MicroRNA signatures in human cancers
Tóm tắt
Từ khóa
Tài liệu tham khảo
Furuno, M. et al. Clusters of internally primed transcripts reveal novel long noncoding RNAs. PLoS Genet. 2, e37 (2006).
Lee, R. C., Feinbaum, R. L. & Ambros, V. A short history of a short RNA. Cell S116, S89–S92 (2004). The history of the first ever miRNA identification by Ambros's group.
Berezikov, E., Cuppen, E. & Plasterk, R. H. Approaches to microRNA discovery. Nature Genet. 38, (Suppl.) S2–S7 (2006).
Lagos-Quintana, M., Rauhut, R., Lendeckel, W. & Tuschl, T. Identification of novel genes coding for small expressed RNA. Science 294, 853–858 (2001).
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).
Lee, R. C. & Ambros, V. An extensive class of small RNAs in Caenorhabditis elegans. Science 294, 862–864 (2001).
Pasquinelli, A. E., Hunter, S. & Bracht, J. MicroRNAs: a developing story. Curr. Opin. Genet. Dev. 15, 200–205 (2005).
Bartel, D. P. & Chen, C. Z. Micromanagers of gene expression: the potentially widespread influence of metazoan microRNAs. Nature Rev. Genet. 5, 396–400 (2004). An interesting perspective on how miRNAs influence gene expression.
Lim, L. P. et al. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433, 769–773 (2005).
Griffiths-Jones, S., Grocock, R. J., van Dongen, S., Bateman, A. & Enright, A. J. miRBase: microRNA sequences, targets and gene nomenclature. NAR Database Issue, D140–D144 (2006). A description of miRBase, the extensive database of all annotated miRNAs.
Lim, L. P., Glasner, M. E., Yekta, S., Burge, C. B. & Bartel, D. P. Vertebrate microRNA genes. Science 299, 1540 (2003).
Xie, X. et al. Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. Nature 434, 338–345 (2005).
Berezikov, E. et al. Phylogenetic shadowing and computational identification of human microRNA genes. Cell 120, 21–24 (2005).
Bentwich, I. et al. Identification of hundreds of conserved and nonconserved human microRNAs. Nature Genet. 37, 766–770 (2005).
Calin, G. A. et al. Frequent deletions and down-regulation of micro- RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia. Proc. Natl Acad. Sci. USA 99, 15524–15529 (2002). The first demonstration of a link between miRNA genes and cancer.
Berezikov, E. & Plasterk, R. H. Camels and zebrafish, viruses and cancer: a microRNA update. Hum. Mol. Genet. 14, R183–R190 (2005).
Calin, G. A. & Croce, C. M. MicroRNA-cancer connection: the beginning of a new tale. Cancer Res. 66, 7390–7394 (2006).
Calin, G. A., Garzon, R., Cimmino, A., Fabbri, M. & Croce, C. M. MicroRNAs and leukemias: how strong is the connection? Leuk. Res. 30, 653–655 (2005).
Hwang, H. W. & Mendell, J. T. MicroRNAs in cell proliferation, cell death, and tumorigenesis. Br. J. Cancer. 94, 776–780 (2006).
Esquela-Kerscher, A. & Slack, F. J. Oncomirs- microRNAs with a role in cancer. Nature Rev. Cancer 6, 259–269 (2006). An excellent review on the role of miRNAs in human cancers.
Calin, G. A. et al. A unique microRNA signature associated with prognostic factors and disease progression in B cell chronic lymphocytic leukemia. N. Engl. J. Med. 352, 1667–1676 (2005). The first evidence of germline and somatic mutations in miRNA genes.
Diederichs, S. & Haber, D. A. Sequence variations of microRNAs in human cancer: alterations in predicted secondary structure do not affect processing. Cancer Res. 66, 6097–6104 (2006).
He, H. et al. The role of microRNA genes in papillary thyroid carcinoma. Proc. Natl Acad. Sci. USA 102, 19075–19080 (2005). The first report about germline alterations in miRNA-recognition sequences located in a messenger RNA.
Abelson, J. F. et al. Sequence variants in SLITRK1 are associated with Tourette's syndrome. Science 310, 317–320 (2005).
Liu, C.-G. et al. An oligonucleotide microchip for genome-wide miRNA profiling in human and mouse tissues. Proc. Natl Acad. Sci. USA 101, 9740–9744 (2004). The first study to report on miRNA profiling using an oligonucleotide microchip.
Lu, J. et al. MicroRNA expression profiles classify human cancers. Nature 435, 834–838 (2005). A comprehensive study of miRNA expression in various human cancers by a new method: bead-based miRNA profiling.
Schmittgen, T. D., Jiang, J., Liu, Q. & yang, L. A high-throughput method to monitor the expression of microRNA precursor. Nucleic Acids Res. 32, 43–53 (2004). The first quantitative real-time PCR developed for miRNA profiling, designed for the amplification of precursor molecules.
Chen, C. et al. Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res. 33, e179 (2005).
Raymond, C. K., Roberts, B. S., Garrett-Engele, P., Lim, L. P. & Johnson, J. M. Simple, quantitative primer-extension PCR assay for the direct monitoring of microRNAs and short-interfering RNAs. RNA 11, 1737–1744 (2005).
Nelson P. T. et al. Microarray-based, high-throughput gene expression profiling of microRNAs. Nature Methods 1, 155–161 (2004).
Volinia, S. et al. A microRNA expression signature of human solid tumors define cancer gene targets. Proc. Natl Acad. Sci. USA 103, 2257–2261 (2006).
Garzon, R. et al. MicroRNA fingerprints during human megakaryocytopoiesis. Proc. Natl Acad. Sci. USA 103, 5078–5083 (2006).
Calin, G. A. et al. MicroRNA profiling reveals distinct signatures in B cell chronic lymphocytic leukemias. Proc. Natl Acad. Sci. USA 101, 11755–11760 (2004). The first paper to explore, by using genome-wide miRNA profiling by microarray, the potential importance of miRNAs in the diagnosis and prognosis of a human malignancy.
Iorio, M. V. et al. microRNA gene expression deregulation in human breast cancer. Cancer Res. 65, 7065–7070 (2005).
Ciafre, S. A. et al. Extensive modulation of a set of microRNAs in primary glioblastoma. Biochem. Biophys. Res. Commun. 334, 1351–1358 (2005).
Murakami, Y. et al. Comprehensive analysis of microRNA expression patterns in hepatocellular carcinoma and non-tumorous tissues. Oncogene 25, 2537–2545 (2006).
Yanaihara, N. et al. microRNA signature in lung cancer diagnosis and prognosis. Cancer Cell 9, 189–198 (2006).
Roldo, C. et al. MicroRNA expression abnormalities in pancreatic endocrine and acinar tumors are associated with distinctive pathological features and clinical behavior. J. Clin. Oncol. 11 Sept. 2006 [epub ahead of print].
Chan, J. A., Krichevsky, A. M. & Kosik, K. S. MicroRNA-21 is an antiapoptotic factor in human glioblastoma cells. Cancer Res. 65, 6029–6033 (2005).
Meng, F. et al. Involvement of human microRNAs in growth and response to chemotherapy in human cholangiocarcinoma cell lines. Gastroenterology 130, 2113–2129 (2006). The first report to show that the chemotherapeutic treatment of human cancer cells can influence miRNA expression.
Ali, I. U., Schriml, L. M. & Dean, M. Mutational spectra of PTEN/MMAC1 gene: a tumor suppressor with lipid phosphatase activity. J. Natl Cancer Inst. 91, 1922–1932 (1999).
Johnson, S. M. et al. RAS is regulated by the let-7 microRNA family. Cell 120, 635–647 (2005). An elegant study that shows a pathogenetic link between miRNAs and target oncogenes.
Voorhoeve, P. M. et al. A genetic screen implicates miRNA-372 and miRNA-373 as oncogenes in testicular germ cell tumors. Cell 124, 1169–1181 (2006). Describes a very powerful method of genetic screening to identify new functions of miRNAs that are important for tumorigenesis.
Costinean, S. et al. Pre B cell proliferation and lymphoblastic leukemia/high grade lymphoma in Emiu miR 155 transgenic mice. Proc. Natl Acad. Sci. USA 103, 7024–7029 (2006). The first paper to show that the deregulation of a single miRNA gene can lead to cancer.
Metzler, M., Wilda, M., Busch, K., Viehmann, S. & Borkhardt, A. High expression of precursor microRNA-155/BIC RNA in children with Burkitt lymphoma. Genes Chromosomes Cancer 39, 167–169 (2004).
Eis, P. S. et al. Accumulation of miR-155 and BIC RNA in human B cell lymphomas. Proc. Natl Acad. Sci. USA 102, 3627–3632 (2005).
Kluiver, J. et al. BIC and miR-155 are highly expressed in Hodgkin, primary mediastinal and diffuse large B cell lymphomas. J. Pathol. 207, 243–249 (2005).
Tam, W., Hughes, S. H., Hayward, W. S. & Besmer, P. Avian bic, a gene isolated from a common retroviral site in avian leukosis virus-induced lymphomas that encodes a noncoding RNA, cooperates with c-myc in lymphomagenesis and erythroleukemogenesis. J. Virol. 76, 4275–4286 (2002).
O'Donnell, K. A., Wentzel, E. A., Zeller, K. I., Dang, C. V. & Mendell, J. T. c-Myc-regulated microRNAs modulate E2F1 expression. Nature 435, 839–843 (2005).
Cimmino, A. et al. miR-15 and miR-16 induce apoptosis by targeting BCL2. Proc. Natl Acad. Sci. USA 102, 13944–13949 (2005).
Jiang, J., Lee, E. J., Gusev, Y. & Schmittgen, T. D. Real-time expression profiling of microRNA precursors in human cancer cell lines. Nucleic Acids Res. 33, 1–10 (2005).
Carpenter, B. et al. The roles of heterogeneous nuclear ribonucleoproteins in tumour development and progression. Biochim. Biophys. Acta 42, 295–309 (2006).
Calin, G. A. et al. Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers. Proc. Natl Acad. Sci. USA 101, 2999–3004 (2004). A genome-wide study proving that half of the annotated human miRNAs are located in genomic regions involved in cancer.
Zhang, L. & Al, E. MicroRNAs exhibit high frequency genomic alterations in human cancer. Proc. Natl Acad. Sci. USA 103, 9136–9141 (2006).
Bottoni, A. et al. miR-15a and miR-16–1 down-regulation in pituitary adenomas. J. Cell Physiol. 204, 280–285 (2005).
Tagawa, H. & Seto, M. A microRNA cluster as a target of genomic amplification in malignant lymphoma. Leukemia 19, 2013–2016 (2005).
Hayashita, Y. et al. A polycistronic microRNA cluster, miR-17–92, is overexpressed in human lung cancers and enhances cell proliferation. Cancer Res. 65, 9628–9632 (2005).
Fraga, M. F. & Esteller, M. Towards the human cancer epigenome: a first draft of histone modifications. Cell Cycle 10, 1377–1381 (2005).
Scott, G. K., Mattie, M. D., Berger, C. E., Benz, S. C. & Benz, C. C. Rapid alteration of microRNA levels by histone deacetylase inhibition. Cancer Res. 66, 1277–1281 (2006).
Saito, Y. et al. Specific activation of microRNAs-127 with downregulation of the proto-oncogene BCL6 by chromatin-modifying drugs in human cancer cells. Cancer Cell 9, 435–443 (2006). Shows the link between epigenetic changes that affect miRNAs and target protein-coding genes involved in cell survival.
Thomson, J. M. et al. Extensive post-transcriptional regulation of microRNAs and its implications for cancer. Genes Dev. 20, 2202–2207 (2006).
Karube, Y. et al. Reduced expression of Dicer associated with poor prognosis in lung cancer patients. Cancer Sci. 96, 111–115 (2005).
Harris, K. S., Zhang, Z., McManus, M. T., Harfe, B. D. & Sun, X. Dicer function is essential for lung epithelium morphogenesis. Proc. Natl Acad. Sci. USA 103, 2208–2213 (2006).
Takamizawa, J. et al. Reduced expression of the let-7 microRNAs in human lung cancers in association with shortened postoperative survival. Cancer Res. 64, 3753–3756 (2004).
Harfe, B. D., McManus, M. T., Mansfield, J. H., Hornstein, E. & Tabin, C. J. The RNaseIII enzyme Dicer is required for morphogenesis but not patterning of the vertebrate limb. Proc Natl Acad Sci USA. 102, 10898–10903 (2005).
Kanellopoulou, C. et al. Dicer-deficient mouse embryonic stem cells are defective in differentiation and centromeric silencing. Genes Dev. 19, 489–501 (2005).
Lau, N. C. et al. Characterization of the piRNA complex from rat testes. Science 313, 363–367 (2006).
Girard, A., Sachidanandam, R., Hannon, G. J. & Carmell, M. A. A germline-specific class of small RNAs binds mammalian Piwi proteins. Nature 442, 199–202 (2006).
Aravin, A. et al. A novel class of small RNAs bind to MILI protein in mouse testes. Nature 442, 203–207 (2006).
Watanabe, T. et al. Identification and characterization of two novel classes of small RNAs in the mouse germline: retrotransposon-derived siRNAs in oocytes and germline small RNAs in testes. Genes Dev. 20, 1732–1743 (2006).
Grivna, S. T., Beyret, E., Wang, Z. & Lin, H. A novel class of small RNAs in mouse spermatogenic cells. Genes Dev. 20, 1709–1714 (2006).
Qiao, D., Zeeman, A. M., Deng, W., Looijenga, L. H. & Lin, H. Molecular characterization of hiwi, a human member of the piwi gene family whose overexpression is correlated to seminomas. Oncogene 21, 3988–3999 (2002).
Liu, X. et al. Expression of hiwi gene in human gastric cancer was associated with proliferation of cancer cells. Int. J. Cancer 118, 1922–1929 (2006).
Pavlidisa, N. & Fizazib, K. Cancer of unknown primary (CUP). Crit. Rev. Oncol. Hematol. 54, 243–250 (2005).
Chiorazzi, N., Rai, K. R. & Ferrarini, M. Chronic lymphocytic leukemia. N. Engl. J. Med. 352, 804–815 (2005).
Kipps, T. J. in Williams hematology (eds Beutler, E., Lichtman, M. A., Coller, B. S., Kipps, T. J. & Seligson, U.) 1163–1194 (McGraw-Hill, New York, 2001).
Tsimberidou, A. M. & Keating, M. J. Richter syndrome: biology, incidence, and therapeutic strategies. Cancer 103, 216–228 (2005).
Cheson, B. D. et al. National Cancer Institute-sponsored Working Group guidelines for chronic lymphocytic leukemia: revised guidelines for diagnosis and treatment. Blood 87, 4990–4997 (1996).
Dohner, H. et al. Genomic aberrations and survival in chronic lymphocytic leukemia. N. Engl. J. Med. 343, 1910–1916 (2000).
Herling, M. et al. TCL1 shows a regulated expression pattern in chronic lymphocytic leukemia that correlates with molecular subtypes and proliferative state. Leukemia 20, 280–285 (2006).
Nagy, B. et al. Abnormal expression of apoptosis-related genes in haematological malignancies: overexpression of MYC is poor prognostic sign in mantle cell lymphoma. Br. J. Haematol. 120, 434–441 (2003).
Adachi, M., Tefferi, A., Greipp, P. R., Kipps, T. J. & Tsujimoto, Y. Preferential linkage of bcl-2 to immunoglobulin light chain gene in chronic lymphocytic leukemia. J. Exp. Med. 171, 559–564 (1990).
Beasley, M. B., Brambilla, E. & Travis, W. D. The 2004 World Health Organization classification of lung tumors. Semin. Roentgenol. 40, 90–97 (2005).
Mascaux, C. et al. The role of RAS oncogene in survival of patients with lung cancer: a systematic review of the literature with meta-analysis. Br. J. Cancer 92, 131–139 (2005).
Orom, U. A., Kauppinen, S. & Lund, A. H. LNA-modified oligonucleotides mediate specific inhibition of microRNA function. Gene 372, 137–141 (2006).
Weiler, J., Hunziker, J. & Hall, J. Anti-miRNA oligonucleotides (AMOs): ammunition to target miRNAs implicated in human disease? Gene Ther. 13, 496–502 (2005).
Krutzfeldt, J. et al. Silencing of microRNAs in vivo with 'antagomirs'. Nature. 438, 685–689 (2005).
Cheung, V. G. et al. Natural variation in human gene expression assessed in lymphoblastoid cells. Nature Genet. 33, 422–425 (2003).
Morley, M. et al. Genetic analysis of genome-wide variation in human gene expression. Nature 430, 743–747 (2004).
Stankovic, T. et al. Inactivation of ataxia telangiectasia mutated gene in B-cell chronic lymphocytic leukaemia. Lancet 353, 26–29 (1999).
Bullrich, F. et al. ATM mutations in B-cell chronic lymphocytic leukemia. Cancer Res. 59, 24–27 (1999).
Calin, G. A. et al. Familial cancer associated with a polymorphism in ARLTS1. N. Engl. J. Med. 352, 1667–1676 (2005).
French, D. B. & Jones, L. A. Minority issues in prostate disease. Med. Clin. North Am. 89, 805–816 (2005).
Gottwein, E., Cai, X. & Cullen, B. R. A novel assay for viral microRNAs function identifies a single nucleotide polymorphism that affects Drosha processing. J. Virol. 80, 5321–5326 (2006).
Dews, M. et al. Augmentation of tumor angiogenesis by a Myc-activated microRNAs cluster. Nature Genet. 38, 1060–1065 (2006).