High throughput microRNAs profiling in cancers

doi:10.1017/CBO9780511541766.026

23 - High throughput microRNAs profiling in cancers

from V - MicroRNAs in disease biology

Published online by Cambridge University Press: 22 August 2009

Muller Fabbri ,

Ramiro Garzon ,

Amelia Cimmino ,

George Adrian Calin and

Carlo Maria Croce

Edited by

Krishnarao Appasani

Foreword by

Sidney Altman and

Victor R. Ambros

Show author details

Muller Fabbri: Affiliation:
Center for Human Cancer Genetics The Ohio State University Comprehensive Cancer Center 385L Comprehensive Cancer Center 410 West 10th Avenue Columbus, OH 43210 USA
Ramiro Garzon: Affiliation:
Center for Human Cancer Genetics The Ohio State University Comprehensive Cancer Center 385L Comprehensive Cancer Center 410 West 10th Avenue Columbus, OH 43210 USA
Amelia Cimmino: Affiliation:
Center for Human Cancer Genetics The Ohio State University Comprehensive Cancer Center 385L Comprehensive Cancer Center 410 West 10th Avenue Columbus, OH 43210 USA
George Adrian Calin: Affiliation:
Center for Human Cancer Genetics The Ohio State University Comprehensive Cancer Center 385L Comprehensive Cancer Center 410 West 10th Avenue Columbus, OH 43210 USA
Carlo Maria Croce: Affiliation:
Center for Human Cancer Genetics The Ohio State University Comprehensive Cancer Center 385L Comprehensive Cancer Center 410 West 10th Avenue Columbus, OH 43210 USA

Book contents

Get access

Summary

Introduction

MicroRNAs are small noncoding RNAgenes (18–24 nucleotides in length) that have been identified in different organisms from the nematode C. elegans to humans (for reviews see Bartel, 2004; He and Hannon, 2004). Recently it has become more and more evident that microRNAs play important roles in regulating the translation and degradation of mRNAs through base pairing to perfectly (in plants) or partially (in mammals) complementary sites, mainly but not exclusively in the untranslated region (UTR) of the target mRNA (Lagos-Quintana et al., 2001; Lau et al., 2001; Lee and Ambros, 2001). MicroRNAs are initially transcribed by RNA polymerase II (pol II) as long primary transcripts called primary-miRNAs (pri-miRNAs). A double-stranded RNA-specific ribonuclease called Drosha is responsible for the processing of pri-miRNAs into hairpin RNAs of 70–100bp known as pre-miRNAs, which contain a two nucleotide 3′ overhang characteristic of RNase III cleavage products (Cullen, 2004). Pre-miRNAs are transported to the cytoplasm by the nuclear export factor exportin 5. Once in the cytoplasm pre-miRNAs are processed by a second, double-stranded specific ribonuclease III called Dicer in a 18–24 nucleotide duplex. The product of Dicer's cleavage is incorporated into a large protein complex called RISC (RNA-induced silencing complex), which includes as core components the Argonaute proteins (Ago1–4 in humans). One strand of the miRNA duplex remains stably associated with RISC and becomes the mature miRNA. The opposite strand, called passenger strand or miRNA, is discarded through two different mechanisms.

Type: Chapter
Information: MicroRNAs
From Basic Science to Disease Biology
, pp. 309 - 321

DOI: https://doi.org/10.1017/CBO9780511541766.026 [Opens in a new window]

Publisher: Cambridge University Press

Print publication year: 2007

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Bartel, D. P. (2004). MicroRNAs: genomics, biogenesis, mechanism, and function. Cell, 23, 281–297.Google Scholar

Calin, G. A. and Croce, C. M. (2006a). MicroRNA – cancer connection: the beginning of a new tale. Cancer Research. (In press.)Google Scholar

Calin, G. A. and Croce, C. M. (2006b). Genomics of CLL: MicroRNAs as new players with clinical significance. Seminars in Oncology, 33, 167–173.Google Scholar

Calin, G. A., Dumitru, C. D., Shimizu, M.et al. (2002). Frequent deletions and down-regulation of micro-RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia. Proceedings of the National Academy of Sciences USA, 99, 15 524–15 529.Google Scholar

Calin, G. A., Sevignani, C., Dumitru, C. D.et al. (2004). Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers. Proceedings of the National Academy of Sciences USA, 101, 2999–3004.Google Scholar

Calin, G. A., Ferracin, M., Cimmino, A.et al. (2005). A microRNA signature associated with prognosis and progression in chronic lymphocytic leukemia. New England Journal of Medicine, 353, 1793–1801.Google Scholar

Chan, J. A., Krichevsky, A. M. and Kosik, K. S. (2005). MicroRNA-21 is an antiapoptotic factor in human glioblastoma cells. Cancer Research, 65, 6029–6033.Google Scholar

Ciafrè, S. A., Galardi, S., Mangiola, A.et al. (2005). Extensive modulation of a set of microRNAs in primary glioblastoma. Biochemical Biophysical Research Communications, 334, 1351–1358.Google Scholar

Cimmino, A., Calin, G. A., Fabbri, M.et al. (2005). MiR-15 and miR-16 induce apoptosis by targeting BCL2. Proceedings of the National Academy of Sciences USA, 102, 13 944–13 949.Google Scholar

Costinean, S., Zanesi, N., Pekarsky, Y.et al. (2006). Pre B cell proliferation and lymphoblastic leucemia/high grade lymphoma in Eμ miR155 transgenic mice. Proceedings of the National Academy of Sciences USA, 2006 Apr 25 [Epub ahead of print].Google Scholar

Croce, C. M. and Calin, G. A. (2006). miRNAs, cancer, and stem cell division. Cell, 15, 122, 6–7.Google Scholar

Cullen, B. R. (2004). Transcription and processing of human microRNA precursors. Molecular Cell, 16, 861–865.Google Scholar

Dong, J. T., Boyd, J. C. and Frierson, H. F. Jr. (2001). Loss of heterozygosity at 13q14 and 13q21 in high grade, high stage prostate cancer. Prostate, 49, 166–171.Google Scholar

Eis, P. S., Tam, W., Sun, L.et al. (2005). Accumulation of miR-155 and BIC RNA in human B cell lymphomas. Proceedings of the National Academy of Sciences USA, 102, 3627–3632.Google Scholar

Elnenaei, M. O., Hamoudi, R. A., Swansbury, J.et al. (2003). Delineation of the minimal region of loss at 13q14 in multiple myeloma. Genes Chromosomes Cancer, 36, 99–106.Google Scholar

Esquela-Kerscher, A. and Slack, F. J. (2004). The age of high-throughput microRNA profiling. Nature Methods, 1, 106–107.Google Scholar

Fazi, F., Rosa, A., Fatica, A.et al. (2005). A minicircuitry comprised of microRNA-223 and transcription factors NFI-A and C/EBPalpha regulates human granulopoiesis. Cell, 123, 819–831.Google Scholar

Felli, N., Fontana, L., Pelosi, E.et al. (2005). MicroRNAs 221 and 222 inhibit normal erythropoiesis and erythroleukemic cell growth via kit receptor down-modulation. Proceedings of the National Academy of Sciences USA, 102, 18 081–18 086.Google Scholar

Garzon, R., Pichiorri, F., Palumbo, T.et al. (2006). MicroRNA fingerprints during human megakaryocytopoiesis. Proceedings of the National Academy of Sciences USA, 103, 5078–5083.Google Scholar

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.Google Scholar

Hayashita, Y., Osada, H., Tatematsu, Y.et al. (2005). A polycistronic microRNA cluster, miR-17-92, is overexpressed in human lung cancers and enhances cell proliferation. Cancer Research, 65, 9628–9632.Google Scholar

He, H., Jazdzewski, K., Li, W.et al. (2005). The role of microRNA genes in papillary thyroid carcinoma. Proceedings of the National Academy of Sciences USA, 102, 19 075–19 080.Google Scholar

He, L. and Hannon, G. J. (2004). MicroRNAs: small RNAs with a big role in gene regulation. Nature Reviews Genetics, 5, 522–531.Google Scholar

He, L., Thomson, J. M., Hemann, M. T.et al. (2005). A microRNA polycistron as a potential human oncogene. Nature, 435, 828–833.Google Scholar

Iorio, M. V., Ferracin, M., Liu, C. G.et al. (2005). MicroRNA gene expression deregulation in human breast cancer. Cancer Research, 65, 7065–7070.Google Scholar

Johnson, S. M., Grosshans, H., Shingara, J.et al. (2005). RAS is regulated by the let-7 microRNA family. Cell, 120, 635–647.Google Scholar

Joos, S., Haluska, F. G., Falk, M. H.et al. (1992). Mapping chromosomal breakpoints of Burkitt's t(8;14) translocations far upstream of c-myc. Cancer Res, 52, 6547–6552.Google Scholar

Kluiver, J., Poppema, S., Jong, D.et al. (2005). BIC and miR-155 are highly expressed in Hodgkin, primary mediastinal and diffuse large B cell lymphomas. Journal of Pathology, 207, 243–249.Google Scholar

Kluiver, J., Haralambieva, E., Jong, D.et al. (2006). Lack of BIC and microRNA miR-155 expression in primary cases of Burkitt lymphoma. Genes Chromosomes Cancer, 45, 147–153.Google Scholar

Lagos-Quintana, M., Rauhut, R., Lendeckel, W. and Tuschl, T. (2001). Identification of novel genes coding for small expressed RNAs. Science, 294, 853–858.Google Scholar

Lagos-Quintana, M., Rauhut, R., Yalcin, A.et al. (2002). Identification of tissue-specific microRNAs from mouse. Current Biology, 12, 735–739.Google Scholar

Lau, N. C., Lim, L. P., Weinstein, E. G. and Bartel, D. P. (2001). An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science, 294, 858–862.Google Scholar

Lee, R. C. and Ambros, V. (2001). An extensive class of small RNAs in Caenorhabditis elegans. Science, 294, 862–864.Google Scholar

Liu, C. G., Calin, G. A., Meloon, B.et al. (2004). An oligonucleotide microchip for genome-wide microRNA profiling in human and mouse tissues. Proceedings of the National Academy of Sciences USA, 101, 9740–9744.Google Scholar

Lu, J., Getz, G., Miska, E. A.et al. (2005). MicroRNA expression profiles classify human cancers. Nature, 435, 834–838.Google Scholar

Matranga, C., Tomari, Y., Shin, C., Bartel, D. P. and Zamore, P. D. (2005). Passenger-strand cleavage facilitates assembly of siRNA into Ago2-containing RNAi enzyme complexes. Cell, 123, 607–620.Google Scholar

Metzler, M., Wilda, M., Busch, K., Viehmann, S. and Borkhardt, A. (2004). High expression of precursor microRNA-155/BIC RNA in children with Burkitt lymphoma. Genes Chromosomes Cancer, 39, 167–169.Google Scholar

Michael, M. Z., O' Connor, S. M., Pellekaan, Holst N. G., Young, G. P. and James, R. J. (2003). Reduced accumulation of specific microRNAs in colorectal neoplasia. Molecular Cancer Research, 1, 882–891.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.Google Scholar

Rand, T. A., Petersen, S., Du, F. and Wang, X. (2005). Argonaute2 cleaves the anti-guide strand of siRNA during RISC activation. Cell, 123, 621–629.Google Scholar

Sanchez-Beato, M., Sanchez-Aguilera, A. and Piris, M. A. (2003). Cell cycle deregulation in B-cell lymphomas. Blood, 101, 1220–1235.Google Scholar

Sanchez-Izquierdo, D., Buchonnet, G., Siebert, R.et al. (2003). MALT1 is deregulated by both chromosomal translocation and amplification in B-cell non-Hodgkin lymphoma. Blood, 101, 4539–4546.Google Scholar

Seitz, H., Royo, H., Bortolin, M. L.et al. (2004). A large imprinted microRNA gene cluster at the mouse Dlk1-Gtl2 domain. Genome Research, 14, 1741–1748.Google Scholar

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

Stilgenbauer, S., Nickolenko, J., Wilhelm, J.et al. (1998). Expressed sequences as candidates for a novel tumor suppressor gene at band 13q14 in B-cell chronic lymphocytic leukemia and mantle cell lymphoma. Oncogene, 16, 1891–1897.Google Scholar

Takamizawa, J., Konishi, H., Yanagisawa, K.et al. (2004). Reduced expression of the let-7 microRNAs in human lung cancers in association with shortened postoperative survival. Cancer Research, 64, 3753–3756.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.Google Scholar

Volinia, S., Calin, G. A., Liu, C. G.et al. (2005). A microRNA expression signature of human solid tumors defines cancer gene targets. Proceedings of the National Academy of Sciences USA, 103, 2257–2261.Google Scholar

Yanaihara, N., Caplen, N., Bowman, E.et al. (2006). Unique microRNA molecular profiles in lung cancer diagnosis and prognosis. Cancer Cell, 9, 189–198.Google Scholar

Book contents

23 - High throughput microRNAs profiling in cancers

Summary

Access options

References

Save book to Kindle

Save book to Dropbox

Save book to Google Drive