Long non-coding RNA: a new player in cancer

Davidson EH, Britten RJ: Regulation of gene expression: possible role of repetitive sequences. Science. 1979, 204 (4397): 1052-1059. 10.1126/science.451548. Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE: Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007, 447 (7146): 799-816. 10.1038/nature05874. Mercer TR, Dinger ME, Mattick JS: Long non-coding RNAs: insights into functions. Nat Rev Genet. 2009, 10 (3): 155-159. 10.1038/nrg2521. Wu Q, Kim YC, Lu J, Xuan Z, Chen J, Zheng Y, Zhou T, Zhang MQ, Wu CI, Wang SM: Poly A-transcripts expressed in HeLa cells. PLoS One. 2008, 3 (7): e2803-10.1371/journal.pone.0002803. Ponting CP, Oliver PL, Reik W: Evolution and functions of long noncoding RNAs. Cell. 2009, 136 (4): 629-641. 10.1016/j.cell.2009.02.006. Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG: The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res. 2012, 22 (9): 1775-1789. 10.1101/gr.132159.111. Mizutani R, Wakamatsu A, Tanaka N, Yoshida H, Tochigi N, Suzuki Y, Oonishi T, Tani H, Tano K, Ijiri K: Identification and characterization of novel genotoxic stress-inducible nuclear long noncoding RNAs in mammalian cells. PLoS One. 2012, 7 (4): e34949-10.1371/journal.pone.0034949. Klattenhoff CA, Scheuermann JC, Surface LE, Bradley RK, Fields PA, Steinhauser ML, Ding H, Butty VL, Torrey L, Haas S: Braveheart, a long noncoding RNA required for cardiovascular lineage commitment. Cell. 2013, 152 (3): 570-583. 10.1016/j.cell.2013.01.003. Dinger ME, Amaral PP, Mercer TR, Pang KC, Bruce SJ, Gardiner BB, Askarian-Amiri ME, Ru K, Soldà G, Simons C: Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Res. 2008, 18 (9): 1433-1445. 10.1101/gr.078378.108. Willingham AT, Orth AP, Batalov S, Peters EC, Wen BG, Aza-Blanc P, Hogenesch JB, Schultz PG: A strategy for probing the function of noncoding RNAs finds a repressor of NFAT. Science. 2005, 309 (5740): 1570-1573. 10.1126/science.1115901. Tripathi V, Ellis JD, Shen Z, Song DY, Pan Q, Watt AT, Freier SM, Bennett CF, Sharma A, Bubulya PA: The nuclearretained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. Mol Cell. 2010, 39 (6): 925-938. 10.1016/j.molcel.2010.08.011. Cabianca DS, Casa V, Bodega B, Xynos A, Ginelli E, Tanaka Y, Gabellini D: A long ncRNA links copy number variation to a polycomb/trithorax epigenetic switch in FSHD muscular dystrophy. Cell. 2012, 149 (4): 819-831. 10.1016/j.cell.2012.03.035. Gong C, Maquat LE: lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3′ UTRs via Alu elements. Nature. 2011, 470 (7333): 284-288. 10.1038/nature09701. Meola N, Pizzo M, Alfano G, Surace EM, Banfi S: The long noncoding RNA Vax2os1 controls the cell cycle progression of photoreceptor progenitors in the mouse retina. RNA. 2012, 18 (1): 111-123. 10.1261/rna.029454.111. Hung T, Wang Y, Lin MF, Koegel AK, Kotake Y, Grant GD, Horlings HM, Shah N, Umbricht C, Wang P: Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters. Nat Genet. 2011, 43 (7): 621-629. 10.1038/ng.848. Gupta RA, Shah N, Wang KC, Kim J, Horlings HM, Wong DJ, Tsai MC, Hung T, Argani P, Rinn JL: Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature. 2010, 464 (7291): 1071-1076. 10.1038/nature08975. Kino T, Hurt DE, Ichijo T, Nader N, Chrousos GP: Noncoding RNA gas5 is a growth arrest- and starvation-associated repressor of the glucocorticoid receptor. Sci Signal. 2010, 3 (107): ra8-10.1126/scisignal.2000568. Prensner JR, Chinnaiyan AM: The emergence of lncRNAs in cancer biology. Cancer Discov. 2011, 1 (5): 391-407. 10.1158/2159-8290.CD-11-0209. Qi P, Du X: The long non-coding RNAs, a new cancer diagnostic and therapeutic gold mine. Mod Pathol. 2013, 26 (2): 155-165. 10.1038/modpathol.2012.160. Bartel DP: MicroRNAs: genomics, biogenesis, mechanism, and function. Cell. 2004, 116 (2): 281-297. 10.1016/S0092-8674(04)00045-5. Pang KC, Frith MC, Mattick JS: Rapid evolution of noncoding RNAs: lack of conservation does not mean lack of function. Trends Genet. 2006, 22 (1): 1-5. 10.1016/j.tig.2005.10.003. Koziol MJ, Rinn JL: RNA traffic control of chromatin complexes. Curr Opin Genet Dev. 2010, 20 (2): 142-148. 10.1016/j.gde.2010.03.003. 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 (5902): 750-756. 10.1126/science.1163045. Nagano T, Mitchell JA, Sanz LA, Pauler FM, Ferguson-Smith AC, Feil R, Fraser P: The Air noncoding RNA epigenetically silences transcription by targeting G9a to chromatin. Science. 2008, 322 (5908): 1717-1720. 10.1126/science.1163802. Pandey RR, Mondal T, Mohammad F, Enroth S, Redrup L, Komorowski J, Nagano T, Mancini-Dinardo D, Kanduri C: Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level control. Mol Cell. 2008, 32 (2): 232-246. 10.1016/j.molcel.2008.08.022. Wang KC, Yang YW, Liu B, Sanyal A, Corces-Zimmerman R, Chen Y, Lajoie BR, Protacio A, Flynn RA, Gupta RA: A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature. 2011, 472 (7341): 120-124. 10.1038/nature09819. Prensner JR, Iyer MK, Balbin OA, Dhanasekaran SM, Cao Q, Brenner JC, Laxman B, Asangani IA, Grasso CS, Kominsky HD: Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression. Nat Biotechnol. 2011, 29 (8): 742-749. 10.1038/nbt.1914. Tian D, Sun S, Lee JT: The long noncoding RNA, Jpx, is a molecular switch for X chromosome inactivation. Cell. 2010, 143 (3): 390-403. 10.1016/j.cell.2010.09.049. Huarte M, Guttman M, Feldser D, Garber M, Koziol MJ, Kenzelmann-Broz D, Khalil AM, Zuk O, Amit I, Rabani M: A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell. 2010, 142 (3): 409-419. 10.1016/j.cell.2010.06.040. Hawkins PG, Morris KV: Transcriptional regulation of Oct4 by a long non-coding RNA antisense to Oct4-pseudogene 5. Transcription. 2010, 1 (3): 165-175. 10.4161/trns.1.3.13332. Yap KL, Li S, Muñoz-Cabello AM, Raguz S, Zeng L, Mujtaba S, Gil J, Walsh MJ, Zhou MM: Molecular interplay of the noncoding RNA ANRIL and methylated histone H3 lysine 27 by polycomb CBX7 in transcriptional silencing of INK4a. Mol Cell. 2010, 38 (5): 662-674. 10.1016/j.molcel.2010.03.021. Kotake Y, Nakagawa T, Kitagawa K, Suzuki S, Liu N, Kitagawa M, Xiong Y: Long non-coding RNA ANRIL is required for the PRC2 recruitment to and silencing of p15 (INK4B) tumor suppressor gene. Oncogene. 2011, 30 (16): 1956-1962. 10.1038/onc.2010.568. Clemson CM, Hutchinson JN, Sara SA, Ensminger AW, Fox AH, Chess A, Lawrence JB: An architectural role for a nuclear noncoding RNA: NEAT1 RNA is essential for the structure of paraspeckles. Mol Cell. 2009, 33 (6): 717-726. 10.1016/j.molcel.2009.01.026. Khalil AM, Guttman M, Huarte M, Garber M, Raj A, Rivea Morales D, Thomas K, Presser A, Bernstein BE, van Oudenaarden A: Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci USA. 2009, 106 (28): 11667-11672. 10.1073/pnas.0904715106. Preker P, Nielsen J, Kammler S, Lykke-Andersen S, Christensen MS, Mapendano CK, Schierup MH, Jensen TH: RNA exosome depletion reveals transcription upstream of active human promoters. Science. 2008, 322 (5909): 1851-1854. 10.1126/science.1164096. Kim TK, Hemberg M, Gray JM, Costa AM, Bear DM, Wu J, Harmin DA, Laptewicz M, Barbara-Haley K, Kuersten S: Widespread transcription at neuronal activity-regulated enhancers. Nature. 2010, 465 (7295): 182-187. 10.1038/nature09033. Faghihi MA, Modarresi F, Khalil AM, Wood DE, Sahagan BG, Morgan TE, Finch CE, St Laurent G, Kenny PJ, Wahlestedt C: Expression of a noncoding RNA is elevated in Alzheimer’s disease and drives rapid feed-forward regulation of beta-secretase. Nat Med. 2008, 14 (7): 723-730. 10.1038/nm1784. Korneev SA, Park JH, O’Shea M: Neuronal expression of neural nitric oxide synthase (nNOS) protein is suppressed by an antisense RNA transcribed from an NOS pseudogene. J Neurosci. 1999, 19 (18): 7711-7720. Cesana M, Cacchiarelli D, Legnini I, Santini T, Sthandier O, Chinappi M, Tramontano A, Bozzoni I: A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA. Cell. 2011, 147 (2): 358-369. 10.1016/j.cell.2011.09.028. Poliseno L, Salmena L, Zhang J, Carver B, Haveman WJ, Pandolfi PP: A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature. 2010, 465 (7301): 1033-1038. 10.1038/nature09144. Gibb EA, Vucic EA, Enfield KS, Stewart GL, Lonergan KM, Kennett JY, Becker-Santos DD, MacAulay CE, Lam S, Brown CJ: Human cancer long non-coding RNA transcriptomes. PLoS One. 2011, 6 (10): e25915-10.1371/journal.pone.0025915. Yuan SX, Yang F, Yang Y, Tao QF, Zhang J, Huang G, Yang Y, Wang RY, Yang S, Huo XS: Long noncoding RNA associated with microvascular invasion in hepatocellular carcinoma promotes angiogenesis and serves as a predictor for hepatocellular carcinoma patients’ poor recurrence-free survival after hepatectomy. Hepatology. 2012, 56 (6): 2231-2241. 10.1002/hep.25895. de Kok JB, Verhaegh GW, Roelofs RW, Hessels D, Kiemeney LA, Aalders TW, Swinkels DW, Schalken JA: DD3 (PCA3), a very sensitive and specific marker to detect prostate tumors. Cancer Res. 2002, 62 (9): 2695-2698. Geng YJ, Xie SL, Li Q, Ma J, Wang GY: Large intervening non-coding RNA HOTAIR is associated with hepatocellular carcinoma progression. J Int Med Res. 2011, 39 (6): 2119-2128. 10.1177/147323001103900608. Ishibashi M, Kogo R, Shibata K, Sawada G, Takahashi Y, Kurashige J, Akiyoshi S, Sasaki S, Iwaya T, Sudo T: Clinical significance of the expression of long non-coding RNA HOTAIR in primary hepatocellular carcinoma. Oncol Rep. 2013, 29 (3): 946-950. Kogo R, Shimamura T, Mimori K, Kawahara K, Imoto S, Sudo T, Tanaka F, Shibata K, Suzuki A, Komune S: Long noncoding RNA HOTAIR regulates polycomb-dependent chromatin modification and is associated with poor prognosis in colorectal cancers. Cancer Res. 2011, 71 (20): 6320-6326. 10.1158/0008-5472.CAN-11-1021. Niinuma T, Suzuki H, Nojima M, Nosho K, Yamamoto H, Takamaru H, Yamamoto E, Maruyama R, Nobuoka T, Miyazaki Y: Upregulation of miR-196a and HOTAIR drive malignant character in gastrointestinal stromal tumors. Cancer Res. 2012, 72 (5): 1126-1136. 10.1158/0008-5472.CAN-11-1803. Tsai MC, Manor O, Wan Y, Mosammaparast N, Wang JK, Lan F, Shi Y, Segal E, Chang HY: Long noncoding RNA as modular scaffold of histone modification complexes. Science. 2010, 329 (5992): 689-693. 10.1126/science.1192002. Müller-Tidow C, Diederichs S, Thomas M, Serve H: Genome-wide screening for prognosis-predicting genes in early-stage non-small-cell lung cancer. Lung Cancer. 2004, 45 (Suppl 2): 145-150. Schmidt LH, Spieker T, Koschmieder S, Schäffers S, Humberg J, Jungen D, Bulk E, Hascher A, Wittmer D, Marra A: The long noncoding MALAT-1 RNA indicates a poor prognosis in non-small cell lung cancer and induces migration and tumor growth. J Thorac Oncol. 2011, 6 (12): 1984-1992. 10.1097/JTO.0b013e3182307eac. Lai MC, Yang Z, Zhou L, Zhu QQ, Xie HY, Zhang F, Wu LM, Chen LM, Zheng SS: Long non-coding RNA MALAT-1 overexpression predicts tumor recurrence of hepatocellular carcinoma after liver transplantation. Med Oncol. 2012, 29 (3): 1810-1816. 10.1007/s12032-011-0004-z. Gutschner T, Hämmerle M, Diederichs S: MALAT1 - a paradigm for long noncoding RNA function in cancer. J Mol Med (Berl). 2013, 10.1007/s00109-013-1028-y. 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 (3): 577-586. 10.1093/carcin/bgs381. 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 (9): e845-10.1371/journal.pone.0000845. Gibb EA, Brown CJ, Lam WL: The functional role of long non-coding RNA in human carcinomas. Mol Cancer. 2011, 10: 38-10.1186/1476-4598-10-38. Braconi C, Valeri N, Kogure T, Gasparini P, Huang N, Nuovo GJ, Terracciano L, Croce CM, Patel T: Expression and functional role of a transcribed noncoding RNA with an ultraconserved element in hepatocellular carcinoma. Proc Natl Acad Sci USA. 2011, 108 (2): 786-791. 10.1073/pnas.1011098108. Flockhart RJ, Webster DE, Qu K, Mascarenhas N, Kovalski J, Kretz M, Khavari PA: BRAFV600E remodels the melanocyte transcriptome and induces BANCR to regulate melanoma cell migration. Genome Res. 2012, 22 (6): 1006-1014. 10.1101/gr.140061.112. Yang F, Yi F, Zheng Z, Ling Z, Ding J, Guo J, Mao W, Wang X, Wang X, Ding X: Characterization of a carcinogenesis-associated long non-coding RNA. RNA Biol. 2012, 9 (1): 110-116. Ellis BC, Molloy PL, Graham LD: CRNDE: A Long Non-Coding RNA Involved in CanceR, Neurobiology, and DEvelopment. Front Genet. 2012, 3: 270- Yang F, Xue X, Bi J, Zheng L, Zhi K, Gu Y, Fang G: Long noncoding RNA CCAT1, which could be, promotes the progression of gastric carcinoma. J Cancer Res Clin Oncol. 2013, 139 (3): 437-445. 10.1007/s00432-012-1324-x. Du Y, Kong G, You X, Zhang S, Zhang T, Gao Y, Ye L, Zhang X: Elevation of highly up-regulated in liver cancer (HULC) by hepatitis B virus X protein promotes hepatoma cell proliferation via down-regulating p18. Biol Chem. 2012, 287 (31): 26302-26311. 10.1074/jbc.M112.342113. Wang Y, Chen W, Yang C, Wu W, Wu S, Qin X, Li X: Long non-coding RNA UCA1a(CUDR) promotes proliferation and tumorigenesis of bladder cancer. Int J Oncol. 2012, 41 (1): 276-284. Mourtada-Maarabouni M, Pickard MR, Hedge VL, Farzaneh F, Williams GT: GAS5, a non-protein-coding RNA, controls apoptosis and is downregulated in breast cancer. Oncogene. 2009, 28 (2): 195-208. 10.1038/onc.2008.373. Zhang X, Gejman R, Mahta A, Zhong Y, Rice KA, Zhou Y, Cheunsuchon P, Louis DN, Klibanski A: Maternally expressed gene 3, an imprinted noncoding RNA gene, is associated with meningioma pathogenesis and progression. Cancer Res. 2010, 70 (6): 2350-2358. 10.1158/0008-5472.CAN-09-3885. Wang P, Ren Z, Sun P: Overexpression of the long non-coding RNA MEG3 impairs in vitro glioma cell proliferation. J Cell Biochem. 2012, 113 (6): 1868-1874. 10.1002/jcb.24055. Braconi C, Kogure T, Valeri N, Huang N, Nuovo G, Costinean S, Negrini M, Miotto E, Croce CM, Patel T: microRNA-29 can regulate expression of the long non-coding RNA gene MEG3 in hepatocellular cancer. Oncogene. 2011, 30 (47): 4750-4756. 10.1038/onc.2011.193. Benetatos L, Hatzimichael E, Dasoula A, Dranitsaris G, Tsiara S, Syrrou M, Georgiou I, Bourantas KL: CpG methylation analysis of the MEG3 and SNRPN imprinted genes in acute myeloid leukemia and myelodysplastic syndromes. Leuk Res. 2010, 34 (2): 148-153. 10.1016/j.leukres.2009.06.019. Jendrzejewski J, He H, Radomska HS, Li W, Tomsic J, Liyanarachchi S, Davuluri RV, Nagy R, de la Chapelle A: The polymorphism rs944289 predisposes to papillary thyroid carcinoma through a large intergenic noncoding RNA gene of tumor suppressor type. Proc Natl Acad Sci USA. 2012, 109 (22): 8646-8651. 10.1073/pnas.1205654109. Pasmant E, Sabbagh A, Masliah-Planchon J, Ortonne N, Laurendeau I, Melin L, Ferkal S, Hernandez L, Leroy K, Valeyrie-Allanore L: Role of noncoding RNA ANRIL in genesis of plexiform neurofibromas in neurofibromatosis type 1. J Natl Cancer Inst. 2011, 103 (22): 1713-1722. 10.1093/jnci/djr416. Liu Y, Pan S, Liu L, Zhai X, Liu J, Wen J, Zhang Y, Chen J, Shen H, Hu Z: A genetic variant in long non-coding RNA HULC contributes to risk of HBV-related hepatocellular carcinoma in a Chinese population. PLoS One. 2012, 7 (4): e35145-10.1371/journal.pone.0035145. Zhu Z, Gao X, He Y, Zhao H, Yu Q, Jiang D, Zhang P, Ma X, Huang H, Dong D: An insertion/deletion polymorphism within RERT-lncRNA modulates hepatocellular carcinoma risk. Cancer Res. 2012, 72 (23): 6163-6172. 10.1158/0008-5472.CAN-12-0010. Xue Y, Wang M, Kang M, Wang Q, Wu B, Chu H, Zhong D, Qin C, Yin C, Zhang Z: Association between lncrna PCGEM1 polymorphisms and prostate cancer risk. Prostate Cancer Prostatic Dis. 2013, 10.1038/pcan.2013.6. Wang J, Liu X, Wu H, Ni P, Gu Z, Qiao Y, Chen N, Sun F, Fan Q: CREB up-regulates long non-coding RNA, HULC expression through interaction with microRNA-372 in liver cancer. Nucleic Acids Res. 2010, 38 (16): 5366-5383. 10.1093/nar/gkq285. Park BJ, Kang JW, Lee SW, Choi SJ, Shin YK, Ahn YH, Choi YH, Choi D, Lee KS, Kim S: The haploinsufficient tumor suppressor p18 upregulates p53 via interactions with ATM/ATR. Cell. 2005, 120 (2): 209-221. 10.1016/j.cell.2004.11.054. Yang C, Li X, Wang Y, Zhao L, Chen W: Long non-coding RNA UCA1 regulated cell cycle distribution via CREB through PI3-K dependent pathway in bladder carcinoma cells. Gene. 2012, 496 (1): 8-16. 10.1016/j.gene.2012.01.012. Han L, Zhang K, Shi Z, Zhang J, Zhu J, Zhu S, Zhang A, Jia Z, Wang G, Yu S: LncRNA profile of glioblastoma reveals the potential role of lncRNAs in contributing to glioblastoma pathogenesis. Int J Oncol. 2012, 40 (6): 2004-2012. Tahira AC, Kubrusly MS, Faria MF, Dazzani B, Fonseca RS, Maracaja-Coutinho V, Verjovski-Almeida S, Machado MC, Reis EM: Long noncoding intronic RNAs are differentially expressed in primary and metastatic pancreatic cancer. Mol Cancer. 2011, 10: 141-10.1186/1476-4598-10-141.