A study of microRNAs in silico and in vivo: Diagnostic and therapeutic applications in cancer

FEBS Journal

Volumn 276, Issue 8, 2009, Pages 2157-2164

  Waldman, Scott A ^a,b   Terzic, Andre ^c  

^a Thomas Jefferson University ^*  (United States)

^b THOMAS JEFFERSON UNIVERSITY   (United States)

^c MAYO CLINIC   (United States)

Author keywords

Biomarkers; Cancer; Diagnosis; Individualized therapy; MicroRNA; Prediction; Prognosis

Indexed keywords

ANTINEOPLASTIC AGENT; ANTISENSE OLIGODEOXYNUCLEOTIDE; CYCLIN D; MICRORNA; PHOSPHATIDYLINOSITOL 3,4,5 TRISPHOSPHATE 3 PHOSPHATASE; PROTEIN BCL 2; RAS PROTEIN; RETINOBLASTOMA PROTEIN; TRANSCRIPTION FACTOR E2F1; TRANSFORMING GROWTH FACTOR BETA; TUMOR MARKER;

B CELL LEUKEMIA; BREAST CANCER; CANCER CHEMOTHERAPY; CANCER CLASSIFICATION; CANCER DIAGNOSIS; CANCER GROWTH; CANCER SURVIVAL; CANCER THERAPY; CARCINOGENESIS; CELL CYCLE REGULATION; CHRONIC LYMPHATIC LEUKEMIA; COLON CANCER; COMPUTER MODEL; DNA FINGERPRINTING; GENE EXPRESSION PROFILING; GENE MUTATION; GENE TARGETING; GLIOBLASTOMA; HOMEOSTASIS; HUMAN; IN VIVO STUDY; LEIOMYOMA; LUNG CANCER; MANTLE CELL LYMPHOMA; MULTIPLE MYELOMA; NONHUMAN; ONCOGENE; ONCOGENE C MYC; ONCOGENE K RAS; PANCREAS CANCER; PRIORITY JOURNAL; PROGNOSIS; PROSTATE CANCER; SHORT SURVEY; STOMACH CANCER; TREATMENT RESPONSE; TUMOR SUPPRESSOR GENE;

ANIMALS; GENE EXPRESSION PROFILING; HUMANS; MICRORNAS; MODELS, BIOLOGICAL; NEOPLASMS; TUMOR MARKERS, BIOLOGICAL;

EID: 63049115244     PISSN: 1742464X     EISSN: 17424658     Source Type: Journal    
DOI: 10.1111/j.1742-4658.2009.06934.x     Document Type: Short Survey

References (63)

1. American Cancer Society (2006) Cancer Statistics 2006. American Cancer Society, Atlanta, GA.
2. Dalton WS Friend SH (2006) Cancer biomarkers - an invitation to the table. Science 312, 1165 1168.
3. Mathers CD Loncar D (2006) Projections of global mortality and burden of disease from 2002 to 2030. PLoS Med 3, e442.
4. Wilson C, Schulz S Waldman SA (2007) Biomarker development, commercialization, and regulation: individualization of medicine lost in translation. Clin Pharmacol Ther 81, 153 155.
5. Wagner J, Williams S Webster C (2007) Biomarkers and surrogate endpoints for development and regulatory evaluation of new drugs. Clin Pharmacol Ther 81, 104 107.
6. Waldman SA, Terzic MR Terzic A (2007) Molecular medicine hones therapeutic arts to science. Clin Pharmacol Ther 82, 343 347.
7. Garraway LA Sellers WR (2006) Lineage dependency and lineage-survival oncogenes in human cancer. Nat Rev Cancer 6, 593 602.
8. Calin GA Croce CM (2006) MicroRNA signatures in human cancers. Nat Rev Cancer 6, 857 866.
9. Chen CZ (2005) MicroRNAs as oncogenes and tumor suppressors. N Engl J Med 353, 1768 1771.
10. Harfe BD (2005) MicroRNAs in vertebrate development. Curr Opin Genet Dev 15, 410 415.
11. Pasquinelli AE, Hunter S Bracht J (2005) MicroRNAs: a developing story. Curr Opin Genet Dev 15, 200 205.
12. Faustino RS, Nelson TJ, Terzic A Perez-Terzic C (2007) Nuclear transport: target for therapy. Clin Pharmacol Ther 81, 880 886.
13. Waldman SA Terzic A (2008) MicroRNA signatures as diagnostic and therapeutic targets. Clin Chem 54, 943 944.
14. Bishop JM (1991) Molecular themes in oncogenesis. Cell 64, 235 248.
15. Weinberg RA (1991) Tumor suppressor genes. Science 254, 1138 1146.
16. Lu J, Getz G, Miska EA, Alvarez-Saavedra E, Lamb J, Peck D, Sweet-Cordero A, Ebert BL, Mak RH, Ferrando AA et al. (2005) MicroRNA expression profiles classify human cancers. Nature 435, 834 838.
17. Volinia S, Calin GA, Liu CG, Ambs S, Cimmino A, Petrocca F, Visone R, Iorio M, Roldo C, Ferracin M et al. (2006) A microRNA expression signature of human solid tumors defines cancer gene targets. Proc Natl Acad Sci USA 103, 2257 2261.
18. He H, Jazdzewski K, Li W, Liyanarachchi S, Nagy R, Volinia S, Calin GA, Liu CG, Franssila K, Suster S et al. (2005) The role of microRNA genes in papillary thyroid carcinoma. Proc Natl Acad Sci USA 102, 19075 19080.
19. Iorio MV, Ferracin M, Liu CG, Veronese A, Spizzo R, Sabbioni S, Magri E, Pedriali M, Fabbri M, Campiglio M et al. (2005) MicroRNA gene expression deregulation in human breast cancer. Cancer Res 65, 7065 7070.
20. Murakami Y, Yasuda T, Saigo K, Urashima T, Toyoda H, Okanoue T Shimotohno K (2006) Comprehensive analysis of microRNA expression patterns in hepatocellular carcinoma and non-tumorous tissues. Oncogene 25, 2537 2545.
21. Roldo C, Missiaglia E, Hagan JP, Falconi M, Capelli P, Bersani S, Calin GA, Volinia S, Liu CG, Scarpa A et al. (2006) MicroRNA expression abnormalities in pancreatic endocrine and acinar tumors are associated with distinctive pathologic features and clinical behavior. J Clin Oncol 24, 4677 4684.
22. Yanaihara N, Caplen N, Bowman E, Seike M, Kumamoto K, Yi M, Stephens RM, Okamoto A, Yokota J, Tanaka T et al. (2006) Unique microRNA molecular profiles in lung cancer diagnosis and prognosis. Cancer Cell 9, 189 198.
23. Johnson SM, Grosshans H, Shingara J, Byrom M, Jarvis R, Cheng A, Labourier E, Reinert KL, Brown D Slack FJ (2005) RAS is regulated by the let-7 microRNA family. Cell 120, 635 647.
24. Kim S, Hwang DW Lee DS (2009) A study of microRNAs in silico and in vivo: bioimaging of microRNA biogenesis and regulation. FEBS J 276, doi :.
25. Waldman SA Terzic A (2007) Translating MicroRNA discovery into clinical biomarkers in cancer. JAMA 297, 1923 1925.
26. Esquela-Kerscher A Slack FJ (2006) Oncomirs - microRNAs with a role in cancer. Nat Rev Cancer 6, 259 269.
27. Kent OA Mendell JT (2006) A small piece in the cancer puzzle: microRNAs as tumor suppressors and oncogenes. Oncogene 25, 6188 6196.
28. Calin GA Croce CM (2007) Chromosomal rearrangements and microRNAs: a new cancer link with clinical implications. J Clin Invest 117, 2059 2066.
29. Calin GA, Dumitru CD, Shimizu M, Bichi R, Zupo S, Noch E, Aldler H, Rattan S, Keating M, Rai K et al. (2002) Frequent deletions and down-regulation of micro- RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia. Proc Natl Acad Sci USA 99, 15524 15529.
30. Dong JT, Boyd JC Frierson HF Jr. (2001) Loss of heterozygosity at 13q14 and 13q21 in high grade, high stage prostate cancer. Prostate 49, 166 171.
31. Sanchez-Beato M, Sanchez-Aguilera A Piris MA (2003) Cell cycle deregulation in B-cell lymphomas. Blood 101, 1220 1235.
32. Cimmino A, Calin GA, Fabbri M, Iorio MV, Ferracin M, Shimizu M, Wojcik SE, Aqeilan RI, Zupo S, Dono M et al. (2005) miR-15 and miR-16 induce apoptosis by targeting BCL2. Proc Natl Acad Sci USA 102, 13944 13949.
33. Raveche ES, Salerno E, Scaglione BJ, Manohar V, Abbasi F, Lin YC, Fredrickson T, Landgraf P, Ramachandra S, Huppi K et al. (2007) Abnormal microRNA-16 locus with synteny to human 13q14 linked to CLL in NZB mice. Blood 109, 5079 5086.
34. Reinhart BJ, Slack FJ, Basson M, Pasquinelli AE, Bettinger JC, Rougvie AE, Horvitz HR Ruvkun G (2000) The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403, 901 906.
35. Calin GA, Sevignani C, Dumitru CD, Hyslop T, Noch E, Yendamuri S, Shimizu M, Rattan S, Bullrich F, Negrini M et al. (2004) Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers. Proc Natl Acad Sci USA 101, 2999 3004.
36. Takamizawa J, Konishi H, Yanagisawa K, Tomida S, Osada H, Endoh H, Harano T, Yatabe Y, Nagino M, Nimura Y et al. (2004) Reduced expression of the let-7 microRNAs in human lung cancers in association with shortened postoperative survival. Cancer Res 64, 3753 3756.
37. Ota A, Tagawa H, Karnan S, Tsuzuki S, Karpas A, Kira S, Yoshida Y Seto M (2004) Identification and characterization of a novel gene, C13orf25, as a target for 13q31-q32 amplification in malignant lymphoma. Cancer Res 64, 3087 3095.
38. He L, Thomson JM, Hemann MT, Hernando-Monge E, Mu D, Goodson S, Powers S, Cordon-Cardo C, Lowe SW, Hannon GJ et al. (2005) A microRNA polycistron as a potential human oncogene. Nature 435, 828 833.
39. Hayashita Y, Osada H, Tatematsu Y, Yamada H, Yanagisawa K, Tomida S, Yatabe Y, Kawahara K, Sekido Y Takahashi T (2005) A polycistronic microRNA cluster, miR-17-92, is overexpressed in human lung cancers and enhances cell proliferation. Cancer Res 65, 9628 9632.
40. Pajic A, Spitkovsky D, Christoph B, Kempkes B, Schuhmacher M, Staege MS, Brielmeier M, Ellwart J, Kohlhuber F, Bornkamm GW et al. (2000) Cell cycle activation by c-myc in a burkitt lymphoma model cell line. Int J Cancer 87, 787 793.
41. Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP Burge CB (2003) Prediction of mammalian microRNA targets. Cell 115, 787 798.
42. O'Donnell KA, Wentzel EA, Zeller KI, Dang CV Mendell JT (2005) c-Myc-regulated microRNAs modulate E2F1 expression. Nature 435, 839 843.
43. Bracken AP, Ciro M, Cocito A Helin K (2004) E2F target genes: unraveling the biology. Trends Biochem Sci 29, 409 417.
44. Hemann MT, Fridman JS, Zilfou JT, Hernando E, Paddison PJ, Cordon-Cardo C, Hannon GJ Lowe SW (2003) An epi-allelic series of p53 hypomorphs created by stable RNAi produces distinct tumor phenotypes in vivo. Nat Genet 33, 396 400.
45. Ciafre SA, Galardi S, Mangiola A, Ferracin M, Liu CG, Sabatino G, Negrini M, Maira G, Croce CM Farace MG (2005) Extensive modulation of a set of microRNAs in primary glioblastoma. Biochem Biophys Res Commun 334, 1351 1358.
46. Krichevsky AM, King KS, Donahue CP, Khrapko K Kosik KS (2003) A microRNA array reveals extensive regulation of microRNAs during brain development. RNA 9, 1274 1281.
47. Wang T, Zhang X, Obijuru L, Laser J, Aris V, Lee P, Mittal K, Soteropoulos P Wei JJ (2007) A micro-RNA signature associated with race, tumor size, and target gene activity in human uterine leiomyomas. Genes Chromosomes Cancer 46, 336 347.
48. Meng F, Henson R, Lang M, Wehbe H, Maheshwari S, Mendell JT, Jiang J, Schmittgen TD Patel T (2006) Involvement of human micro-RNA in growth and response to chemotherapy in human cholangiocarcinoma cell lines. Gastroenterology 130, 2113 2129.
49. Si ML, Zhu S, Wu H, Lu Z, Wu F Mo YY (2007) miR-21-mediated tumor growth. Oncogene 26, 2799 2803.
50. Zhu S, Si ML, Wu H Mo YY (2007) MicroRNA-21 targets the tumor suppressor gene tropomyosin 1 (TPM1). J Biol Chem 282, 14328 14336.
51. Chan JA, Krichevsky AM Kosik KS (2005) MicroRNA-21 is an antiapoptotic factor in human glioblastoma cells. Cancer Res 65, 6029 6033.
52. Fabbri M, Croce CM Calin GA (2008) MicroRNAs. Cancer J 14, 1 6.
53. Bloomston M, Frankel W, Ptrocca F, Volinia S, Alder H, Liu C, Bhat D, Taccioli C, Jenkins H Croce C (2007) MicroRNA expression patterns differentiate pancreatic adenocarcinoma from normal pancreas and chronic pancreatitis. JAMA 297, 1901 1908.
54. Schetter AJ, Leung SY, Sohn JJ, Zanetti KA, Bowman ED, Yanaihara N, Yuen ST, Chan TL, Kwong DL, Au GK et al. (2008) MicroRNA expression profiles associated with prognosis and therapeutic outcome in colon adenocarcinoma. JAMA 299, 425 436.
55. Zhang L, Huang J, Yang N, Greshock J, Megraw MS, Giannakakis A, Liang S, Naylor TL, Barchetti A, Ward MR et al. (2006) microRNAs exhibit high frequency genomic alterations in human cancer. Proc Natl Acad Sci USA 103, 9136 9141.
56. Lujambio A, Ropero S, Ballestar E, Fraga MF, Cerrato C, Setien F, Casado S, Suarez-Gauthier A, Sanchez-Cespedes M, Git A et al. (2007) Genetic unmasking of an epigenetically silenced microRNA in human cancer cells. Cancer Res 67, 1424 1429.
57. Saito Y, Liang G, Egger G, Friedman JM, Chuang JC, Coetzee GA Jones PA (2006) Specific activation of microRNA-127 with downregulation of the proto-oncogene BCL6 by chromatin-modifying drugs in human cancer cells. Cancer Cell 9, 435 443.
58. Harris KS, Zhang Z, McManus MT, Harfe BD Sun X (2006) Dicer function is essential for lung epithelium morphogenesis. Proc Natl Acad Sci USA 103, 2208 2213.
59. Karube Y, Tanaka H, Osada H, Tomida S, Tatematsu Y, Yanagisawa K, Yatabe Y, Takamizawa J, Miyoshi S, Mitsudomi T et al. (2005) Reduced expression of Dicer associated with poor prognosis in lung cancer patients. Cancer Sci 96, 111 115.
60. Kumar MS, Lu J, Mercer KL, Golub TR Jacks T (2007) Impaired microRNA processing enhances cellular transformation and tumorigenesis. Nat Genet 39, 673 677.
61. Weiler J, Hunziker J Hall J (2006) Anti-miRNA oligonucleotides (AMOs): ammunition to target miRNAs implicated in human disease? Gene Ther 13, 496 502.
62. Naguibneva I, Ameyar-Zazoua M, Nonne N, Polesskaya A, Ait-Si-Ali S, Groisman R, Souidi M, Pritchard LL Harel-Bellan A (2006) An LNA-based loss-of-function assay for micro-RNAs. Biomed Pharmacother 60, 633 638.
63. Krutzfeldt J, Rajewsky N, Braich R, Rajeev KG, Tuschl T, Manoharan M Stoffel M (2005) Silencing of microRNAs in vivo with 'antagomirs'. Nature 438, 685 689.