Recent technological advancements and methodologies have been developed to perform global analysis of tissue-specific ‘signatures’ of microRNAs in humans. The emerging view from such studies is that altered miRNA expression commonly occurs in a variety of cancers, which underscores the potential utility of miRNA profiling for diagnostic and prognostic applications. We present here a high-throughput methodology for miRNA profiling that is sufficiently sensitive for routine use on clinical specimens with limited starting material.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Ambros, V. 2003. MicroRNA pathways in flies and worms: growth, death, fat, stress, and timing.Cell 113: 673–676
Bartel, D. 2004. MicroRNAs: genomics, biogenesis,mechanism, and function.Cell 116: 281–297
Bartel, B., and Bartel, D.P. 2003. MicroRNAs: at the root of plant development?Plant Physiol.132: 709–717
Baskerville, S., and Bartel, D.P. 2005. Microarray profiling of microRNAs reveals frequent coex-pression with neighboring miRNAs and host genes.RNA 11: 241–247
Bentwich, I., Avniel, A., Karov, Y. , Aharonov, R.,Gilad, S., Barad, O., Barzilai, A., Einat, P.,Einav, U., Meiri, E., Sharon, E., Spector, Y., and Bentwich, Z. 2005. Identification of hundreds of conserved and nonconserved human microR-NAs.Nat. Genet.37: 766–770
Bohnsack, M.T., Czaplinsk, K., and Gorlich, D.2004. Exportin 5 is a RanGTP-dependent dsRNA-binding protein that mediates nuclear export of pre-miRNAs.RNA 10: 185–191
Cai, X., Hagedorn, C.H., and Cullen, B.R. 2004.Human microRNAs are processed from capped,polyadenylated transcripts that can also function as mRNAs.RNA 12: 1957–1966
Calin, G.A., Dumitru, C.D., Shimizu, M., Bichi,R., Zupo, S., Noch, E., Aldler, H., Rattan, S.,Keating, M., Rai, K., Rassenti, L., Kipps, T.,Negrini, M., Bullrich, F., and Croce, C.M. 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
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., Iuliano, R., Palumbo,T., Pichiorri, F., Roldo, C., Garzon, R., Sevignani,C., Rassenti, L., Alder, H., Volinia, S., Liu, C.G.,Kipps, T.J., Negrini, M., and Croce, C.M. 2005.A microRNA signature associated with prognosis and progression in chronic lymphocytic leukemia.N. Engl. J. Med.353: 1793–1801
Cao, X., Yeo, G., Muotri, A.R., Kuwabara, T., and Gage, F.H. 2006. Noncoding RNAs in mammalian central nervous system.Annul. Rev.Neurosci.29: 77–103
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., Lao, K.Q.,Livak, K.J., and Guegler, K.J. 2005. Real-time quantification of microRNAs by stemloop RT-PCR.Nucl. Acids Res.33: e179
Davison, T.S., Johnson, C.D., and Andruss, B.F. 2006. Analyzing microRNA expression using microarrays.Meth. Enzymol.411: 14–34
Einat, P. 2006. Methodologies for high-throughput expression profiling of microRNAs.Meth. Mol.Biol. 342: 139–157
Goff, L.A., Bowers, J., Schwalm, J., Howerton, K., Getts, R.C., and Hart, R.P. 2004. Evaluation of sense-strand mRNA amplification by comparative quantitative PCR.BMC Genomics 5: 76–80
Goff, L.A., Yang, M., Bowers, J., Getts, R.C.,Padgett, R.W., and Hart, R.P. 2005. Rational probe optimization and enhanced detection strategy for microRNAs using microarrays.RNA Biol. 2: E9–E16
Gregory, R.I., Chendrimada, T.P., Cooch, N., and Shiekhattar, R. 2005. Human RISC couples microRNA biogenesis and posttranscriptional gene silencing.Cell 123: 631–640
Griffiths-Jones, S., Grocock, R.J., van Dongen, S.,Bateman, A., and Enright, A.J. 2006. miRBase:microRNA sequences, targets and gene nomenclature.Nucl. Acids Res. 34: D140–D144
Hutvagner, G., and Zamore, P.D. 2002. A micro-RNA in a multiple turnover RNAi enzyme complex.Science 297: 2056–2060
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
John, B., Enright, A.J., Aravin, A., Tuschl, T.,Sander, C., and Marks, D.S. 2004. Human microRNA targets.PLoS 2:e363
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 thelet-7microRNA family.Cell 120: 635–647
Ketting, R.F., Fischer, S.E., Bernstein, E., Sijen, T.,Hannon, G.J., and Plasterk, R.H. 2001. Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans.Genes Dev.15: 2654–2659
Landgraf, P., Rusu, M., Sheridan, R., Sewer, A.,Iovino, N., Aravin, A., Pfeffer, S., Rice, A.,Kamphorst, A.O., Landthaler, M., Lin, C., Socci,N., Hermida, L., Fulci, V. , Chiaretti, S., Foa, R.,Schliwks, J., Fuchs, U., Novosel, A., Muller, R.-U., Schermer, B., Bissels, U., Inman, J., Phan,Q., Chien, M., Weir, D.B., Choksi, R., De Vita,G., Frezzetti, D., Trompeter, H.-I., Hornung,V., Teng, G., Hartmann, G., Palkovits, M., Di Lauro, R., Wernet, P., Macino, G., Rogler, C.E.,Nagle, J.W., Ju, J., Papavasilliou, F.N., Benzing,T., Lichter, P., Tam, W., Brownstein, M.J.,Bosio, A., Borkhardt, A., Russo, J.J., Sander, C.,Zavolan, M., and Tuschl, T. 2007. A mammalian microRNA expression atlas based on small RNA library sequencing.Cell 129: 1401–1414
Lawrie, C.H., Soneji, S., Marafioti, T., Cooper, C.D.,Palazzo, S., Paterson, J.C., Cattan, H., Enver,T., Mager, R., Boultwood, J., Wainscoat, J.S.,and Hatton, C.S. 2007. MicroRNA expression distinguishes between germinal center B celllike and activated B cell-like subtypes of diffuse large B cell lymphoma.Intl. J. Cancer 121:1156–1161
Lee, Y., Kim, M., Han, J., Yeom, K.H., Lee, S.,Baek, S.H., and Kim, V.N. 2004. MicroRNA genes are transcribed by RNA polymerase II.EMBO J.23: 4051–4060
Lewis, B.P., Shih, I.H., Jones-Rhoades, M.W., Bartel,D.P., and Burge, C.B. 2003. Prediction of mammalian microRNA targets.Cell 115: 787–798
Lin, S.L., Chang, D., and Ying, S.Y. 2005.Asymmetry of intronic pre-miRNA structures in functional RISC assembly.Gene 356:32–38
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., and Golub, T.R. 2005.MicroRNA expression profiles classify human cancers.Nature 435: 834–838
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
Nilsen, T.W., Grazel, J., and Prensky, W. 1997.Dendritic Nucleic Acid Structures.J. Theor.Biol.187: 273–284
Olsen, P.H., and Ambros, V. 1999. Thelin-4regulatory RNA controls developmental timing inCaenorhabditis elegansby blocking LIN-14 protein synthesis after the initiation of translation.Dev. Biol.216: 671–680
Plasterk, R.H. 2006. MicroRNAs in animal development.Cell 124: 877–881
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
Schmittgen, T.D., Jiang, J., Liu, Q., and Yang, L.2004. A high-throughput method to monitor the expression of microRNA precursors.Nucl. Acids Res.32: e43
Shi, R., and Chiang, V.L. 2005. Facile means for quantifying microRNA expression by real-time PCR.Biotechniques 39: 519–525
Shivdasani, R.A. 2006. MicroRNAs: regulators of gene expression and cell differentiation.Blood 108: 3646–3653
Stears, R.L., Getts, R.C., and Gullans, S.R. 2000.A novel, sensitive detection system for high-density microarrays using dendrimer technology.Physiol. Genomics 3: 93–99
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 thelet-7microRNAs in human lung cancers in association with shortened postoperative survival.Cancer Res.64: 3753–3756
Wilson, J.F. 2006. The rocky road to useful cancer biomarkers.Ann. Intern. Med.144:945–948
Yanaihara, N., Caplen, N., Bowman, E., Seike, M.,Kumanoto, K., Yi, M., Stephens, R., Okamoto,A., Yokota, J., Tanaka, T., Calin, G., Liu, C.,Croce, C., and Harris, C. 2006. Unique micro-RNA molecular profiles in lung cancer diagnosis and prognosis.Cancer Cell 9: 189–198
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2008 Springer Science + Business Media B.V.
About this chapter
Cite this chapter
Mattie, M.D., Getts, R.C. (2008). Breast and Prostate Biopsies: Use of Optimized High-Throughput MicroRNA Expression for Diagnosis (Methodology). In: Hayat, M.A. (eds) Methods of Cancer Diagnosis, Therapy and Prognosis. Methods of Cancer Diagnosis, Therapy and Prognosis, vol 1. Springer, Dordrecht. https://doi.org/10.1007/978-1-4020-8369-3_5
Download citation
DOI: https://doi.org/10.1007/978-1-4020-8369-3_5
Publisher Name: Springer, Dordrecht
Print ISBN: 978-1-4020-8368-6
Online ISBN: 978-1-4020-8369-3
eBook Packages: MedicineMedicine (R0)