Integrated analysis of the differential cellular and EBV miRNA expression profiles in microdissected nasopharyngeal carcinoma and non-cancerous nasopharyngeal tissues

Oncology Reports

Volumn 34, Issue 5, 2015, Pages 2585-2601

  Wan, Xun Xun ^a,b   Yi, Hong ^a   Qu, Jia Quan ^a   He, Qiu Yan ^a   Xiao, Zhi Qiang ^a  

^a CENTRAL SOUTH UNIVERSITY   (China)

^b HUNAN NORMAL UNIVERSITY   (China)

Author keywords

Epstein Barr virus; Microarray; MiRNA; Nasopharyngeal carcinoma

Indexed keywords

ALPHA2 INTEGRIN; CELLULAR MICRORNA; FOCAL ADHESION KINASE; MICRORNA; MICRORNA 18A; MICRORNA 200A; MICRORNA 200B; MICRORNA 31; MICRORNA 34B; MICRORNA 34C; MICRORNA 449A; MICRORNA BART3; MICRORNA BART5; MICRORNA LET 7; MITOGEN ACTIVATED PROTEIN KINASE; PROTEIN P53; RNA; SOMATOMEDIN BINDING PROTEIN 5; TRANSCRIPTION FACTOR FKHR; TRANSFORMING GROWTH FACTOR BETA; UNCLASSIFIED DRUG; VIRUS RNA; TP53 PROTEIN, HUMAN;

APOPTOSIS; ARHGEF12 GENE; ARTICLE; CARCINOGENESIS; CELL PROLIFERATION; CELL SURVIVAL; CLINICAL ARTICLE; COMPARATIVE STUDY; CONTROLLED STUDY; DHCR24 GENE; DOWN REGULATION; EPITHELIUM; EPSTEIN BARR VIRUS; FOXO1 GENE; FZD4 GENE; GENE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE INTERACTION; GENE ONTOLOGY; GENE REGULATORY NETWORK; GENETIC ANALYSIS; GENETIC ASSOCIATION; HUMAN; HUMAN TISSUE; IGFBP5 GENE; INTEGRATED ANALYSIS; INTRACELLULAR SIGNALING; ITGA2 GENE; LASER CAPTURE MICRODISSECTION; MICROARRAY ANALYSIS; NASOPHARYNGEAL EPITHELIAL TISSUE; NASOPHARYNX CARCINOMA; NONHUMAN; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SH3GLB1 GENE; UPREGULATION; VALIDATION PROCESS; WNT SIGNALING PATHWAY; CELL CYCLE; DNA MICROARRAY; EPSTEIN BARR VIRUS INFECTION; FOCAL ADHESION; GENETICS; NASOPHARYNX TUMOR; PATHOLOGY; PROCEDURES; SIGNAL TRANSDUCTION; VIROLOGY;

CELL CYCLE; CELL PROLIFERATION; EPSTEIN-BARR VIRUS INFECTIONS; FOCAL ADHESIONS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENE REGULATORY NETWORKS; HERPESVIRUS 4, HUMAN; HUMANS; MAP KINASE SIGNALING SYSTEM; MICRORNAS; NASOPHARYNGEAL NEOPLASMS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RNA, VIRAL; TRANSFORMING GROWTH FACTOR BETA; TUMOR SUPPRESSOR PROTEIN P53; WNT SIGNALING PATHWAY;

EID: 84941947679     PISSN: 1021335X     EISSN: 17912431     Source Type: Journal    
DOI: 10.3892/or.2015.4237     Document Type: Article

References (58)

1. Ambros V: The functions of animal microRNAs. Nature 431: 350-355, 2004.
2. Croce CM and Calin GA: miRNAs, cancer, and stem cell division. Cell 122: 6-7, 2005.
3. Bushati N and Cohen SM: microRNA functions. Annu Rev Cell Dev Biol 23: 175-205, 2007.
4. Chen CZ: MicroRNAs as oncogenes and tumor suppressors. N Engl J Med 353: 1768-1771, 2005.
5. Calin GA, Sevignani C, Dumitru CD, Hyslop T, Noch E, Yendamuri S, Shimizu M, Rattan S, Bullrich F, Negrini M, et al: Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers. Proc Natl Acad Sci USA 101: 2999-3004, 2004.
6. Lu J, Getz G, Miska EA, Alvarez-Saavedra E, Lamb J, Peck D, Sweet-Cordero A, Ebert BL, Mak RH, Ferrando AA, et al: MicroRNA expression profiles classify human cancers. Nature 435: 834-838, 2005.
7. Murakami Y, Yasuda T, Saigo K, Urashima T, Toyoda H, Okanoue T and Shimotohno K: Comprehensive analysis of microRNA expression patterns in hepatocellular carcinoma and non-tumorous tissues. Oncogene 25: 2537-2545, 2006.
8. Kida Y and Han YP: MicroRNA expression in colon adenocarcinoma. JAMA 299: 2628-2629, 2008.
9. Yanaihara N, Caplen N, Bowman E, Seike M, Kumamoto K, Yi M, Stephens RM, Okamoto A, Yokota J, Tanaka T, et al: Unique microRNA molecular profiles in lung cancer diagnosis and prognosis. Cancer Cell 9: 189-198, 2006.
10. Schetter AJ, Leung SY, Sohn JJ, Zanetti KA, Bowman ED, Yanaihara N, Yuen ST, Chan TL, Kwong DLW, Au GKH, et al: MicroRNA expression profiles associated with prognosis and therapeutic outcome in colon adenocarcinoma. JAMA 299: 425-436, 2008.
11. Sengupta S, den Boon JA, Chen IH, Newton MA, Stanhope SA, Cheng YJ, Chen CJ, Hildesheim A, Sugden B and Ahlquist P: MicroRNA 29c is down-regulated in nasopharyngeal carcinomas, up-regulating mRNAs encoding extracellular matrix proteins. Proc Natl Acad Sci USA 105: 5874-5878, 2008.
12. Alajez NM, Lenarduzzi M, Ito E, Hui AB, Shi W, Bruce J, Yue S, Huang SH, Xu W, Waldron J, et al: miR-218 suppresses nasopharyngeal cancer progression through downregulation of survivin and the SLIT2-ROBO1 pathway. Cancer Res 71: 2381-2391, 2011.
13. Lu J, He ML, Wang L, Chen Y, Liu X, Dong Q, Chen YC, Peng Y, Yao KT, Kung HF, et al: MiR-26a inhibits cell growth and tumorigenesis of nasopharyngeal carcinoma through repression of EZH2. Cancer Res 71: 225-233, 2011.
14. Yi C, Wang Q, Wang L, Huang Y, Li L, Liu L, Zhou X, Xie G, Kang T, Wang H, et al: miR-663, a microRNA targeting p21WAF1/CIP1, promotes the proliferation and tumorigenesis of nasopharyngeal carcinoma. Oncogene 31: 4421-4433, 2012.
15. Wong TS, Man OY, Tsang CM, Tsao SW, Tsang RK, Chan JY, Ho WK, Wei WI and To VS: MicroRNA let-7 suppresses nasopharyngeal carcinoma cells proliferation through downregulating c-Myc expression. J Cancer Res Clin Oncol 137: 415-422, 2011.
16. Zhang L, Deng T, Li X, Liu H, Zhou H, Ma J, Wu M, Zhou M, Shen S, Li X, et al: microRNA-141 is involved in a nasopharyngeal carcinoma-related genes network. Carcinogenesis 31: 559-566, 2010.
17. Deng M, Tang H, Zhou Y, Zhou M, Xiong W, Zheng Y, Ye Q, Zeng X, Liao Q, Guo X, et al: miR-216b suppresses tumor growth and invasion by targeting KRAS in nasopharyngeal carcinoma. J Cell Sci 124: 2997-3005, 2011.
18. Xia H, Ng SS, Jiang S, Cheung WK, Sze J, Bian XW, Kung HF and Lin MC: miR-200a-mediated downregulation of ZEB2 and CTNNB1 differentially inhibits nasopharyngeal carcinoma cell growth, migration and invasion. Biochem Biophys Res Commun 391: 535-541, 2010.
19. Busson P, Keryer C, Ooka T and Corbex M: EBV-associated nasopharyngeal carcinomas: From epidemiology to virustargeting strategies. Trends Microbiol 12: 356-360, 2004.
20. Wei WI and Sham JS: Nasopharyngeal carcinoma. Lancet 365: 2041-2054, 2005.
21. Qiu J, Cosmopoulos K, Pegtel M, Hopmans E, Murray P, Middeldorp J, Shapiro M and Thorley-Lawson DA: A novel persistence associated EBV miRNA expression profile is disrupted in neoplasia. PLoS Pathog 7: e1002193, 2011.
22. Barth S, Meister G and Grässer FA: EBV-encoded miRNAs. Biochim Biophys Acta 1809: 631-640, 2011.
23. Xia T, O'Hara A, Araujo I, Barreto J, Carvalho E, Sapucaia JB, Ramos JC, Luz E, Pedroso C, Manrique M, et al: EBV microRNAs in primary lymphomas and targeting of CXCL-11 by ebv-mir-BHRF1-3. Cancer Res 68: 1436-1442, 2008.
24. Nachmani D, Stern-Ginossar N, Sarid R and Mandelboim O: Diverse herpesvirus microRNAs target the stress-induced immune ligand MICB to escape recognition by natural killer cells. Cell Host Microbe 5: 376-385, 2009.
25. Choy EY, Siu KL, Kok KH, Lung RW, Tsang CM, To KF, Kwong DL, Tsao SW and Jin DY: An Epstein-Barr virus-encoded microRNA targets PUMA to promote host cell survival. J Exp Med 205: 2551-2560, 2008.
26. Li Z, Chen X, Li L, Liu S, Yang L, Ma X, Tang M, Bode AM, Dong Z, Sun L, et al: EBV encoded miR-BHRF1-1 potentiates viral lytic replication by downregulating host p53 in nasopharyngeal carcinoma. Int J Biochem Cell Biol 44: 275-279, 2012.
27. Lo AK, To KF, Lo KW, Lung RW, Hui JW, Liao G and Hayward SD: Modulation of LMP1 protein expression by EBV-encoded microRNAs. Proc Natl Acad Sci USA 104: 16164-16169, 2007.
28. Barth S, Pfuhl T, Mamiani A, Ehses C, Roemer K, Kremmer E, Jäker C, Höck J, Meister G and Grässer FA: Epstein-Barr virusencoded microRNA miR-BART2 down-regulates the viral DNA polymerase BALF5. Nucleic Acids Res 36: 666-675, 2008.
29. Lung RWM, Tong JHM, Sung YM, Leung PS, Ng DCH, Chau SL, Chan AWH, Ng EKO, Lo KW and To KF: Modulation of LMP2A expression by a newly identified Epstein-Barr virusencoded microRNA miR-BART22. Neoplasia 11: 1174-1184, 2009.
30. Lo AK, Dawson CW, Jin DY and Lo KW: The pathological roles of BART miRNAs in nasopharyngeal carcinoma. J Pathol 227: 392-403, 2012.
31. Marquitz AR and Raab-Traub N: The role of miRNAs and EBV BARTs in NPC. Semin Cancer Biol 22: 166-172, 2012.
32. Chen HC, Chen GH, Chen YH, Liao WL, Liu CY, Chang KP, Chang YS and Chen SJ: MicroRNA deregulation and pathway alterations in nasopharyngeal carcinoma. Br J Cancer 100: 1002-1011, 2009.
33. Luo Z, Zhang L, Li Z, Li X, Li G, Yu H, Jiang C, Dai Y, Guo X, Xiang J, et al: An in silico analysis of dynamic changes in microRNA expression profiles in stepwise development of nasopharyngeal carcinoma. BMC Med Genomics 5: 3, 2012.
34. Liu N, Chen NY, Cui RX, Li WF, Li Y, Wei RR, Zhang MY, Sun Y, Huang BJ, Chen M, et al: Prognostic value of a microRNA signature in nasopharyngeal carcinoma: A microRNA expression analysis. Lancet Oncol 13: 633-641, 2012.
35. Zeng X, Xiang J, Wu M, Xiong W, Tang H, Deng M, Li X, Liao Q, Su B, Luo Z, et al: Circulating miR-17, miR-20a, miR-29c, and miR-223 combined as non-invasive biomarkers in nasopharyngeal carcinoma. PLoS One 7: e46367, 2012.
36. Li T, Chen JX, Fu XP, Yang S, Zhang Z, Chen KhH and Li Y: microRNA expression profiling of nasopharyngeal carcinoma. Oncol Rep 25: 1353-1363, 2011.
37. Chen SJ, Chen GH, Chen YH, Liu CY, Chang KP, Chang YS and Chen HC: Characterization of Epstein-Barr virus miRNAome in nasopharyngeal carcinoma by deep sequencing. PLoS One 5: e12745, 2010.
38. Zhu JY, Pfuhl T, Motsch N, Barth S, Nicholls J, Grässer F and Meister G: Identification of novel Epstein-Barr virus microRNA genes from nasopharyngeal carcinomas. J Virol 83: 3333-3341, 2009.
39. Wong AM, Kong KL, Tsang JW, Kwong DL and Guan XY: Profiling of Epstein-Barr virus-encoded microRNAs in nasopharyngeal carcinoma reveals potential biomarkers and oncomirs. Cancer 118: 698-710, 2012.
40. Cheng AL, Huang WG, Chen ZC, Peng F, Zhang PF, Li MY, Li F, Li JL, Li C, Yi H, et al: Identification of novel biomarkers for differentiation and prognosis of nasopharyngeal carcinoma by laser capture microdissection and proteomic analysis. Clin Cancer Res 14: 435-445, 2008.
41. Elefant N, Berger A, Shein H, Hofree M, Margalit H and Altuvia Y: RepTar: A database of predicted cellular targets of host and viral miRNAs. Nucleic Acids Res 39: D188-D194, 2011.
42. Maragkakis M, Reczko M, Simossis VA, Alexiou P, Papadopoulos GL, Dalamagas T, Giannopoulos G, Goumas G, Koukis E, Kourtis K, et al: DIANA-microT web server: Elucidating microRNA functions through target prediction. Nucleic Acids Res 37: W273-W276, 2009.
43. Yang JH, Li JH, Shao P, Zhou H, Chen YQ and Qu LH: starBase: A database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data. Nucleic Acids Res 39: D202-D209, 2011.
44. Kim H, Park S, Min H and Yoon S: vHoT: A database for predicting interspecies interactions between viral microRNA and host genomes. Arch Virol 157: 497-501, 2012.
45. Baek D, Villén J, Shin C, Camargo FD, Gygi SP and Bartel DP: The impact of microRNAs on protein output. Nature 455: 64-71, 2008.
46. Selbach M, Schwanhäusser B, Thierfelder N, Fang Z, Khanin R and Rajewsky N: Widespread changes in protein synthesis induced by microRNAs. Nature 455: 58-63, 2008.
47. Cloonan N, Brown MK, Steptoe AL, Wani S, Chan WL, Forrest AR, Kolle G, Gabrielli B and Grimmond SM: The miR-17-5p microRNA is a key regulator of the G1/S phase cell cycle transition. Genome Biol 9: R127, 2008.
48. Liu Q, Fu H, Sun F, Zhang H, Tie Y, Zhu J, Xing R, Sun Z and Zheng X: miR-16 family induces cell cycle arrest by regulating multiple cell cycle genes. Nucleic Acids Res 36: 5391-5404, 2008.
49. Gusev Y, Schmittgen TD, Lerner M, Postier R and Brackett D: Computational analysis of biological functions and pathways collectively targeted by co-expressed microRNAs in cancer. BMC Bioinformatics 8 (Suppl 7): S16, 2007.
50. Chang TC, Wentzel EA, Kent OA, Ramachandran K, Mullendore M, Lee KH, Feldmann G, Yamakuchi M, Ferlito M, Lowenstein CJ, et al: Transactivation of miR-34a by p53 broadly influences gene expression and promotes apoptosis. Mol Cell 26: 745-752, 2007.
51. Dews M, Homayouni A, Yu D, Murphy D, Sevignani C, Wentzel E, Furth EE, Lee WM, Enders GH, Mendell JT, et al: Augmentation of tumor angiogenesis by a Myc-activated microRNA cluster. Nat Genet 38: 1060-1065, 2006.
52. Johnson CD, Esquela-Kerscher A, Stefani G, Byrom M, Kelnar K, Ovcharenko D, Wilson M, Wang X, Shelton J, Shingara J, et al: The let-7 microRNA represses cell proliferation pathways in human cells. Cancer Res 67: 7713-7722, 2007.
53. O'Day E and Lal A: MicroRNAs and their target gene networks in breast cancer. Breast Cancer Res 12: 201, 2010.
54. Lei T, Yuen KS, Xu R, Tsao SW, Chen H, Li M, Kok KH and Jin DY: Targeting of DICE1 tumor suppressor by Epstein-Barr virus-encoded miR-BART3 microRNA in nasopharyngeal carcinoma. Int J Cancer 133: 79-87, 2013.
55. Zhang G, Zong J, Lin S, Verhoeven RJ, Tong S, Chen Y, Ji M, Cheng W, Tsao SW, Lung M, et al: Circulating Epstein-Barr virus microRNAs miR-BART7 and miR-BART13 as biomarkers for nasopharyngeal carcinoma diagnosis and treatment. Int J Cancer 136: E301-E312, 2015.
56. Zeng ZY, Zhou YH, Zhang WL, Xiong W, Fan SQ, Li XL, Luo XM, Wu MH, Yang YX, Huang C, et al: Gene expression profiling of nasopharyngeal carcinoma reveals the abnormally regulated Wnt signaling pathway. Hum Pathol 38: 120-133, 2007.
57. Meulmeester E and Ten Dijke P: The dynamic roles of TGF-β in cancer. J Pathol 223: 205-218, 2011.
58. Chou J, Lin YC, Kim J, You L, Xu Z, He B and Jablons DM: Nasopharyngeal carcinoma - review of the molecular mechanisms of tumorigenesis. Head Neck 30: 946-963, 2008.