In-depth characterization of the microRNA transcriptome in a leukemia progression model

Genome Research

Volumn 18, Issue 11, 2008, Pages 1787-1797

  Kuchenbauer, Florian ^a   Morin, Ryan D ^b   Argiropoulos, Bob ^a   Petriv, Oleh I ^c   Griffith, Malachi ^b   Heuser, Michael ^a   Yung, Eric ^a   Piper, Jessica ^a   Delaney, Allen ^b   Prabhu, Anna Liisa ^b   Zhao, Yongjun ^b   McDonald, Helen ^b   Zeng, Thomas ^b   Hirst, Martin ^b   Hansen, Carl L ^c   Marra, Marco A ^b   Humphries, R Keith ^a  

^a BRITISH COLUMBIA CANCER AGENCY   (Canada)

^b BRITISH COLUMBIA CANCER AGENCY   (Canada)

^c UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

DNA BINDING PROTEIN; HYBRID PROTEIN; LUCIFERASE; MICRORNA; NUCLEOPORIN 98; PROTEIN HOXD13; TRANSCRIPTOME; UNCLASSIFIED DRUG;

ACUTE GRANULOCYTIC LEUKEMIA; ANIMAL CELL; ANIMAL EXPERIMENT; ANIMAL MODEL; ARTICLE; CANCER GROWTH; CONTROLLED STUDY; GENE OVEREXPRESSION; GENE SEQUENCE; GENE TARGETING; GENETIC ENGINEERING; GENETIC TRANSDUCTION; GENETIC VARIABILITY; MOLECULAR CLONING; MOUSE; MYELOID PROGENITOR CELL; NONHUMAN; ONCOGENE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FUNCTION;

ANIMALS; BASE SEQUENCE; CELL LINE, TUMOR; GENE EXPRESSION PROFILING; GENETIC ENGINEERING; GENETIC VARIATION; HOMEODOMAIN PROTEINS; LEUKEMIA, EXPERIMENTAL; LEUKEMIA, MYELOID, ACUTE; MICE; MICRORNAS; MODELS, GENETIC; NEOPLASM PROTEINS; NUCLEAR PORE COMPLEX PROTEINS; ONCOGENE PROTEINS, FUSION; RNA, NEOPLASM; TRANSCRIPTION FACTORS;

MURINAE;

EID: 55549129277     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.077578.108     Document Type: Article

References (65)

1. Akao, Y., Nakagawa, Y., and Naoe, T. 2006. let-7 microRNA functions as a potential growth suppressor in human colon cancer cells. Biol. Pharm. Bull. 29: 903-906.
2. Aravin, A. and Tuschl, T. 2005. Identification and characterization of small RNAs involved in RNA silencing. FEBS Lett. 579: 5830-5840.
3. Argiropoulos, B., Palmqvist, L., Yung, E., Kuchenbauer, F., Heuser, M., Sly, L.M., Wan, A., Krystal, G., and Humphries, R.K. 2008. Linkage of Meis1 leukemogenic activity to multiple downstream effectors including Trib2 and Ccl3. Exp. Hematol. 36: 845-859.
4. Bandres, E., Agirre, X., Ramirez, N., Zarate, R., and Garcia-Foncillas, J. 2007. MicroRNAs as cancer players: Potential clinical and biological effects. DNA Cell Biol. 26: 273-282.
5. Bartel, D.P. 2004. MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell 116: 281-297.
6. Berezikov, E., Cuppen, E., and Plasterk, R.H. 2006a. Approaches to microRNA discovery. Nat. Genet. 38: S2-S7.
7. Berezikov, E., Thuemmler, F., van Laake, L.W., Kondova, I., Bontrop, R., Cuppen, E., and Plasterk, R.H. 2006b. Diversity of microRNAs in human and chimpanzee brain. Nat. Genet. 38: 1375-1377.
8. Calin, G.A., Dumitru, C.D., 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. 99: 15524-15529.
9. Calin, G.A., Liu, C.G., Sevignani, C., Ferracin, M., Felli, N., Dumitru, C.D., Shimizu, M., Cimmino, A., Zupo, S., Dono, M., et al. 2004. MicroRNA profiling reveals distinct signatures in B cell chronic lymphocytic leukemias. Proc. Natl. Acad. Sci. 101: 11755-11760.
10. Calin, G.A., Ferracin, M., Cimmino, A., Di Leva, G., Shimizu, M., Wojcik, S.E., Iorio, M.V., Visone, R., Sever, N.I., Fabbri, M., et al. 2005. A microRNA signature associated with prognosis and progression in chronic lymphocytic leukemia. N. Engl. J. Med. 353: 1793-1801.
11. Chan, J.A., Krichevsky, A.M., and Kosik, K.S. 2005. MicroRNA-21 is an antiapoptotic factor in human glioblastoma cells. Cancer Res. 65: 6029-6033.
12. Davison, T.S., Johnson, C.D., and Andruss, B.F. 2006. Analyzing micro-RNA expression using microarrays. Methods Enzymol. 411: 14-34.
13. Debernardi, S., Skoulakis, S., Molloy, G., Chaplin, T., Dixon-McIver, A., and Young, B.D. 2007. MicroRNA miR-181a correlates with morphological sub-class of acute myeloid leukaemia and the expression of its target genes in global genome-wide analysis. Leukemia 21: 912-916.
14. Fazi, F., Rosa, A., Fatica, A., Gelmetti, V., De Marchis, M.L., Nervi, C., and Bozzoni, I. 2005. A minicircuitry comprised of microRNA-223 and transcription factors NFI-A and C/EBPalpha regulates human granulopoiesis. Cell 123: 819-831.
15. Fazi, F., Racanicchi, S., Zardo, G., Starnes, L.M., Mancini, M., Travaglini, L., Diverio, D., Ammatuna, E., Cimino, G., Lo-Coco, F., et al. 2007. Epigenetic silencing of the myelopoiesis regulator microRNA-223 by the AML1/ETO oncoprotein. Cancer Cell 12: 457-466.
16. Fontana, L., Pelosi, E., Greco, P., Racanicchi, S., Testa, U., Liuzzi, F., Croce, C.M., Brunetti, E., Grignani, F., and Peschle, C. 2007. MicroRNAs 17-5p-20a-106a control monocytopoiesis through AML1 targeting and M-CSF receptor upregulation. Nat. Cell Biol. 9: 775-787.
17. Fu, H., Tie, Y., Xu, C., Zhang, Z., Zhu, J., Shi, Y., Jiang, H., Sun, Z., and Zheng, X. 2005. Identification of human fetal liver miRNAs by a novel method. FEBS Lett. 579: 3849-3854.
18. Futreal, P.A., Coin, L., Marshall, M., Down, T., Hubbard, T., Wooster, R., Rahman, N., and Stratton, M.R. 2004. A census of human cancer genes. Nat. Rev. Cancer 4: 177-183.
19. Garzon, R., Volinia, S., Liu, C.G., Fernandez-Cymering, C., Palumbo, T., Pichiorri, F., Fabbri, M., Coombes, K., Alder, H., Nakamura, T., et al. 2008. MicroRNA signatures associated with cytogenetics and prognosis in acute myeloid leukemia. Blood 111: 3183-3189.
20. Griffiths-Jones, S. 2006. miRBase: The microRNA sequence database. Methods Mol. Biol. 342: 129-138.
21. Grimson, A., Farh, K.K., Johnston, W.K., Garrett-Engele, P., Lim, L.P., and Bartel, D.P. 2007. MicroRNA targeting specificity in mammals: Determinants beyond seed pairing. Mol. Cell 27: 91-105.
22. Hernando, E. 2007. MicroRNAs and cancer: Role in tumorigenesis, patient classification and therapy. Clin. Transl. Oncol. 9: 155-160.
23. Ibarra, I., Erlich, Y., Muthuswamy, S.K., Sachidanandam, R., and Hannon, G.J. 2007. A role for microRNAs in maintenance of mouse mammary epithelial progenitor cells. Genes & Dev. 21: 3238-3243.
24. Isken, F., Steffen, B., Merk, S., Dugas, M., Markus, B., Tidow, N., Zuhlsdorf, M., Illmer, T., Thiede, C., Berdel, W.E., et al. 2008. Identification of acute myeloid leukaemia associated microRNA expression patterns. Br. J. Haematol. 140: 153-161.
25. Jay, C., Nemunaitis, J., Chen, P., Fulgham, P., and Tong, A.W. 2007. miRNA profiling for diagnosis and prognosis of human cancer. DNA Cell Biol. 26: 293-300.
26. Johnson, S.M., Grosshans, H., Shingara, J., Byrom, M., Jarvis, R., Cheng, A., Labourier, E., Reinert, K.L., Brown, D., and Slack, F.J. 2005. RAS is regulated by the let-7 microRNA family. Cell 120: 635-647.
27. Jongen-Lavrencic, M., Sun, S.M., Dijkstra, M.K., Valk, P.J., and Lowenberg, B. 2008. MicroRNA expression profiling in relation to the genetic heterogeneity of acute myeloid leukemia. Blood 111: 5078-5085.
28. Kawahara, Y., Zinshteyn, B., Chendrimada, T.P., Shiekhattar, R., and Nishikura, K. 2007. RNA editing of the microRNA-151 precursor blocks cleavage by the Dicer-TRBP complex. EMBO Rep. 8: 763-769.
29. Landgraf, P., Rusu, M., Sheridan, R., Sewer, A., Iovino, N., Aravin, A., Pfeffer, S., Rice, A., Kamphorst, A.O., Landthaler, M., et al. 2007. A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 129: 1401-1414.
30. Lee, Y.S. and Dutta, A. 2006. MicroRNAs: Small but potent oncogenes or tumor suppressors. Curr. Opin. Investig. Drugs 7: 560-564.
31. Lee, Y.S. and Dutta, A. 2007. The tumor suppressor microRNA let-7 represses the HMGA2 oncogene. Genes & Dev. 21: 1025-1030.
32. Long, D., Lee, R., Williams, P., Chan, C.Y., Ambros, V., and Ding, Y. 2007. Potent effect of target structure on microRNA function. Nat. Struct. Mol. Biol. 14: 287-294.
33. Looijenga, L.H., Gillis, A.J., Stoop, H., Hersmus, R., and Oosterhuis, J.W. 2007. Relevance of microRNAs in normal and malignant development, including human testicular germ cell tumours. Int J Androl. 30: 304-314.
34. Lu, J., Getz, G., Miska, E.A., Alvarez-Saavedra, E., Lamb, J., Peck, D., Sweet-Cordero, A., Ebert, B.L., Mak, R.H., Ferrando, A.A., et al. 2005. MicroRNA expression profiles classify human cancers. Nature 435: 834-838.
35. Lui, W.O., Pourmand, N., Patterson, B.K., and Fire, A. 2007. Patterns of known and novel small RNAs in human cervical cancer. Cancer Res. 67: 6031-6043.
36. Lund, E., Guttinger, S., Calado, A., Dahlberg, J.E., and Kutay, U. 2004. Nuclear export of microRNA precursors. Science 303: 95-98.
37. Ma, L., Teruya-Feldstein, J., and Weinberg, R.A. 2007. Tumour invasion and metastasis initiated by microRNA-10b in breast cancer. Nature 449: 682-688.
38. Mansfield, J.H., Harfe, B.D., Nissen, R., Obenauer, J., Srineel, J., Chaudhuri, A., Farzan-Kashani, R., Zuker, M., Pasquinelli, A.E., Ruvkun, G., et al. 2004. MicroRNA-responsive "sensor" transgenes uncover Hox-like and other developmentally regulated patterns of vertebrate microRNA expression. Nat. Genet. 36: 1079-1083.
39. Margulies, M., Egholm, M., Altman, W.E., Attiya, S., Bader, J.S., Bemben, L.A., Berka, J., Braverman, M.S., Chen, Y.J., Chen, Z., et al. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380.
40. Mayr, C., Hemann, M.T., and Bartel, D.P. 2007. Disrupting the pairing between let-7 and Hmga2 enhances oncogenic transformation. Science 315: 1576-1579.
41. Mi, S., Lu, J., Sun, M., Li, Z., Zhang, H., Neilly, M.B., Wang, Y., Qian, Z., Jin, J., Zhang, Y., et al. 2007. MicroRNA expression signatures accurately discriminate acute lymphoblastic leukemia from acute myeloid leukemia. Proc. Natl. Acad. Sci. 104: 19971-19976.
42. Morin, R.D., O'Connor, M.D., Griffith, M., Kuchenbauer, F., Delaney, A., Prabhu, A.L., Zhao, Y., McDonald, H., Zeng, T., Hirst, M., et al. 2008. Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Res. 18: 610-621.
43. Mullican, S.E., Zhang, S., Konopleva, M., Ruvolo, V., Andreeff, M., Milbrandt, J., and Conneely, O.M. 2007. Abrogation of nuclear receptors Nr4a3 and Nr4a1 leads to development of acute myeloid leukemia. Nat. Med. 13: 730-735.
44. Negrini, M., Ferracin, M., Sabbioni, S., and Croce, C.M. 2007. MicroRNAs in human cancer: From research to therapy. J. Cell Sci. 120: 1833-1840.
45. Okamura, K., Phillips, M.D., Tyler, D.M., Duan, H., Chou, Y.T., and Lai, E.C. 2008. The regulatory activity of microRNA* species has substantial influence on microRNA and 3′ UTR evolution. Nat. Struct. Mol. Biol. 15: 354-363.
46. O'Toole, A.S., Miller, S., Haines, N., Zink, M.C., and Serra, M.J. 2006. Comprehensive thermodynamic analysis of 3′ double-nucleotide overhangs neighboring Watson-Crick terminal base pairs. Nucleic Acids Res. 34: 3338-3344.
47. Park, J.K., Liu, X., Strauss, T.J., McKearin, D.M., and Liu, Q. 2007. The miRNA pathway intrinsically controls self-renewal of Drosophila germline stem cells. Curr. Biol. 17: 533-538.
48. Pfeffer, S., Sewer, A., Lagos-Quintana, M., Sheridan, R., Sander, C., Grasser, F.A., van Dyk, L.F., Ho, C.K., Shuman, S., Chien, M., et al. 2005. Identification of microRNAs of the herpesvirus family. Nat. Methods 2: 269-276.
49. Pineault, N., Buske, C., Feuring-Buske, M., Abramovich, C., Rosten, P., Hogge, D.E., Aplan, P.D., and Humphries, R.K. 2003. Induction of acute myeloid leukemia in mice by the human leukemia-specific fusion gene NUP98-HOXD13 in concert with Meis1. Blood 101: 4529-4538.
50. Pineault, N., Abramovich, C., and Humphries, R.K. 2005. Transplantable cell lines generated with NUP98-Hox fusion genes undergo leukemic progression by Meis1 independent of its binding to DNA. Leukemia 19: 636-643.
51. Porkka, K.P., Pfeiffer, M.J., Waltering, K.K., Vessella, R.L., Tammela, T.L., and Visakorpi, T. 2007. MicroRNA expression profiling in prostate cancer. Cancer Res. 67: 6130-6135.
52. Ro, S., Park, C., Young, D., Sanders, K.M., and Yan, W. 2007. Tissue-dependent paired expression of miRNAs. Nucleic Acids Res. 35: 5944-5953.
53. Ruby, J.G., Jan, C., Player, C., Axtell, M.J., Lee, W., Nusbaum, C., Ge, H., and Bartel, D.P. 2006. Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell 127: 1193-1207.
54. Seitz, H., Ghildiyal, M., and Zamore, P.D. 2008. Argonaute loading improves the 5′ precision of both microRNAs and their miRNA strands in flies. Curr. Biol. 18: 147-151.
55. Sevignani, C., Calin, G.A., Nnadi, S.C., Shimizu, M., Davuluri, R.V., Hyslop, T., Demant, P., Croce, C.M., and Siracusa, L.D. 2007. MicroRNA genes are frequently located near mouse cancer susceptibility loci. Proc. Natl. Acad. Sci. 104: 8017-8022.
56. Shell, S., Park, S.M., Radjabi, A.R., Schickel, R., Kistner, E.O., Jewell, D.A., Feig, C., Lengyel, E., and Peter, M.E. 2007. Let-7 expression defines two differentiation stages of cancer. Proc. Natl. Acad. Sci. 104: 11400-11405.
57. Tang, F., Hajkova, P., Barton, S.C., O'Carroll, D., Lee, C., Lao, K., and Surani, M.A. 2006. 220-plex microRNA expression profile of a single cell. Nat. Protocols 1: 1154-1159.
58. Tang, F., Kaneda, M., O'Carroll, D., Hajkova, P., Barton, S.C., Sun, Y.A., Lee, C., Tarakhovsky, A., Lao, K., and Surani, M.A. 2007. Maternal microRNAs are essential for mouse zygotic development. Genes & Dev. 21: 644-648.
59. Thatcher, E.J., Flynt, A.S., Li, N., Patton, J.R., and Patton, J.G. 2007. miRNA expression analysis during normal zebrafish development and following inhibition of the Hedgehog and Notch signaling pathways. Dev. Dyn. 236: 2172-2180.
60. Tran, N., McLean, T., Zhang, X., Zhao, C.J., Thomson, J.M., O'Brien, C., and Rose, B. 2007. MicroRNA expression profiles in head and neck cancer cell lines. Biochem. Biophys. Res. Commun. 358: 12-17.
61. Wang, Y., Medvid, R., Melton, C., Jaenisch, R., and Blelloch, R. 2007. DGCR8 is essential for microRNA biogenesis and silencing of embryonic stem cell self-renewal. Nat. Genet. 39: 380-385.
62. Yu, J., Wang, F., Yang, G.H., Wang, F.L., Ma, Y.N., Du, Z.W., and Zhang, J.W. 2006. Human microRNA clusters: Genomic organization and expression profile in leukemia cell lines. Biochem. Biophys. Res. Commun. 349: 59-68.
63. Yu, F., Yao, H., Zhu, P., Zhang, X., Pan, Q., Gong, C., Huang, Y., Hu, X., Su, F., Lieberman, J., et al. 2007a. let-7 regulates self renewal and tumorigenicity of breast cancer cells. Cell 131: 1109-1123.
64. Yu, S.L., Chen, H.Y., Yang, P.C., and Chen, J.J. 2007b. Unique MicroRNA signature and clinical outcome of cancers. DNA Cell Biol. 26: 283-292.
65. Zuker, M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31: 3406-3415.