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http://dx.doi.org/10.5483/BMBRep.2012.45.11.227

Long noncoding RNA involvement in cancer  

Maruyama, Reo (Department of Molecular Biology, Sapporo Medical University)
Suzuki, Hiromu (Department of Molecular Biology, Sapporo Medical University)
Publication Information
BMB Reports / v.45, no.11, 2012 , pp. 604-611 More about this Journal
Abstract
Recent advances in genome and transcriptome analysis have enabled identification of numerous members of a new class of noncoding RNA, long noncoding RNA (lncRNA). lncRNAs are broadly defined as RNA molecules greater than 200 nt in length and lacking an open reading frame. Recent studies provide evidence that lncRNAs play central roles in a wide range of cellular processes through interaction with key component proteins in the gene regulatory system, and that alteration of their cell- or tissue-specific expression and/or their primary or secondary structures is thought to promote cell proliferation, invasion and metastasis. The biological and molecular characteristics of the large majority of lncRNAs remains unknown, and it is anticipated that improved understanding of the roles played by lncRNAs in cancer will lead to the development of novel biomarkers and effective therapeutic strategies.
Keywords
Biomarker; Cancer; Gene regulation; Histone modification; LincRNA; Long noncoding RNA; Oncogene; Tumor suppressor;
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1 Gabory, A., Ripoche, M. A., Yoshimizu, T. and Dandolo, L. (2006) The H19 gene: regulation and function of a non-coding RNA. Cytogenet. Genome Res. 113, 188-193.   DOI   ScienceOn
2 Gejman, R., Ansell, P. J., Zhao, J., Weng, C. and Klibanski, A. (2007) Activation of p53 by MEG3 non-coding RNA. J. Biol. Chem. 282, 24731-24742.   DOI   ScienceOn
3 Zhang, X., Gejman, R., Mahta, A., Zhong, Y., Rice, K. A., Zhou, Y., Cheunsuchon, P., Louis, D. N. and Klibanski, A. (2010) Maternally expressed gene 3, an imprinted noncoding RNA gene, is associated with meningioma pathogenesis and progression. Cancer Res. 70, 2350-2358.   DOI
4 Wang, J., Liu, X., Wu, H., Ni, P., Gu, Z., Qiao, Y., Chen, N., Sun, F. and Fan, Q. (2010) CREB up-regulates long non-coding RNA, HULC expression through interaction with microRNA-372 in liver cancer. Nucleic Acids Res. 38, 5366-5383.   DOI
5 Panzitt, K., Tschernatsch, M. M., Guelly, C., Moustafa, T., Stradner, M., Strohmaier, H. M., Buck, C. R., Denk, H., Schroeder, R., Trauner, M. and Zatloukal, K. (2007) Characterization of HULC, a novel gene with striking up-regulation in hepatocellular carcinoma, as noncoding RNA. Gastroenterology 132, 330-342.   DOI   ScienceOn
6 Tomlins, S. A., Aubin, S. M., Siddiqui, J., Lonigro, R. J., Sefton-Miller, L., Miick, S., Williamsen, S., Hodge, P., Meinke, J., Blase, A., Penabella, Y., Day, J. R., Varambally, R., Han, B., Wood, D., Wang, L., Sanda, M. G., Rubin, M. A., Rhodes, D. R., Hollenbeck, B., Sakamoto, K., Silberstein, J. L., Fradet, Y., Amberson, J. B., Meyers, S., Palanisamy, N., Rittenhouse, H., Wei, J. T., Groskopf, J. and Chinnaiyan, A. M. (2011) Urine TMPRSS2:ERG fusion transcript stratifies prostate cancer risk in men with elevated serum PSA. Sci. Transl. Med. 3, 94ra72.   DOI
7 Esteller, M. (2011) Non-coding RNAs in human disease. Nat. Rev. Genet. 12, 861-874.
8 Cabili, M. N., Trapnell, C., Goff, L., Koziol, M., Tazon-Vega, B., Regev, A. and Rinn, J. L. (2011) Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 25, 1915-1927.   DOI   ScienceOn
9 Mercer, T. R., Dinger, M. E., Sunkin, S. M., Mehler, M. F. and Mattick, J. S. (2008) Specific expression of long noncoding RNAs in the mouse brain. Proc. Natl. Acad. Sci. U.S.A. 105, 716-721.   DOI   ScienceOn
10 Hung, T., Wang, Y., Lin, M. F., Koegel, A. K., Kotake, Y., Grant, G. D., Horlings, H. M., Shah, N., Umbricht, C., Wang, P., Kong, B., Langerod, A., Borresen-Dale, A. L., Kim, S. K., van de Vijver, M., Sukumar, S., Whitfield, M. L., Kellis, M., Xiong, Y., Wong, D. J. and Chang, H. Y. (2011) Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters. Nat. Genet. 43, 621-629.   DOI   ScienceOn
11 Gutschner, T. and Diederichs, S. (2012) The Hallmarks of Cancer: A long non-coding RNA point of view. RNA Biol. 9, 703-719. doi: 10.4161/rna.20481.   DOI
12 Wang, K. C. and Chang, H. Y. (2011) Molecular mechanisms of long noncoding RNAs. Mol. Cell 43, 904-914.   DOI   ScienceOn
13 Zhao, J., Sun, B. K., Erwin, J. A., Song, J. J. and Lee, J. T. (2008) Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome. Science 322, 750-756.   DOI   ScienceOn
14 Gupta, R. A., Shah, N., Wang, K. C., Kim, J., Horlings, H. M., Wong, D. J., Tsai, M. C., Hung, T., Argani, P., Rinn, J. L., Wang, Y., Brzoska, P., Kong, B., Li, R., West, R. B., van de Vijver, M. J., Sukumar, S. and Chang, H. Y. (2010) Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 464, 1071-1076.   DOI   ScienceOn
15 Nagano, T., Mitchell, J. A., Sanz, L. A., Pauler, F. M., Ferguson-Smith, A. C., Feil, R. and Fraser, P. (2008) The Air noncoding RNA epigenetically silences transcription by targeting G9a to chromatin. Science 322, 1717-1720.   DOI   ScienceOn
16 Wang, K. C., Yang, Y. W., Liu, B., Sanyal, A., Corces- Zimmerman, R., Chen, Y., Lajoie, B. R., Protacio, A., Flynn, R. A., Gupta, R. A., Wysocka, J., Lei, M., Dekker, J., Helms, J. A. and Chang, H. Y. (2011) A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature 472, 120-124.   DOI   ScienceOn
17 Huarte, M., Guttman, M., Feldser, D., Garber, M., Koziol, M. J., Kenzelmann-Broz, D., Khalil, A. M., Zuk, O., Amit, I., Rabani, M., Attardi, L. D., Regev, A., Lander, E. S., Jacks, T. and Rinn, J. L. (2010) A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell 142, 409-419.   DOI   ScienceOn
18 Niland, C. N., Merry, C. R. and Khalil, A. M. (2012) Emerging roles for long non-coding rnas in cancer and neurological disorders. Front Genet. 3, 25.
19 Chu, C., Qu, K., Zhong, F. L., Artandi, S. E. and Chang, H. Y. (2011) Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. Mol. Cell 44, 667-678.   DOI   ScienceOn
20 Yap, K. L., Li, S., Munoz-Cabello, A. M., Raguz, S., Zeng, L., Mujtaba, S., Gil, J., Walsh, M. J. and Zhou, M. M. (2010) Molecular interplay of the noncoding RNA ANRIL and methylated histone H3 lysine 27 by polycomb CBX7 in transcriptional silencing of INK4a. Mol. Cell 38, 662-674.   DOI   ScienceOn
21 Tsai, M. C., Manor, O., Wan, Y., Mosammaparast, N., Wang, J. K., Lan, F., Shi, Y., Segal, E. and Chang, H. Y. (2010) Long noncoding RNA as modular scaffold of histone modification complexes. Science 329, 689-693.   DOI   ScienceOn
22 Kotake, Y., Nakagawa, T., Kitagawa, K., Suzuki, S., Liu, N., Kitagawa, M. and Xiong, Y. (2011) Long non-coding RNA ANRIL is required for the PRC2 recruitment to and silencing of p15(INK4B) tumor suppressor gene. Oncogene 30, 1956-1962.   DOI   ScienceOn
23 Pandey, R. R., Mondal, T., Mohammad, F., Enroth, S., Redrup, L., Komorowski, J., Nagano, T., Mancini-Dinardo, D. and Kanduri, C. (2008) Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation. Mol. Cell 32, 232-246.   DOI   ScienceOn
24 A. W., Fox, A. H., Chess, A. and Lawrence, J. B. (2009) An architectural role for a nuclear noncoding RNA: NEAT1 RNA is essential for the structure of paraspeckles. Mol. Cell 33, 717-726.   DOI   ScienceOn
25 Khalil, A. M., Guttman, M., Huarte, M., Garber, M., Raj, A., Rivea Morales, D., Thomas, K., Presser, A., Bernstein, B. E., van Oudenaarden, A., Regev, A., Lander, E. S. and Rinn, J. L. (2009) Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc. Natl. Acad. Sci. U.S.A. 106, 11667-11672.   DOI   ScienceOn
26 Guttman, M., Donaghey, J., Carey, B. W., Garber, M., Grenier, J. K., Munson, G., Young, G., Lucas, A. B., Ach, R., Bruhn, L., Yang, X., Amit, I., Meissner, A., Regev, A., Rinn, J. L., Root, D. E. and Lander, E. S. (2011) lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature 477, 295-300.   DOI   ScienceOn
27 Kino, T., Hurt, D. E., Ichijo, T., Nader, N. and Chrousos, G. P. (2010) Noncoding RNA gas5 is a growth arrest- and starvation- associated repressor of the glucocorticoid receptor. Sci. Signal. 3, ra8.   DOI   ScienceOn
28 Song, M. S., Carracedo, A., Salmena, L., Song, S. J., Egia, A., Malumbres, M. and Pandolfi, P. P. (2011) Nuclear PTEN regulates the APC-CDH1 tumor-suppressive complex in a phosphatase-independent manner. Cell 144, 187-199.   DOI   ScienceOn
29 Redon, S., Reichenbach, P. and Lingner, J. (2010) The non-coding RNA TERRA is a natural ligand and direct inhibitor of human telomerase. Nucleic Acids Res. 38, 5797-5806.   DOI
30 Poliseno, L., Salmena, L., Zhang, J., Carver, B., Haveman, W. J. and Pandolfi, P. P. (2010) A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature 465, 1033-1038.   DOI   ScienceOn
31 Rinn, J. L., Kertesz, M., Wang, J. K., Squazzo, S. L., Xu, X., Brugmann, S. A., Goodnough, L. H., Helms, J. A., Farnham, P. J., Segal, E. and Chang, H. Y. (2007) Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 129, 1311-1323.   DOI   ScienceOn
32 Yang, Z., Zhou, L., Wu, L. M., Lai, M. C., Xie, H. Y., Zhang, F. and Zheng, S. S. (2011) Overexpression of long non-coding rna hotair predicts tumor recurrence in hepatocellular carcinoma patients following liver transplantation. Ann. Surg. Oncol. 18, 1243-1250.   DOI
33 Kogo, R., Shimamura, T., Mimori, K., Kawahara, K., Imoto, S., Sudo, T., Tanaka, F., Shibata, K., Suzuki, A., Komune, S., Miyano, S. and Mori, M. (2011) Long noncoding RNA HOTAIR regulates polycomb-dependent chromatin modification and is associated with poor prognosis in colorectal cancers. Cancer Res. 71, 6320-6326.   DOI
34 Kim, K., Jutooru, I., Chadalapaka, G., Johnson, G., Frank, J., Burghardt, R., Kim, S. and Safe, S. (2012) HOTAIR is a negative prognostic factor and exhibits pro-oncogenic activity in pancreatic cancer. Oncogene [Epub ahead of print].
35 Popov, N. and Gil, J. (2010) Epigenetic regulation of the INK4b-ARF-INK4a locus: in sickness and in health. Epigenetics 5, 685-690.   DOI
36 Niinuma, T., Suzuki, H., Nojima, M., Nosho, K., Yamamoto, H., Takamaru, H., Yamamoto, E., Maruyama, R., Nobuoka, T., Miyazaki, Y., Nishida, T., Bamba, T., Kanda, T., Ajioka, Y., Taguchi, T., Okahara, S., Takahashi, H., Nishida, Y., Hosokawa, M., Hasegawa, T., Tokino, T., Hirata, K., Imai, K., Toyota, M. and Shinomura, Y. (2012) Upregulation of miR-196a and HOTAIR drive malignant character in gastrointestinal stromal tumors. Cancer Res. 72, 1126-1136.   DOI
37 Pasmant, E., Laurendeau, I., Heron, D., Vidaud, M., Vidaud, D. and Bieche, I. (2007) Characterization of a germ-line deletion, including the entire INK4/ARF locus, in a melanoma-neural system tumor family: identification of ANRIL, an antisense noncoding RNA whose expression coclusters with ARF. Cancer Res. 67, 3963-3969.   DOI   ScienceOn
38 Yu, W., Gius, D., Onyango, P., Muldoon-Jacobs, K., Karp, J., Feinberg, A. P. and Cui, H. (2008) Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA. Nature 451, 202-206.   DOI   ScienceOn
39 Iacobucci, I., Sazzini, M., Garagnani, P., Ferrari, A., Boattini, A., Lonetti, A., Papayannidis, C., Mantovani, V., Marasco, E., Ottaviani, E., Soverini, S., Girelli, D., Luiselli, D., Vignetti, M., Baccarani, M. and Martinelli, G. (2011) A polymorphism in the chromosome 9p21 ANRIL locus is associated to Philadelphia positive acute lymphoblastic leukemia. Leuk. Res. 35, 1052-1059.   DOI   ScienceOn
40 Pasmant, E., Sabbagh, A., Masliah-Planchon, J., Ortonne, N., Laurendeau, I., Melin, L., Ferkal, S., Hernandez, L., Leroy, K., Valeyrie-Allanore, L., Parfait, B., Vidaud, D., Bieche, I., Lantieri, L., Wolkenstein, P. and Vidaud, M. (2011) Role of noncoding RNA ANRIL in genesis of plexiform neurofibromas in neurofibromatosis type 1. J. Natl. Cancer Inst. 103, 1713-1722.   DOI   ScienceOn
41 Pasmant, E., Sabbagh, A., Vidaud, M. and Bieche, I. (2011) ANRIL, a long, noncoding RNA, is an unexpected major hotspot in GWAS. FASEB J. 25, 444-448.   DOI   ScienceOn
42 Muller-Tidow, C., Diederichs, S., Thomas, M. and Serve, H. (2004) Genome-wide screening for prognosis-predicting genes in early-stage non-small-cell lung cancer. Lung Cancer 45(Suppl 2), S145-150.   DOI   ScienceOn
43 Ji, P., Diederichs, S., Wang, W., Boing, S., Metzger, R., Schneider, P. M., Tidow, N., Brandt, B., Buerger, H., Bulk, E., Thomas, M., Berdel, W. E., Serve, H. and Muller-Tidow, C. (2003) MALAT-1, a novel noncoding RNA and thymosin beta4 predict metastasis and survival in early-stage non-small cell lung cancer. Oncogene 22, 8031-8041.   DOI   ScienceOn
44 Yamada, K., Kano, J., Tsunoda, H., Yoshikawa, H., Okubo, C., Ishiyama, T. and Noguchi, M. (2006) Phenotypic characterization of endometrial stromal sarcoma of the uterus. Cancer Sci. 97, 106-112.   DOI   ScienceOn
45 Lin, R., Maeda, S., Liu, C., Karin, M. and Edgington, T. S. (2007) A large noncoding RNA is a marker for murine hepatocellular carcinomas and a spectrum of human carcinomas. Oncogene 26, 851-858.   DOI   ScienceOn
46 Tano, K., Mizuno, R., Okada, T., Rakwal, R., Shibato, J., Masuo, Y., Ijiri, K. and Akimitsu, N. (2010) MALAT-1 enhances cell motility of lung adenocarcinoma cells by influencing the expression of motility-related genes. FEBS Lett. 584, 4575-4580.   DOI   ScienceOn
47 Tripathi, V., Ellis, J. D., Shen, Z., Song, D. Y., Pan, Q., Watt, A. T., Freier, S. M., Bennett, C. F., Sharma, A., Bubulya, P. A., Blencowe, B. J., Prasanth, S. G. and Prasanth, K. V. (2010) The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. Mol. Cell 39, 925-938.   DOI   ScienceOn
48 Prensner, J. R., Iyer, M. K., Balbin, O. A., Dhanasekaran, S. M., Cao, Q., Brenner, J. C., Laxman, B., Asangani, I. A., Grasso, C. S., Kominsky, H. D., Cao, X., Jing, X., Wang, X., Siddiqui, J., Wei, J. T., Robinson, D., Iyer, H. K., Palanisamy, N., Maher, C. A. and Chinnaiyan, A. M. (2011) Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression. Nat. Biotechnol. 29, 742-749.   DOI   ScienceOn
49 Mourtada-Maarabouni, M., Pickard, M. R., Hedge, V. L., Farzaneh, F. and Williams, G. T. (2009) GAS5, a non-protein-coding RNA, controls apoptosis and is downregulated in breast cancer. Oncogene 28, 195-208.   DOI   ScienceOn
50 Schneider, C., King, R. M. and Philipson, L. (1988) Genes specifically expressed at growth arrest of mammalian cells. Cell 54, 787-793.   DOI   ScienceOn
51 Morrison, L. E., Jewell, S. S., Usha, L., Blondin, B. A., Rao, R. D., Tabesh, B., Kemper, M., Batus, M. and Coon, J. S. (2007) Effects of ERBB2 amplicon size and genomic alterations of chromosomes 1, 3 and 10 on patient response to trastuzumab in metastatic breast cancer. Genes Chromosomes Cancer 46, 397-405.   DOI   ScienceOn
52 Smedley, D., Sidhar, S., Birdsall, S., Bennett, D., Herlyn, M., Cooper, C. and Shipley, J. (2000) Characterization of chromosome 1 abnormalities in malignant melanomas. Genes Chromosomes Cancer 28, 121-125.   DOI
53 Luo, J. H., Ren, B., Keryanov, S., Tseng, G. C., Rao, U. N., Monga, S. P., Strom, S., Demetris, A. J., Nalesnik, M., Yu, Y. P., Ranganathan, S. and Michalopoulos, G. K. (2006) Transcriptomic and genomic analysis of human hepatocellular carcinomas and hepatoblastomas. Hepatology 44, 1012-1024.
54 Petrovics, G., Zhang, W., Makarem, M., Street, J. P., Connelly, R., Sun, L., Sesterhenn, I. A., Srikantan, V., Moul, J. W. and Srivastava, S. (2004) Elevated expression of PCGEM1, a prostate-specific gene with cell growth-promoting function, is associated with high-risk prostate cancer patients. Oncogene 23, 605-611.   DOI   ScienceOn
55 Srikantan, V., Zou, Z., Petrovics, G., Xu, L., Augustus, M., Davis, L., Livezey, J. R., Connell, T., Sesterhenn, I. A., Yoshino, K., Buzard, G. S., Mostofi, F. K., McLeod, D. G., Moul, J. W. and Srivastava, S. (2000) PCGEM1, a prostate-specific gene, is overexpressed in prostate cancer. Proc. Natl. Acad. Sci. U.S.A. 97, 12216-12221.   DOI   ScienceOn
56 Yu, M., Ohira, M., Li, Y., Niizuma, H., Oo, M. L., Zhu, Y., Ozaki, T., Isogai, E., Nakamura, Y., Koda, T., Oba, S., Yu, B. and Nakagawara, A. (2009) High expression of ncRAN, a novel non-coding RNA mapped to chromosome 17q25.1, is associated with poor prognosis in neuroblastoma. Int. J. Oncol. 34, 931-938.
57 Braconi, C., Valeri, N., Kogure, T., Gasparini, P., Huang, N., Nuovo, G. J., Terracciano, L., Croce, C. M. and Patel, T. (2011) Expression and functional role of a transcribed noncoding RNA with an ultraconserved element in hepatocellular carcinoma. Proc. Natl. Acad. Sci. U.S.A. 108, 786-791.   DOI   ScienceOn
58 Calin, G. A., Liu, C. G., Ferracin, M., Hyslop, T., Spizzo, R., Sevignani, C., Fabbri, M., Cimmino, A., Lee, E. J., Wojcik, S. E., Shimizu, M., Tili, E., Rossi, S., Taccioli, C., Pichiorri, F., Liu, X., Zupo, S., Herlea, V., Gramantieri, L., Lanza, G., Alder, H., Rassenti, L., Volinia, S., Schmittgen, T. D., Kipps, T. J., Negrini, M. and Croce, C. M. (2007) Ultraconserved regions encoding ncRNAs are altered in human leukemias and carcinomas. Cancer Cell 12, 215-229.   DOI   ScienceOn
59 Khaitan, D., Dinger, M. E., Mazar, J., Crawford, J., Smith, M. A., Mattick, J. S. and Perera, R. J. (2011) The melanoma-upregulated long noncoding RNA SPRY4-IT1 modulates apoptosis and invasion. Cancer Res. 71, 3852-3862.   DOI
60 Zhu, Y., Yu, M., Li, Z., Kong, C., Bi, J., Li, J. and Gao, Z. (2011) ncRAN, a newly identified long noncoding RNA, enhances human bladder tumor growth, invasion and survival. Urology 77, 510.e1-5.   DOI   ScienceOn
61 Chung, S., Nakagawa, H., Uemura, M., Piao, L., Ashikawa, K., Hosono, N., Takata, R., Akamatsu, S., Kawaguchi, T., Morizono, T., Tsunoda, T., Daigo, Y., Matsuda, K., Kamatani, N., Nakamura, Y. and Kubo, M. (2011) Association of a novel long non-coding RNA in 8q24 with prostate cancer susceptibility. Cancer Sci. 102, 245-252.   DOI   ScienceOn
62 Matouk, I. J., DeGroot, N., Mezan, S., Ayesh, S., Abu-lail, R., Hochberg, A. and Galun, E. (2007) The H19 non-coding RNA is essential for human tumor growth. PLoS One 2, e845.   DOI