown), which is exported to the cytoplasm and translated to PTEN protein that acts as a negative regulator of cell growth. The 3′-untranslated region of PTEN mRNA contains binding sites (red/black dashed line) for microRNAs (miRNAs) from the miR-106b-93-25 cluster. (2) PTENP1 pseudogene, highly homologous to PTEN, is encoded at chromosome 9 and coexpressed with PTEN in normal and malignant prostate tissues. Three lncRNAs (in green) are simultaneously transcribed from PTENP1: one in sense: PTENP1-Ψ, and two in antisense: PTENP1-ASα and PTENP1-ASβ. The PTENP1-Ψ sequence is similar to PTEN mRNA and also contains binding sites for the miR-106b-93-25 cluster. (3) Two protein-coding genes, CNOT6L and VAPA (in orange), encoded at chromosomes 4 and 18, respectively, contain binding sites for the miR-106b-93-25 cluster. (4) The miRNA cluster miR-106b-93-25 (in red) targeting PTEN mRNA is intronically encoded at the MCM7 gene at chromosome 7. When overexpressed, miRNAs from the miR-106b-93-25 cluster are exported to the cytoplasm where they associate with the RNA-induced silencing complex (RISC) (in blue), cause the downregulation of PTEN mRNA, and promote prostate tumorigenesis. (A) In the nucleus, PTENP1-ASα acts as a trans-acting epigenetic repressor that localises to the PTEN promoter and recruits the chromatin repressive protein complex EZH2 (in yellow). EZH2 silences the transcription of PTEN by introducing repressive histone marks (lollypops) at the PTEN promoter. (B) The structure of PTENP1-ψ is stabilised by PTENP1-ASβ by the formation of a double-stranded RNA:RNA tandem, which is exported to the cytoplasm. (C) In the cytoplasm, this tandem functions as a miRNA sponge and sequesters miR-106b, miR-93, and miR-25. This leads to the de-repression of PTEN mRNA, higher levels of PTEN protein, and subsequent growth inhibition. In addition, independently of their coding potential, the VAPA and CNOT6L mRNAs can also function as miRNA sponges for PTEN. European Urology 2014 65, 1140-1151DOI: (10.1016/j.eururo.2013.12.003) Copyright © 2013 European Association of Urology Terms and Conditions

Fig. 3 Genomic imprinting at the 11p15.5 locus harboring the insulin-like growth factor 2 (IGF2) and imprinted maternally expressed transcript (H19) genes in normal cells, Wilms tumours, and bladder carcinomas. Either silencing or overexpression of H19 can cause tumour growth. In normal cells, IGF2 and H19 are separated by the genomic imprinting control region (ICR) recognised by the transcriptional regulator CTCF. IGF and H19 demonstrate monoallelic coexpression during embryogenesis and are under the control of the same enhancer elements (E) located downstream of H19. ICR is methylated on the paternal chromosome (lollypops), which blocks binding of CTCF, prevents transcription of H19, and allows activation of IGF2 by the distal enhancer. Instead, CTCF binds to the maternal chromosome and promotes H19 transcription. In this way, the methylation status of H19 balances in cis the expression of IGF2 residing on the same chromosome. In Wilms tumours, H19 is methylated at both chromosomes, which leads to expression of IGF2 from both alleles, accumulation of IGF2 protein, and cell growth stimulation. In bladder cancer, the H19 promoter region and ICR are hypomethylated, which blocks expression of IGF2 and causes the accumulation of H19 lncRNA. European Urology 2014 65, 1140-1151DOI: (10.1016/j.eururo.2013.12.003) Copyright © 2013 European Association of Urology Terms and Conditions