Roles of IncRNA in breast cancer

Frontiers in Bioscience - Scholar

Volumn 7S, Issue 1, 2015, Pages 94-108

  Liu, Yin ^a   Sharma, Sambad ^a   Watabe, Kounosuke ^a  

^a WAKE FOREST SCHOOL OF MEDICINE   (United States)

Author keywords

Breast cancer; Long non coding rnas

Indexed keywords

LONG UNTRANSLATED RNA; LSINCT5 PROTEIN; PROTEIN; SMAD7 PROTEIN; STEROID RECEPTOR; UNCLASSIFIED DRUG; ZFAS1 PROTEIN; FAL1 PROTEIN; GAS5 PROTEIN; RNA H19; SOX2OT PROTEIN; SRA PROTEIN; TRANSCRIPTION FACTOR SOX2; UCA1 PROTEIN; XIST PROTEIN;

ANCHORAGE INDEPENDENT GROWTH; APOPTOSIS; BREAST CANCER; BREAST EPITHELIUM CELL; CANCER CELL; CANCER GROWTH; CELL PROLIFERATION; CLONOGENESIS; EPIGENETICS; EXON; GENE EXPRESSION; GENE FUNCTION; HUMAN; METASTASIS; NONHUMAN; PROTEIN SYNTHESIS; REVIEW; RNA PROCESSING; RNA TRANSLATION; TRANSCRIPTION REGULATION; TUMOR INVASION; X CHROMOSOME INACTIVATION; ANIMAL; BREAST TUMOR; EXPERIMENTAL MAMMARY NEOPLASM; FEMALE; GENE EXPRESSION REGULATION; GENETICS; ARTICLE; CANCER INHIBITION; CANCER STEM CELL;

ANIMALS; BREAST NEOPLASMS; FEMALE; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; MAMMARY NEOPLASMS, EXPERIMENTAL; RNA, LONG NONCODING;

EID: 84931268799     PISSN: 19450516     EISSN: 19450524     Source Type: Journal    
DOI: 10.2741/427     Document Type: Review

References (107)

1. P. Kapranov, J. Cheng, S. Dike, D. A. Nix, R. Duttagupta, A. T. Willingham, P. F. Stadler, J. Hertel, J. Hackermuller, I. L. Hofacker, I. Bell, E. Cheung, J. Drenkow, E. Dumais, S. Patel, G. Helt, M. Ganesh, S. Ghosh, A. Piccolboni, V. Sementchenko, H. Tammana and T. R. Gingeras: RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science, 316(5830), 1484-8 (2007)
2. P. Carninci, T. Kasukawa, S. Katayama, J. Gough, M. C. Frith, N. Maeda, R. Oyama, T. Ravasi, B. Lenhard, C. Wells, R. Kodzius, K. Shimokawa, V. B. Bajic, S. E. Brenner, S. Batalov, et al.: The transcriptional landscape of the mammalian genome. Science, 309(5740), 1559-63 (2005)
3. M. Guttman, I. Amit, M. Garber, C. French, M. F. Lin, D. Feldser, M. Huarte, O. Zuk, B. W. Carey, J. P. Cassady, M. N. Cabili, R. Jaenisch, T. S. Mikkelsen, T. Jacks, N. Hacohen, B. E. Bernstein, M. Kellis, A. Regev, J. L. Rinn and E. S. Lander: Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature, 458(7235), 223-7 (2009) DOI: 10.1038/nature07672
4. M. B. Gerstein, A. Kundaje, M. Hariharan, S. G. Landt, K. K. Yan, C. Cheng, X. J. Mu, E. Khurana, J. Rozowsky, R. Alexander, R. Min, P. Alves, A. Abyzov, N. Addleman, N. Bhardwaj, A. P. Boyle, P. Cayting, A. Charos, D. Z. Chen, Y. Cheng, D. Clarke, C. Eastman, G. Euskirchen, S. Frietze, Y. Fu, J. Gertz, F. Grubert, A. Harmanci, P. Jain, M. Kasowski, P. Lacroute, J. Leng, J. Lian, H. Monahan, H. O'Geen, Z. Ouyang, E. C. Partridge, D. Patacsil, F. Pauli, D. Raha, L. Ramirez, T. E. Reddy, B. Reed, M. Shi, T. Slifer, J. Wang, L. Wu, X. Yang, K. Y. Yip, G. Zilberman-Schapira, S. Batzoglou, A. Sidow, P. J. Farnham, R. M. Myers, S. M. Weissman and M. Snyder: Architecture of the human regulatory network derived from ENCODE data. Nature, 489(7414), 91-100 (2012) DOI: 10.1038/nature11245
5. M. N. Cabili, C. Trapnell, L. Goff, M. Koziol, B. Tazon-Vega, A. Regev and J. L. Rinn: Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev, 25(18), 1915-27 (2011) DOI: 10.1101/gad.17446611
6. A. M. Khalil, M. Guttman, M. Huarte, M. Garber, A. Raj, D. Rivea Morales, K. Thomas, A. Presser, B. E. Bernstein, A. van Oudenaarden, A. Regev, E. S. Lander and J. L. Rinn: Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci U S A, 106(28), 11667-72 (2009) DOI: 10.1073/pnas.0904715106
7. P. P. Amaral, M. B. Clark, D. K. Gascoigne, M. E. Dinger and J. S. Mattick: lncRNAdb: a reference database for long noncoding RNAs. Nucleic Acids Res, 39(Database issue), D146-51 (2011) DOI: 10.1093/nar/gkq1138
8. B. E. Bernstein, A. Meissner and E. S. Lander: The mammalian epigenome. Cell, 128(4), 669-81 (2007)
9. S. B. Baylin and J. E. Ohm: Epigenetic gene silencing in cancer - a mechanism for early oncogenic pathway addiction? Nat Rev Cancer, 6(2), 107-16 (2006)
10. J. L. Rinn, M. Kertesz, J. K. Wang, S. L. Squazzo, X. Xu, S. A. Brugmann, L. H. Goodnough, J. A. Helms, P. J. Farnham, E. Segal and H. Y. Chang: Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell, 129(7), 1311-23 (2007)
11. J. T. Lee: Epigenetic regulation by long noncoding RNAs. Science, 338(6113), 1435-9 (2012) DOI: 10.1126/science.1231776
12. J. Tan, X. Yang, L. Zhuang, X. Jiang, W. Chen, P. L. Lee, R. K. Karuturi, P. B. Tan, E. T. Liu and Q. Yu: Pharmacologic disruption of Polycomb-repressive complex 2-mediated gene repression selectively induces apoptosis in cancer cells. Genes Dev, 21(9), 1050-63 (2007)
13. J. S. Mattick: The genetic signatures of noncoding RNAs. PLoS Genet, 5(4), e1000459 (2009) DOI: 10.1371/journal.pgen.1000459
14. C. Chu, K. Qu, F. L. Zhong, S. E. Artandi and H. Y. Chang: Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. Mol Cell, 44(4), 667-78 (2011) DOI: 10.1016/j.molcel.2011.08.027
15. Kuersten, E. Markenscoff-Papadimitriou, D. Kuhl, H. Bito, P. F. Worley, G. Kreiman and M. E. Greenberg: Widespread transcription at neuronal activity-regulated enhancers. Nature, 465(7295), 182-7 (2010) DOI: 10.1038/nature09033
16. D. Wang, I. Garcia-Bassets, C. Benner, W. Li, X. Su, Y. Zhou, J. Qiu, W. Liu, M. U. Kaikkonen, K. A. Ohgi, C. K. Glass, M. G. Rosenfeld and X. D. Fu: Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA. Nature, 474(7351), 390-4 (2011) DOI: 10.1038/nature10006
17. C. A. Melo, J. Drost, P. J. Wijchers, H. van de Werken, E. de Wit, J. A. Oude Vrielink, R. Elkon, S. A. Melo, N. Leveille, R. Kalluri, W. de Laat and R. Agami: eRNAs are required for p53-dependent enhancer activity and gene transcription. Mol Cell, 49(3), 524-35 (2013) DOI: 10.1016/j.molcel.2012.11.021
18. F. Yang, L. Zhang, X. S. Huo, J. H. Yuan, D. Xu, S. X. Yuan, N. Zhu, W. P. Zhou, G. S. Yang, Y. Z. Wang, J. L. Shang, C. F. Gao, F. R. Zhang, F. Wang and S. H. Sun: Long noncoding RNA high expression in hepatocellular carcinoma facilitates tumor growth through enhancer of zeste homolog 2 in humans. Hepatology, 54(5), 1679-89 (2011) DOI: 10.1002/hep.24563
19. U. A. Orom, T. Derrien, M. Beringer, K. Gumireddy, A. Gardini, G. Bussotti, F. Lai, M. Zytnicki, C. Notredame, Q. Huang, R. Guigo and R. Shiekhattar: Long noncoding RNAs with enhancer-like function in human cells. Cell, 143(1), 46-58 (2010) DOI: 10.1016/j.cell.2010.09.001
20. C. S. Bond and A. H. Fox: Paraspeckles: nuclear bodies built on long noncoding RNA. J Cell Biol, 186(5), 637-44 (2009) DOI: 10.1083/jcb.200906113
21. Y. S. Mao, H. Sunwoo, B. Zhang and D. L. Spector: Direct visualization of the co-transcriptional assembly of a nuclear body by noncoding RNAs. Nat Cell Biol, 13(1), 95-101 (2011) DOI: 10.1038/ncb2140
22. K. V. Prasanth, S. G. Prasanth, Z. Xuan, S. Hearn, S. M. Freier, C. F. Bennett, M. Q. Zhang and D. L. Spector: Regulating gene expression through RNA nuclear retention. Cell, 123(2), 249-63 (2005)
23. Y. T. Sasaki, T. Ideue, M. Sano, T. Mituyama and T. Hirose: MENepsilon/beta noncoding RNAs are essential for structural integrity of nuclear paraspeckles. Proc Natl Acad Sci U S A, 106(8), 2525-30 (2009) DOI: 10.1073/pnas.0807899106
24. C. M. Clemson, J. N. Hutchinson, S. A. Sara, A. W. Ensminger, A. H. Fox, A. Chess and J. B. Lawrence: An architectural role for a nuclear noncoding RNA: NEAT1 RNA is essential for the structure of paraspeckles. Mol Cell, 33(6), 717-26 (2009) DOI: 10.1016/j.molcel.2009.01.026
25. C. Carrieri, L. Cimatti, M. Biagioli, A. Beugnet, S. Zucchelli, S. Fedele, E. Pesce, I. Ferrer, L. Collavin, C. Santoro, A. R. Forrest, P. Carninci, S. Biffo, E. Stupka and S. Gustincich: Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat. Nature, 491(7424), 454-7 (2012) DOI: 10.1038/nature11508
26. J. H. Yoon, K. Abdelmohsen, S. Srikantan, X. Yang, J. L. Martindale, S. De, M. Huarte, M. Zhan, K. G. Becker and M. Gorospe: LincRNA-p21 suppresses target mRNA translation. Mol Cell, 47(4), 648-55 (2012) DOI: 10.1016/j.molcel.2012.06.027
27. G. Wu, J. Cai, Y. Han, J. Chen, Z. P. Huang, C. Chen, Y. Cai, H. Huang, Y. Yang, Y. Liu, Z. Xu, D. He, X. Zhang, X. Hu, L. Pinello, D. Zhong, F. He, G. C. Yuan, D. Z. Wang and C. Zeng: LincRNA-p21 Regulates Neointima Formation, Vascular Smooth Muscle Cell Proliferation, Apoptosis, and Atherosclerosis by Enhancing p53 Activity. Circulation, 130(17), 1452-65 (2014) DOI: 10.1161/CIRCULATIONAHA.114.011675
28. K. Wang, T. Sun, N. Li, Y. Wang, J. X. Wang, L. Y. Zhou, B. Long, C. Y. Liu, F. Liu and P. F. Li: MDRL lncRNA regulates the processing of miR-484 primary transcript by targeting miR-361. PLoS Genet, 10(7), e1004467 (2014) DOI: 10.1371/journal.pgen.1004467
29. J. Wang, C. Gong and L. E. Maquat: Control of myogenesis by rodent SINE-containing lncRNAs. Genes Dev, 27(7), 793-804 (2013) DOI: 10.1101/gad.212639.112
30. E. Park and L. E. Maquat: Staufen-mediated mRNA decay. Wiley Interdiscip Rev RNA, 4(4), 423-35 (2013) DOI: 10.1002/wrna.1168
31. J. H. Yuan, F. Yang, F. Wang, J. Z. Ma, Y. J. Guo, Q. F. Tao, F. Liu, W. Pan, T. T. Wang, C. C. Zhou, S. B. Wang, Y. Z. Wang, Y. Yang, N. Yang, W. P. Zhou, G. S. Yang and S. H. Sun: A long noncoding RNA activated by TGF-beta promotes the invasion-metastasis cascade in hepatocellular carcinoma. Cancer Cell, 25(5), 666-81 (2014) DOI: 10.1016/j.ccr.2014.03.010
32. I. Legnini, M. Morlando, A. Mangiavacchi, A. Fatica and I. Bozzoni: A feedforward regulatory loop between HuR and the long noncoding RNA linc-MD1 controls early phases of myogenesis. Mol Cell, 53(3), 506-14 (2014) DOI: 10.1016/j.molcel.2013.12.012
33. C. A. Edwards and A. C. Ferguson-Smith: Mechanisms regulating imprinted genes in clusters. Curr Opin Cell Biol, 19(3), 281-9 (2007)
34. A. Gabory, H. Jammes and L. Dandolo: The H19 locus: role of an imprinted non-coding RNA in growth and development. Bioessays, 32(6), 473-80 (2010) DOI: 10.1002/bies.200900170
35. R. Feil: Epigenetic asymmetry in the zygote and mammalian development. Int J Dev Biol, 53(2-3), 191-201 (2009) DOI: 10.1387/ijdb.082654rf
36. P. Monnier, C. Martinet, J. Pontis, I. Stancheva, S. Ait-Si-Ali and L. Dandolo: H19 lncRNA controls gene expression of the Imprinted Gene Network by recruiting MBD1. Proc Natl Acad Sci U S A, 110(51), 20693-8 (2013) DOI: 10.1073/pnas.1310201110
37. P. A. Jones and S. B. Baylin: The fundamental role of epigenetic events in cancer. Nat Rev Genet, 3(6), 415-28 (2002)
38. H. Cui, P. Onyango, S. Brandenburg, Y. Wu, C. L. Hsieh and A. P. Feinberg: Loss of imprinting in colorectal cancer linked to hypomethylation of H19 and IGF2. Cancer Res, 62(22), 6442-6 (2002)
39. K. Hibi, H. Nakamura, A. Hirai, Y. Fujikake, Y. Kasai, S. Akiyama, K. Ito and H. Takagi: Loss of H19 imprinting in esophageal cancer. Cancer Res, 56(3), 480-2 (1996)
40. S. Lottin, E. Adriaenssens, T. Dupressoir, N. Berteaux, C. Montpellier, J. Coll, T. Dugimont and J. J. Curgy: Overexpression of an ectopic H19 gene enhances the tumorigenic properties of breast cancer cells. Carcinogenesis, 23(11), 1885-95 (2002) DOI: 10.1093/carcin/23.11.1885
41. C. E. van Roozendaal, A. J. Gillis, J. G. Klijn, B. van Ooijen, C. J. Claassen, A. M. Eggermont, S. C. Henzen-Logmans, J. W. Oosterhuis, J. A. Foekens and L. H. Looijenga: Loss of imprinting of IGF2 and not H19 in breast cancer, adjacent normal tissue and derived fibroblast cultures. FEBS Lett, 437(1-2), 107-11 (1998)
42. N. Berteaux, S. Lottin, D. Monte, S. Pinte, B. Quatannens, J. Coll, H. Hondermarck, J. J. Curgy, T. Dugimont and E. Adriaenssens: H19 mRNA-like noncoding RNA promotes breast cancer cell proliferation through positive control by E2F1. J Biol Chem, 280(33), 29625-36 (2005)
43. D. Barsyte-Lovejoy, S. K. Lau, P. C. Boutros, F. Khosravi, I. Jurisica, I. L. Andrulis, M. S. Tsao and L. Z. Penn: The c-Myc oncogene directly induces the H19 noncoding RNA by allele-specific binding to potentiate tumorigenesis. Cancer Res, 66(10), 5330-7 (2006)
44. T. Yoshimizu, A. Miroglio, M. A. Ripoche, A. Gabory, M. Vernucci, A. Riccio, S. Colnot, C. Godard, B. Terris, H. Jammes and L. Dandolo: The H19 locus acts in vivo as a tumor suppressor. Proc Natl Acad Sci U S A, 105(34), 12417-22 (2008) DOI: 10.1073/pnas.0801540105
45. Y. Hao, T. Crenshaw, T. Moulton, E. Newcomb and B. Tycko: Tumour-suppressor activity of H19 RNA. Nature, 365(6448), 764-7 (1993) DOI: 10.1038/365764a0
46. A. N. Kallen, X. B. Zhou, J. Xu, C. Qiao, J. Ma, L. Yan, L. Lu, C. Liu, J. S. Yi, H. Zhang, W. Min, A. M. Bennett, R. I. Gregory, Y. Ding and Y. Huang: The imprinted H19 lncRNA antagonizes let-7 microRNAs. Mol Cell, 52(1), 101-12 (2013) DOI: 10.1016/j.molcel.2013.08.027
47. F. Yu, H. Yao, P. Zhu, X. Zhang, Q. Pan, C. Gong, Y. Huang, X. Hu, F. Su, J. Lieberman and E. Song: let-7 regulates self renewal and tumorigenicity of breast cancer cells. Cell, 131(6), 1109-23 (2007)
48. A. Keniry, D. Oxley, P. Monnier, M. Kyba, L. Dandolo, G. Smits and W. Reik: The H19 lincRNA is a developmental reservoir of miR-675 that suppresses growth and Igf1r. Nat Cell Biol, 14(7), 659-65 (2012) DOI: 10.1038/ncb2521
49. W. P. Tsang, E. K. Ng, S. S. Ng, H. Jin, J. Yu, J. J. Sung and T. T. Kwok: Oncofetal H19-derived miR-675 regulates tumor suppressor RB in human colorectal cancer. Carcinogenesis, 31(3), 350-8 (2010) DOI: 10.1093/carcin/bgp181
50. I. V. Novikova, S. P. Hennelly and K. Y. Sanbonmatsu: Structural architecture of the human long non-coding RNA, steroid receptor RNA activator. Nucleic Acids Res, 40(11), 5034-51 (2012) DOI: 10.1093/nar/gks071
51. J. Sharif, M. Muto, S. Takebayashi, I. Suetake, A. Iwamatsu, T. A. Endo, J. Shinga, Y. Mizutani-Koseki, T. Toyoda, K. Okamura, S. Tajima, K. Mitsuya, M. Okano and H. Koseki: The SRA protein Np95 mediates epigenetic inheritance by recruiting Dnmt1 to methylated DNA. Nature, 450(7171), 908-12 (2007)
52. G. P. Vicent, A. S. Nacht, R. Zaurin, J. Font-Mateu, D. Soronellas, F. Le Dily, D. Reyes and M. Beato: Unliganded progesterone receptor-mediated targeting of an RNA-containing repressive complex silences a subset of hormone-inducible genes. Genes Dev, 27(10), 1179-97 (2013) DOI: 10.1101/gad.215293.113
53. R. B. Lanz, N. J. McKenna, S. A. Onate, U. Albrecht, J. Wong, S. Y. Tsai, M. J. Tsai and B. W. O'Malley: A steroid receptor coactivator, SRA, functions as an RNA and is present in an SRC-1 complex. Cell, 97(1), 17-27 (1999)
54. C. Cooper, J. Guo, Y. Yan, S. Chooniedass-Kothari, F. Hube, M. K. Hamedani, L. C. Murphy, Y. Myal and E. Leygue: Increasing the relative expression of endogenous non-coding Steroid Receptor RNA Activator (SRA) in human breast cancer cells using modified oligonucleotides. Nucleic Acids Res, 37(13), 4518-31 (2009) DOI: 10.1093/nar/gkp441
55. S. M. Colley and P. J. Leedman: Steroid Receptor RNA Activator - A nuclear receptor coregulator with multiple partners: Insights and challenges. Biochimie, 93(11), 1966-72 (2011) DOI: 10.1016/j.biochi.2011.07.004
56. R. B. Lanz, S. S. Chua, N. Barron, B. M. Soder, F. DeMayo and B. W. O'Malley: Steroid receptor RNA activator stimulates proliferation as well as apoptosis in vivo. Mol Cell Biol, 23(20), 7163-76 (2003) DOI: 10.1128/MCB.23.20.7163-7176.2003
57. J. M. Silva, N. J. Boczek, M. W. Berres, X. Ma and D. I. Smith: LSINCT5 is over expressed in breast and ovarian cancer and affects cellular proliferation. RNA Biol, 8(3), 496-505 (2011)
58. G. Dieci, G. Fiorino, M. Castelnuovo, M. Teichmann and A. Pagano: The expanding RNA polymerase III transcriptome. Trends Genet, 23(12), 614-22 (2007)
59. M. E. Askarian-Amiri, J. Crawford, J. D. French, C. E. Smart, M. A. Smith, M. B. Clark, K. Ru, T. R. Mercer, E. R. Thompson, S. R. Lakhani, A. C. Vargas, I. G. Campbell, M. A. Brown, M. E. Dinger and J. S. Mattick: SNORD-host RNA Zfas1 is a regulator of mammary development and a potential marker for breast cancer. RNA, 17(5), 878-91 (2011) DOI: 10.1261/rna.2528811
60. M. Arase, K. Horiguchi, S. Ehata, M. Morikawa, S. Tsutsumi, H. Aburatani, K. Miyazono and D. Koinuma: Transforming growth factor-beta-induced lncRNA-Smad7 inhibits apoptosis of mouse breast cancer JygMC(A) cells. Cancer Sci, 105(8), 974-82 (2014) DOI: 10.1111/cas.12454
61. K. Augoff, B. McCue, E. F. Plow and K. Sossey-Alaoui: miR-31 and its host gene lncRNA LOC554202 are regulated by promoter hypermethylation in triple-negative breast cancer. Mol Cancer, 11, 5 (2012) DOI: 10.1186/1476-4598-11-5
62. Y. Shi, J. Lu, J. Zhou, X. Tan, Y. He, J. Ding, Y. Tian, L. Wang and K. Wang: Long non-coding RNA Loc554202 regulates proliferation and migration in breast cancer cells. Biochem Biophys Res Commun, 446(2), 448-53 (2014) DOI: 10.1016/j.bbrc.2014.02.144
63. S. Kaneko, G. Li, J. Son, C. F. Xu, R. Margueron, T. A. Neubert and D. Reinberg: Phosphorylation of the PRC2 component Ezh2 is cell cycle-regulated and up-regulates its binding to ncRNA. Genes Dev, 24(23), 2615-20 (2010) DOI: 10.1038/cddis.2013.541
64. S. He, S. Liu and H. Zhu: The sequence, structure and evolutionary features of HOTAIR in mammals. BMC Evol Biol, 11, 102 (2011) DOI: 10.1186/1471-2148-11-102
65. L. Wu, P. Murat, D. Matak-Vinkovic, A. Murrell and S. Balasubramanian: Binding interactions between long noncoding RNA HOTAIR and PRC2 proteins. Biochemistry, 52(52), 9519-27 (2013) DOI: 10.1021/bi401085h
66. R. Kogo, T. Shimamura, K. Mimori, K. Kawahara, S. Imoto, T. Sudo, F. Tanaka, K. Shibata, A. Suzuki, S. Komune, S. Miyano and M. Mori: Long noncoding RNA HOTAIR regulates polycomb-dependent chromatin modification and is associated with poor prognosis in colorectal cancers. Cancer Res, 71(20), 6320-6 (2011) DOI: 10.1158/0008-5472.CAN-11-1021
67. M. Cantile, G. Pettinato, A. Procino, I. Feliciello, L. Cindolo and C. Cillo: In vivo expression of the whole HOX gene network in human breast cancer. Eur J Cancer, 39(2), 257-64 (2003)
68. R. A. Gupta, N. Shah, K. C. Wang, J. Kim, H. M. Horlings, D. J. Wong, M. C. Tsai, T. Hung, P. Argani, J. L. Rinn, Y. Wang, P. Brzoska, B. Kong, R. Li, R. B. West, M. J. van de Vijver, S. Sukumar and H. Y. Chang: Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature, 464(7291), 1071-6 (2010) DOI: 10.1038/nature08975
69. K. P. Sorensen, M. Thomassen, Q. Tan, M. Bak, S. Cold, M. Burton, M. J. Larsen and T. A. Kruse: Long non-coding RNA HOTAIR is an independent prognostic marker of metastasis in estrogen receptor-positive primary breast cancer. Breast Cancer Res Treat, 142(3), 529-36 (2013) DOI: 10.1007/s10549-013-2776-7
70. K. M. Chisholm, Y. Wan, R. Li, K. D. Montgomery, H. Y. Chang and R. B. West: Detection of long non-coding RNA in archival tissue: correlation with polycomb protein expression in primary and metastatic breast carcinoma. PLoS ONE, 7(10), e47998 (2012) DOI: 10.1371/journal.pone.0047998
71. L. Lu, G. Zhu, C. Zhang, Q. Deng, D. Katsaros, S. T. Mayne, H. A. Risch, L. Mu, E. M. Canuto, G. Gregori, C. Benedetto and H. Yu: Association of large noncoding RNA HOTAIR expression and its downstream intergenic CpG island methylation with survival in breast cancer. Breast Cancer Res Treat, 136(3), 875-83 (2012) DOI: 10.1007/s10549-012-2314-z
72. P. P. Amaral, C. Neyt, S. J. Wilkins, M. E. Askarian-Amiri, S. M. Sunkin, A. C. Perkins and J. S. Mattick: Complex architecture and regulated expression of the Sox2ot locus during vertebrate development. RNA, 15(11), 2013-27 (2009) DOI: 10.1261/rna.1705309
73. M. E. Askarian-Amiri, V. Seyfoddin, C. E. Smart, J. Wang, J. E. Kim, H. Hansji, B. C. Baguley, G. J. Finlay and E. Y. Leung: Emerging role of long non-coding RNA SOX2OT in SOX2 regulation in breast cancer. PLoS ONE, 9(7), e102140 (2014) DOI: 10.1371/journal.pone.0102140
74. J. Yu, M. A. Vodyanik, K. Smuga-Otto, J. Antosiewicz-Bourget, J. L. Frane, S. Tian, J. Nie, G. A. Jonsdottir, V. Ruotti, R. Stewart, Slukvin, II and J. A. Thomson: Induced pluripotent stem cell lines derived from human somatic cells. Science, 318(5858), 1917-20 (2007)
75. X. Hu, Y. Feng, D. Zhang, S. D. Zhao, Z. Hu, J. Greshock, Y. Zhang, L. Yang, X. Zhong, L. P. Wang, S. Jean, C. Li, Q. Huang, D. Katsaros, K. T. Montone, J. L. Tanyi, Y. Lu, J. Boyd, K. L. Nathanson, H. Li, G. B. Mills and L. Zhang: A functional genomic approach identifies FAL1 as an oncogenic long noncoding RNA that associates with BMI1 and represses p21 expression in cancer. Cancer Cell, 26(3), 344-57 (2014) DOI: 10.1016/j.ccr.2014.07.009
76. J. Godlewski, M. O. Nowicki, A. Bronisz, S. Williams, A. Otsuki, G. Nuovo, A. Raychaudhury, H. B. Newton, E. A. Chiocca and S. Lawler: Targeting of the Bmi-1 oncogene/stem cell renewal factor by microRNA-128 inhibits glioma proliferation and self-renewal. Cancer Res, 68(22), 9125-30 (2008) DOI: 10.1158/0008-5472.CAN-08-2629
77. T. Kino, D. E. Hurt, T. Ichijo, N. Nader and G. P. Chrousos: Noncoding RNA gas5 is a growth arrest- and starvation-associated repressor of the glucocorticoid receptor. Sci Signal, 3(107), ra8 (2010) DOI: 10.1126/scisignal.2000568
78. C. Schneider, R. M. King and L. Philipson: Genes specifically expressed at growth arrest of mammalian cells. Cell, 54(6), 787-93 (1988)
79. M. Mourtada-Maarabouni, M. R. Pickard, V. L. Hedge, F. Farzaneh and G. T. Williams: GAS5, a non-protein-coding RNA, controls apoptosis and is downregulated in breast cancer. Oncogene, 28(2), 195-208 (2009) DOI: 10.1038/onc.2008.373
80. E. Ozgur, U. Mert, M. Isin, M. Okutan, N. Dalay and U. Gezer: Differential expression of long non-coding RNAs during genotoxic stress-induced apoptosis in HeLa and MCF-7 cells. Clin Exp Med, 13(2), 119-26 (2013) DOI: 10.1007/s10238-012-0181-x
81. H. L. Piao and L. Ma: Non-coding RNAs as regulators of mammary development and breast cancer. J Mammary Gland Biol Neoplasia, 17(1), 33-42 (2012) DOI: 10.1007/s10911-012-9245-5
82. Z. Zhang, Z. Zhu, K. Watabe, X. Zhang, C. Bai, M. Xu, F. Wu and Y. Y. Mo: Negative regulation of lncRNA GAS5 by miR-21. Cell Death Differ, 20(11), 1558-68 (2013) DOI: 10.1038/cdd.2013.110
83. F. Meng, R. Henson, H. Wehbe-Janek, K. Ghoshal, S. T. Jacob and T. PaTel: MicroRNA-21 regulates expression of the PTEN tumor suppressor gene in human hepatocellular cancer. Gastroenterology, 133(2), 647-58 (2007)
84. R. I. Gregory, T. P. Chendrimada, N. Cooch and R. Shiekhattar: Human RISC couples microRNA biogenesis and posttranscriptional gene silencing. Cell, 123(4), 631-40 (2005)
85. G. D. Penny, G. F. Kay, S. A. Sheardown, S. Rastan and N. Brockdorff: Requirement for Xist in X chromosome inactivation. Nature, 379(6561), 131-7 (1996) DOI: 10.1038/379131a0
86. Y. Jeon and J. T. Lee: YY1 tethers Xist RNA to the inactive X nucleation center. Cell, 146(1), 119-33 (2011) DOI: 10.1016/j.cell.2011.06.026
87. S. Ganesan, D. P. Silver, R. A. Greenberg, D. Avni, R. Drapkin, A. Miron, S. C. Mok, V. Randrianarison, S. Brodie, J. Salstrom, T. P. Rasmussen, A. Klimke, C. Marrese, Y. Marahrens, C. X. Deng, J. Feunteun and D. M. Livingston: BRCA1 supports XIST RNA concentration on the inactive X chromosome. Cell, 111(3), 393-405 (2002)
88. C. Xiao, J. A. Sharp, M. Kawahara, A. R. Davalos, M. J. Difilippantonio, Y. Hu, W. Li, L. Cao, K. Buetow, T. Ried, B. P. Chadwick, C. X. Deng and B. Panning: The XIST noncoding RNA functions independently of BRCA1 in X inactivation. Cell, 128(5), 977-89 (2007)
89. D. P. Silver, S. D. Dimitrov, J. Feunteun, R. Gelman, R. Drapkin, S. D. Lu, E. Shestakova, S. Velmurugan, N. Denunzio, S. Dragomir, J. Mar, X. Liu, S. Rottenberg, J. Jonkers, S. Ganesan and D. M. Livingston: Further evidence for BRCA1 communication with the inactive X chromosome. Cell, 128(5), 991-1002 (2007)
90. G. J. Pageau, L. L. Hall and J. B. Lawrence: BRCA1 does not paint the inactive X to localize XIST RNA but may contribute to broad changes in cancer that impact XIST and Xi heterochromatin. J Cell Biochem, 100(4), 835-50 (2007) DOI: 10.1002/jcb.21188
91. S. Ganesan, D. P. Silver, R. Drapkin, R. Greenberg, J. Feunteun and D. M. Livingston: Association of BRCA1 with the inactive X chromosome and XIST RNA. Philos Trans R Soc Lond B Biol Sci, 359(1441), 123-8 (2004) DOI: 10.1098/rstb.2003.1371
92. S. M. Sirchia, L. Ramoscelli, F. R. Grati, F. Barbera, D. Coradini, F. Rossella, G. Porta, E. Lesma, A. Ruggeri, P. Radice, G. Simoni and M. Miozzo: Loss of the inactive X chromosome and replication of the active X in BRCA1-defective and wild-type breast cancer cells. Cancer Res, 65(6), 2139-46 (2005) DOI: 10.1371/journal.pone.0005559
93. S. M. Sirchia, S. Tabano, L. Monti, M. P. Recalcati, M. Gariboldi, F. R. Grati, G. Porta, P. Finelli, P. Radice and M. Miozzo: Misbehaviour of XIST RNA in breast cancer cells. PLoS ONE, 4(5), e5559 (2009)
94. A. L. Richardson, Z. C. Wang, A. De Nicolo, X. Lu, M. Brown, A. Miron, X. Liao, J. D. Iglehart, D. M. Livingston and S. Ganesan: X chromosomal abnormalities in basal-like human breast cancer. Cancer Cell, 9(2), 121-32 (2006)
95. R. Maruyama, M. Shipitsin, S. Choudhury, Z. Wu, A. Protopopov, J. Yao, P. K. Lo, M. Bessarabova, A. Ishkin, Y. Nikolsky, X. S. Liu, S. Sukumar and K. Polyak: Altered antisense-to-sense transcript ratios in breast cancer. Proc Natl Acad Sci U S A, 109(8), 2820-4 (2012) DOI: 10.1073/pnas.1010559107
96. W. Zhao, J. Luo and S. Jiao: Comprehensive characterization of cancer subtype associated long non-coding RNAs and their clinical implications. Sci Rep, 4, 6591 (2014) DOI: 10.1038/srep06591
97. X. Su, G. G. Malouf, Y. Chen, J. Zhang, H. Yao, V. Valero, J. N. Weinstein, J. P. Spano, F. Meric-Bernstam, D. Khayat and F. J. Esteva: Comprehensive analysis of long non-coding RNAs in human breast cancer clinical subtypes. Oncotarget, 5(20), 9864-9876 (2014)
98. K. Reiche, K. Kasack, S. Schreiber, T. Luders, E. U. Due, B. Naume, M. Riis, V. N. Kristensen, F. Horn, A. L. Borresen-Dale, J. Hackermuller and L. O. Baumbusch: Long Non-Coding RNAs Differentially Expressed between Normal versus Primary Breast Tumor Tissues Disclose Converse Changes to Breast Cancer-Related Protein-Coding Genes. PLoS ONE, 9(9), e106076 (2014) DOI: 10.1371/journal.pone.0106076
99. P. T. Simpson, J. S. Reis-Filho, T. Gale and S. R. Lakhani: Molecular evolution of breast cancer. J Pathol, 205(2), 248-54 (2005) DOI: 10.1002/path.1691
100. S. Gout and J. Huot: Role of cancer microenvironment in metastasis: focus on colon cancer. Cancer Microenviron, 1(1), 69-83 (2008) DOI: 10.1007/s12307-008-0007-2
101. R. Spizzo, M. I. Almeida, A. Colombatti and G. A. Calin: Long non-coding RNAs and cancer: a new frontier of translational research? Oncogene, 31(43), 4577-87 (2012) DOI: 10.1038/onc.2011.621
102. X. Huang, T. Yuan, M. Tschannen, Z. Sun, H. Jacob, M. Du, M. Liang, R. L. Dittmar, Y. Liu, M. Kohli, S. N. Thibodeau, L. Boardman and L. Wang: Characterization of human plasma-derived exosomal RNAs by deep sequencing. BMC Genomics, 14, 319 (2013) DOI: 10.1186/1471-2164-14-319
103. J. R. Prensner, M. K. Iyer, O. A. Balbin, S. M. Dhanasekaran, Q. Cao, J. C. Brenner, B. Laxman, I. A. Asangani, C. S. Grasso, H. D. Kominsky, X. Cao, X. Jing, X. Wang, J. Siddiqui, J. T. Wei, D. Robinson, H. K. Iyer, N. Palanisamy, C. A. Maher and A. M. Chinnaiyan: Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression. Nat Biotechnol, 29(8), 742-9 (2011) DOI: 10.1038/nbt.1914
104. M. C. Lai, Z. Yang, L. Zhou, Q. Q. Zhu, H. Y. Xie, F. Zhang, L. M. Wu, L. M. Chen and S. S. Zheng: Long non-coding RNA MALAT-1 overexpression predicts tumor recurrence of hepatocellular carcinoma after liver transplantation. Med Oncol, 29(3), 1810-6 (2012) DOI: 10.1007/s12032-011-0004-z
105. R. J. Platt, S. Chen, Y. Zhou, M. J. Yim, L. Swiech, H. R. Kempton, J. E. Dahlman, O. Parnas, T. M. Eisenhaure, M. Jovanovic, D. B. Graham, S. Jhunjhunwala, M. Heidenreich, R. J. Xavier, R. Langer, D. G. Anderson, N. Hacohen, A. Regev, G. Feng, P. A. Sharp and F. Zhang: CRISPR-Cas9 Knockin Mice for Genome Editing and Cancer Modeling. Cell, 159(2), 440-55 (2014) DOI: 10.1016/j.eururo.2004.06.004
106. J. Han, J. Zhang, L. Chen, B. Shen, J. Zhou, B. Hu, Y. Du, P. H. Tate, X. Huang and W. Zhang: Efficient in vivo deletion of a large imprinted lncRNA by CRISPR/Cas9. RNA Biol, 11(7), 829-35 (2014) DOI: 10.1053/j.gastro.2006.08.026
107. Y. Niu, B. Shen, Y. Cui, Y. Chen, J. Wang, L. Wang, Y. Kang, X. Zhao, W. Si, W. Li, A. P. Xiang, J. Zhou, X. Guo, Y. Bi, C. Si, B. Hu, G. Dong, H. Wang, Z. Zhou, T. Li, T. Tan, X. Pu, F. Wang, S. Ji, Q. Zhou, X. Huang, W. Ji and J. Sha: Generation of gene-modified cynomolgus monkey via Cas9/RNA-mediated gene targeting in one-cell embryos. Cell, 156(4), 836-43 (2014) DOI: 10.1016/j.cell.2014.09.014