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Significance of Aberrant Expression of MicroRNAs in Cancer Cells

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Bioinformatics in Cancer and Cancer Therapy

Abstract

Alterations in miRNA genes and other non-coding RNAs play a critical role in the pathophysiology of all human cancers: cancer initiation and progression can involve microRNAs (miRNAs) – small non-coding RNAs that can regulate gene expression. At present, the main mechanism of microRNoma (defined as the full complement of microRNAs present in a genome) alteration in cancer cells seems to be represented by aberrant gene expression, characterized by abnormal levels of expression for mature and/or precursor miRNA sequences in comparison with the corresponding normal tissues. MicroRNAs expression profiling has been exploited to identify miRNAs that are potentially involved in the pathogenesis of human cancers. MicroRNAs and other non-coding RNAs profiling achieved by various methods has allowed the identification of signatures associated with diagnosis, staging, progression, prognosis, and response to treatment of human tumors.

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References

  • Allawi, H.T., Dahlberg, J.E., Olson, S., Lund, E., Olson, M., Ma, W.P., Takova, T., Neri, B.P., and Lyamichev, V.I. 2004. Quantitation of microRNAs using a modified Invader assay. RNA 10, 1153–1161.

    Article  PubMed  CAS  Google Scholar 

  • Ambros, V. 2003. MicroRNA pathways in flies and worms: growth, death, fat, stress, and timing. Cell 113, 673–676.

    Article  PubMed  CAS  Google Scholar 

  • Ambros, V. 2004. The functions of animal microRNAs. Nature 431, 350–355.

    Article  PubMed  CAS  Google Scholar 

  • Bartel, D.P. 2004. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116, 281–297.

    Article  PubMed  CAS  Google Scholar 

  • Bentwich, I., Avniel, A., Karov, Y., Aharonov, R., Gilad, S., Barad, O., Barzilai, A., Einat, P., Einav, U., Meiri, E., . et al. 2005. Identification of hundreds of conserved and nonconserved human microRNAs. Nat Genet 37, 766–770.

    Article  PubMed  CAS  Google Scholar 

  • Berezikov, E., and Plasterk, R.H. 2005. Camels and zebrafish, viruses and cancer: a microRNA update. Hum Mol Genet 14, R183–R190.

    Article  PubMed  CAS  Google Scholar 

  • Berezikov, E., Guryev, V., van de Belt, J., Wienholds, E., Plasterk, R.H., and Cuppen, E. 2005. Phylogenetic shadowing and computational identification of human microRNA genes. Cell 120, 21–24.

    Article  PubMed  CAS  Google Scholar 

  • Bottoni, A., Piccin, D., Tagliati, F., Luchin, A., Zatelli, M.C., and degli Uberti, E.C. 2005. . miR-15a and miR-16–1 down-regulation in pituitary adenomas J Cell Physiol 204, 280–285.

    Article  PubMed  CAS  Google Scholar 

  • Brennecke, J., Hipfner, D.R., Russell, rk, A., Cohen, R.B., S.M.S., A.Russell, R.B., and Cohen, S.M. 2003. Bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila. Cell 113, 25–36.

    Article  PubMed  CAS  Google Scholar 

  • 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 USA 99, 15524–15529.

    Article  PubMed  CAS  Google Scholar 

  • Calin, G.A., Sevignani, C., Dumitru, C.D., 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.

    Article  PubMed  CAS  Google Scholar 

  • 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. 2005a. A MicroRNA signature associated with prognosis and progression in chronic lymphocytic leukemia. N Engl J Med 353, 1793–1801.

    Article  CAS  Google Scholar 

  • Calin, G.A., Garzon, R., Cimmino, A., Fabbri, M., and Croce, C.M. 2005b. MicroRNAs and leukemias: How strong is the connection? Leuk Res30, 653–655.

    Article  Google Scholar 

  • Chen, C.Z. 2005. MicroRNAs as oncogenes and tumor suppressors. N Engl J Med 353, 1768–1771.

    Article  PubMed  CAS  Google Scholar 

  • Chen, C.Z., Li, L., Lodish, H.F., and Bartel, D.P. 2004. MicroRNAs modulate hematopoietic lineage differentiation. Science 303, 83–86.

    Article  PubMed  CAS  Google Scholar 

  • Chen, C., Ridzon, D.A., Broomer, A.J., Zhou, Z., Lee, D.H., Nguyen, J.T., Barbisin, M., Xu, N.L., Mahuvakar, V.R., Andersen, M.R., . et al. 2005. Real-time quant ification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res 33, e179.

    Article  PubMed  Google Scholar 

  • Cimmino, A., Calin, G.A., Fabbri, M., Iorio, M.V., Ferracin, M., Shimizu, M., Wojcik, S.E., Aqeilan, R., Zupo, S., Dono, M., . et al. 2005. miR-15 and miR-16 induce apoptosis by targeting BCL2. Proc Natl Acad Sc USA 102, 13944–13949.

    Article  CAS  Google Scholar 

  • Cory, S., Huang, D.C.S., and Adams, J.M. 2003. The BCL2 family: roles in cell survival and oncogenesis. Oncogene 22, 8590–8607.

    Article  PubMed  CAS  Google Scholar 

  • Croce, C.M., and Calin, G.A. 2005. miRNAs, Cancer, and Stem Cell Division. Cell 122, 6–7.

    Article  PubMed  CAS  Google Scholar 

  • Dang, C.V., O’Donnell, K.A., and Juopperi, T. 2005. The great MYC escape in tumorigenesis. Cancer Cell 8, 177–178.

    Article  PubMed  CAS  Google Scholar 

  • Eis, P.S., Tam, W., Sun, L., Chadburn, A., Li, Z., Gomez, M.F., Lund, E., and Dahlberg, J.E. 2005. Accumulation of miR-155 and BIC RNA in human B cell lymphomas. Proc Natl Acad Sci USA 102, 3627–3632.

    Article  PubMed  CAS  Google Scholar 

  • Esquela-Kerscher, A., and Slack, F.J. 2004. The age of high-throughput microRNA profiling. Nat Methods 1, 106–107.

    Article  PubMed  CAS  Google Scholar 

  • Felli, N., Fontana, L., Pelosi, E., Botta, R., Bonci, D., Facchiano, F., Liuzzi, F., Lulli, V., Morsilli, O., Santoro, S., . et al. 2005. MicroRNAs 221 and 222 inhibit normal erythropoiesis and erythroleukemic cell growth via kit receptor down-modulation. Proc Natl Acad Sci USA 102, 18081–18086.

    Article  PubMed  CAS  Google Scholar 

  • Fodde, R., and Smits, R. 2002. Cancer biology. A matter of dosage. Science 298, 761–763.

    Article  PubMed  CAS  Google Scholar 

  • Gregory, R.I., and Shiekhattar, R. 2005. MicroRNA biogenesis and cancer. Cancer Res 65, 3509–3512.

    Article  PubMed  CAS  Google Scholar 

  • Griffiths-Jones, S., Grocock, R.J., van Dongen, S., Bateman, A., and Enright, A.J. 2006. miRBase: microRNA sequences, targets and gene nomenclature. NAR Database Issue, D140–D144.

    Google Scholar 

  • Hammond, S.M. 2006. MicroRNAs as oncogenes. Curr Opin Genet Dev 16, 4–9.

    Article  PubMed  CAS  Google Scholar 

  • Harfe, B.D. 2005. MicroRNAs in vertebrate development. Curr Opin Genet Dev 15, 410–415.

    Article  PubMed  CAS  Google Scholar 

  • He, H., Jazdzewski, K., Li, W., Liyanarachchi, S., Nagy, R., Volinia, S., Calin, G.A., Liu, C.G., Franssila, K., Suster, S., . et al. 2005a.. The role of microRNA genes in papillary thyroid carcinoma Proc Natl Acad Sci USA 102, 19075–19080.

    Article  CAS  Google Scholar 

  • He, L., Thomson, J.M., Hemann, M.T., Hernando-Monge, E., Mu, D., Goodson, S., Powers, S., Cordon-Cardo, C., Lowe, S.W., Hannon, G.J., . et al. 2005b. A microRNA polycistron as a potential human oncogene. Nature 435, 828–833.

    Article  CAS  Google Scholar 

  • Hwang, H.W., and Mendell, J.T. 2006. MicroRNAs in cell proliferation, cell death, and tumorigenesis. Br J Cancer 94, 776–780.

    Article  PubMed  CAS  Google Scholar 

  • Iorio, M.V., Ferracin, M., Liu, C.G., 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.

    Article  PubMed  CAS  Google Scholar 

  • John, B., Enright, A.J., Aravin, A., Tuschl, T., Sander, C., and Marks, D.S. 2004. Human MicroRNA targets. PLoS Biol 2, e363.

    Article  PubMed  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Jopling, C.L., Yi, M., Lancaster, A.M., Lemon, S.M., and Sarnow, P. 2005. Modulation of hepatitis C virus RNA abundance by a liver-specific MicroRNA. Science 309, 1577–1581.

    Article  PubMed  CAS  Google Scholar 

  • Kim, H., Emi, M., Tanabe, K., and Toge, T. 2004. Therapeutic potential of antisense Bcl-2 as a chemosensitizer for cancer therapy. Cancer 101, 2491–2502.

    Article  PubMed  CAS  Google Scholar 

  • Kiriakidou, M., Nelson, P.T., Kouranov, A., Fitziev, P., Bouyioukos, C., Mourelatos, Z., and Hatzigeorgiou, A. 2004. A combined computational-experimental approach predicts human microRNA targets. Genes Dev 18, 1165–1178.

    Article  PubMed  CAS  Google Scholar 

  • Kloosterman, W.P., Wienholds, E., de Bruijn, E., Kauppinen, S., and Plasterk, R.H. 2006. In situ detection of miRNAs in animal embryos using LNA-modified oligonucleotide probes. Cell 3, 27–29.

    CAS  Google Scholar 

  • Kluiver, J., Poppema, S., de Jong, D., Blokzijl, T., Harms, G., Jacobs, S., Kroesen, B.J., and van den Berg, A. 2005. BIC and miR-155 are highly expressed in Hodgkin, primary mediastinal and diffuse large B cell lymphomas. J Pathol 207, 243–249.

    Article  PubMed  CAS  Google Scholar 

  • Krek, A., Grun, D., Poy, M.N., Wolf, R., Rosenberg, L., Epstein, E.J., MacMenamin, P., da Piedade, I., Gunsalus, K.C., Stoffel, M.,et al. 2005. Combinatorial microRNA target predictions. Nat Genet37, 495–500.

    Article  PubMed  CAS  Google Scholar 

  • Krichevsky, A.M., King, K.S., Donahue, C.P., Khrapko, K., and Kosik, K.S. 2003. A microRNA array reveals extensive regulation of microRNAs during brain development. RNA 9, 1274–1281.

    Article  PubMed  CAS  Google Scholar 

  • Krutzfeldt, J., Rajewsky, N., Braich, R., Rajeev, K.G., Tuschl, T., Manoharan, M., and Stoffel, M. 2005. Silencing of microRNAs in vivo with ‘antagomirs’. Nature 438, 685–689.

    Article  PubMed  Google Scholar 

  • Lao, K., Xu, N.L., Yeung, V., Chen, C., Livak, K.J., and Straus, N.A. 2006. Multiplexing RT-PCR for the detection of multiple miRNA species in small samples. Biochem Biophys Res Commun, 34385–89.

    Article  CAS  Google Scholar 

  • Lee, R.C., Feinbaum, R.L., and Ambros, V. 1993. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75, 843–854.

    Article  PubMed  CAS  Google Scholar 

  • Lewis, B.P., Burge, C.B., and Bartel, D.P. 2005. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120, 15–20.

    Article  PubMed  CAS  Google Scholar 

  • Lim, L.P., Lau, N.C., Garrett-Engele, P., Grimson, A., Schelter, J.M., Castle, J., Bartel, D.P., Linsley, P.S., and Johnson, J.M. 2005. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433, 769–773.

    Article  PubMed  CAS  Google Scholar 

  • Liu, C.G., Calin, G.A., Meloon, B., Gamliel, N., Sevignani, C., Ferracin, M., Dumitru, C.D., Shimizu, M., Zupo, S., Dono, M.,et al. 2004. An oligonucleotide microchip for genome-wide microRNA profiling in human and mouse tissues. Proc Natl Acad Sci USA 101, 9740–9744.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Malumbres, M., and Barbacid, M. 2003. RAS oncogenes: the first 30 years. Nat Rev Cancer 3, 459–465.

    Article  PubMed  CAS  Google Scholar 

  • Miska, E.A. 2005. How microRNAs control cell division, differentiation and death. Curr Opin Genet Dev 15, 563–568.

    Article  PubMed  CAS  Google Scholar 

  • Murakami, Y., Yasuda, T., Saigo, K., Urashima, T., Toyoda, H., Okanoue, T., and Shimotohno, K. 2006. Comprehensive analysis of microRNA expression patterns in hepatocellular carcinoma and non-tumorous tissues. Oncogene 25, 2537–2545.

    Article  PubMed  CAS  Google Scholar 

  • Neely, L.A., Patel, S., Garver, J., Gallo, M., Hackett, M., McLaughlin, S., Nadel, M., Harris, J., Gullans, S., and Rooke, J. 2006. A single-molecule method for the quantitation of microRNA gene expression. Nat Methods 3, 41–46.

    Article  PubMed  CAS  Google Scholar 

  • O’Donnell, K.A., Wentzel, E.A., Zeller, K.I., Dang, C.V., and Mendell, J.T. 2005. c-Myc-regulated microRNAs modulate E2F1 expression. Nature 435, 839–843.

    Article  PubMed  Google Scholar 

  • Orom, U.A., Kauppinen, S., and Lund, A.H. 2006. LNA-modified oligonucleotides mediate specific inhibition of microRNA function. Gene372, 137–141.

    Article  PubMed  CAS  Google Scholar 

  • Pasquinelli, A.E. 2002. MicroRNAs: deviants no longer. Trends Genet 18, 171–173.

    Article  PubMed  CAS  Google Scholar 

  • Raymond, C.K., Roberts, B.S., Garrett-Engele, P., Lim, L.P., and Johnson, J.M. 2005. Simple, quantitative primer-extension PCR assay for direct monitoring of microRNAs and short-interfering RNAs. RNA 11, 1737–1744.

    Article  PubMed  CAS  Google Scholar 

  • Rodriguez, A., Griffiths-Jones, S., Ashurst, J.L., and Bradley, A. 2004. Identification of mammalian microRNA host genes and transcription units. Genome Res 14, 1902–1910.

    Article  PubMed  CAS  Google Scholar 

  • Sattler, M., and Salgia, R. 2003. Targeting c-Kit mutations: basic science to novel therapies. Leuk Res 28, S11–S20.

    Article  Google Scholar 

  • Schmittgen, T.D., Jiang, J., Liu, Q., and yang, L. 2004. A high-throughput method to monitor the expression of microRNA precursor. Nucleic Acid Res 32, 43–53.

    Article  Google Scholar 

  • Sethupathy, P., Corda, B., and Hatziegeorgiou, A.G. 2006. TarBase: A comprehensive database of experimentally supported animal microRNA targets. RNA 12, 192–197.

    Article  PubMed  CAS  Google Scholar 

  • Sevignani, C., Calin, G.A., Siracusa, L.D., and Croce, C.M. 2006. Mammalian microRNAs: a small world for fine-tuning gene expression. Mamm Genome 17, 189–202.

    Article  PubMed  CAS  Google Scholar 

  • Sioud, M., and Rosok, O. 2004. Profiling microRNA expression using sensitive cDNA probes and filter arrays. Biotechniques 37, 574–576, 578–580.

    Google Scholar 

  • Slack, F.J., and Weidhans, J.B. 2006. . MicroRNAs as a potential magic bullet in cancer Future Med 2, 73–82.

    CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Tsujimoto, Y., Finger, L.R., Yunis, J., Nowell, P.C., and Croce, C.M. 1984. Cloning of the chromosome breakpoint of neoplastic B cells with the t 14;18 chromosome translocation. Science 226, 1097–1099.

    Article  PubMed  CAS  Google Scholar 

  • Tsujimoto, Y., Cossman, J., Jaffe, E., and Croce, C.M. 1985. Involvement of the bcl-2 gene in human follicular lymphoma. Science 228, 1440–1443.

    Article  PubMed  CAS  Google Scholar 

  • Volinia, S., Calin, G.A., Liu, C.G., 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.

    Article  PubMed  CAS  Google Scholar 

  • Weiler, J., Hunziker, J., and Hall, J. 2005. Anti-miRNA oligonucleotides AMOs: ammunition to target miRNAs implicated in human disease? Gene Ther13, 496–502.

    Article  Google Scholar 

  • Xu, P., Vernooy, S.Y., Guo, M., and Hay, B.A. 2003. The drosophila MicroRNA Mir-14 suppresses cell death and is required for normal fat metabolism. Curr Biol 13, 790–795.

    Article  PubMed  CAS  Google Scholar 

  • Yanaihara, N., Caplen, N., Bowman, E., Kumamoto, K., Okamoto, A., Yokota, J., Tanaka, T., Calin, G.A., Liu, C.G., Croce, C.M.,et al. 2006. microRNA Signature in lung cancer diagnosis and prognosis. Cancer Cell 9, 189–198.

    Article  PubMed  CAS  Google Scholar 

  • Yekta, S., Hshih, I., and Bartel, D.P. 2004. MicroRNA-directed cleavaga of HOXB8 mRNA. Science 304, 594–596.

    Article  PubMed  CAS  Google Scholar 

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Acknowledgements

Dr Calin is supported by the CLL Global Research Foundation and by an MD Anderson Trust grant.

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Calin, G., Liu, Cg., Ferracin, M., Volinia, S., Negrini, M., Croce, C. (2009). Significance of Aberrant Expression of MicroRNAs in Cancer Cells. In: Gordon, G. (eds) Bioinformatics in Cancer and Cancer Therapy. Cancer Drug Discovery and Development. Humana Press. https://doi.org/10.1007/978-1-59745-576-3_5

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