Advertisement

The Role and Use of MicroRNA in Cancer Diagnosis

  • Michał Świerniak
  • Andrzej Świerniak
Part of the Advances in Intelligent Systems and Computing book series (AISC, volume 230)

Abstract

MicroRNAs (miRNAs) are small RNA molecules that posttranscriptionally regulate gene expression. The aim of this paper is to present a survey on published application of these molecules in cancer diagnosis including our own results in this area. As an illustrative example of the use of miRNA in cancer diagnosis we present some main points from our study related to thyroid carcinoma.

Keywords

Medical diagnosis cancer MiRNAs system biology 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Fire, A., Xu, S., Montgomery, M.K., Kostas, S.A., Driver, S.E., Mello, C.C.: Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391, 806–811 (1998)CrossRefGoogle Scholar
  2. 2.
    Lee, R.C., Feinbaum, R.L., Ambros, V.: The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75, 843–854 (1993)CrossRefGoogle Scholar
  3. 3.
    Reinhart, B.J., Slack, F.J., Basson, M., Pasquinelli, A.E., Bettinger, J.C., Rougvie, A.E., Horvitz, H.R., Ruvkun, G.: The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403, 901–906 (2000)CrossRefGoogle Scholar
  4. 4.
    Pasquinelli, A.E., Reinhart, B.J., Slack, F., Martindale, M.Q., Kuroda, M.I., Maller, B., Hayward, D.C., Ball, E.E., Degnan, B., Muller, P., Spring, J., Srinivasan, A., Fishman, M., Finnerty, J., Corbo, J., Levine, M., Leahy, P., Davidson, E., Ruvkun, G.: Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature 408, 86–89 (2000)CrossRefGoogle Scholar
  5. 5.
    Lau, N.C., Lim, L.P., Weinstein, E.G., Bartel, D.P.: An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294, 858–862 (2001)CrossRefGoogle Scholar
  6. 6.
    Lee, R.C., Ambros, V.: An extensive class of small RNAs in Caenorhabditis elegans. Science 294, 862–864 (2001)CrossRefGoogle Scholar
  7. 7.
    Bartel, D.P.: MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116, 281–297 (2004)CrossRefGoogle Scholar
  8. 8.
    Beitzinger, M., Peters, L., Zhu, J.Y., Kremmer, E., Meister, G.: Identification of Human microRNA targets from isolated Argonaute protein complexes. RNA Biol. 4(2), 76–84 (2007)CrossRefGoogle Scholar
  9. 9.
    Lewis, B.P., Burge, C.B., Bartel, D.P.: Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120(1), 15–20 (2005)CrossRefGoogle Scholar
  10. 10.
    Griffiths-Jones, S.: miRBase: the microRNA sequence database. Methods Mol. Biol. 342, 129–138 (2006)Google Scholar
  11. 11.
    Brennecke, J., Stark, A., Russell, R.B., Cohen, S.M.: Principles of microRNA-target recognition. PLoS Biol. 3, e85 (2005)Google Scholar
  12. 12.
    Calin, G.A., Croce, C.M.: MicroRNA signatures in human cancers. Nat. Rev. Cancer 6, 857–866 (2006)CrossRefGoogle Scholar
  13. 13.
    Calin, G.A., Sevignani, C., Dumitru, C.D., Hyslop, T., Noch, E., Yendamuri, S., Shimizu, M., Rattan, S., Bullrich, F., Negrini, M., Croce, C.M.: Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers. Proc. Natl. Acad. Sci. USA 101, 2999–3004 (2004)CrossRefGoogle Scholar
  14. 14.
    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., Hammond, S.M.: A microRNA polycistron as a potential human oncogene. Nature 435, 828–833 (2005)CrossRefGoogle Scholar
  15. 15.
    Ota, A., Tagawa, H., Karnan, S., Tsuzuki, S., Karpas, A., Kira, S., Yoshida, Y., Seto, M.: Identification and characterization of a novel gene, C13orf25, as a target for 13q31-q32 amplification in malignant lymphoma. Cancer Res. 64, 3087–3095 (2004)CrossRefGoogle Scholar
  16. 16.
    Matsubara, H., Takeuchi, T., Nishikawa, E., Yanagisawa, K., Hayashita, Y., Ebi, H., Yamada, H., Suzuki, M., Nagino, M., Nimura, Y., Osada, H., Takahashi, T.: Apoptosis induction by antisense oligonucleotides against miR-17-5p and miR-20a in lung cancers overexpressing miR-17-92. Oncogene 26, 6099–6105 (2007)CrossRefGoogle Scholar
  17. 17.
    Chen, C.Z., Li, L., Lodish, H.F., Bartel, D.P.: MicroRNAs modulate hematopoietic lineage differentiation. Science 303, 83–86 (2004)CrossRefGoogle Scholar
  18. 18.
    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., Downing, J.R., Jacks, T., Horvitz, H.R., Golub, T.R.: MicroRNA expression profiles classify human cancers. Nature 435, 834–838 (2005)CrossRefGoogle Scholar
  19. 19.
    Volinia, S., Galasso, M., Sana, M.E., Wise, T.F., Palatini, J., Huebner, K., Croce, C.M.: Breast cancer signatures for invasiveness and prognosis defined by deep sequencing of microRNA. Proc. Natl. Acad. Sci. USA 109, 3024–3029 (2012)CrossRefGoogle Scholar
  20. 20.
    Blenkiron, C., Goldstein, L.D., Thorne, N.P., Spiteri, I., Chin, S.F., Dunning, M.J., Barbosa-Morais, N.L., Teschendorff, A.E., Green, A.R., Ellis, I.O., Tavare, S., Caldas, C., Miska, E.A.: MicroRNA expression profiling of human breast cancer identifies new markers of tumor subtype. Genome. Biol. 8, R214 (2007)Google Scholar
  21. 21.
    Lowery, A.J., Miller, N., Devaney, A., McNeill, R.E., Davoren, P.A., Lemetre, C., Benes, V., Schmidt, S., Blake, J., Ball, G., Kerin, M.J.: MicroRNA signatures predict oestrogen receptor, progesterone receptor and HER2/neu receptor status in breast cancer. Breast Cancer Res. 11, R27 (2009)Google Scholar
  22. 22.
    Foekens, J.A., Sieuwerts, A.M., Smid, M., Look, M.P., de Weerd, V., Boersma, A.W., Klijn, J.G., Wiemer, E.A., Martens, J.W.: Four miRNAs associated with aggressiveness of lymph node negative, estrogen receptor-positive human breast cancer. Proc. Natl. Acad. Sci. USA 105, 13021–13026 (2008)CrossRefGoogle Scholar
  23. 23.
    Qian, B., Katsaros, D., Lu, L., Preti, M., Durando, A., Arisio, R., Mu, L., Yu, H.: High miR-21 expression in breast cancer associated with poor disease-free survival in early stage disease and high TGF-beta1. Breast Cancer Res. Treat 117, 131–140 (2009)CrossRefGoogle Scholar
  24. 24.
    He, H., Jazdzewski, K., Li, W., Liyanarachchi, S., Nagy, R., Volinia, S., Calin, G.A., Liu, C.G., Franssila, K., Suster, S., Kloos, R.T., Croce, C.M., de la Chapelle, A.: The role of micro-RNA genes in papillary thyroid carcinoma. Proc. Natl. Acad. Sci. USA 102, 19075–19080 (2005)CrossRefGoogle Scholar
  25. 25.
    de la Chapelle, A., Jazdzewski, K.: MicroRNAs in thyroid cancer. J. Clin. Endocrinol. Metab. 96, 3326–3336 (2011)CrossRefGoogle Scholar
  26. 26.
    Jazdzewski, K., Liyanarachchi, S., Swierniak, M., Pachucki, J., Ringel, M.D., Jarzab, B., de la Chapelle, A.: Polymorphic mature microRNAs from passenger strand of pre-miR-146a contribute to thyroid cancer. Proc. Natl. Acad. Sci. USA 106, 1502–1505 (2009)CrossRefGoogle Scholar
  27. 27.
    Swierniak, M., Wojcicka, A., Czetwertynska, M., Stachlewska, E., Maciag, M., Wiechno, W., Gornicka, B., Bogdanska, M., Koperski, L., de la Chapelle, A., Jazdzewski, K.: In-depth characterization of the microRNA transcriptome in normal thyroid and papillary thyroid carcinoma. J. Clin. Endocrinol. Metab. (in print)Google Scholar
  28. 28.
    Langmead, B., Trapnell, C., Pop, M., Salzberg, S.L.: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome. Biol. 10(3), R25 (2009)Google Scholar
  29. 29.
    Li, H., Durbin, R.: Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics 25, 1754–1760 (2009)CrossRefGoogle Scholar
  30. 30.
    Goecks, J., Nekrutenko, A., Taylor, J.: The Galaxy Team: Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome. Biol. 11(8), R86 (2010)Google Scholar
  31. 31.
    Blankenberg, D., Von Kuster, G., Coraor, N., Ananda, G., Lazarus, R., Mangan, M., Nekrutenko, A., Taylor, J.: Galaxy: a web-based genome analysis tool for experimentalists. Curr. Protoc. in Mol. Biol. Chapter 19, Unit 19.10.1-21 (2010)Google Scholar
  32. 32.
    Giardine, B., Riemer, C., Hardison, R.C., Burhans, R., Elnitski, L., Shah, P., Zhang, Y., Blankenberg, D., Albert, I., Taylor, J., Miller, W., Kent, W.J., Nekrutenko, A.: Galaxy: a platform for interactive large-scale genome analysis. Genome Research 15(10), 1451–1455 (2005)CrossRefGoogle Scholar
  33. 33.
  34. 34.
    Martin, M.M.: Cutadapt removes adaptor sequences from high-throughput sequencing reads. EMBnet. Journal 17.1, 10–12 (2011)Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Michał Świerniak
    • 1
    • 2
  • Andrzej Świerniak
    • 3
  1. 1.Department of Nuclear Medicine and Endocrine OncologyMaria Sklodowska-Curie Memorial, Cancer Center and Institute of OncologyGliwicePoland
  2. 2.Department of General, Transplant, and Liver SurgeryMedical University of WarsawWarsawPoland
  3. 3.Department of Automatic ControlSilesian University of TechnologyGliwicePoland

Personalised recommendations