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32 - Microarray analysis and RNA silencing to determine genes functionally important in mesothelioma

Published online by Cambridge University Press:  31 July 2009

By
Maria E. Ramos-Nino  and
Brooke T. Mossman
Edited by
Krishnarao Appasani
Foreword by
Andrew Fire  and
Marshall Nirenberg
Maria E. Ramos-Nino
Affiliation:
Environmental Pathology Program, Department of Pathology, University of Vermont, College of Medicine
Brooke T. Mossman
Affiliation:
Environmental Pathology Program, Department of Pathology, University of Vermont, College of Medicine
Krishnarao Appasani
Affiliation:
GeneExpression Systems, Inc., Massachusetts
Andrew Fire
Affiliation:
Stanford University, California
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Summary

Introduction

The most important event in science in this decade has been the publication of the sequence of the human genome by two independent initiatives (Lander et al., 2001; Venter et al., 2001). However, the sequence of the human genome and other species can contribute to our understanding of human biology only if it can be linked with functional information on the roles of encoded proteins. A major goal of science in the “post-genomic era” is to unravel the functions of the many genes discovered by sequencing. Although sequence- or structure-based comparisons are enabling the generation of hypotheses on the biochemical functions of many gene products, determining the role of a large set of genes is still a challenge.

Recently, RNA interference (RNAi) technology has been developed for the down-regulation of selected gene expression in mammalian cells. This technology offers a rapid way to gain insight to loss-of-function phenotypes associated with specific genes. Furthermore, the combination of RNAi with other functional genomic approaches such as gene expression profiling is providing a powerful tool in our efforts to establish the function of genes in the pathogenesis of many diseases. In this chapter, we will summarize the contributions that RNAi and microarrays have had in cancer research, particularly in understanding the mechanisms and pathogenesis of malignant mesothelioma, a devastating tumor of the serosal cells lining the pleural, peritoneal and pericardial cavities (Mossman and Gee, 1989).

Type
Chapter
Information
RNA Interference Technology
From Basic Science to Drug Development
 , pp. 447 - 469
Publisher: Cambridge University Press
Print publication year: 2005

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References

Abe, J., Kusuhara, M., Ulevitch, R. J., Berk, B. C. and Lee, J. D. (1996). Bigmitogen-activated protein kinase 1 (BMK1) is a redox-sensitive kinase. Journal of Biological Chemistry, 271, 16586–16590CrossRefGoogle Scholar
Adamson, I. and Bakowska, J. (2001). KGF and HGF are growth factors for mesothelial cells in pleural lavage fluid after intratracheal asbestos. Experimental Lung Research, 27, 605–616Google ScholarPubMed
Alizadeh, A. A., Eisen, M. B., Davis, R. E., Ma, C., Lossos, I. S., Rosenwald, A. et al. (2000). Distincttypes of diffuse large B-cell lymphoma identified by gene expression profiling. Nature, 403, 503–511CrossRefGoogle ScholarPubMed
Alon, U., Barkai, N., Notterman, D. A., Gish, K., Ybarra, S., Mack, D., et al. (1999). Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proceedings of the National Academy of Sciences USA, 96, 6745–6750CrossRefGoogle ScholarPubMed
Battista, S., Nigris, F., Fedele, M., Chiappetta, G., Scala, S., Vallone, D., et al. (1998). Increase in AP-1 activity is a general event in thyroid cell transformation in vitro and in vivo. Oncogene, 17, 377–385CrossRefGoogle ScholarPubMed
Bennett, A. and Tonks, N. (1997). Regulation of distinct stages of skeletal muscle differentiation by mitogen-activated protein kinases. Science, 278, 1288–1291CrossRefGoogle ScholarPubMed
Bergers, G., Graninger, P., Braselmann, S., Wrighton, C. and Busslinger, M. (1995). Transcriptional activation of the fra-1 gene by AP-1 is mediated by regulatory sequences in the first intron. Molecular and Cellular Biology, 15, 3748–3758CrossRefGoogle ScholarPubMed
Bernstein, E., Denli, A. M. and Hannon, G. J. (2001). Therest is silence. RNA, 7, 1509–1521Google Scholar
Bhat, N. and Zhang, P. (1999). Hydrogen peroxide activation of multiple mitogen-activated protein kinases in an oligodendrocyte cell line: Role of extracellular signal-regulated kinase in hydrogen peroxide-induced cell death. Journal of Neurochemistry, 72, 112–119CrossRefGoogle Scholar
Bos, J. L. (1989). rasoncogenes in human cancer: A review. Cancer Research, 49, 4682–4689Google Scholar
Braasch, D. A. and Corey, D. R. (2002). Novel antisense and peptide nucleic acid strategies for controlling gene expression. Biochemistry, 41, 4503–4510CrossRefGoogle ScholarPubMed
Branch, A. D. (1998). A good antisense molecule is hard to find. Trends in Biochemical Sciences, 23, 45–50CrossRefGoogle ScholarPubMed
Brummelkamp, T. R., Bernards, R. and Agami, R. (2002). A system for stable expression of short interfering RNAs in mammalian cells. Science, 296, 550–553CrossRefGoogle ScholarPubMed
Butz, K., Ristriani, T., Hengstermann, A., Denk, C., Scheffner, M. and Hoppe-Seyler, F. (2003). siRNA targeting of the viral E6 oncogene efficiently kills human papillomavirus-positive cancer cells. Oncogene, 22, 5938–5945CrossRefGoogle ScholarPubMed
Cacciotti, P., Libener, R., Betta, P., Martini, F., Porta, C., Procopio, A., et al. (2001). SV40 replication in human mesothelial cells induces HGF/Met receptor activation: A model for viral-related carcinogenesis of human malignant mesothelioma. Proceedings of the National Academy of Sciences USA, 98, 12032–12037CrossRefGoogle ScholarPubMed
Caplen, N. J., Parrish, S., Imani, F., Fire, A. and Morgan, R. A. (2001). Specific inhibition of gene expression by small double-stranded RNAs in invertebrate and vertebrate systems. Proceedings of the National Academy of Sciences USA, 98, 9742–9747CrossRefGoogle ScholarPubMed
Carbone, M., Kratzke, R. and Testa, J. (2002). Thepathogenesis of mesothelioma. Seminars in Oncology, 29, 2–17CrossRefGoogle Scholar
Carmichael, G. G. (2002). Medicine: Silencing viruses with RNA. Nature, 418, 379–380CrossRefGoogle ScholarPubMed
Chase, D., Serafinas, C., Ashcroft, N., Kosinski, M., Longo, D., Ferris, D. K., et al. (2000). Thepolo-like kinase PLK-1 is required for nuclear envelope breakdown and the completion of meiosis in Caenorhabditis elegans. Genetics, 26, 26–41Google ScholarPubMed
Chen, Y., Stamatoyannopoulos, G. and Song, C. Z. (2003). Down-regulation of CXCR4 by inducible small interfering RNA inhibits breast cancer cell invasion in vitro. Cancer Research, 63, 4801–4804Google ScholarPubMed
Chi, J. T., Chang, H. Y., Wang, N. N., Chang, D. S., Dunphy, N. and Brown, P. O. (2003). Genome wide view of gene silencing by small interfering RNAs. Proceedings of the National Academy of Sciences USA, 100, 6343–6346CrossRefGoogle Scholar
Chin, B., Choi, M., Burdick, M., Strieter, R., Risby, T. and Choi, A. (1998). Induction of apoptosis by particulate matter: Role of TNF-alpha and MAPK. American Journal of Physiology (Lung Cellular and Molecular Physiology), 275, L942–L949CrossRefGoogle ScholarPubMed
Cowley, S., Paterson, H., Kemp, P. and Marshall, C. (1994). Activation of MAP kinase kinase is necessary and sufficient for PC12 differentiation and for transformation of NIH 3T3 cells. Cell, 77, 841–852CrossRefGoogle ScholarPubMed
Craighead, J., Akley, N., Gould, L. and Libbus, B. (1987). Characteristics of tumors and tumor cells cultured from experimental asbestos-induced mesothelioma in rats. American Journal of Pathology, 129, 448–462Google ScholarPubMed
Schrijver, E., Brusselmans, K., Heyns, W., Verhoeven, G. and Swinnen, J. V. (2003). RNA interference-mediated silencing of the fatty acid synthase gene attenuates growth and induces morphological changes and apoptosis of LNCaP prostate cancer cells. Cancer Research, 63, 3799–3804Google ScholarPubMed
Denhardt, D. (1996). Signal transducing protein phosphorylation cascades mediated by Ras/Rho proteins in the mammalian cell: The potential for multiplex signaling. Biochemical Journal, 318, 729–747CrossRefGoogle Scholar
Dillin, A. (2003). The specifics of small interfering RNA specificity. Proceedings of the National Academy of Sciences USA, 100, 6289–6291CrossRefGoogle ScholarPubMed
Doench, J. G., Petersen, C. P. and Sharp, P. A. (2003). siRNAs can function as miRNAs. Genes & Development, 17, 438–442CrossRefGoogle ScholarPubMed
Elbashir, S. M., Harborth, J., Lendeckel, W., Yalcin, A., Weber, K. and Tuschl, T. (2001). Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature, 411, 494–498CrossRefGoogle ScholarPubMed
Elbashir, S. M., Lendeckel, W. and Tuschl, T. (2001). RNA interference is mediated by 21- and 22-nucleotide RNAs. Genes & Development, 15, 188–200CrossRefGoogle ScholarPubMed
Ellis, C. A. and Clark, G. (2000). The importance of being K-Ras. Cellular Signaling, 12, 425–434CrossRefGoogle ScholarPubMed
English, J., Pearson, G., Hockenberry, T., Shivakumar, L., White, M. and Cobb, M. (1999). Contribution of the ERK5/MEK5 pathway to Ras/Raf signaling and growth control. Journal of Biological Chemistry, 274, 31588–31592CrossRefGoogle ScholarPubMed
Esparis-Ogando, A., Diaz-Rodriguez, E., Montero, J., Yuste, L., Crespo, P. and Pandiella, A. (2002). Erk5 participates in neuregulin signal transduction and is constitutively active in breast cancer cells overexpressing ErbB2. Molecular and Cellular Biology, 22, 270–285CrossRefGoogle ScholarPubMed
Faassen, A., Schrager, J., Klein, D., Oegema, T., Couchman, J. and McCarthy, J. (1992). A cell surface chondroitin sulfate proteoglycan, immunologically related to CD44, is involved in type I collagen-mediated melanoma cell motility and invasion. Journal of Cell Biology, 116, 521–531CrossRefGoogle ScholarPubMed
Fire, A., Xu, S., Montgomery, M. K., Kostas, S. A., Driver, S. E. and Mello, C. C. (1998). Potentand specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature, 391, 806–811CrossRefGoogle ScholarPubMed
Gil, J. and Esteban, M. (2000). Induction of apoptosis by the dsRNA-dependent protein kinase (PKR): Mechanism of action. Apoptosis, 5, 107–114CrossRefGoogle ScholarPubMed
Gille, H., Sharrocks, A. and Shaw, P. (1992). Phosphorylation of transcription factor p62TCF by MAP kinase stimulates ternary complex formation at c-fos promoter. Nature, 358, 414–417CrossRefGoogle ScholarPubMed
Golub, T. R., Slonim, D. K., Tamayo, P., Huard, C., Gaasenbeek, M., Mesirov, J. P., et al. (1999). Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring. Science, 286, 531–537CrossRefGoogle ScholarPubMed
Gordon, G. J., Jensen, R. V., Hsiao, L. L., Gullans, S. R., Blumenstock, J. E., Ramaswamy, S., et al. (2002). Translation of microarray data into clinically relevant cancer diagnostic tests using gene expression ratios in lung cancer and mesothelioma. Cancer Research, 62, 4963–4967Google ScholarPubMed
Gordon, G. J., Jensen, R. V., Hsiao, L. L., Gullans, S. R., Blumenstock, J. E., Richards, W. G., et al. (2003). Usinggene expression ratios to predict outcome among patients with mesothelioma. Journal of the National Cancer Institute, 95, 598–605CrossRefGoogle ScholarPubMed
Grishok, A., Pasquinelli, A. E., Conte, D., Li, N., Parrish, S., Ha, I., Baillie, D. L., Fire, A., Ruvkun, G. and Mello, C. C. (2001). Genesand mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell, 106, 23–34CrossRefGoogle Scholar
Gunthert, U., Hofmann, M., Rudy, W., Reber, S., Zoller, M., Haussmann, I., et al. (1991). A new variant of glycoprotein CD44 confers metastatic potential to rat carcinoma cells. Cell, 65, 13–24CrossRefGoogle ScholarPubMed
Guo, Y., Ma, J., Wang, J., Che, X., Narula, J., Bigby, M., et al. (1994). Inhibition of human melanoma growth and metastasis in vivo by anti-CD44 monoclonal antibody. Cancer Research, 54, 1561–1565Google ScholarPubMed
Harvey, A. and Crompton, M. (2003). Use of RNA interference to validate Brk as novel therapeutic target in breast cancer: Brk promotes breast carcinoma cell proliferation. Oncogene, 22, 5006–5010CrossRefGoogle ScholarPubMed
Harvey, P., Clark, I., Jaurand, M., Warn, R. and Edwards, D. (2000). Hepatocyte growth factor/scatter factor enhances the invasion of mesothelioma cell lines and the expression of matrix metalloproteinases. British Journal of Cancer, 83, 1147–1153CrossRefGoogle ScholarPubMed
Hasuwa, H., Kaseda, K., Einarsdottir, T. and Okabe, M. (2002). Small interfering RNA and gene silencing in transgenic mice and rats. Federation of European Biochemical Society Letters, 532, 227–230CrossRefGoogle ScholarPubMed
Heintz, N., Janssen, Y. and Mossman, B. (1993). Persistent induction of c-fos and c-jun expression by asbestos. Proceedings of the National Academy of Sciences USA, 90, 3299–3303CrossRefGoogle ScholarPubMed
Hemann, M. T., Fridman, J. S., Zilfou, J. T., Hernando, E., Paddison, P. J., Cordon-Cardo, C., et al. (2003). Anepi-allelic series of p53 hypomorphs created by stable RNAi produces distinct tumor phenotypes in vivo. Nature Genetics, 33, 396–400CrossRefGoogle ScholarPubMed
Hofmann, M., Rudy, W., Gunthert, U., Zimmer, S., Zawadzki, V., Zoller, M., et al. (1993). A link between ras and metastatic behavior of tumor cells: Ras induces CD44 promoter activity and leads to low-level expression of metastasis-specific variants of CD44 in CREF cells. Cancer Research, 53, 1516–1521Google ScholarPubMed
Hunter, T. (1991). Cooperation between oncogenes. Cell, 64, 249–270CrossRefGoogle ScholarPubMed
Hütvagner, G., McLachlan, J., Pasquinelli, A. E., Balint, E., Tuschl, T. and Zamore, P. D. (2001). A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science, 293, 834–838CrossRefGoogle ScholarPubMed
Ilves, H., Barske, C., Junker, U., Bohnlein, E. and Veres, G. (1996). Retroviral vectors designed for targeted expression of RNA polymerase III-driven transcripts: A comparative study. Gene, 171, 203–208CrossRefGoogle ScholarPubMed
Jennings, P. A. and Molloy, P. L. (1987). Inhibition of SV40 replicon function by engineered antisense RNA transcribed by RNA polymerase III. European Molecular Biology Organization Journal, 6, 3043–3047Google ScholarPubMed
Jimenez, L., Zanella, C., Fung, H., Janssen, Y., Vacek, P., Charland, C., et al. (1997). Role of extracellular signal-regulated protein kinases in apoptosis by asbestos and H2O2. American Journal of Physiology (Lung Cellular and Molecular Physiology), 273, L1029–L1035CrossRefGoogle ScholarPubMed
Jochum, W., David, J., Elliott, C., Wutz, A., Plenk, H. J., Matsuo, K., et al. (2000). Increased bone formation and osteosclerosis in mice overexpressing the transcription factor Fra-1. Nature Medicine, 6, 980–984CrossRefGoogle ScholarPubMed
Jorgensen, R. A., Cluster, P. D., English, J., Que, Q. and Napoli, C. A. (1996). Chalconesynthase cosuppression phenotypes in petunia flowers: Comparison of sense vs. antisense constructs and single-copy vs. complex T-DNA sequences. Plant Molecular Biology, 31, 957–73CrossRefGoogle ScholarPubMed
Kamakura, S., Moriguchi, T. and Nishida, E. (1999). Activation of the protein kinase ERK5/BMK1 by receptor tyrosine kinases. Identification and characterization of a signaling pathway to the nucleus. Journal of Biological Chemistry, 274, 26563–26571CrossRefGoogle ScholarPubMed
Kamath, R. S., Fraser, A. G., Dong, Y., Poulin, G., Durbin, R., Gotta, M., et al. (2003). Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature, 421, 231–237CrossRefGoogle ScholarPubMed
Karin, M., Liu, Z. and Zandi, E. (1997). AP-1 function and regulation. Current Opinion in Cell Biology, 9, 240–246CrossRefGoogle ScholarPubMed
Kato, Y., Tapping, R., Huang, S., Watson, M., Ulevitch, R. and Lee, J. (1998). BMK1/ERK5 is required for cell proliferation induced by epidermal growth factor. Nature, 395, 713–716CrossRefGoogle ScholarPubMed
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 & Development, 15, 2654–2659CrossRefGoogle ScholarPubMed
Ketting, R. F., Haverkamp, T. H., Luenen, H. G. and Plasterk, R. H. (1999). Mut-7 of C. elegans, required for transposon silencing and RNA interference, is a homolog of Werner syndrome helicase and RNaseD. Cell, 99, 133–141CrossRefGoogle ScholarPubMed
Ketting, R. F. and Plasterk, R. H. (2000). A genetic link between co-suppression and RNA interference in C. elegans. Nature, 404, 296–298CrossRefGoogle ScholarPubMed
Klein, G., Powers, A. and Croce, C. (2002). Association of SV40 with human tumors. Oncogene, 21, 1141–1149CrossRefGoogle ScholarPubMed
Klominek, J., Baskin, B., Liu, Z. and Hauzenberger, D. (1998). Hepatocyte growth factor/scatter factor stimulates chemotaxis and growth of malignant mesothelioma cells through c-met receptor. International Journal of Cancer, 76, 240–2493.0.CO;2-G>CrossRefGoogle ScholarPubMed
Knight, S. W. and Bass, B. L. (2001). A role for the RNase III enzyme DCR-1 in RNA interference and germ line development in Caenorhabditis elegans. Science, 293, 2269–2271CrossRefGoogle ScholarPubMed
Lamb, R., Hennigan, R., Turnbull, K., Katsanakis, K., MacKenzie, E., Birnie, G., et al. (1997). AP-1 mediated invasion requires increased expression of the hyaluronan receptor CD44. Molecular and Cellular Biology, 17, 963–976CrossRefGoogle ScholarPubMed
Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., et al. (2001). Initial sequencing and analysis of the human genome. Nature, 409, 860–921CrossRefGoogle ScholarPubMed
Lebedeva, I. and Stein, C. A. (2001). Antisenseoligonucleotides: Promise and reality. Annual Review of Pharmacology and Toxicology, 41, 403–419CrossRefGoogle Scholar
Lee, N. S., Dohjima, T., Bauer, G., Li, H., Li, M. J., Ehsani, A., et al. (2002). Expression of small interfering RNAs targeted against HIV-1 rev transcripts in human cells. Nature Biotechnology, 20, 500–505CrossRefGoogle ScholarPubMed
Lewis, C., Townsend, P. and Isacke, C. (2001). Ca(2+)/calmodulin-dependent protein kinase mediates the phosphorylation of CD44 required for cell migration on hyaluronan. Biochemical Journal, 357, 843–850CrossRefGoogle ScholarPubMed
Li, Y. and Heldin, P. (2001). Hyaluronanproduction increases the malignant properties of mesothelioma cells. British Journal of Cancer, 85, 600–607CrossRefGoogle ScholarPubMed
Liu, L., Liu, Z., Jiang, H., Zhang, W., Qi, S., Hu, J., et al. (2003). Gene expession profiles of hepatoma cell lines HLE. World Journal of Gastroenterology, 9, 683–687CrossRefGoogle Scholar
Lloyd, A., Yancheva, N. and Wasylyk, B. (1991). Transformation suppressor activity of a Jun transcription factor lacking its activation domain. Nature, 352, 635–638CrossRefGoogle ScholarPubMed
Malumbres, M. and Pellicer, A. (1998). RAS pathways to cell cycle control and cell transformation. Frontiers of Bioscience, 3, 887–912Google ScholarPubMed
Mansour, S., Matten, W., Hermann, A., Candia, J., Rong, S., Fukasawa, K., et al. (1994). Transformation of mammalian cells by constitutively active MAP kinase kinase. Science, 265, 966–970CrossRefGoogle ScholarPubMed
Marais, R., Wynne, J. and Treisman, R. (1993). The SRF accessory protein Elk-1 contains a growth factor-regulated transcriptional activation domain. Cell, 73, 381–393CrossRefGoogle ScholarPubMed
McCormick, F. (1999). Signalling networks that cause cancer. Trends in Cellular Biology, 9, M53–M56CrossRefGoogle ScholarPubMed
McDonald, J. and Wagner, A. (1996). The epidemiology of mesothelioma in historical context. European Respiratory Journal, 9, 1932–1942CrossRefGoogle ScholarPubMed
McManus, M. T. and Sharp, P. A. (2002). Gene silencing in mammals by small interfering RNAs. Nature Reviews Genetics, 3, 737–747CrossRefGoogle ScholarPubMed
Mechta, F., Lallemand, D., Pfarr, C. and Yaniv, M. (1997). Transformation by ras modifies AP-1 composition and activity. Oncogene, 14, 837–847CrossRefGoogle ScholarPubMed
Mehta, P., Jenkins, B., McCarthy, L., Thilak, L., Robson, C., Neal, D., et al. (2003). MEK5 overexpression is associated with metastatic prostate cancer, and stimulates proliferation, MMP-9 expression and invasion. Oncogene, 22, 1381–1389CrossRefGoogle ScholarPubMed
Miyagishi, M. and Taira, K. (2002). U6 promoter-driven siRNAs with four uridine 3′ overhangs efficiently suppress targeted gene expression in mammalian cells. Nature Biotechnology, 20, 497–500CrossRefGoogle ScholarPubMed
Mohr, S. and Rihn, B. (2001). Geneexpression profiling in human mesothelioma cells using DNA microarray and high-density filter array technologies. Bulletin du Cancer, 88, 305–313Google Scholar
Mossman, B., Bignon, J., Corn, M., Seaton, A. and Gee, J. (1990). Asbestos: Scientific developments and implications for public policy. Science, 247, 294–301CrossRefGoogle ScholarPubMed
Mossman, B. and Gee, J. (1989). Asbestosrelated disease. New England Journal of Medicine, 320, 1721–1730CrossRefGoogle Scholar
Mossman, B. and Gruenert, D. (2002). SV40, growth factors, and mesothelioma – Another piece of the puzzle. American Journal of Respiratory Cell and Molecular Biology, 26, 167–170CrossRefGoogle ScholarPubMed
Mulloy, R., Salinas, S., Philips, A. and Hipskind, R. A. (2003). Activation of cyclin D1 expression by the ERK5 cascade. Oncogene, 22, 5387–5398CrossRefGoogle ScholarPubMed
Nagy, P., Arndt-Jovin, D. J. and Jovin, T. M. (2003). Small interfering RNAs suppress the expression of endogenous and GFP-fused epidermal growth factor receptor (erbB1) and induce apoptosis in erbB1-overexpressing cells. Experimental Cell Research, 285, 39–49CrossRefGoogle ScholarPubMed
Napoli, C., Lemieux, C. and Jorgensen, R. (1990). Introduction of a chimeric chalcone synthase gene into petunia results in reversible co-suppression of homologous genes in trans. Plant Cell, 2, 279–289CrossRefGoogle ScholarPubMed
Ojwang, J. O., Hampel, A., Looney, D. J., Wong-Staal, F. and Rappaport, J. (1992). Inhibition of human immunodeficiency virus type 1 expression by a hairpin ribozyme. Proceedings of the National Academy of Sciences USA, 89, 10802–10806CrossRefGoogle ScholarPubMed
Pache, J., Janssen, Y., Walsh, E., Quinlan, T., Zanella, C., Low, R., et al. (1998). Increase depidermal growth factor-receptor (EGF-R) protein in a human mesothelial cell line in response to long asbestos fibers. American Journal of Pathology, 152, 333–340Google Scholar
Paddison, P. J., Caudy, A. A., Bernstein, E., Hannon, G. J. and Conklin, D. S. (2002). Shorthairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells. Genes & Development, 16, 948–958CrossRefGoogle Scholar
Pass, H., Donington, J., Wu, P., Rizzo, P., Nishimura, M., Kennedy, R., et al. (1998). Humanmesotheliomas contain the simian virus-40 regulatory region and large tumor antigen DNA sequences. Journal of Thoracic and Cardiovascular Surgery, 116, 854–849CrossRefGoogle ScholarPubMed
Patterson, T., Vuong, H., Liaw, Y., Wu, R., Kalvakolanu, D. and Reddy, S. (2001). Mechanism of repression of squamous differentiation marker, SPRR1B, in malignant bronchial epithelial cells: Role of critical TRE-sites and its transacting factors. Oncogene, 20, 634–644CrossRefGoogle ScholarPubMed
Paul, C. P., Good, P. D., Winer, I. and Engelke, D. R. (2002). Effective expression of small interfering RNA in human cells. Nature Biotechnology, 20, 505–508CrossRefGoogle ScholarPubMed
Pearson, G., English, J. M., White, M. A. and Cobb, M. H. (2001). ERK5 and ERK2 cooperate to regulate NF-kappaB and cell transformation. Journal of Biological Chemistry, 276, 7927–7931CrossRefGoogle ScholarPubMed
Perou, C. M., Sorlie, T., Eisen, M. B., Rijn, M., Jeffrey, S. S., Rees, C. A., et al. (2000). Molecular portraits of human breast tumours. Nature, 406, 747–752CrossRefGoogle ScholarPubMed
Pollack, J. R., Perou, C. M., Alizadeh, A. A., Eisen, M. B., Pergamenschikov, A., Williams, C. F., et al. (1999). Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nature Genetics, 23, 41–46CrossRefGoogle ScholarPubMed
Ramaswamy, S., Tamayo, P., Rifkin, R., Mukherjee, S., Yeang, C. H., Angelo, M., et al. (2001). Multiclasscancer diagnosis using tumor gene expression signatures. Proceedings of the National Academy of Sciences USA, 98, 15149–15154CrossRefGoogle ScholarPubMed
Ramos-Nino, M., Timblin, C. and Mossman, B. (2002). Mesothelial cell transformation requires increased AP-1 binding activity and ERK-dependent Fra-1 expression. Cancer Research, 62, 6065–6069Google ScholarPubMed
Ramos-Nino, M. E., Haegens, A., Shukla, A. and Mossman, B. T. (2002). Role of mitogen-activated protein kinases (MAPK) in cell injury and proliferation by environmental particulates. Molecular and Cellular Biochemistry, 234–235, 111–118CrossRefGoogle ScholarPubMed
Ramos-Nino, M. E., Scapoli, L., Martinelli, M., Land, S. and Mossman, B. T. (2003). Micro arrayanalysis and RNA silencing link fra-1 to cd44 and c-met expression in mesothelioma. Cancer Research, 63, 3539–3545Google Scholar
Reddy, S. and Mossman, B. (2002). Roleand regulation of activator protein-1 (AP-1) in toxicant-induced responses of the lung. American Journal of Physiology (Lung Cellular and Molecular Physiology), 283, L1161–L1178CrossRefGoogle Scholar
Regan, C. P., Li, W., Boucher, D. M., Spatz, S., Su, M. S. and Kuida, K. (2002). Erk5 null mice display multiple extraembryonic vascular and embryonic cardiovascular defects. Proceedings of the National Academy of Sciences, USA, 99, 9248–9253CrossRefGoogle ScholarPubMed
Rihn, B. H., Mohr, S., McDowell, S. A., Binet, S., Loubinoux, J., Galateau, F., et al. (2000). Differential gene expression in mesothelioma. Federation of European Biochemical Society Letters, 480, 95–100CrossRefGoogle ScholarPubMed
Rincón, M., Flavell, R. and Davis, R. (2000). The JNK and p38 MAP kinase signaling pathways in T-cell mediated immune responses. Free Radical Biology and Medicine, 28, 1328–1337CrossRefGoogle ScholarPubMed
Risse-Hackl, G., Adamkiewicz, J., Wimmel, A. and Schuermann, M. (1998). Transition from SCLC to NSCLC phenotype is accompanied by an increased TRE-binding activity and recruitment of specific AP-1 proteins. Oncogene, 16, 3057–3068CrossRefGoogle ScholarPubMed
Robinson, D., He, F., Pretlow, T. and Kung, H. J. (1996). A tyrosine kinase profile of prostate carcinoma. Proceedings of the National Academy of Sciences USA, 93, 5958–5962CrossRefGoogle ScholarPubMed
Sandhu, H., Dehnen, W., Roller, M., Abel, J. and Unfried, K. (2000). mRNA expression patterns in different stages of asbestos-induced carcinogenesis in rats. Carcinogenesis, 21, 1023–1029CrossRefGoogle ScholarPubMed
Scapoli, L., Ramos-Nino, M., Martinelli, M. and Mossman, B. (2004). Src-dependent ERK5 and Src/EGFR-dependent ERK1/2 activation is required for cell proliferation by asbestos. Oncogene, 23, 805–813CrossRefGoogle ScholarPubMed
Schaeffer, H. and , MJ W. (1999). Mitogen-activated protein kinases: Specific messages from ubiquitous messengers. Molecular and Cellular Biology, 19, 2435–2444CrossRefGoogle ScholarPubMed
Sebolt-Leopold, J., Dudley, D., Herrera, R., Becelaere, K., Wiland, A., Gowan, R., et al. (1999). Blockade of the MAP kinase pathway suppresses growth of colon tumors in vivo. Nature Medicine, 5, 810–816CrossRefGoogle ScholarPubMed
Semizarov, D., Frost, L., Sarthy, A., Kroeger, P., Halbert, D. N. and Fesik, S. W. (2003). Specificity of short interfering RNA determined through gene expression signatures. Proceedings of the National Academy of Sciences USA, 100, 6347–6352CrossRefGoogle ScholarPubMed
Sharp, P. A. (2001). RNA interference – 2001. Genes & Development, 15, 485–490CrossRefGoogle ScholarPubMed
Shukla, A., Timblin, C., Hubbard, A., Bravman, J. and Mossman, B. (2001). Silica-induced activation of c-Jun-NH2-terminal amino kinases, protracted expression of the activator protein-1 proto-oncogene, fra-1, and S-phase alterations are mediated via oxidative stress. Cancer Research, 61, 1791–1795Google ScholarPubMed
Singhal, S., Wiewrodt, R., Malden, L. D., Amin, K. M., Matzie, K., Friedberg, J., et al. (2003). Geneexpression profiling of malignant mesothelioma. Clinical Cancer Research, 9, 3080–3097Google Scholar
Sohn, S. J., Sarvis, B. K., Cado, D. and Winoto, A. (2002). ERK5 MAPK regulates embryonic angiogenesis and acts as a hypoxia-sensitive repressor of vascular endothelial growth factor expression. Journal of Biological Chemistry, 277, 43344–43351CrossRefGoogle ScholarPubMed
Spankuch-Schmitt, B., Bereiter-Hahn, J., Kaufmann, M. and Strebhardt, K. (2002). Effect of RNA silencing of polo-like kinase-1 (PLK1) on apoptosis and spindle formation in human cancer cells. Journal of the National Cancer Institute, 94, 1863–1877CrossRefGoogle ScholarPubMed
Sun, B., Nishihira, J., Suzuki, M., Fukushima, N., Ishibashi, T., Kondo, M., et al. (2003). Induction of macrophage migration inhibitory factor by lysophosphatidic acid: Relevance to tumor growth and angiogenesis. International Journal of Molecular Medicine, 12, 633–641Google ScholarPubMed
Thomas, L., Etoh, T., Stamenkovic, I., Mihm, M. J. and Byers, H. (1993). Migration of human melanoma cells on hyaluronate is related to CD44 expression. Journal of Investigative Dermatology, 100, 115–120CrossRefGoogle ScholarPubMed
Timblin, C., Guthrie, G., Janssen, Y., Walsh, E., Vacek, P. and Mossman, B. (1998). Patterns of c-fos and c-jun protooncogene expression, apoptosis and proliferation in rat pleural mesothelial cells exposed to erionite or asbestos fibers. Toxicology and Applied Pharmacology, 151, 88–97CrossRefGoogle ScholarPubMed
Tolnay, E., Kuhnen, C., Wiethege, T., Konig, J., Voss, B. and Muller, K. (1998). Hepatocyte growth factor/scatter factor and its receptor c-Met are overexpressed and associated with an increased microvessel density in malignant pleural mesothelioma. Journal of Cancer Research and Clinical Oncology, 124, 291–296CrossRefGoogle ScholarPubMed
Treinies, I., Paterson, H., Hooper, S., Wilson, R. and Marshall, C. (1999). Activated MEK stimulates expression of AP-1 components independently of phosphatidylinositol 3-kinase (PI3-kinase) but requires a PI3-kinase signal To stimulate DNA synthesis. Molecular and Cellular Biology, 19, 321–329CrossRefGoogle ScholarPubMed
Tuschl, T. and Borkhardt, A. (2002). Small interfering RNAs a revolutionary tool for the analyiss of gene function and gene therapy. Molecular Interventions, 2, 158–167CrossRefGoogle Scholar
Dartel, M., Cornelissen, P. W., Redeker, S., Tarkkanen, M., Knuutila, S., Hogendoorn, P. C., et al. (2002). Amplification of 17p11.2 approximately p12, including PMP22, TOP3A, and MAPK7, in high-grade osteosarcoma. Cancer Genetics and Cytogenetics, 139, 91–96CrossRefGoogle ScholarPubMed
Krol, A., Mur, L., Beld, M., Mol, J. and Stuitje, A. (1990). Flavonoidgenes in petunia: Addition of a limited number of gene copies may lead to a suppression of gene expression. Plant Cell, 2, 291–299CrossRefGoogle ScholarPubMed
‘t Veer, L. J., Dai, H., Vijver, M. J., He, Y. D., Hart, A. A., Mao, M., et al. (2002). Gene expression profiling predicts clinical outcome of breast cancer. Nature, 415, 530–536CrossRefGoogle ScholarPubMed
Venter, J. C., Adams, M. D., Myers, E. W., Li, P. W., Mural, R. J., Sutton, G. G., et al. (2001). The sequence of the human genome. Science, 291, 1304–1351CrossRefGoogle ScholarPubMed
Vuong, H., Patterson, T., Adiseshaiah, P., Shapiro, P., Kalvakolanu, D. and Reddy, S. (2002). JNK1 and AP-1 regulate PMA-inducible squamous differentiation marker expression in Clara-like H441 cells. American Journal of Physiology (Lung Cellular and Molecular Physiology), 282, L215–L225CrossRefGoogle ScholarPubMed
Watts, R., Huang, C., Young, M., Li, J., Dong, Z., Pennie, W., et al. (1998). Expression of dominant negative ERK2 inhibits AP-1 transactivation and neoplastic transformation. Oncogene, 17, 3493–3498CrossRefGoogle ScholarPubMed
Weg-Remers, S., Ponta, H., Herrlich, P. and Konig, H. (2001). Regulation of alternative pre-mRNA splicing by the ERK MAP-kinase pathway. European Molecular Biology Organization Journal, 20, 4194–4203CrossRefGoogle ScholarPubMed
Whalen, A., Galasinski, S., Shapiro, P., Nahreini, T. and Ahn, N. (1997). Megakaryocytic differentiation induced by constitutive activation of mitogen-activated protein kinase kinase. Molecular and Cellular Biology, 17, 1947–1958CrossRefGoogle ScholarPubMed
Williams, B. R. (1997). Role of the double-stranded RNA-activated protein kinase (PKR) in cell regulation. Biochemical Society Transactions, 25, 509–513CrossRefGoogle Scholar
Williams, N. S., Gaynor, R. B., Scoggin, S., Verma, U., Gokaslan, T., Simmang, C., et al. (2003). Identification and validation of genes involved in the pathogenesis of colorectal cancer using cDNA microarrays and RNA interference. Clinical Cancer Research, 9, 931–946Google ScholarPubMed
Wisdom, R. and Verma, I. (1993). Transformation by Fos proteins requires a c-terminal transactivation domain. Molecular and Cellular Biology, 13, 7429–7438CrossRefGoogle Scholar
Wu-Scharf, D., Jeong, B., Zhang, C. and Cerutti, H. (2000). Transgene and transposon silencing in Chlamydomonas reinhardtii by a DEAH-box RNA helicase. Science, 290, 1159–1162CrossRefGoogle ScholarPubMed
Xia, H., Mao, Q., Paulson, H. L. and Davidson, B. L. (2002). siRNA-mediated gene silencing in vitro and in vivo. Nature Biotechnology, 20, 1006–1010CrossRefGoogle ScholarPubMed
Yan, C., Takahashi, M., Okuda, M., Lee, J. D. and Berk, B. C. (1999). Fluids hear stress stimulates big mitogen-activated protein kinase 1 (BMK1) activity in endothelial cells. Dependence on tyrosine kinases and intracellular calcium. Journal of Biological Chemistry, 274, 143–150CrossRefGoogle Scholar
Yu, J. Y., DeRuiter, S. L. and Turner, D. L. (2002). RNA interference by expression of short-interfering RNAs and hairpin RNAs in mammalian cells. Proceedings of the National Academy of Sciences USA, 99, 6047–6052CrossRefGoogle ScholarPubMed
Zamore, P. D. (2001). RNA interference: Listening to the sound of silence. Nature Structural Biology, 8, 746–750CrossRefGoogle ScholarPubMed
Zanella, C., Posada, J., Tritton, T. and Mossman, B. (1996). Asbestos causes stimulation of the ERK-1 mitogen-activated protein kinase cascade after phosphorylation of the epidermal growth factor receptor. Cancer Research, 56, 5334–5338Google ScholarPubMed
Zanella, C., Timblin, C., Cummins, A., Jung, M., Goldberg, J., Raabe, R., et al. (1999). Asbestos-induced phosphorylation of epidermal growth factor receptor is linked to c-fos expression and apoptosis. American Journal of Physiology (Lung Cellular and Molecular Physiology), 277, L684–L693CrossRefGoogle ScholarPubMed
Zhang, L., Yang, N., Mohamed-Hadley, A., Rubin, S. C. and Coukos, G. (2003). Vector-based RNAi, a novel tool for isoform-specific knock-down of VEGF and anti-angiogenesis gene therapy of cancer. Biochemical and Biophysical Research Communications, 303, 1169–1178CrossRefGoogle Scholar

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