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Review

Clinical significance of the interaction between non-coding RNAs and the epigenetics machinery

Challenges and opportunities in oncology

, &
Pages 75-80 | Received 19 Aug 2013, Accepted 13 Sep 2013, Published online: 11 Oct 2013

References

  • Jeltsch A. Beyond Watson and Crick: DNA methylation and molecular enzymology of DNA methyltransferases. Chembiochem 2002; 3:274 - 93; http://dx.doi.org/10.1002/1439-7633(20020402)3:4<274::AID-CBIC274>3.0.CO;2-S; PMID: 11933228
  • Goldberg AD, Allis CD, Bernstein E. Epigenetics: a landscape takes shape. Cell 2007; 128:635 - 8; http://dx.doi.org/10.1016/j.cell.2007.02.006; PMID: 17320500
  • Costa FF. Non-coding RNAs: Meet thy masters. Bioessays 2010; 32:599 - 608; http://dx.doi.org/10.1002/bies.200900112; PMID: 20544733
  • Wahlestedt C. Targeting long non-coding RNA to therapeutically upregulate gene expression. Nat Rev Drug Discov 2013; 12:433 - 46; http://dx.doi.org/10.1038/nrd4018; PMID: 23722346
  • Carninci P, Yasuda J, Hayashizaki Y. Multifaceted mammalian transcriptome. Curr Opin Cell Biol 2008; 20:274 - 80; http://dx.doi.org/10.1016/j.ceb.2008.03.008; PMID: 18468878
  • Cheng J, Kapranov P, Drenkow J, Dike S, Brubaker S, Patel S, Long J, Stern D, Tammana H, Helt G, et al. Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 2005; 308:1149 - 54; http://dx.doi.org/10.1126/science.1108625; PMID: 15790807
  • Röther S, Meister G. Small RNAs derived from longer non-coding RNAs. Biochimie 2011; 93:1905 - 15; http://dx.doi.org/10.1016/j.biochi.2011.07.032; PMID: 21843590
  • Graifer D, Karpova G. Structural and functional topography of the human ribosome. Acta Biochim Biophys Sin (Shanghai) 2012; 44:281 - 99; http://dx.doi.org/10.1093/abbs/gmr118; PMID: 22257731
  • Lee RC, Feinbaum RL, Ambros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 1993; 75:843 - 54; http://dx.doi.org/10.1016/0092-8674(93)90529-Y; PMID: 8252621
  • Wightman B, Ha I, Ruvkun G. Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 1993; 75:855 - 62; http://dx.doi.org/10.1016/0092-8674(93)90530-4; PMID: 8252622
  • Kunej T, Godnic I, Horvat S, Zorc M, Calin GA. Cross talk between microRNA and coding cancer genes. Cancer J 2012; 18:223 - 31; http://dx.doi.org/10.1097/PPO.0b013e318258b771; PMID: 22647358
  • Berry B, Deddouche S, Kirschner D, Imler JL, Antoniewski C. Viral suppressors of RNA silencing hinder exogenous and endogenous small RNA pathways in Drosophila. PLoS One 2009; 4:e5866; http://dx.doi.org/10.1371/journal.pone.0005866; PMID: 19516905
  • Pauli A, Rinn JL, Schier AF. Non-coding RNAs as regulators of embryogenesis. Nat Rev Genet 2011; 12:136 - 49; http://dx.doi.org/10.1038/nrg2904; PMID: 21245830
  • Calin GA, Croce CM. MicroRNA signatures in human cancers. Nat Rev Cancer 2006; 6:857 - 66; http://dx.doi.org/10.1038/nrc1997; PMID: 17060945
  • Calin GA, Ferracin M, Cimmino A, Di Leva G, Shimizu M, Wojcik SE, Iorio MV, Visone R, Sever NI, Fabbri M, et al. A MicroRNA signature associated with prognosis and progression in chronic lymphocytic leukemia. N Engl J Med 2005; 353:1793 - 801; http://dx.doi.org/10.1056/NEJMoa050995; PMID: 16251535
  • Calin GA, Trapasso F, Shimizu M, Dumitru CD, Yendamuri S, Godwin AK, Ferracin M, Bernardi G, Chatterjee D, Baldassarre G, et al. Familial cancer associated with a polymorphism in ARLTS1. N Engl J Med 2005; 352:1667 - 76; http://dx.doi.org/10.1056/NEJMoa042280; PMID: 15843669
  • Lu CY, Lin KY, Tien MT, Wu CT, Uen YH, Tseng TL. Frequent DNA methylation of MiR-129-2 and its potential clinical implication in hepatocellular carcinoma. Genes Chromosomes Cancer 2013; 52:636 - 43; PMID: 23580407
  • Hanahan D, Weinberg RA. The hallmarks of cancer. Cell 2000; 100:57 - 70; http://dx.doi.org/10.1016/S0092-8674(00)81683-9; PMID: 10647931
  • Wong KY, Yim RL, Kwong YL, Leung CY, Hui PK, Cheung F, Liang R, Jin DY, Chim CS. Epigenetic inactivation of the MIR129-2 in hematological malignancies. J Hematol Oncol 2013; 6:16; http://dx.doi.org/10.1186/1756-8722-6-16; PMID: 23406679
  • Agirre X, Martínez-Climent JA, Odero MD, Prósper F. Epigenetic regulation of miRNA genes in acute leukemia. Leukemia 2012; 26:395 - 403; http://dx.doi.org/10.1038/leu.2011.344; PMID: 22143672
  • Gebauer K, Peters I, Dubrowinskaja N, Hennenlotter J, Abbas M, Scherer R, Tezval H, Merseburger AS, Stenzl A, Kuczyk MA, et al. Hsa-mir-124-3 CpG island methylation is associated with advanced tumours and disease recurrence of patients with clear cell renal cell carcinoma. Br J Cancer 2013; 108:131 - 8; http://dx.doi.org/10.1038/bjc.2012.537; PMID: 23321515
  • Agirre X, Vilas-Zornoza A, Jiménez-Velasco A, Martin-Subero JI, Cordeu L, Gárate L, San José-Eneriz E, Abizanda G, Rodríguez-Otero P, Fortes P, et al. Epigenetic silencing of the tumor suppressor microRNA Hsa-miR-124a regulates CDK6 expression and confers a poor prognosis in acute lymphoblastic leukemia. Cancer Res 2009; 69:4443 - 53; http://dx.doi.org/10.1158/0008-5472.CAN-08-4025; PMID: 19435910
  • Siemens H, Neumann J, Jackstadt R, Mansmann U, Horst D, Kirchner T, Hermeking H. Detection of miR-34a promoter methylation in combination with elevated expression of c-Met and β-catenin predicts distant metastasis of colon cancer. Clin Cancer Res 2013; 19:710 - 20; http://dx.doi.org/10.1158/1078-0432.CCR-12-1703; PMID: 23243217
  • Lujambio A, Calin GA, Villanueva A, Ropero S, Sánchez-Céspedes M, Blanco D, Montuenga LM, Rossi S, Nicoloso MS, Faller WJ, et al. A microRNA DNA methylation signature for human cancer metastasis. Proc Natl Acad Sci U S A 2008; 105:13556 - 61; http://dx.doi.org/10.1073/pnas.0803055105; PMID: 18768788
  • Incoronato M, Urso L, Portela A, Laukkanen MO, Soini Y, Quintavalle C, Keller S, Esteller M, Condorelli G. Epigenetic regulation of miR-212 expression in lung cancer. PLoS One 2011; 6:e27722; http://dx.doi.org/10.1371/journal.pone.0027722; PMID: 22110741
  • Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F, et al. Landscape of transcription in human cells. Nature 2012; 489:101 - 8; http://dx.doi.org/10.1038/nature11233; PMID: 22955620
  • Beckedorff FC, Amaral MS, Deocesano-Pereira C, Verjovski-Almeida S. Long non-coding RNAs and their implications in cancer epigenetics. Biosci Rep 2013; 33:e00061; http://dx.doi.org/10.1042/BSR20130054; PMID: 23875687
  • Matouk IJ, DeGroot N, Mezan S, Ayesh S, Abu-lail R, Hochberg A, Galun E. The H19 non-coding RNA is essential for human tumor growth. PLoS One 2007; 2:e845; http://dx.doi.org/10.1371/journal.pone.0000845; PMID: 17786216
  • Zhang L, Yang F, Yuan JH, Yuan SX, Zhou WP, Huo XS, Xu D, Bi HS, Wang F, Sun SH. Epigenetic activation of the MiR-200 family contributes to H19-mediated metastasis suppression in hepatocellular carcinoma. Carcinogenesis 2013; 34:577 - 86; http://dx.doi.org/10.1093/carcin/bgs381; PMID: 23222811
  • Zhang XQSS, Sun S, Lam KF, Kiang KM, Pu JK, Ho AS, Lui WM, Fung CF, Wong TS, Leung GK. A long non-coding RNA signature in glioblastoma multiforme predicts survival. Neurobiol Dis 2013; 58:123 - 31; http://dx.doi.org/10.1016/j.nbd.2013.05.011; PMID: 23726844
  • Beroukhim R, Mermel CH, Porter D, Wei G, Raychaudhuri S, Donovan J, Barretina J, Boehm JS, Dobson J, Urashima M, et al. The landscape of somatic copy-number alteration across human cancers. Nature 2010; 463:899 - 905; http://dx.doi.org/10.1038/nature08822; PMID: 20164920
  • Bignell GR, Greenman CD, Davies H, Butler AP, Edkins S, Andrews JM, Buck G, Chen L, Beare D, Latimer C, et al. Signatures of mutation and selection in the cancer genome. Nature 2010; 463:893 - 8; http://dx.doi.org/10.1038/nature08768; PMID: 20164919
  • Popov N, Gil J. Epigenetic regulation of the INK4b-ARF-INK4a locus: in sickness and in health. Epigenetics 2010; 5:685 - 90; http://dx.doi.org/10.4161/epi.5.8.12996; PMID: 20716961
  • Fabbri M, Garzon R, Cimmino A, Liu Z, Zanesi N, Callegari E, Liu S, Alder H, Costinean S, Fernandez-Cymering C, et al. MicroRNA-29 family reverts aberrant methylation in lung cancer by targeting DNA methyltransferases 3A and 3B. Proc Natl Acad Sci U S A 2007; 104:15805 - 10; http://dx.doi.org/10.1073/pnas.0707628104; PMID: 17890317
  • Garzon R, Heaphy CE, Havelange V, Fabbri M, Volinia S, Tsao T, Zanesi N, Kornblau SM, Marcucci G, Calin GA, et al. MicroRNA 29b functions in acute myeloid leukemia. Blood 2009; 114:5331 - 41; http://dx.doi.org/10.1182/blood-2009-03-211938; PMID: 19850741
  • Zhang J, Yang Y, Yang T, Liu Y, Li A, Fu S, Wu M, Pan Z, Zhou W. microRNA-22, downregulated in hepatocellular carcinoma and correlated with prognosis, suppresses cell proliferation and tumourigenicity. Br J Cancer 2010; 103:1215 - 20; http://dx.doi.org/10.1038/sj.bjc.6605895; PMID: 20842113
  • Noonan EJ, Place RF, Pookot D, Basak S, Whitson JM, Hirata H, Giardina C, Dahiya R. miR-449a targets HDAC-1 and induces growth arrest in prostate cancer. Oncogene 2009; 28:1714 - 24; http://dx.doi.org/10.1038/onc.2009.19; PMID: 19252524
  • Guo Y, Ying L, Tian Y, Yang P, Zhu Y, Wang Z, Qiu F, Lin J. miR-144 downregulation increases bladder cancer cell proliferation by targeting EZH2 and regulating Wnt signaling. FEBS J 2013; 280:4531 - 8; http://dx.doi.org/10.1111/febs.12417; PMID: 23815091
  • Friedman JM, Liang G, Liu CC, Wolff EM, Tsai YC, Ye W, Zhou X, Jones PA. The putative tumor suppressor microRNA-101 modulates the cancer epigenome by repressing the polycomb group protein EZH2. Cancer Res 2009; 69:2623 - 9; http://dx.doi.org/10.1158/0008-5472.CAN-08-3114; PMID: 19258506
  • Varambally S, Cao Q, Mani RS, Shankar S, Wang X, Ateeq B, Laxman B, Cao X, Jing X, Ramnarayanan K, et al. Genomic loss of microRNA-101 leads to overexpression of histone methyltransferase EZH2 in cancer. Science 2008; 322:1695 - 9; http://dx.doi.org/10.1126/science.1165395; PMID: 19008416
  • Ren G, Baritaki S, Marathe H, Feng J, Park S, Beach S, Bazeley PS, Beshir AB, Fenteany G, Mehra R, et al. Polycomb protein EZH2 regulates tumor invasion via the transcriptional repression of the metastasis suppressor RKIP in breast and prostate cancer. Cancer Res 2012; 72:3091 - 104; http://dx.doi.org/10.1158/0008-5472.CAN-11-3546; PMID: 22505648
  • Braconi C, Huang N, Patel T. MicroRNA-dependent regulation of DNA methyltransferase-1 and tumor suppressor gene expression by interleukin-6 in human malignant cholangiocytes. Hepatology 2010; 51:881 - 90; PMID: 20146264
  • Stumpel DJ, Schotte D, Lange-Turenhout EA, Schneider P, Seslija L, de Menezes RX, Marquez VE, Pieters R, den Boer ML, Stam RW. Hypermethylation of specific microRNA genes in MLL-rearranged infant acute lymphoblastic leukemia: major matters at a micro scale. Leukemia 2011; 25:429 - 39; http://dx.doi.org/10.1038/leu.2010.282; PMID: 21116279
  • Duursma AM, Kedde M, Schrier M, le Sage C, Agami R. miR-148 targets human DNMT3b protein coding region. RNA 2008; 14:872 - 7; http://dx.doi.org/10.1261/rna.972008; PMID: 18367714
  • Brown CJ, Hendrich BD, Rupert JL, Lafrenière RG, Xing Y, Lawrence J, Willard HF. The human XIST gene: analysis of a 17 kb inactive X-specific RNA that contains conserved repeats and is highly localized within the nucleus. Cell 1992; 71:527 - 42; http://dx.doi.org/10.1016/0092-8674(92)90520-M; PMID: 1423611
  • Siddiqi S, Matushansky I. Piwis and piwi-interacting RNAs in the epigenetics of cancer. J Cell Biochem 2012; 113:373 - 80; http://dx.doi.org/10.1002/jcb.23363; PMID: 21928326
  • Zhao J, Sun BK, Erwin JA, Song JJ, Lee JT. Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome. Science 2008; 322:750 - 6; http://dx.doi.org/10.1126/science.1163045; PMID: 18974356
  • Lind GE, Skotheim RI, Lothe RA. The epigenome of testicular germ cell tumors. APMIS 2007; 115:1147 - 60; http://dx.doi.org/10.1111/j.1600-0463.2007.apm_660.xml.x; PMID: 18042148
  • Li D, Feng J, Wu T, Wang Y, Sun Y, Ren J, Liu M. Long intergenic noncoding RNA HOTAIR is overexpressed and regulates PTEN methylation in laryngeal squamous cell carcinoma. Am J Pathol 2013; 182:64 - 70; http://dx.doi.org/10.1016/j.ajpath.2012.08.042; PMID: 23141928
  • Gupta RA, Shah N, Wang KC, Kim J, Horlings HM, Wong DJ, Tsai MC, Hung T, Argani P, Rinn JL, et al. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 2010; 464:1071 - 6; http://dx.doi.org/10.1038/nature08975; PMID: 20393566
  • He W, Wang Z, Wang Q, Fan Q, Shou C, Wang J, Giercksky KE, Nesland JM, Suo Z. Expression of HIWI in human esophageal squamous cell carcinoma is significantly associated with poorer prognosis. BMC Cancer 2009; 9:426; http://dx.doi.org/10.1186/1471-2407-9-426; PMID: 19995427

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