Long noncoding RNAs and neuroblastoma

Oncotarget

Volumn 6, Issue 21, 2015, Pages 18265-18275

  Pandey, Gaurav Kumar ^a   Kanduri, Chandrasekhar ^a  

^a UNIVERSITY OF GOTHENBURG   (Sweden)

Author keywords

MYCN; NBAT1; Neuroblastoma; Neuronal differentiation; Noncoding RNA

Indexed keywords

LONG UNTRANSLATED RNA; RNA; TRANSCRIBED ULTRA CONSERVED REGION; UNCLASSIFIED DRUG; MYCN PROTEIN, HUMAN; N MYC PROTO ONCOGENE PROTEIN; NUCLEAR PROTEIN; ONCOPROTEIN; TUMOR MARKER;

ARTICLE; CANCER DIAGNOSIS; CANCER PROGNOSIS; CANCER RISK; CARCINOGENESIS; CELL DIFFERENTIATION; CHROMOSOME 11Q; CHROMOSOME 1P; CHROMOSOME 2P; CHROMOSOME 6P; DISEASE ACTIVITY; DISEASE MARKER; GENE EXPRESSION; GENE FUNCTION; GENE IDENTIFICATION; GENE LOCUS; GENE MAPPING; HIGH RISK PATIENT; HUMAN; MOLECULAR PATHOLOGY; NEURAL CREST CELL; NEUROBLASTOMA; NONHUMAN; PROMOTER REGION; RISK ASSESSMENT; RISK FACTOR; SINGLE NUCLEOTIDE POLYMORPHISM; BIOLOGICAL MODEL; CHROMOSOME ABERRATION; GENE EXPRESSION REGULATION; GENETICS; PROGNOSIS;

BIOMARKERS, TUMOR; CHROMOSOME ABERRATIONS; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; MODELS, GENETIC; N-MYC PROTO-ONCOGENE PROTEIN; NEUROBLASTOMA; NUCLEAR PROTEINS; ONCOGENE PROTEINS; PROGNOSIS; RISK FACTORS; RNA, LONG NONCODING;

EID: 84938778653     PISSN: None     EISSN: 19492553     Source Type: Journal    
DOI: 10.18632/oncotarget.4251     Document Type: Article

References (69)

1. Kamijo T, Nakagawara A. Molecular and genetic bases of neuroblastoma. International journal of clinical oncology. 2012; 17:190-195.
2. Brodeur GM. Neuroblastoma: biological insights into a clinical enigma. Nature reviews Cancer. 2003; 3:203-216.
3. Cohn SL, Pearson AD, London WB, Monclair T, Ambros PF, Brodeur GM, Faldum A, Hero B, Iehara T, Machin D, Mosseri V, Simon T, Garaventa A, Castel V, Matthay KK, Force IT. The International Neuroblastoma Risk Group (INRG) classification system: an INRG Task Force report. Journal of clinical oncology: official journal of the American Society of Clinical Oncology. 2009; 27:289-297.
4. Monclair T, Brodeur GM, Ambros PF, Brisse HJ, Cecchetto G, Holmes K, Kaneko M, London WB, Matthay KK, Nuchtern JG, von Schweinitz D, Simon T, Cohn SL, Pearson AD, Force IT. The International Neuroblastoma Risk Group (INRG) staging system: an INRG Task Force report. Journal of clinical oncology: official journal of the American Society of Clinical Oncology. 2009; 27:298-303.
5. Brodeur GM, Seeger RC, Schwab M, Varmus HE, Bishop JM. Amplification of N-myc in untreated human neuroblastomas correlates with advanced disease stage. Science. 1984; 224:1121-1124.
6. Bagatell R, Beck-Popovic M, London WB, Zhang Y, Pearson AD, Matthay KK, Monclair T, Ambros PF, Cohn SL International Neuroblastoma Risk G. Significance of MYCN amplification in international neuroblastoma staging system stage 1 and 2 neuroblastoma: a report from the International Neuroblastoma Risk Group database. Journal of clinical oncology: official journal of the American Society of Clinical Oncology. 2009; 27:365-370.
7. Bordow SB, Norris MD, Haber PS, Marshall GM, Haber M. Prognostic significance of MYCN oncogene expression in childhood neuroblastoma. Journal of clinical oncology : official journal of the American Society of Clinical Oncology. 1998; 16:3286-3294.
8. Schwab M. Amplification of N-myc as a prognostic marker for patients with neuroblastoma. Seminars in cancer biology. 1993; 4:13-18.
9. Caron H. Allelic loss of chromosome 1 and additional chromosome 17 material are both unfavourable prognostic markers in neuroblastoma. Medical and pediatric oncology. 1995; 24:215-221.
10. Schleiermacher G, Mosseri V, London WB, Maris JM, Brodeur GM, Attiyeh E, Haber M, Khan J, Nakagawara A, Speleman F, Noguera R, Tonini GP, Fischer M, Ambros I, Monclair T, Matthay KK, et al. Segmental chromosomal alterations have prognostic impact in neuroblastoma: a report from the INRG project. British journal of cancer. 2012; 107:1418-1422.
11. Maris JM, Matthay KK. Molecular biology of neuroblastoma. Journal of clinical oncology: official journal of the American Society of Clinical Oncology. 1999; 17:2264-2279.
12. Maris JM, White PS, Beltinger CP, Sulman EP, Castleberry RP, Shuster JJ, Look AT, Brodeur GM. Significance of chromosome 1p loss of heterozygosity in neuroblastoma. Cancer research. 1995; 55:4664-4669.
13. Theissen J, Oberthuer A, Hombach A, Volland R, Hertwig F, Fischer M, Spitz R, Zapatka M, Brors B, Ortmann M, Simon T, Hero B, Berthold F. Chromosome 17/17q gain and unaltered profiles in high resolution array-CGH are prognostically informative in neuroblastoma. Genes, chromosomes & cancer. 2014; 53:639-649.
14. Diskin SJ, Capasso M, Schnepp RW, Cole KA, Attiyeh EF, Hou C, Diamond M, Carpenter EL, Winter C, Lee H, Jagannathan J, Latorre V, Iolascon A, Hakonarson H, Devoto M, Maris JM. Common variation at 6q16 within HACE1 and LIN28B influences susceptibility to neuroblastoma. Nature genetics. 2012; 44:1126-1130.
15. Maris JM, Mosse YP, Bradfield JP, Hou C, Monni S, Scott RH, Asgharzadeh S, Attiyeh EF, Diskin SJ, Laudenslager M, Winter C, Cole KA, Glessner JT, Kim C, Frackelton EC, Casalunovo T, et al. Chromosome 6p22 locus associated with clinically aggressive neuroblastoma. The New England journal of medicine. 2008; 358:2585-2593.
16. Molenaar JJ, Domingo-Fernandez R, Ebus ME, Lindner S, Koster J, Drabek K, Mestdagh P, van Sluis P, Valentijn LJ, van Nes J, Broekmans M, Haneveld F, Volckmann R, Bray I, Heukamp L, Sprussel A, et al. LIN28B induces neuroblastoma and enhances MYCN levels via let-7 suppression. Nature genetics. 2012; 44:1199-1206.
17. Pandey GK, Mitra S, Subhash S, Hertwig F, Kanduri M, Mishra K, Fransson S, Ganeshram A, Mondal T, Bandaru S, Ostensson M, Akyurek LM, Abrahamsson J, Pfeifer S, Larsson E, Shi L, et al. The risk-associated long noncoding RNA NBAT-1 controls neuroblastoma progression by regulating cell proliferation and neuronal differentiation. Cancer cell. 2014; 26:722-737.
18. Maris JM. Recent advances in neuroblastoma. The New England journal of medicine. 2010; 362:2202-2211.
19. Morris KV, Mattick JS. The rise of regulatory RNA. Nature reviews Genetics. 2014; 15:423-437.
20. Mercer TR, Dinger ME, Mattick JS. Long non-coding RNAs: insights into functions. Nature reviews Genetics. 2009; 10:155-159.
21. Batista PJ, Chang HY. Long noncoding RNAs: cellular address codes in development and disease. Cell. 2013; 152:1298-1307.
22. Kanduri C. Long noncoding RNA and epigenomics. Advances in experimental medicine and biology. 2011; 722:174-195.
23. Mohammad F, Mondal T, Kanduri C. Epigenetics of imprinted long noncoding RNAs. Epigenetics: official journal of the DNA Methylation Society. 2009; 4:277-286.
24. Whitehead J, Pandey GK, Kanduri C. Regulation of the mammalian epigenome by long noncoding RNAs. Biochimica et biophysica acta. 2009; 1790:936-947.
25. Ohms S, Rangasamy D. Silencing of LINE-1 retrotransposons contributes to variation in small noncoding RNA expression in human cancer cells. Oncotarget. 2014; 5:4103-4117.
26. Prensner JR, Chinnaiyan AM. The emergence of lncRNAs in cancer biology. Cancer discovery. 2011; 1:391-407.
27. Spizzo R, Almeida MI, Colombatti A, Calin GA. Long noncoding RNAs and cancer: a new frontier of translational research? Oncogene. 2012; 31:4577-4587.
28. Taft RJ, Pang KC, Mercer TR, Dinger M, Mattick JS. Noncoding RNAs: regulators of disease. The Journal of pathology. 2010; 220:126-139.
29. Xue Y, Ma G, Zhang Z, Hua Q, Chu H, Tong N, Yuan L, Qin C, Yin C, Zhang Z, Wang M. A novel antisense long noncoding RNA regulates the expression of MDC1 in bladder cancer. Oncotarget. 2015; 6:484-493.
30. Pandey GK, Kanduri C. Fighting Neuroblastomas with NBAT1 Oncoscience. 2015; 2:79-80.
31. Liu B, Sun L, Liu Q, Gong C, Yao Y, Lv X, Lin L, Yao H, Su F, Li D, Zeng M, Song E. A cytoplasmic NF-kappaB interacting long noncoding RNA blocks IkappaB phosphorylation and suppresses breast cancer metastasis. Cancer cell. 2015; 27:370-381.
32. Lee KS, Park JL, Lee K, Richardson LE, Johnson BH, Lee HS, Lee JS, Kim SB, Kwon OH, Song KS, Kim YS, Ashktorab H, Smoot DT, Jeon SH, Kim SY, Lee YS. nc886, a non-coding RNA of anti-proliferative role, is suppressed by CpG DNA methylation in human gastric cancer. Oncotarget. 2014; 5:3944-3955.
33. Lee HS, Lee K, Jang HJ, Lee GK, Park JL, Kim SY, Kim SB, Johnson BH, Zo JI, Lee JS, Lee YS. Epigenetic silencing of the non-coding RNA nc886 provokes oncogenes during human esophageal tumorigenesis. Oncotarget. 2014; 5:3472-3481.
34. Wu Y, Liu H, Shi X, Yao Y, Yang W, Song Y. The long non-coding RNA HNF1A-AS1 regulates proliferation and metastasis in lung adenocarcinoma. Oncotarget. 2015; 6:9160-9172.
35. Mazar J, Zhao W, Khalil AM, Lee B, Shelley J, Govindarajan SS, Yamamoto F, Ratnam M, Aftab MN, Collins S, Finck BN, Han X, Mattick JS, Dinger ME, Perera RJ. The functional characterization of long noncoding RNA SPRY4-IT1 in human melanoma cells. Oncotarget. 2014; 5:8959-8969.
36. Guo H, Zhang X, Dong R, Liu X, Li Y, Lu S, Xu L, Wang Y, Wang X, Hou D, Wei JJ, Shao C, Liu Z. Integrated analysis of long noncoding RNAs and mRNAs reveals their potential roles in the pathogenesis of uterine leiomyomas. Oncotarget. 2014; 5:8625-8636.
37. Li H, Yu B, Li J, Su L, Yan M, Zhu Z, Liu B. Overexpression of lncRNA H19 enhances carcinogenesis and metastasis of gastric cancer. Oncotarget. 2014; 5:2318-2329.
38. Buechner J, Einvik C. N-myc and noncoding RNAs in neuroblastoma. Molecular cancer research: MCR. 2012; 10:1243-1253.
39. Castelnuovo M, Massone S, Tasso R, Fiorino G, Gatti M, Robello M, Gatta E, Berger A, Strub K, Florio T, Dieci G, Cancedda R, Pagano A. An Alu-like RNA promotes cell differentiation and reduces malignancy of human neuroblastoma cells. FASEB journal: official publication of the Federation of American Societies for Experimental Biology. 2010; 24:4033-4046.
40. Liu PY, Erriquez D, Marshall GM, Tee AE, Polly P, Wong M, Liu B, Bell JL, Zhang XD, Milazzo G, Cheung BB, Fox A, Swarbrick A, Huttelmaier S, Kavallaris M, Perini G, et al. Effects of a novel long noncoding RNA, lncUSMycN, on N-Myc expression and neuroblastoma progression. Journal of the National Cancer Institute. 2014; 106.
41. Iyer MK, Niknafs YS, Malik R, Singhal U, Sahu A, Hosono Y, Barrette TR, Prensner JR, Evans JR, Zhao S, Poliakov A, Cao X, Dhanasekaran SM, Wu YM, Robinson DR, Beer DG, et al. The landscape of long noncoding RNAs in the human transcriptome. Nature genetics. 2015; 47:199-208.
42. 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 regulation. Molecular cell. 2008; 32:232-246.
43. Gibb EA, Brown CJ, Lam WL. The functional role of long non-coding RNA in human carcinomas. Molecular cancer. 2011; 10:38.
44. Bejerano G, Pheasant M, Makunin I, Stephen S, Kent WJ, Mattick JS, Haussler D. Ultraconserved elements in the human genome. Science. 2004; 304:1321-1325.
45. Calin GA, Liu CG, Ferracin M, Hyslop T, Spizzo R, Sevignani C, Fabbri M, Cimmino A, Lee EJ, Wojcik SE, Shimizu M, Tili E, Rossi S, Taccioli C, Pichiorri F, Liu X, et al. Ultraconserved regions encoding ncRNAs are altered in human leukemias and carcinomas. Cancer cell. 2007; 12:215-229.
46. Scaruffi P, Stigliani S, Moretti S, Coco S, De Vecchi C, Valdora F, Garaventa A, Bonassi S, Tonini GP. Transcribed-Ultra Conserved Region expression is associated with outcome in high-risk neuroblastoma. BMC cancer. 2009; 9:441.
47. Mestdagh P, Fredlund E, Pattyn F, Rihani A, Van Maerken T, Vermeulen J, Kumps C, Menten B, De Preter K, Schramm A, Schulte J, Noguera R, Schleiermacher G, Janoueix-Lerosey I, Laureys G, Powel R, et al. An integrative genomics screen uncovers ncRNA T-UCR functions in neuroblastoma tumours. Oncogene. 2010; 29:3583-3592.
48. Watters KM, Bryan K, Foley NH, Meehan M, Stallings RL. Expressional alterations in functional ultra-conserved non-coding RNAs in response to all-trans retinoic acid-induced differentiation in neuroblastoma cells. BMC cancer. 2013; 13:184.
49. Bown N, Cotterill S, Lastowska M, O'Neill S, Pearson AD, Plantaz D, Meddeb M, Danglot G, Brinkschmidt C, Christiansen H, Laureys G, Speleman F, Nicholson J, Bernheim A, Betts DR, Vandesompele J, et al. Gain of chromosome arm 17q and adverse outcome in patients with neuroblastoma. The New England journal of medicine. 1999; 340:1954-1961.
50. Azuhata T, Scott D, Takamizawa S, Wen J, Davidoff A, Fukuzawa M, Sandler A. The inhibitor of apoptosis protein survivin is associated with high-risk behavior of neuroblastoma. Journal of pediatric surgery. 2001; 36:1785-1791.
51. Saito-Ohara F, Imoto I, Inoue J, Hosoi H, Nakagawara A, Sugimoto T, Inazawa J. PPM1D is a potential target for 17q gain in neuroblastoma. Cancer research. 2003; 63:1876-1883.
52. Yu M, Ohira M, Li Y, Niizuma H, Oo ML, 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. International journal of oncology. 2009; 34:931-938.
53. Seeger RC, Brodeur GM, Sather H, Dalton A, Siegel SE, Wong KY, Hammond D. Association of multiple copies of the N-myc oncogene with rapid progression of neuroblastomas. The New England journal of medicine. 1985; 313:1111-1116.
54. Tseng YY, Moriarity BS, Gong W, Akiyama R, Tiwari A, Kawakami H, Ronning P, Reuland B, Guenther K, Beadnell TC, Essig J, Otto GM, O'Sullivan MG, Largaespada DA, Schwertfeger KL, Marahrens Y, et al. PVT1 dependence in cancer with MYC copy-number increase. Nature. 2014; 512:82-86.
55. Attiyeh EF, London WB, Mosse YP, Wang Q, Winter C, Khazi D, McGrady PW, Seeger RC, Look AT, Shimada H, Brodeur GM, Cohn SL, Matthay KK, Maris JM Children's Oncology G. Chromosome 1p and 11q deletions and outcome in neuroblastoma. The New England journal of medicine. 2005; 353:2243-2253.
56. Caren H, Kryh H, Nethander M, Sjoberg RM, Trager C, Nilsson S, Abrahamsson J, Kogner P, Martinsson T. Highrisk neuroblastoma tumors with 11q-deletion display a poor prognostic, chromosome instability phenotype with later onset. Proceedings of the National Academy of Sciences of the United States of America. 2010; 107:4323-4328.
57. Barnhill LM, Williams RT, Cohen O, Kim Y, Batova A, Mielke JA, Messer K, Pu M, Bao L, Yu AL, Diccianni MB. High expression of CAI2, a 9p21-embedded long noncoding RNA, contributes to advanced-stage neuroblastoma. Cancer research. 2014; 74:3753-3763.
58. Atmadibrata B, Liu PY, Sokolowski N, Zhang L, Wong M, Tee AE, Marshall GM, Liu T. The novel long noncoding RNA linc00467 promotes cell survival but is down-regulated by N-Myc. PloS one. 2014; 9:e88112.
59. Tee AE, Ling D, Nelson C, Atmadibrata B, Dinger ME, Xu N, Mizukami T, Liu PY, Liu B, Cheung B, Pasquier E, Haber M, Norris MD, Suzuki T, Marshall GM, Liu T. The histone demethylase JMJD1A induces cell migration and invasion by up-regulating the expression of the long noncoding RNA MALAT1. Oncotarget. 2014; 5:1793-1804.
60. Zhao Z, Ma X, Hsiao TH, Lin G, Kosti A, Yu X, Suresh U, Chen Y, Tomlinson GE, Pertsemlidis A, Du L. A highcontent morphological screen identifies novel microRNAs that regulate neuroblastoma cell differentiation. Oncotarget. 2014; 5:2499-2512.
61. Ng SY, Johnson R, Stanton LW. Human long non-coding RNAs promote pluripotency and neuronal differentiation by association with chromatin modifiers and transcription factors. The EMBO journal. 2012; 31:522-533.
62. Ng SY, Bogu GK, Soh BS, Stanton LW. The long noncoding RNA RMST interacts with SOX2 to regulate neurogenesis. Molecular cell. 2013; 51:349-359.
63. Vance KW, Sansom SN, Lee S, Chalei V, Kong L, Cooper SE, Oliver PL, Ponting CP. The long non-coding RNA Paupar regulates the expression of both local and distal genes. The EMBO journal. 2014; 33:296-311.
64. 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 research. 2002; 62:2695-2698.
65. Vitiello M, Tuccoli A, Poliseno L. Long non-coding RNAs in cancer: implications for personalized therapy. Cellular oncology. 2014.
66. Wang F, Ren S, Chen R, Lu J, Shi X, Zhu Y, Zhang W, Jing T, Zhang C, Shen J, Xu C, Wang H, Wang H, Wang Y, Liu B, Li Y, et al. Development and prospective multicenter evaluation of the long noncoding RNA MALAT-1 as a diagnostic urinary biomarker for prostate cancer. Oncotarget. 2014; 5:11091-11102.
67. Zhang EB, Kong R, Yin DD, You LH, Sun M, Han L, Xu TP, Xia R, Yang JS, De W, Chen J. Long noncoding RNA ANRIL indicates a poor prognosis of gastric cancer and promotes tumor growth by epigenetically silencing of miR-99a/miR-449a. Oncotarget. 2014; 5:2276-2292.
68. Hu Y, Chen HY, Yu CY, Xu J, Wang JL, Qian J, Zhang X, Fang JY. A long non-coding RNA signature to improve prognosis prediction of colorectal cancer. Oncotarget. 2014; 5:2230-2242.
69. Crea F, Watahiki A, Quagliata L, Xue H, Pikor L, Parolia A, Wang Y, Lin D, Lam WL, Farrar WL, Isogai T, Morant R, Castori-Eppenberger S, Chi KN, Wang Y, Helgason CD. Identification of a long non-coding RNA as a novel biomarker and potential therapeutic target for metastatic prostate cancer. Oncotarget. 2014; 5:764-774.