The role and use of microRNA in cancer diagnosis

Advances in Intelligent Systems and Computing

Volumn 230, Issue , 2014, Pages 225-233

  Świerniak, Michał ^a,b   Świerniak, Andrzej ^c  

^a INSTITUTE OF ONCOLOGY   (Poland)

^b MEDICAL UNIVERSITY OF WARSAW   (Poland)

^c SILESIAN UNIVERSITY OF TECHNOLOGY   (Poland)

Author keywords

Cancer; Medical diagnosis; MiRNAs; System biology

Indexed keywords

DIAGNOSIS; DISEASES; GENE EXPRESSION; MOLECULES;

CANCER; CANCER DIAGNOSIS; MICRORNAS; MIRNAS; SMALL RNA; SYSTEM BIOLOGY; THYROID CARCINOMA;

RNA;

EID: 84949114858     PISSN: 21945357     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-3-642-39881-0_18     Document Type: Conference Paper

References (34)

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)
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)
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)
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)
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)
6. Lee, R.C., Ambros, V.: An extensive class of small RNAs in Caenorhabditis elegans. Science 294, 862–864 (2001)
7. Bartel, D.P.: MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116, 281–297 (2004)
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)
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)
10. Griffiths-Jones, S.: miRBase: the microRNA sequence database. Methods Mol. Biol. 342, 129–138 (2006)
11. Brennecke, J., Stark, A., Russell, R.B., Cohen, S.M.: Principles of microRNA-target recognition. PLoS Biol. 3, e85 (2005)
12. Calin, G.A., Croce, C.M.: MicroRNA signatures in human cancers. Nat. Rev. Cancer 6, 857–866 (2006)
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)
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)
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)
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)
17. Chen, C.Z., Li, L., Lodish, H.F., Bartel, D.P.: MicroRNAs modulate hematopoietic lineage differentiation. Science 303, 83–86 (2004)
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)
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)
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)
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)
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)
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-beta 1. Breast Cancer Res. Treat 117, 131–140 (2009)
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)
25. de la Chapelle, A., Jazdzewski, K.: MicroRNAs in thyroid cancer. J. Clin. Endocrinol. Metab. 96, 3326–3336 (2011)
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)
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)
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)
29. Li, H., Durbin, R.: Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics 25, 1754–1760 (2009)
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)
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)
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)
33. Andrews, S.: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
34. Martin, M.M.: Cutadapt removes adaptor sequences from high-throughput sequencing reads. EMBnet. Journal 17.1, 10–12 (2011)