LncRNA: A link between RNA and cancer

Biochimica et Biophysica Acta - Gene Regulatory Mechanisms

Volumn 1839, Issue 11, 2014, Pages 1097-1109

  Yang, Guodong ^a   Lu, Xiaozhao ^b   Yuan, Lijun ^c  

^a FOURTH MILITARY MEDICAL UNIVERSITY   (China)

^b The 323 Hospital of PLA   (China)

^c FOURTH MILITARY MEDICAL UNIVERSITY   (China)

Author keywords

Cancer; Cancer diagnosis and therapy; Epigenetics; Long non coding RNAs; Posttranscriptional regulation; Transcriptional regulation

Indexed keywords

LONG UNTRANSLATED RNA; MESSENGER RNA; MICRORNA; SMALL UNTRANSLATED RNA; RNA; TUMOR MARKER;

ARTICLE; CANCER CELL; CANCER DIAGNOSIS; CANCER GROWTH; CANCER RISK; CANCER THERAPY; CARCINOGENESIS; CHROMATIN; GENE CONTROL; GENE EXPRESSION; GENE FUNCTION; HUMAN; INTERACTIONS WITH RNA; METASTASIS; NEOPLASM; NONHUMAN; RNA SEQUENCE; TRANSCRIPTION REGULATION; ANIMAL; CELL TRANSFORMATION; GENE EXPRESSION REGULATION; GENETICS; MOLECULAR DIAGNOSIS; MOLECULARLY TARGETED THERAPY; NEOPLASMS; PHYSIOLOGY; PROCEDURES;

ANIMALS; CELL TRANSFORMATION, NEOPLASTIC; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; MOLECULAR DIAGNOSTIC TECHNIQUES; MOLECULAR TARGETED THERAPY; NEOPLASMS; RNA; RNA, LONG NONCODING; TUMOR MARKERS, BIOLOGICAL;

EID: 84907500489     PISSN: 18749399     EISSN: 18764320     Source Type: Journal    
DOI: 10.1016/j.bbagrm.2014.08.012     Document Type: Review

References (153)

1. Crick F.H., Barnett L., Brenner S., Watts-Tobin R.J. General nature of the genetic code for proteins. Nature 1961, 192:1227-1232.
2. Carninci P., Hayashizaki Y. Noncoding RNA transcription beyond annotated genes. Curr. Opin. Genet. Dev. 2007, 17:139-144.
3. Eddy S.R. Noncoding RNA genes. Curr. Opin. Genet. Dev. 1999, 9:695-699.
4. Griffiths-Jones S. Annotating noncoding RNA genes. Annu. Rev. Genomics Hum. Genet. 2007, 8:279-298.
5. Pauli A., Rinn J.L., Schier A.F. Non-coding RNAs as regulators of embryogenesis. Nat. Rev. Genet. 2011, 12:136-149.
6. Brown C.J., Hendrich B.D., Rupert J.L., Lafreniere R.G., Xing Y., Lawrence J., Willard H.F. The human XIST gene: analysis of a 17kb inactive X-specific RNA that contains conserved repeats and is highly localized within the nucleus. Cell 1992, 71:527-542.
7. Feil R., Walter J., Allen N.D., Reik W. Developmental control of allelic methylation in the imprinted mouse Igf2 and H19 genes. Development 1994, 120:2933-2943.
8. Bernstein B.E., Birney E., Dunham I., Green E.D., Gunter C., Snyder M. An integrated encyclopedia of DNA elements in the human genome. Nature 2012, 489:57-74.
9. Derrien T., Johnson R., Bussotti G., Tanzer A., Djebali S., Tilgner H., Guernec G., Martin D., Merkel A., Knowles D.G., Lagarde J., Veeravalli L., Ruan X., Ruan Y., Lassmann T., Carninci P., Brown J.B., Lipovich L., Gonzalez J.M., Thomas M., Davis C.A., Shiekhattar R., Gingeras T.R., Hubbard T.J., Notredame C., Harrow J., Guigo R. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res. 2012, 22:1775-1789.
10. Mercer T.R., Dinger M.E., Mattick J.S. Long non-coding RNAs: insights into functions. Nat. Rev. Genet. 2009, 10:155-159.
11. Tsai M.C., Spitale R.C., Chang H.Y. Long intergenic noncoding RNAs: new links in cancer progression. Cancer Res. 2011, 71:3-7.
12. Volders P.J., Helsens K., Wang X., Menten B., Martens L., Gevaert K., Vandesompele J., Mestdagh P. LNCipedia: a database for annotated human lncRNA transcript sequences and structures. Nucleic Acids Res. 2013, 41:D246-D251.
13. Guttman M., Amit I., Garber M., French C., Lin M.F., Feldser D., Huarte M., Zuk O., Carey B.W., Cassady J.P., Cabili M.N., Jaenisch R., Mikkelsen T.S., Jacks T., Hacohen N., Bernstein B.E., Kellis M., Regev A., Rinn J.L., Lander E.S. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 2009, 458:223-227.
14. Qureshi I.A., Mehler M.F. Emerging roles of non-coding RNAs in brain evolution, development, plasticity and disease. Nat. Rev. Neurosci. 2012, 13:528-541.
15. Sati S., Ghosh S., Jain V., Scaria V., Sengupta S. Genome-wide analysis reveals distinct patterns of epigenetic features in long non-coding RNA loci. Nucleic Acids Res. 2012, 40:10018-10031.
16. 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., Rinn J.L. A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell 2010, 142:409-419.
17. Anno Y.N., Myslinski E., Ngondo-Mbongo R.P., Krol A., Poch O., Lecompte O., Carbon P. Genome-wide evidence for an essential role of the human Staf/ZNF143 transcription factor in bidirectional transcription. Nucleic Acids Res. 2011, 39:3116-3127.
18. Hiller M., Findeiss S., Lein S., Marz M., Nickel C., Rose D., Schulz C., Backofen R., Prohaska S.J., Reuter G., Stadler P.F. Conserved introns reveal novel transcripts in Drosophila melanogaster. Genome Res. 2009, 19:1289-1300.
19. Kageyama Y., Kondo T., Hashimoto Y. Coding vs non-coding: translatability of short ORFs found in putative non-coding transcripts. Biochimie 2011, 93:1981-1986.
20. Candeias M.M. The can and can't dos of p53 RNA. Biochimie 2011, 93:1962-1965.
21. Cooper C., Vincett D., Yan Y., Hamedani M.K., Myal Y., Leygue E. Steroid receptor RNA activator bi-faceted genetic system: heads or Tails?. Biochimie 2011, 93:1973-1980.
22. Rinn J.L., Chang H.Y. Genome regulation by long noncoding RNAs. Annu. Rev. Biochem. 2012, 81:145-166.
23. Hung T., Chang H.Y. Long noncoding RNA in genome regulation: prospects and mechanisms. RNA Biol. 2010, 7:582-585.
24. Yang Y., Zhou X., Jin Y. ADAR-mediated RNA editing in non-coding RNA sequences. Sci China Life Sci 2013, 56:944-952.
25. Beltran M., Puig I., Pena C., Garcia J.M., Alvarez A.B., Pena R., Bonilla F., de Herreros A.G. A natural antisense transcript regulates Zeb2/Sip1 gene expression during Snail1-induced epithelial-mesenchymal transition. Genes Dev. 2008, 22:756-769.
26. 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., Prasanth K.V. The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. Mol. Cell 2010, 39:925-938.
27. Jalali S., Jayaraj G.G., Scaria V. Integrative transcriptome analysis suggest processing of a subset of long non-coding RNAs to small RNAs. Biol. Direct 2012, 7:25.
28. Steck E., Boeuf S., Gabler J., Werth N., Schnatzer P., Diederichs S., Richter W. Regulation of H19 and its encoded microRNA-675 in osteoarthritis and under anabolic and catabolic in vitro conditions. J. Mol. Med. (Berl) 2012, 90:1185-1195.
29. Augoff K., McCue B., Plow E.F., Sossey-Alaoui K. miR-31 and its host gene lncRNA LOC554202 are regulated by promoter hypermethylation in triple-negative breast cancer. Mol. Cancer 2012, 11:5.
30. Wilusz J.E., Freier S.M., Spector D.L. 3' end processing of a long nuclear-retained noncoding RNA yields a tRNA-like cytoplasmic RNA. Cell 2008, 135:919-932.
31. Ebert M.S., Sharp P.A. Emerging roles for natural microRNA sponges. Curr. Biol. 2010, 20:R858-R861.
32. Jeggari A., Marks D.S., Larsson E. miRcode: a map of putative microRNA target sites in the long non-coding transcriptome. Bioinformatics 2012, 28:2062-2063.
33. 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, 38:5366-5383.
34. Ioffe Y.J., Chiappinelli K.B., Mutch D.G., Zighelboim I., Goodfellow P.J. Phosphatase and tensin homolog (PTEN) pseudogene expression in endometrial cancer: a conserved regulatory mechanism important in tumorigenesis?. Gynecol. Oncol. 2012, 124:340-346.
35. Poliseno L., Salmena L., Zhang J., Carver B., Haveman W.J., Pandolfi P.P. A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature 2010, 465:1033-1038.
36. Hansen T.B., Wiklund E.D., Bramsen J.B., Villadsen S.B., Statham A.L., Clark S.J., Kjems J. miRNA-dependent gene silencing involving Ago2-mediated cleavage of a circular antisense RNA. EMBO J. 2011, 30:4414-4422.
37. Yoon J.H., Abdelmohsen K., Srikantan S., Yang X., Martindale J.L., De S., Huarte M., Zhan M., Becker K.G., Gorospe M. LincRNA-p21 suppresses target mRNA translation. Mol. Cell 2012, 47:648-655.
38. Faghihi M.A., Zhang M., Huang J., Modarresi F., Van der Brug M.P., Nalls M.A., Cookson M.R., St-Laurent G., Wahlestedt C. Evidence for natural antisense transcript-mediated inhibition of microRNA function. Genome Biol. 2010, 11:R56.
39. Gong C., Maquat L.E. lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3' UTRs via Alu elements. Nature 2011, 470:284-288.
40. Carrieri C., Cimatti L., Biagioli M., Beugnet A., Zucchelli S., Fedele S., Pesce E., Ferrer I., Collavin L., Santoro C., Forrest A.R., Carninci P., Biffo S., Stupka E., Gustincich S. Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat. Nature 2012, 491:454-457.
41. Huarte M. LncRNAs have a say in protein translation. Cell Res. 2013, 23:449-451.
42. Wang X., Arai S., Song X., Reichart D., Du K., Pascual G., Tempst P., Rosenfeld M.G., Glass C.K., Kurokawa R. Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription. Nature 2008, 454:126-130.
43. Yao H., Brick K., Evrard Y., Xiao T., Camerini-Otero R.D., Felsenfeld G. Mediation of CTCF transcriptional insulation by DEAD-box RNA-binding protein p68 and steroid receptor RNA activator SRA. Genes Dev. 2010, 24:2543-2555.
44. Tsai M.C., Manor O., Wan Y., Mosammaparast N., Wang J.K., Lan F., Shi Y., Segal E., Chang H.Y. Long noncoding RNA as modular scaffold of histone modification complexes. Science 2010, 329:689-693.
45. Zhao J., Sun B.K., Erwin J.A., Song J.J., Lee J.T. Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome. Science 2008, 322:750-756.
46. Kino T., Hurt D.E., Ichijo T., Nader N., Chrousos G.P. Noncoding RNA gas5 is a growth arrest- and starvation-associated repressor of the glucocorticoid receptor. Sci. Signal. 2010, 3:ra8.
47. 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., Chang H.Y. Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters. Nat. Genet. 2011, 43:621-629.
48. Wapinski O., Chang H.Y. Long noncoding RNAs and human disease. Trends Cell Biol. 2011, 21:354-361.
49. Pasic I., Shlien A., Durbin A.D., Stavropoulos D.J., Baskin B., Ray P.N., Novokmet A., Malkin D. Recurrent focal copy-number changes and loss of heterozygosity implicate two noncoding RNAs and one tumor suppressor gene at chromosome 3q13.31 in osteosarcoma. Cancer Res. 2010, 70:160-171.
50. Higashimoto K., Soejima H., Saito T., Okumura K., Mukai T. Imprinting disruption of the CDKN1C/KCNQ1OT1 domain: the molecular mechanisms causing Beckwith-Wiedemann syndrome and cancer. Cytogenet. Genome Res. 2006, 113:306-312.
51. Poliseno L., Haimovic A., Christos P.J., Vega Y.S.d.M.E.C., Shapiro R., Pavlick A., Berman R.S., Darvishian F., Osman I. Deletion of PTENP1 pseudogene in human melanoma. J. Invest. Dermatol. 2011, 131:2497-2500.
52. 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., Nakagawara A. High expression of ncRAN, a novel non-coding RNA mapped to chromosome 17q25.1, is associated with poor prognosis in neuroblastoma. Int. J. Oncol. 2009, 34:931-938.
53. Akrami R., Jacobsen A., Hoell J., Schultz N., Sander C., Larsson E. Comprehensive analysis of long non-coding RNAs in ovarian cancer reveals global patterns and targeted DNA amplification. PLoS ONE 2013, 8:e80306.
54. Cabianca D.S., 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, 149:819-831.
55. Cabianca D.S., Casa V., Gabellini D. A novel molecular mechanism in human genetic disease: a DNA repeat-derived lncRNA point-of-view. RNA Biol. 2012, 9.
56. Jendrzejewski J., He H., Radomska H.S., Li W., Tomsic J., Liyanarachchi S., Davuluri R.V., 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. U. S. A. 2012, 109:8646-8651.
57. 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., Kubo M. Association of a novel long non-coding RNA in 8q24 with prostate cancer susceptibility. Cancer Sci. 2011, 102:245-252.
58. 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:e35145.
59. Zhang X., Zhou L., Fu G., Sun F., Shi J., Wei J., Lu C., Zhou C., Yuan Q., Yang M. The identification of an ESCC susceptibility SNP rs920778 that regulates the expression of lncRNA HOTAIR via a novel intronic enhancer. Carcinogenesis 2014, [Epub ahead of print].
60. Shen J., Ambrosone C.B., DiCioccio R.A., Odunsi K., Lele S.B., Zhao H. A functional polymorphism in the miR-146a gene and age of familial breast/ovarian cancer diagnosis. Carcinogenesis 2008, 29:1963-1966.
61. Autuoro J.M., Pirnie S.P., Carmichael G.G. Long noncoding RNAs in imprinting and X chromosome inactivation. Biomolecules 2014, 4:76-100.
62. Chen B., Yu M., Chang Q., Lu Y., Thakur C., Ma D., Yi Z., Chen F. Mdig de-represses H19 large intergenic non-coding RNA (lincRNA) by down-regulating H3K9me3 and heterochromatin. Oncotarget 2013, 4:1427-1437.
63. Wijnen M., Alders M., Zwaan C.M., Wagner A., van den Heuvel-Eibrink M.M. KCNQ1OT1 hypomethylation: a novel disguised genetic predisposition in sporadic pediatric adrenocortical tumors?. Pediatr. Blood Cancer 2012, 59:565-566.
64. Weksberg R., Nishikawa J., Caluseriu O., Fei Y.L., Shuman C., Wei C., Steele L., Cameron J., Smith A., Ambus I., Li M., Ray P.N., Sadowski P., Squire J. Tumor development in the Beckwith-Wiedemann syndrome is associated with a variety of constitutional molecular 11p15 alterations including imprinting defects of KCNQ1OT1. Hum. Mol. Genet. 2001, 10:2989-3000.
65. Nakano S., Murakami K., Meguro M., Soejima H., Higashimoto K., Urano T., Kugoh H., Mukai T., Ikeguchi M., Oshimura M. Expression profile of LIT1/KCNQ1OT1 and epigenetic status at the KvDMR1 in colorectal cancers. Cancer Sci. 2006, 97:1147-1154.
66. Benetatos L., Vartholomatos G., Hatzimichael E. MEG3 imprinted gene contribution in tumorigenesis. Int. J. Cancer 2011, 129:773-779.
67. Yuan J.H., Yang F., Wang F., Ma J.Z., Guo Y.J., Tao Q.F., Liu F., Pan W., Wang T.T., Zhou C.C., Wang S.B., Wang Y.Z., Yang Y., Yang N., Zhou W.P., Yang G.S., Sun S.H. A long noncoding RNA activated by TGF-beta promotes the invasion-metastasis cascade in hepatocellular carcinoma. Cancer Cell 2014, 25:666-681.
68. Cayre A., Rossignol F., Clottes E., Penault-Llorca F. aHIF but not HIF-1alpha transcript is a poor prognostic marker in human breast cancer. Breast Cancer Res. 2003, 5:R223-R230.
69. Rossignol F., Vache C., Clottes E. Natural antisense transcripts of hypoxia-inducible factor 1alpha are detected in different normal and tumour human tissues. Gene 2002, 299:135-140.
70. Span P.N., Rao J.U., Oude Ophuis S.B., Lenders J.W., Sweep F.C., Wesseling P., Kusters B., van Nederveen F.H., de Krijger R.R., Hermus A.R., Timmers H.J. Overexpression of the natural antisense hypoxia-inducible factor-1alpha transcript is associated with malignant pheochromocytoma/paraganglioma. Endocrinol. Relat. Cancer 2011, 18:323-331.
71. Thrash-Bingham C.A., Tartof K.D. aHIF: a natural antisense transcript overexpressed in human renal cancer and during hypoxia. J. Natl. Cancer Inst. 1999, 91:143-151.
72. Zolk O., Solbach T.F., Eschenhagen T., Weidemann A., Fromm M.F. Activation of negative regulators of the hypoxia-inducible factor (HIF) pathway in human end-stage heart failure. Biochem. Biophys. Res. Commun. 2008, 376:315-320.
73. Matouk I.J., 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.
74. Barsyte-Lovejoy D., Lau S.K., Boutros P.C., Khosravi F., Jurisica I., Andrulis I.L., Tsao M.S., Penn L.Z. The c-Myc oncogene directly induces the H19 noncoding RNA by allele-specific binding to potentiate tumorigenesis. Cancer Res. 2006, 66:5330-5337.
75. 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. J. Biol. Chem. 2012, 287:26302-26311.
76. Braconi C., Kogure T., Valeri N., Huang N., Nuovo G., Costinean S., Negrini M., Miotto E., Croce C.M., Patel T. microRNA-29 can regulate expression of the long non-coding RNA gene MEG3 in hepatocellular cancer. Oncogene 2011, 30:4750-4756.
77. Hanahan D., Weinberg R.A. Hallmarks of cancer: the next generation. Cell 2011, 144:646-674.
78. Yang G., Lu X., Fu H., Jin L., Yao L., Lu Z. Concerns about targeting cancer stem cell for cancer therapy. Med. Hypotheses 2011, 76:457.
79. Tang D.G. Understanding cancer stem cell heterogeneity and plasticity. Cell Res. 2012, 22:457-472.
80. Dinger M.E., Amaral P.P., Mercer T.R., Pang K.C., Bruce S.J., Gardiner B.B., Askarian-Amiri M.E., Ru K., Solda G., Simons C., Sunkin S.M., Crowe M.L., Grimmond S.M., Perkins A.C., Mattick J.S. Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Res. 2008, 18:1433-1445.
81. Trimarchi T., Bilal E., Ntziachristos P., Fabbri G., Dalla-Favera R., Tsirigos A., Aifantis I. Genome-wide mapping and characterization of notch-regulated long noncoding RNAs in acute leukemia. Cell 2014, 158:593-606.
82. Richly H., Aloia L., Di Croce L. Roles of the Polycomb group proteins in stem cells and cancer. Cell Death Dis. 2011, 2:e204.
83. 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., Rinn J.L. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc. Natl. Acad. Sci. U. S. A. 2009, 106:11667-11672.
84. 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, 30:1956-1962.
85. Aguilo F., Zhou M.M., Walsh M.J. Long noncoding RNA, polycomb, and the ghosts haunting INK4b-ARF-INK4a expression. Cancer Res. 2011, 71:5365-5369.
86. 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., Chang H.Y. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 2010, 464:1071-1076.
87. Sampieri K., Fodde R. Cancer stem cells and metastasis. Semin. Cancer Biol. 2012, 22:187-193.
88. Sheik Mohamed J., Gaughwin P.M., Lim B., Robson P., Lipovich L. Conserved long noncoding RNAs transcriptionally regulated by Oct4 and Nanog modulate pluripotency in mouse embryonic stem cells. RNA 2010, 16:324-337.
89. Schoppy D.W., Ruzankina Y., Brown E.J. Removing all obstacles: a critical role for p53 in promoting tissue renewal. Cell Cycle 2010, 9:1313-1319.
90. Chiou S.H., Wang M.L., Chou Y.T., Chen C.J., Hong C.F., Hsieh W.J., Chang H.T., Chen Y.S., Lin T.W., Hsu H.S., Wu C.W. Coexpression of Oct4 and Nanog enhances malignancy in lung adenocarcinoma by inducing cancer stem cell-like properties and epithelial-mesenchymal transdifferentiation. Cancer Res. 2010, 70:10433-10444.
91. 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., Chinnaiyan A.M. Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression. Nat. Biotechnol. 2011, 29:742-749.
92. Fu X., Ravindranath L., Tran N., Petrovics G., Srivastava S. Regulation of apoptosis by a prostate-specific and prostate cancer-associated noncoding gene, PCGEM1. DNA Cell Biol. 2006, 25:135-141.
93. Petrovics G., Zhang W., Makarem M., Street J.P., Connelly R., Sun L., Sesterhenn I.A., Srikantan V., Moul J.W., Srivastava S. Elevated expression of PCGEM1, a prostate-specific gene with cell growth-promoting function, is associated with high-risk prostate cancer patients. Oncogene 2004, 23:605-611.
94. 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., Srivastava S. PCGEM1, a prostate-specific gene, is overexpressed in prostate cancer. Proc. Natl. Acad. Sci. U. S. A. 2000, 97:12216-12221.
95. Mourtada-Maarabouni M., Pickard M.R., Hedge V.L., Farzaneh F., Williams G.T. GAS5, a non-protein-coding RNA, controls apoptosis and is downregulated in breast cancer. Oncogene 2009, 28:195-208.
96. Li C.-Y., Shan S., Huang Q., Braun R.D., Lanzen J., Hu K., Lin P., Dewhirst M.W. Initial stages of tumor cell-induced angiogenesis: evaluation via skin window chambers in rodent models. J. Natl. Cancer Inst. 2000, 92:143-147.
97. Lai M.C., Yang Z., Zhou L., Zhu Q.Q., Xie H.Y., Zhang F., Wu L.M., Chen L.M., Zheng S.S. Long non-coding RNA MALAT-1 overexpression predicts tumor recurrence of hepatocellular carcinoma after liver transplantation. Med. Oncol. 2012, 29:1810-1816.
98. Schmidt L.H., Spieker T., Koschmieder S., Schaffers S., Humberg J., Jungen D., Bulk E., Hascher A., Wittmer D., Marra A., Hillejan L., Wiebe K., Berdel W.E., Wiewrodt R., Muller-Tidow C. 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, 6:1984-1992.
99. Xu C., Yang M., Tian J., Wang X., Li Z. MALAT-1: a long non-coding RNA and its important 3' end functional motif in colorectal cancer metastasis. Int. J. Oncol. 2011, 39:169-175.
100. Michalik K.M., You X., Manavski Y., Doddaballapur A., Zornig M., Braun T., John D., Ponomareva Y., Chen W., Uchida S., Boon R.A., Dimmeler S. Long noncoding RNA MALAT1 regulates endothelial cell function and vessel growth. Circ. Res. 2014, 114:1389-1397.
101. Zhou Y., Zhang X., Klibanski A. MEG3 noncoding RNA: a tumor suppressor. J. Mol. Endocrinol. 2012, 48:R45-R53.
102. Fidler I.J. The pathogenesis of cancer metastasis: the 'seed and soil' hypothesis revisited. Nat. Rev. Cancer 2003, 3:453-458.
103. Kim K., Jutooru I., Chadalapaka G., Johnson G., Frank J., Burghardt R., Kim S., Safe S. HOTAIR is a negative prognostic factor and exhibits pro-oncogenic activity in pancreatic cancer. Oncogene 2012, 32:1616-1625.
104. Geng Y.J., Xie S.L., Li Q., Ma J., Wang G.Y. Large intervening non-coding RNA HOTAIR is associated with hepatocellular carcinoma progression. J. Int. Med. Res. 2011, 39:2119-2128.
105. 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., Shinomura Y. Upregulation of miR-196a and HOTAIR drive malignant character in gastrointestinal stromal tumors. Cancer Res. 2012, 72:1126-1136.
106. Kogo R., Shimamura T., Mimori K., Kawahara K., Imoto S., Sudo T., Tanaka F., Shibata K., Suzuki A., Komune S., Miyano S., Mori M. Long noncoding RNA HOTAIR regulates polycomb-dependent chromatin modification and is associated with poor prognosis in colorectal cancers. Cancer Res. 2011, 71:6320-6326.
107. Yu W., Gius D., Onyango P., Muldoon-Jacobs K., Karp J., Feinberg A.P., Cui H. Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA. Nature 2008, 451:202-206.
108. Yap K.L., Li S., Munoz-Cabello A.M., Raguz S., Zeng L., Mujtaba S., Gil J., Walsh M.J., Zhou M.M. Molecular interplay of the noncoding RNA ANRIL and methylated histone H3 lysine 27 by polycomb CBX7 in transcriptional silencing of INK4a. Mol. Cell 2010, 38:662-674.
109. Lee G.L., Dobi A., Srivastava S. Prostate cancer: diagnostic performance of the PCA3 urine test. Nat. Rev. Urol. 2011, 8:123-124.
110. Crawford E.D., Rove K.O., Trabulsi E.J., Qian J., Drewnowska K.P., Kaminetsky J.C., Huisman T.K., Bilowus M.L., Freedman S.J., Glover W.L., Bostwick D.G. Diagnostic performance of PCA3 to detect prostate cancer in men with increased prostate specific antigen: a prospective study of 1,962 cases. J. Urol. 2012, 188:1726-1731.
111. Matouk I.J., Abbasi I., Hochberg A., Galun E., Dweik H., Akkawi M. Highly upregulated in liver cancer noncoding RNA is overexpressed in hepatic colorectal metastasis. Eur. J. Gastroenterol. Hepatol. 2009, 21:688-692.
112. Panzitt K., Tschernatsch M.M., Guelly C., Moustafa T., Stradner M., Strohmaier H.M., Buck C.R., Denk H., Schroeder R., Trauner M., Zatloukal K. Characterization of HULC, a novel gene with striking up-regulation in hepatocellular carcinoma, as noncoding RNA. Gastroenterology 2007, 132:330-342.
113. Silva J.M., Boczek N.J., Berres M.W., Ma X., Smith D.I. LSINCT5 is over expressed in breast and ovarian cancer and affects cellular proliferation. RNA Biol. 2011, 8:496-505.
114. Zhu Z., Gao X., He Y., Zhao H., Yu Q., Jiang D., Zhang P., Ma X., Huang H., Dong D., Wan J., Gu Z., Jiang X., Yu L., Gao Y. An insertion/deletion polymorphism within RERT-lncRNA modulates hepatocellular carcinoma risk. Cancer Res. 2012, 72:6163-6172.
115. Braconi C., Valeri N., Kogure T., Gasparini P., Huang N., Nuovo G.J., Terracciano L., Croce C.M., Patel T. Expression and functional role of a transcribed noncoding RNA with an ultraconserved element in hepatocellular carcinoma. Proc. Natl. Acad. Sci. U. S. A. 2011, 108:786-791.
116. 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., Croce C.M. Ultraconserved regions encoding ncRNAs are altered in human leukemias and carcinomas. Cancer Cell 2007, 12:215-229.
117. Wang F., Li X., Xie X., Zhao L., Chen W. UCA1, a non-protein-coding RNA up-regulated in bladder carcinoma and embryo, influencing cell growth and promoting invasion. FEBS Lett. 2008, 582:1919-1927.
118. Wang X.S., Zhang Z., Wang H.C., Cai J.L., Xu Q.W., Li M.Q., Chen Y.C., Qian X.P., Lu T.J., Yu L.Z., Zhang Y., Xin D.Q., Na Y.Q., Chen W.F. Rapid identification of UCA1 as a very sensitive and specific unique marker for human bladder carcinoma. Clin. Cancer Res. 2006, 12:4851-4858.
119. 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, 41:276-284.
120. 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, 496:8-16.
121. Yang F., Zhang L., Huo X.S., Yuan J.H., Xu D., Yuan S.X., Zhu N., Zhou W.P., Yang G.S., Wang Y.Z., Shang J.L., Gao C.F., Zhang F.R., Wang F., Sun S.H. Long noncoding RNA high expression in hepatocellular carcinoma facilitates tumor growth through enhancer of zeste homolog 2 in humans. Hepatology 2011, 54:1679-1689.
122. Yuan S.X., Yang F., Yang Y., Tao Q.F., Zhang J., Huang G., Wang R.Y., Yang S., Huo X.S., Zhang L., Wang F., Sun S.H., Zhou W.P. Long non-coding RNA-MVIH promotes angiogenesis and serves as a predictor for HCC patients' poor recurrence-free survival after hepatectomy. Hepatology 2012, 56:2231-2241.
123. Fradet Y., Saad F., Aprikian A., Dessureault J., Elhilali M., Trudel C., Masse B., Piche L., Chypre C. uPM3, a new molecular urine test for the detection of prostate cancer. Urology 2004, 64:311-315. (discussion 315-316).
124. Shappell S.B. Clinical utility of prostate carcinoma molecular diagnostic tests. Rev. Urol. 2008, 10:44-69.
125. Properzi F., Logozzi M., Fais S. Exosomes: the future of biomarkers in medicine. Biomark. Med 2013, 7:769-778.
126. Takahashi K., Yan I.K., Kogure T., Haga H., Patel T. Extracellular vesicle-mediated transfer of long non-coding RNA ROR modulates chemosensitivity in human hepatocellular cancer. FEBS Open Biol. 2014, 4:458-467.
127. Gezer U., Ozgur E., Cetinkaya M., Isin M., Dalay N. Long non-coding RNAs with low expression levels in cells are enriched in secreted exosomes. Cell Biol. Int. 2014, 38:1076-1079.
128. Yang Z., Zhou L., Wu L.M., Lai M.C., Xie H.Y., Zhang F., Zheng S.S. Overexpression of long non-coding RNA HOTAIR predicts tumor recurrence in hepatocellular carcinoma patients following liver transplantation. Ann. Surg. Oncol. 2011, 18:1243-1250.
129. Qi P., Du X. The long non-coding RNAs, a new cancer diagnostic and therapeutic gold mine. Mod. Pathol. 2013, 26:155-165.
130. Gnyszka A., Jastrzebski Z., Flis S. DNA methyltransferase inhibitors and their emerging role in epigenetic therapy of cancer. Anticancer Res. 2013, 33:2989-2996.
131. Moskalev E.A., Schubert M., Hoheisel J.D. RNA-directed epigenomic reprogramming: an emerging principle of a more targeted cancer therapy?. Gene Chromosome Cancer 2012, 51:105-110.
132. Huang S., Ernberg I., Kauffman S. Cancer attractors: a systems view of tumors from a gene network dynamics and developmental perspective. Semin. Cell Dev. Biol. 2009, 20:869-876.
133. Chu C., Quinn J., Chang H.Y. Chromatin isolation by RNA purification (ChIRP). J. Vis. Exp. 2012, 25. pii: 3912.
134. Kleinman M.E., Yamada K., Takeda A., Chandrasekaran V., Nozaki M., Baffi J.Z., Albuquerque R.J., Yamasaki S., Itaya M., Pan Y., Appukuttan B., Gibbs D., Yang Z., Kariko K., Ambati B.K., Wilgus T.A., DiPietro L.A., Sakurai E., Zhang K., Smith J.R., Taylor E.W., Ambati J. Sequence- and target-independent angiogenesis suppression by siRNA via TLR3. Nature 2008, 452:591-597.
135. Castanotto D., Rossi J.J. The promises and pitfalls of RNA-interference-based therapeutics. Nature 2009, 457:426-433.
136. DeVincenzo J., Cehelsky J.E., Alvarez R., Elbashir S., Harborth J., Toudjarska I., Nechev L., Murugaiah V., Van Vliet A., Vaishnaw A.K., Meyers R. Evaluation of the safety, tolerability and pharmacokinetics of ALN-RSV01, a novel RNAi antiviral therapeutic directed against respiratory syncytial virus (RSV). Antivir. Res. 2008, 77:225-231.
137. Leachman S.A., Hickerson R.P., Schwartz M.E., Bullough E.E., Hutcherson S.L., Boucher K.M., Hansen C.D., Eliason M.J., Srivatsa G.S., Kornbrust D.J., Smith F.J., McLean W.I., Milstone L.M., Kaspar R.L. First-in-human mutation-targeted siRNA phase Ib trial of an inherited skin disorder. Mol. Ther. 2010, 18:442-446.
138. Davis M.E., Zuckerman J.E., Choi C.H., Seligson D., Tolcher A., Alabi C.A., Yen Y., Heidel J.D., Ribas A. Evidence of RNAi in humans from systemically administered siRNA via targeted nanoparticles. Nature 2010, 464:1067-1070.
139. Johnsen K.B., Gudbergsson J.M., Skov M.N., Pilgaard L., Moos T., Duroux M. A comprehensive overview of exosomes as drug delivery vehicles-endogenous nanocarriers for targeted cancer therapy. Biochim. Biophys. Acta 2014, 1846:75-87.
140. Alvarez-Erviti L., Seow Y., Yin H., Betts C., Lakhal S., Wood M.J. Delivery of siRNA to the mouse brain by systemic injection of targeted exosomes. Nat. Biotechnol. 2011, 29:341-345.
141. Sun D., Zhuang X., Xiang X., Liu Y., Zhang S., Liu C., Barnes S., Grizzle W., Miller D., Zhang H.G. A novel nanoparticle drug delivery system: the anti-inflammatory activity of curcumin is enhanced when encapsulated in exosomes. Mol. Ther. 2010, 18:1606-1614.
142. Ohno S., Takanashi M., Sudo K., Ueda S., Ishikawa A., Matsuyama N., Fujita K., Mizutani T., Ohgi T., Ochiya T., Gotoh N., Kuroda M. Systemically injected exosomes targeted to EGFR deliver antitumor microRNA to breast cancer cells. Mol. Ther. 2013, 21:185-191.
143. Chung C.C., Chanock S.J. Current status of genome-wide association studies in cancer. Hum. Genet. 2011, 130:59-78.
144. Chung C.C., Magalhaes W.C., Gonzalez-Bosquet J., Chanock S.J. Genome-wide association studies in cancer-current and future directions. Carcinogenesis 2010, 31:111-120.
145. Hindorff L.A., Sethupathy P., Junkins H.A., Ramos E.M., Mehta J.P., Collins F.S., Manolio T.A. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc. Natl. Acad. Sci. U. S. A. 2009, 106:9362-9367.
146. Uno S., Zembutsu H., Hirasawa A., Takahashi A., Kubo M., Akahane T., Aoki D., Kamatani N., Hirata K., Nakamura Y. A genome-wide association study identifies genetic variants in the CDKN2BAS locus associated with endometriosis in Japanese. Nat. Genet. 2010, 42:707-710.
147. Shirasawa S., Harada H., Furugaki K., Akamizu T., Ishikawa N., Ito K., Tamai H., Kuma K., Kubota S., Hiratani H., Tsuchiya T., Baba I., Ishikawa M., Tanaka M., Sakai K., Aoki M., Yamamoto K., Sasazuki T. SNPs in the promoter of a B cell-specific antisense transcript SAS-ZFAT, determine susceptibility to autoimmune thyroid disease. Hum. Mol. Genet. 2004, 13:2221-2231.
148. Garzon R., Marcucci G., Croce C.M. Targeting microRNAs in cancer: rationale, strategies and challenges. Nat. Rev. Drug Discov. 2010, 9:775-789.
149. Ponjavic J., Ponting C.P., Lunter G. Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs. Genome Res. 2007, 17:556-565.
150. Chodroff R.A., Goodstadt L., Sirey T.M., Oliver P.L., Davies K.E., Green E.D., Molnar Z., Ponting C.P. Long noncoding RNA genes: conservation of sequence and brain expression among diverse amniotes. Genome Biol. 2010, 11:R72.
151. Jia H., Osak M., Bogu G.K., Stanton L.W., Johnson R., Lipovich L. Genome-wide computational identification and manual annotation of human long noncoding RNA genes. RNA 2010, 16:1478-1487.
152. Wang K.C., Chang H.Y. Molecular mechanisms of long noncoding RNAs. Mol. Cell 2011, 43:904-914.
153. Geisler S., Coller J. RNA in unexpected places: long non-coding RNA functions in diverse cellular contexts. Nat. Rev. Mol. Cell Biol. 2013, 14:699-712.