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Detection of MicroRNAs in Prostate Cancer Cells by MicroRNA Array

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MicroRNAs in Development

Part of the book series: Methods in Molecular Biology ((MIMB,volume 732))

Abstract

MicroRNAs (miRNAs) are a novel class of small noncoding RNAs that regulate gene expression at the posttranscriptional level and play a critical role in many important biological processes and pathological development. In the past few years, miRNAs have been implicated to play an important role in cancer initiation and development. In this chapter, we describe a protocol for the analysis and characterization of miRNAs in prostate cancer cells using a simple but effective array platform. The array is composed of 553 nonredundant miRNAs encompassing the entire set of known miRNAs in humans and mice. As an example, profiling of miRNAs in four prostate cancer cell lines has revealed that a set of miRNAs were differentially expressed between androgen-dependent and androgen-independent metastatic prostate cancer cells. Among them, the differential expression of miR-205 and miR-200c were further validated by Northern blot analysis in these two types of prostate cancer cells. This comprehensive and easy-to-follow protocol will be useful for studying miRNAs in various cancers and can be readily adapted for miRNA analysis in a variety of human diseases.

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References

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

    Article  PubMed  CAS  Google Scholar 

  2. Berezikov, E., Cuppen, E., and Plasterk, R. H. (2006) Approaches to microRNA discovery. Nat Genet 38 Suppl, S2–7.

    Google Scholar 

  3. Jones-Rhoades, M. W., Bartel, D. P., and Bartel, B. (2006) MicroRNAS and their regulatory roles in plants. Annu Rev Plant Biol 57, 19–53.

    Article  PubMed  CAS  Google Scholar 

  4. Griffiths-Jones, S. (2006) miRBase: the microRNA sequence database. Methods Mol Biol 342, 129–138.

    PubMed  CAS  Google Scholar 

  5. Griffiths-Jones, S., Saini, H. K., van Dongen, S., and Enright, A. J. (2008) miRBase: tools for microRNA genomics. Nucleic Acids Res 36, D154–158.

    Article  PubMed  CAS  Google Scholar 

  6. Bentwich, I. (2005) Prediction and validation of microRNAs and their targets. FEBS Lett 579, 5904–5910.

    Article  PubMed  CAS  Google Scholar 

  7. 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 

  8. Miranda, K. C., Huynh, T., Tay, Y., Ang, Y. S., Tam, W. L., Thomson, A. M., Lim, B., and Rigoutsos, I. (2006) A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes. Cell 126, 1203–1217.

    Article  PubMed  CAS  Google Scholar 

  9. Xie, X., Lu, J., Kulbokas, E. J., Golub, T. R., Mootha, V., Lindblad-Toh, K., Lander, E. S., and Kellis, M. (2005) Systematic discovery of regulatory motifs in human promoters and 3’ UTRs by comparison of several mammals. Nature 434, 338–345.

    Article  PubMed  CAS  Google Scholar 

  10. Calin, G. A., Liu, C. G., Sevignani, C., Ferracin, M., Felli, N., Dumitru, C. D., Shimizu, M., Cimmino, A., Zupo, S., Dono, M., Dell’Aquila, M. L., Alder, H., Rassenti, L., Kipps, T. J., Bullrich, F., Negrini, M., and Croce, C. M. (2004) MicroRNA profiling reveals distinct signatures in B cell chronic lymphocytic leukemias. Proc Natl Acad Sci USA 101, 11755–11760.

    Article  PubMed  CAS  Google Scholar 

  11. Hayashita, Y., Osada, H., Tatematsu, Y., Yamada, H., Yanagisawa, K., Tomida, S., Yatabe, Y., Kawahara, K., Sekido, Y., and 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.

    Article  PubMed  CAS  Google Scholar 

  12. Pallante, P., Visone, R., Ferracin, M., Ferraro, A., Berlingieri, M. T., Troncone, G., Chiappetta, G., Liu, C. G., Santoro, M., Negrini, M., Croce, C. M., and Fusco, A. (2006) MicroRNA deregulation in human thyroid papillary carcinomas. Endocr Relat Cancer 13, 497–508.

    Article  PubMed  CAS  Google Scholar 

  13. Volinia, S., Calin, G. A., Liu, C. G., Ambs, S., Cimmino, A., Petrocca, F., Visone, R., Iorio, M., Roldo, C., Ferracin, M., Prueitt, R. L., Yanaihara, N., Lanza, G., Scarpa, A., Vecchione, A., Negrini, M., Harris, C. C., and Croce, C. M. (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 

  14. Yue, J., and Tigyi, G. (2006) MicroRNA Trafficking and Human Cancer. Cancer Biol Ther 5, 573–578.

    Article  PubMed  CAS  Google Scholar 

  15. Calin, G. A., and Croce, C. M. (2006) MicroRNA-Cancer Connection: The Beginning of a New Tale. Cancer Res 66, 7390–7394.

    Article  PubMed  CAS  Google Scholar 

  16. Croce, C. M. (2009) Causes and consequences of microRNA dysregulation in cancer. Nat Rev Genet 10, 704–714.

    Article  PubMed  CAS  Google Scholar 

  17. Esquela-Kerscher, A., and Slack, F. J. (2006) Oncomirs - microRNAs with a role in cancer. Nat Rev Cancer 6, 259–269.

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  19. McManus, M. T. (2003) MicroRNAs and cancer. Semin Cancer Biol 13, 253–258.

    Article  PubMed  CAS  Google Scholar 

  20. Slack, F. J., and Weidhaas, J. B. (2006) MicroRNAs as a potential magic bullet in cancer. Future Oncol 2, 73–82.

    Article  PubMed  CAS  Google Scholar 

  21. Iorio, M. V., Casalini, P., Tagliabue, E., Menard, S., and Croce, C. M. (2008) MicroRNA profiling as a tool to understand prognosis, therapy response and resistance in breast cancer. Eur J Cancer 44, 2753–2759.

    Article  PubMed  CAS  Google Scholar 

  22. Mattie, M. D., Benz, C. C., Bowers, J., Sensinger, K., Wong, L., Scott, G. K., Fedele, V., Ginzinger, D., Getts, R., and Haqq, C. (2006) Optimized high-throughput microRNA expression profiling provides novel biomarker assessment of clinical prostate and breast cancer biopsies. Mol Cancer 5, 24.

    Article  PubMed  Google Scholar 

  23. Yang, N., Kaur, S., Volinia, S., Greshock, J., Lassus, H., Hasegawa, K., Liang, S., Leminen, A., Deng, S., Smith, L., Johnstone, C. N., Chen, X. M., Liu, C. G., Huang, Q., Katsaros, D., Calin, G. A., Weber, B. L., Butzow, R., Croce, C. M., Coukos, G., and Zhang, L. (2008) MicroRNA microarray identifies Let-7i as a novel biomarker and therapeutic target in human epithelial ovarian cancer. Cancer Res 68, 10307–10314.

    Article  PubMed  CAS  Google Scholar 

  24. Iorio, M. V., Ferracin, M., Liu, C. G., Veronese, A., Spizzo, R., Sabbioni, S., Magri, E., Pedriali, M., Fabbri, M., Campiglio, M., Menard, S., Palazzo, J. P., Rosenberg, A., Musiani, P., Volinia, S., Nenci, I., Calin, G. A., Querzoli, P., Negrini, M., and Croce, C. M. (2005) MicroRNA gene expression deregulation in human breast cancer. Cancer Res 65, 7065–7070.

    Article  PubMed  CAS  Google Scholar 

  25. Ciafre, S. A., Galardi, S., Mangiola, A., Ferracin, M., Liu, C. G., Sabatino, G., Negrini, M., Maira, G., Croce, C. M., and Farace, M. G. (2005) Extensive modulation of a set of microRNAs in primary glioblastoma. Biochem Biophys Res Commun 334, 1351–1358.

    Article  PubMed  CAS  Google Scholar 

  26. Murakami, Y., Yasuda, T., Saigo, K., Urashima, T., Toyoda, H., Okanoue, T., and Shimotohno, K. (2005) Comprehensive analysis of microRNA expression patterns in hepatocellular carcinoma and non-tumorous tissues. 25, 2537–2545.

    Google Scholar 

  27. 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., and de la Chapelle, A. (2005) The role of microRNA genes in papillary ­thyroid carcinoma. Proc Natl Acad Sci USA 102, 19075–19080.

    Article  PubMed  CAS  Google Scholar 

  28. Takamizawa, J., Konishi, H., Yanagisawa, K., Tomida, S., Osada, H., Endoh, H., Harano, T., Yatabe, Y., Nagino, M., Nimura, Y., Mitsudomi, T., and Takahashi, T. (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 

  29. Yanaihara, N., Caplen, N., Bowman, E., Seike, M., Kumamoto, K., Yi, M., Stephens, R. M., Okamoto, A., Yokota, J., Tanaka, T., Calin, G. A., Liu, C. G., Croce, C. M., and Harris, C. C. (2006) Unique microRNA molecular profiles in lung cancer diagnosis and prognosis. Cancer Cell 9, 189–198.

    Article  PubMed  CAS  Google Scholar 

  30. Michael, M. Z., SM, O. C., van Holst Pellekaan, N. G., Young, G. P., and James, R. J. (2003) Reduced accumulation of specific microRNAs in colorectal neoplasia. Mol Cancer Res 1, 882–891.

    PubMed  CAS  Google Scholar 

  31. Bandyopadhyay, S., Mitra, R., Maulik, U., and Zhang, M. (2010) Development of the human cancer microRNA network. Silence 1, 6.

    Article  PubMed  Google Scholar 

  32. Greenlee, R. T., Murray, T., Bolden, S., and Wingo, P. A. (2000) Cancer statistics, 2000. CA Cancer J Clin 50, 7–33.

    Article  PubMed  CAS  Google Scholar 

  33. Jiang, J., Lee, E. J., Gusev, Y., and Schmittgen, T. D. (2005) Real-time expression profiling of microRNA precursors in human cancer cell lines. Nucleic Acids Res 33, 5394–5403.

    Article  PubMed  CAS  Google Scholar 

  34. Leite, K. R., Canavez, J. M., Reis, S. T., Tomiyama, A. H., Piantino, C. B., Sanudo, A., Camara-Lopes, L. H., and Srougi, M. (2010) miRNA analysis of prostate cancer by quantitative real time PCR: Comparison between formalin-fixed paraffin embedded and fresh-frozen tissue. Urol Oncol. doi:10.1016/j.urolonc.2009.05.008.

  35. Lin, S. L., Chang, D., and Ying, S. Y. (2007) Hyaluronan stimulates transformation of androgen-independent prostate cancer. Carcinogenesis, 28, 310–20.

    Article  PubMed  CAS  Google Scholar 

  36. Shi, X. B., Xue, L., Yang, J., Ma, A. H., Zhao, J., Xu, M., Tepper, C. G., Evans, C. P., Kung, H. J., and deVere White, R. W. (2007) An androgen-regulated miRNA suppresses Bak1 expression and induces androgen-independent growth of prostate cancer cells. Proc Natl Acad Sci USA 104, 19983–19988.

    Article  PubMed  CAS  Google Scholar 

  37. Ambs, S., Prueitt, R. L., Yi, M., Hudson, R. S., Howe, T. M., Petrocca, F., Wallace, T. A., Liu, C. G., Volinia, S., Calin, G. A., Yfantis, H. G., Stephens, R. M., and Croce, C. M. (2008) Genomic profiling of microRNA and messenger RNA reveals deregulated microRNA expression in prostate cancer. Cancer Res 68, 6162–6170.

    Article  PubMed  CAS  Google Scholar 

  38. Lee, K. H., Chen, Y. L., Yeh, S. D., Hsiao, M., Lin, J. T., Goan, Y. G., and Lu, P. J. (2009) MicroRNA-330 acts as tumor suppressor and induces apoptosis of prostate cancer cells through E2F1-mediated suppression of Akt phosphorylation. Oncogene 28, 3360–3370.

    Article  PubMed  CAS  Google Scholar 

  39. Li, T., Li, D., Sha, J., Sun, P., and Huang, Y. (2009) MicroRNA-21 directly targets MARCKS and promotes apoptosis resistance and invasion in prostate cancer cells. Biochem Biophys Res Commun 383, 280–285.

    Article  PubMed  CAS  Google Scholar 

  40. Ozen, M., Creighton, C. J., Ozdemir, M., and Ittmann, M. (2008) Widespread deregulation of microRNA expression in human prostate cancer. Oncogene 27, 1788–1793.

    Article  PubMed  CAS  Google Scholar 

  41. 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.

    Article  PubMed  CAS  Google Scholar 

  42. Ribas, J., Ni, X., Haffner, M., Wentzel, E. A., Salmasi, A. H., Chowdhury, W. H., Kudrolli, T. A., Yegnasubramanian, S., Luo, J., Rodriguez, R., Mendell, J. T., and Lupold, S. E. (2009) miR-21: an androgen receptor-regulated microRNA that promotes hormone-dependent and hormone-independent prostate cancer growth. Cancer Res 69, 7165–7169.

    Article  PubMed  CAS  Google Scholar 

  43. Rokhlin, O. W., Scheinker, V. S., Taghiyev, A. F., Bumcrot, D., Glover, R. A., and Cohen, M. B. (2008) MicroRNA-34 mediates AR-dependent p53-induced apoptosis in prostate cancer. Cancer Biol Ther 7, 1288–1296.

    Article  PubMed  CAS  Google Scholar 

  44. Spahn, M., Kneitz, S., Scholz, C. J., Nico, S., Rudiger, T., Strobel, P., Riedmiller, H., and Kneitz, B. (2010) Expression of microRNA-221 is progressively reduced in aggressive prostate cancer and metastasis and predicts clinical recurrence. Int J Cancer. doi: 10.1002/ijc.24715

  45. Sun, T., Wang, Q., Balk, S., Brown, M., Lee, G. S., and Kantoff, P. (2009) The role of microRNA-221 and microRNA-222 in androgen-independent prostate cancer cell lines. Cancer Res 69, 3356–3363.

    Article  PubMed  CAS  Google Scholar 

  46. Wang, G., Wang, Y., Feng, W., Wang, X., Yang, J. Y., Zhao, Y., and Liu, Y. (2008) Transcription factor and microRNA regulation in androgen-dependent and -independent prostate cancer cells. BMC Genomics 9 Suppl 2, S22.

    Google Scholar 

  47. Tang, X., Gal, J., Zhuang, X., Wang, W., Zhu, H., and Tang, G. (2007) A simple array platform for microRNA analysis and its ­application in mouse tissues. RNA 13, 1803–1822.

    Article  PubMed  CAS  Google Scholar 

  48. de Hoon, M. J. L., Imoto, S., Nolan, J., and Miyano, S. (2004) Open source clustering software. Bioinformatics 20, 1453–1454.

    Article  PubMed  Google Scholar 

  49. Saldanha, A. J. (2004) Java Treeview--extensible visualization of microarray data. Bioinformatics 20, 3246–3248.

    Article  PubMed  CAS  Google Scholar 

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Acknowledgments

X. T. is supported by NIH/NIDDK K01 award (K01DK078648) and R03DK08166. G.T. is supported by the Kentucky Tobacco Research and Development Center (KTRDC), the USDA-NRI grants 2006-35301-17115 and 2006-35100-17433, the NSF MCB-0718029 (Subaward No. S-00000260), and an award from the Kentucky Science and Technology Corporation under Contract # KSTC-144-401-08-029. This work was partially supported by DOD Synergistic Idea Development Awards W81XWH-08-1-0430 (to H.Z.) and W81XWH-08-1-0431 (to N.K.).

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Authors and Affiliations

  1. Department of Plant and Soil Sciences & KTRDC, University of Kentucky, Lexington, KY, USA

    Guiliang Tang

Authors
  1. Xiaoqing Tang
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  2. Xiaohu Tang
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  3. Jozsef Gal
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  4. Natasha Kyprianou
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  5. Haining Zhu
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  6. Guiliang Tang
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Correspondence to Guiliang Tang .

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Editors and Affiliations

  1. School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom

    Tamas Dalmay

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© 2011 Humana Press

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Tang, X., Tang, X., Gal, J., Kyprianou, N., Zhu, H., Tang, G. (2011). Detection of MicroRNAs in Prostate Cancer Cells by MicroRNA Array. In: Dalmay, T. (eds) MicroRNAs in Development. Methods in Molecular Biology, vol 732. Humana Press. https://doi.org/10.1007/978-1-61779-083-6_6

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  • DOI: https://doi.org/10.1007/978-1-61779-083-6_6

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  • Publisher Name: Humana Press

  • Print ISBN: 978-1-61779-082-9

  • Online ISBN: 978-1-61779-083-6

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