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Perspective

Noncoding RNA for Personalized Prostate Cancer Treatment: Utilizing the ‘Dark Matters’ of the Genome

, , , , , & show all
Pages 159-169 | Received 24 Oct 2016, Accepted 22 Dec 2016, Published online: 25 Jan 2017

References

  • Siegel RL , MillerKD , JemalA . Cancer statistics, 2016 . CA Cancer J. Clin.66 ( 1 ), 7 – 30 ( 2016 ).
  • Routh JC , LeibovichBC . Adenocarcinoma of the prostate: epidemiological trends, screening, diagnosis, and surgical management of localized disease . Mayo Clin. Proc.80 ( 7 ), 899 – 907 ( 2005 ).
  • Cancer Genome Atlas Research Network . The molecular taxonomy of primary prostate cancer . Cell163 ( 4 ), 1011 – 1025 ( 2015 ).
  • Mottet N , BellmuntJ , BollaMet al. EAU-ESTRO-SIOG guidelines on prostate cancer. Part 1: screening, diagnosis, and local treatment with curative intent . Eur. Urol. doi:10.1016/j.eururo.2016.08.003 ( 2016 ) ( Epub ahead of print ).
  • Attard G , ParkerC , EelesRAet al. Prostate cancer . Lancet387 ( 10013 ), 70 – 82 ( 2016 ).
  • Prensner JR , RubinMA , WeiJT , ChinnaiyanAM . Beyond PSA: the next generation of prostate cancer biomarkers . Sci. Transl. Med.4 ( 127 ), 127rv3 – 127rv3 ( 2012 ).
  • Cornford P , BellmuntJ , BollaMet al. EAU-ESTRO-SIOG guidelines on prostate cancer. Part II: treatment of relapsing, metastatic, and castration-resistant prostate cancer . Eur. Urol. doi:10.1016/j.eururo.2016.08.002 ( 2016 ) ( Epub ahead of print ).
  • Gnanapragasam VJ , LophatananonA , WrightKA , MuirKR , GavinA , GreenbergDC . Improving clinical risk stratification at diagnosis in primary prostate cancer: a prognostic modelling study . PLoS Med.13 ( 8 ), e1002063 ( 2016 ).
  • Boutros PC , FraserM , HardingNJet al. Spatial genomic heterogeneity within localized, multifocal prostate cancer . Nat. Genet.47 ( 7 ), 736 – 745 ( 2015 ).
  • Tang KD , LingM-T . Targeting drug-resistant prostate cancer with dual PI3K/mTOR inhibition . Curr. Med. Chem.21 ( 26 ), 3048 – 3056 ( 2014 ).
  • Mateo J , CarreiraS , SandhuSet al. DNA-repair defects and olaparib in metastatic prostate cancer . N. Engl. J. Med.373 ( 18 ), 1697 – 1708 ( 2015 ).
  • He W , ZhangM-G , WangX-Jet al. AURKA suppression induces DU145 apoptosis and sensitizes DU145 to docetaxel treatment . Am. J. Transl. Res.5 ( 3 ), 359 – 367 ( 2013 ).
  • Esteller M . Non-coding RNAs in human disease . Nat. Rev. Genet.12 ( 12 ), 861 – 874 ( 2011 ).
  • Berezikov E . Evolution of microRNA diversity and regulation in animals . Nat. Rev. Genet.12 ( 12 ), 846 – 860 ( 2011 ).
  • Ulitsky I . Evolution to the rescue: using comparative genomics to understand long non-coding RNAs . Nat. Rev. Genet.17 ( 10 ), 601 – 614 ( 2016 ).
  • Prensner JR , ChinnaiyanAM . The emergence of lncRNAs in cancer biology . Cancer Discov.1 ( 5 ), 391 – 407 ( 2011 ).
  • Guttman M , AmitI , GarberMet al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals . Nature458 ( 7235 ), 223 – 227 ( 2009 ).
  • Djebali S , DavisCA , MerkelAet al. Landscape of transcription in human cells . Nature489 ( 7414 ), 101 – 108 ( 2012 ).
  • Lu J , GetzG , MiskaEAet al. MicroRNA expression profiles classify human cancers . Nature435 ( 7043 ), 834 – 838 ( 2005 ).
  • Waltering KK , PorkkaKP , JalavaSEet al. Androgen regulation of micro-RNAs in prostate cancer . Prostate71 ( 6 ), 604 – 614 ( 2011 ).
  • Tsai M-C , ManorO , WanYet al. Long noncoding RNA as modular scaffold of histone modification complexes . Science329 ( 5992 ), 689 – 693 ( 2010 ).
  • Gupta RA , ShahN , WangKCet al. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis . Nature464 ( 7291 ), 1071 – 1076 ( 2010 ).
  • Ylipää A , KivinummiK , KohvakkaAet al. Transcriptome sequencing reveals PCAT5 as a novel ERG-regulated long noncoding RNA in prostate cancer . Cancer Res.75 ( 19 ), 4026 – 4031 ( 2015 ).
  • Parasramka MA , MajiS , MatsudaA , YanIK , PatelT . Long non-coding RNAs as novel targets for therapy in hepatocellular carcinoma . Pharmacol. Ther.161 , 67 – 78 ( 2016 ).
  • Li Z , RanaTM . Therapeutic targeting of microRNAs: current status and future challenges . Nat. Rev. Drug. Discov.13 ( 8 ), 622 – 638 ( 2014 ).
  • Du Z , FeiT , VerhaakRGWet al. Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer . Nat. Struct. Mol. Biol.20 ( 7 ), 908 – 913 ( 2013 ).
  • Byron SA , Van Keuren-JensenKR , EngelthalerDM , CarptenJD , CraigDW . Translating RNA sequencing into clinical diagnostics: opportunities and challenges . Nat. Rev. Genet.17 ( 5 ), 257 – 271 ( 2016 ).
  • Brown BD , NaldiniL . Exploiting and antagonizing microRNA regulation for therapeutic and experimental applications . Nat. Rev. Genet.10 ( 8 ), 578 – 585 ( 2009 ).
  • Jonas S , IzaurraldeE . Towards a molecular understanding of microRNA-mediated gene silencing . Nat. Rev. Genet.16 ( 7 ), 421 – 433 ( 2015 ).
  • Lee RC , FeinbaumRL , AmbrosV . The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14 . Cell75 ( 5 ), 843 – 854 ( 1993 ).
  • Pasquinelli AE . MicroRNAs and their targets: recognition, regulation and an emerging reciprocal relationship . Nat. Rev. Genet.13 ( 4 ), 271 – 282 ( 2012 ).
  • Ribas J , NiX , HaffnerMet al. miR-21: an androgen receptor-regulated microRNA that promotes hormone-dependent and hormone-independent prostate cancer growth . Cancer Res.69 ( 18 ), 7165 – 7169 ( 2009 ).
  • Okato A , GotoY , KurozumiAet al. Direct regulation of LAMP1 by tumor-suppressive microRNA-320a in prostate cancer . Int. J. Oncol.49 ( 1 ), 111 – 122 ( 2016 ).
  • Kurozumi A , GotoY , MatsushitaRet al. Tumor-suppressive microRNA-223 inhibits cancer cell migration and invasion by targeting ITGA3/ITGB1 signaling in prostate cancer . Cancer Sci.107 ( 1 ), 84 – 94 ( 2016 ).
  • Fabris L , CederY , ChinnaiyanAMet al. The potential of microRNAs as prostate cancer biomarkers . Eur. Urol.70 ( 2 ), 312 – 322 ( 2016 ).
  • Fendler A , StephanC , YousefGM , KristiansenG , JungK . The translational potential of microRNAs as biofluid markers of urological tumours . Nat. Rev. Urol.13 ( 12 ), 734 – 752 ( 2016 ).
  • Mitchell PS , ParkinRK , KrohEMet al. Circulating microRNAs as stable blood-based markers for cancer detection . Proc. Natl Acad. Sci. USA105 ( 30 ), 10513 – 10518 ( 2008 ).
  • Arroyo JD , ChevilletJR , KrohEMet al. Argonaute2 complexes carry a population of circulating microRNAs independent of vesicles in human plasma . Proc. Natl Acad. Sci. USA108 ( 12 ), 5003 – 5008 ( 2011 ).
  • Gallo A , TandonM , AlevizosI , IlleiGG . The majority of microRNAs detectable in serum and saliva is concentrated in exosomes . PLoS ONE7 ( 3 ), e30679 ( 2012 ).
  • Yang Q , LuJ , WangS , LiH , GeQ , LuZ . Application of next-generation sequencing technology to profile the circulating microRNAs in the serum of preeclampsia versus normal pregnant women . Clin. Chim. Acta412 ( 23–24 ), 2167 – 2173 ( 2011 ).
  • Yaman Agaoglu F , KovancilarM , DizdarYet al. Investigation of miR-21, miR-141, and miR-221 in blood circulation of patients with prostate cancer . Tumour Biol.32 ( 3 ), 583 – 588 ( 2011 ).
  • Nguyen HCN , XieW , YangMet al. Expression differences of circulating microRNAs in metastatic castration resistant prostate cancer and low-risk, localized prostate cancer . Prostate73 ( 4 ), 346 – 354 ( 2013 ).
  • Shen J , HrubyGW , McKiernanJMet al. Dysregulation of circulating microRNAs and prediction of aggressive prostate cancer . Prostate72 ( 13 ), 1469 – 1477 ( 2012 ).
  • Zhang XO , WangHB , ZhangY , LuX , ChenLL , YangL . Complementary sequence-mediated exon circularization . Cell159 ( 1 ), 134 – 147 ( 2014 ).
  • Selth LA , TilleyWD , ButlerLM . Circulating microRNAs: macro-utility as markers of prostate cancer?Endocr. Relat. Cancer19 ( 4 ), R99 – R113 ( 2012 ).
  • Goto Y , KojimaS , NishikawaRet al. MicroRNA expression signature of castration-resistant prostate cancer: the microRNA-221/222 cluster functions as a tumour suppressor and disease progression marker . Br. J. Cancer113 ( 7 ), 1055 – 1065 ( 2015 ).
  • Ebert MS , NeilsonJR , SharpPA . MicroRNA sponges: competitive inhibitors of small RNAs in mammalian cells . Nat. Methods4 ( 9 ), 721 – 726 ( 2007 ).
  • Gumireddy K , YoungDD , XiongX , HogeneschJB , HuangQ , DeitersA . Small-molecule inhibitors of microRNA miR-21 function . Angew. Chem. Int. Ed. Engl.47 ( 39 ), 7482 – 7484 ( 2008 ).
  • Ørom UA , KauppinenS , LundAH . LNA-modified oligonucleotides mediate specific inhibition of microRNA function . Gene372 , 137 – 141 ( 2006 ).
  • Wei Y , YangJ , YiLet al. MiR-223-3p targeting SEPT6 promotes the biological behavior of prostate cancer . Sci. Rep.4 , 7546 ( 2014 ).
  • Elmén J , LindowM , SilahtarogluAet al. Antagonism of microRNA-122 in mice by systemically administered LNA-antimiR leads to up-regulation of a large set of predicted target mRNAs in the liver . Nucleic Acids Res.36 ( 4 ), 1153 – 1162 ( 2008 ).
  • Di Martino MT , GullàA , Gallo CantafioMEet al. In vitro and in vivo activity of a novel locked nucleic acid (LNA)-inhibitor-miR-221 against multiple myeloma cells . PLoS ONE9 ( 2 ), e89659 ( 2014 ).
  • Bianchini D , OmlinA , PezaroCet al. First-in-human Phase I study of EZN-4176, a locked nucleic acid antisense oligonucleotide to exon 4 of the androgen receptor mRNA in patients with castration-resistant prostate cancer . Br. J. Cancer109 ( 10 ), 2579 – 2586 ( 2013 ).
  • Juliano RL . The delivery of therapeutic oligonucleotides . Nucleic Acids Res.44 ( 14 ), 6518 – 6548 ( 2016 ).
  • Ozcan G , OzpolatB , ColemanRL , SoodAK , Lopez-BeresteinG . Preclinical and clinical development of siRNA-based therapeutics . Adv. Drug Deliv. Rev.87 , 108 – 119 ( 2015 ).
  • Quinn JJ , ChangHY . Unique features of long non-coding RNA biogenesis and function . Nat. Rev. Genet.17 ( 1 ), 47 – 62 ( 2016 ).
  • Bánfai B , JiaH , KhatunJet al. Long noncoding RNAs are rarely translated in two human cell lines . Genome Res.22 ( 9 ), 1646 – 1657 ( 2012 ).
  • Anderson DM , AndersonKM , ChangC-Let al. A micropeptide encoded by a putative long noncoding RNA regulates muscle performance . Cell160 ( 4 ), 595 – 606 ( 2015 ).
  • Rinn JL , ChangHY . Genome regulation by long noncoding RNAs . Annu. Rev. Biochem.81 ( 1 ), 145 – 166 ( 2012 ).
  • Chen H , XuJ , HongJ , TangR , ZhangX , FangJ-Y . Long noncoding RNA profiles identify five distinct molecular subtypes of colorectal cancer with clinical relevance . Mol. Oncol.8 ( 8 ), 1393 – 1403 ( 2014 ).
  • Iyer MK , NiknafsYS , MalikRet al. The landscape of long noncoding RNAs in the human transcriptome . Nat. Genet.47 ( 3 ), 199 – 208 ( 2015 ).
  • Quek XC , ThomsonDW , MaagJLVet al. lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs . Nucleic Acids Res.43 , D168 – D173 ( 2015 ).
  • de Kok JB , VerhaeghGW , RoelofsRWet al. DD3(PCA3), a very sensitive and specific marker to detect prostate tumors . Cancer Res.62 ( 9 ), 2695 – 2698 ( 2002 ).
  • Prensner JR , ZhaoS , ErhoNet al. RNA biomarkers associated with metastatic progression in prostate cancer: a multi-institutional high-throughput analysis of SChLAP1 . Lancet Oncol.15 ( 13 ), 1469 – 1480 ( 2014 ).
  • Li Q , ShaoY , ZhangXet al. Plasma long noncoding RNA protected by exosomes as a potential stable biomarker for gastric cancer . Tumour Biol.36 ( 3 ), 2007 – 2012 ( 2015 ).
  • Li Y , ZhengQ , BaoCet al. Circular RNA is enriched and stable in exosomes: a promising biomarker for cancer diagnosis . Cell Res.25 ( 8 ), 981 – 984 ( 2015 ).
  • Ahadi A , BrennanS , KennedyPJ , HutvagnerG , TranN . Long non-coding RNAs harboring miRNA seed regions are enriched in prostate cancer exosomes . Sci. Rep.6 , 24922 ( 2016 ).
  • Yang L , LinC , JinCet al. lncRNA-dependent mechanisms of androgen-receptor-regulated gene activation programs . Nature500 ( 7464 ), 598 – 602 ( 2013 ).
  • Prensner JR , IyerMK , SahuAet al. The long noncoding RNA SChLAP1 promotes aggressive prostate cancer and antagonizes the SWI/SNF complex . Nat. Genet.45 ( 11 ), 1392 – 1398 ( 2013 ).
  • Guo H , AhmedM , ZhangFet al. Modulation of long noncoding RNAs by risk SNPs underlying genetic predispositions to prostate cancer . Nat. Genet.48 ( 10 ), 1142 – 1150 ( 2016 ).
  • Takahashi K , YanIK , KogureT , HagaH , PatelT . Extracellular vesicle-mediated transfer of long non-coding RNA ROR modulates chemosensitivity in human hepatocellular cancer . FEBS. Open. Bio4 ( 1 ), 458 – 467 ( 2014 ).
  • Qu L , DingJ , ChenCet al. Exosome-transmitted lncARSR promotes sunitinib resistance in renal cancer by acting as a competing endogenous RNA . Cancer Cell29 ( 5 ), 653 – 668 ( 2016 ).
  • Zhao J , ZhaoY , WangLet al. Alterations of androgen receptor-regulated enhancer RNAs (eRNAs) contribute to enzalutamide resistance in castration-resistant prostate cancer . Oncotarget7 ( 25 ), 38551 – 38565 ( 2016 ).
  • Lennox KA , BehlkeMA . Cellular localization of long non-coding RNAs affects silencing by RNAi more than by antisense oligonucleotides . Nucleic Acids Res.44 ( 2 ), 863 – 877 ( 2016 ).
  • Matsui M , CoreyDR . Non-coding RNAs as drug targets . Nat. Rev. Drug Discov. doi:10.1038/nrd.2016.117 ( 2016 ) ( Epub ahead of print ).
  • Salzman J , GawadC , WangPL , LacayoN , BrownPO . Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types . PLoS ONE7 ( 2 ), e30733 ( 2012 ).
  • Memczak S , JensM , ElefsiniotiAet al. Circular RNAs are a large class of animal RNAs with regulatory potency . Nature495 ( 7441 ), 333 – 338 ( 2013 ).
  • Zheng Q , BaoC , GuoWet al. Circular RNA profiling reveals an abundant circHIPK3 that regulates cell growth by sponging multiple miRNAs . Nat. Commun.7 , 11215 ( 2016 ).
  • Memczak S , PapavasileiouP , PetersO , RajewskyN . Identification and characterization of circular RNAs as a new class of putative biomarkers in human blood . PLoS ONE10 ( 10 ), e0141214 ( 2015 ).
  • Guarnerio J , BezziM , JeongJCet al. Oncogenic role of fusion-circRNAs derived from cancer-associated chromosomal translocations . Cell165 ( 2 ), 289 – 302 ( 2016 ).
  • Song X , ZhangN , HanPet al. Circular RNA profile in gliomas revealed by identification tool UROBORUS . Nucleic Acids Res.44 ( 9 ), e87 – e87 ( 2016 ).
  • Hansen TB , JensenTI , ClausenBHet al. Natural RNA circles function as efficient microRNA sponges . Nature495 ( 7441 ), 384 – 388 ( 2013 ).
  • Zhong Z , LvM , ChenJ . Screening differential circular RNA expression profiles reveals the regulatory role of circTCF25-miR-103a-3p/miR-107-CDK6 pathway in bladder carcinoma . Sci. Rep.6 , 30919 ( 2016 ).
  • Zhang Y , ZhangX-O , ChenTet al. Circular intronic long noncoding RNAs . Mol. Cell.51 ( 6 ), 792 – 806 ( 2013 ).
  • Du Z , SunT , HacisuleymanEet al. Integrative analyses reveal a long noncoding RNA-mediated sponge regulatory network in prostate cancer . Nat. Commun.7 , 10982 ( 2016 ).
  • Leucci E , PatellaF , WaageJet al. microRNA-9 targets the long non-coding RNA MALAT1 for degradation in the nucleus . Sci. Rep.3 , 2535 ( 2013 ).
  • Cesana M , CacchiarelliD , LegniniIet al. A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA . Cell147 ( 2 ), 358 – 369 ( 2011 ).
  • Burd CE , JeckWR , LiuY , SanoffHK , WangZ , SharplessNE . Expression of linear and novel circular forms of an INK4/ARF-associated non-coding RNA correlates with atherosclerosis risk . PLoS Genets.6 ( 12 ), e1001233 ( 2010 ).
  • Qi P , ZhouX-Y , DuX . Circulating long non-coding RNAs in cancer: current status and future perspectives . Mol. Cancer15 ( 1 ), 39 ( 2016 ).
  • Wang L , LiuC , LiCet al. Effects of microRNA-211/222 on cell proliferation and apoptosis in prostate cancer cells . Gene572 ( 2 ), 252 – 258 ( 2015 ).
  • Pesta M , KleckaJ , KuldaVet al. Importance of miR-20a expression in prostate cancer tissue . Anticancer Res.30 ( 9 ), 3579 – 3583 ( 2010 ).
  • Qiang XF , ZhangZW , LiuQet al. miR-20a promotes prostate cancer invasion and migration through targeting ABL2 . J. Cell Biochem.115 ( 7 ), 1269 – 1276 ( 2014 ).
  • Crea F , WatahikiA , QuagliataLet al. Identification of a long non-coding RNA as a novel biomarker and potential therapeutic target for metastatic prostate cancer . Oncotarget5 ( 3 ), 764 – 774 ( 2014 ).
  • Wang F , RenS , ChenRet al. Development and prospective multicenter evaluation of the long noncoding RNA MALAT-1 as a diagnostic urinary biomarker for prostate cancer . Oncotarget5 ( 22 ), 11091 – 11102 ( 2014 ).
  • Wang D , DingL , WangLet al. LncRNA MALAT1 enhances oncogenic activities of EZH2 in castration-resistant prostate cancer . Oncotarget6 ( 38 ), 41045 – 41055 ( 2015 ).
  • Prensner JR , ChenW , HanSet al. The long non-coding RNA PCAT-1 promotes prostate cancer cell proliferation through cMyc . Neoplasia16 ( 11 ), 900 – 908 ( 2014 ).
  • Karantanos T , CornPG , ThompsonTC . Prostate cancer progression after androgen deprivation therapy: mechanisms of castrate resistance and novel therapeutic approaches . Oncogene32 ( 49 ), 5501 – 5511 ( 2013 ).
  • Paralkar VR , TabordaCC , HuangPet al. Unlinking an lncRNA from its associated cis element . Mol. Cell.62 ( 1 ), 104 – 110 ( 2016 ).

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