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

doi:10.1017/CBO9780511546402.035

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

Published online by Cambridge University Press: 31 July 2009

Maria E. Ramos-Nino and

Brooke T. Mossman

Edited by

Krishnarao Appasani

Foreword by

Andrew Fire and

Marshall Nirenberg

Show author details

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

DOI: https://doi.org/10.1017/CBO9780511546402.035 [Opens in a new window]

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, 16586–16590CrossRef Google 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 Scholar PubMed

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, 503–511CrossRef Google Scholar PubMed

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, 6745–6750CrossRef Google Scholar PubMed

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, 377–385CrossRef Google Scholar PubMed

Bennett, A. and Tonks, N. (1997). Regulation of distinct stages of skeletal muscle differentiation by mitogen-activated protein kinases. Science, 278, 1288–1291CrossRef Google Scholar PubMed

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, 3748–3758CrossRef Google Scholar PubMed

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, 112–119CrossRef Google 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, 4503–4510CrossRef Google Scholar PubMed

Branch, A. D. (1998). A good antisense molecule is hard to find. Trends in Biochemical Sciences, 23, 45–50CrossRef Google Scholar PubMed

Brummelkamp, T. R., Bernards, R. and Agami, R. (2002). A system for stable expression of short interfering RNAs in mammalian cells. Science, 296, 550–553CrossRef Google Scholar PubMed

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, 5938–5945CrossRef Google Scholar PubMed

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, 12032–12037CrossRef Google Scholar PubMed

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, 9742–9747CrossRef Google Scholar PubMed

Carbone, M., Kratzke, R. and Testa, J. (2002). Thepathogenesis of mesothelioma. Seminars in Oncology, 29, 2–17CrossRef Google Scholar

Carmichael, G. G. (2002). Medicine: Silencing viruses with RNA. Nature, 418, 379–380CrossRef Google Scholar PubMed

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 Scholar PubMed

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 Scholar PubMed

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, 6343–6346CrossRef Google 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–L949CrossRef Google Scholar PubMed

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, 841–852CrossRef Google Scholar PubMed

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 Scholar PubMed

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 Scholar PubMed

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, 729–747CrossRef Google Scholar

Dillin, A. (2003). The specifics of small interfering RNA specificity. Proceedings of the National Academy of Sciences USA, 100, 6289–6291CrossRef Google Scholar PubMed

Doench, J. G., Petersen, C. P. and Sharp, P. A. (2003). siRNAs can function as miRNAs. Genes & Development, 17, 438–442CrossRef Google Scholar PubMed

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, 494–498CrossRef Google Scholar PubMed

Elbashir, S. M., Lendeckel, W. and Tuschl, T. (2001). RNA interference is mediated by 21- and 22-nucleotide RNAs. Genes & Development, 15, 188–200CrossRef Google Scholar PubMed

Ellis, C. A. and Clark, G. (2000). The importance of being K-Ras. Cellular Signaling, 12, 425–434CrossRef Google Scholar PubMed

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, 31588–31592CrossRef Google Scholar PubMed

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, 270–285CrossRef Google Scholar PubMed

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, 521–531CrossRef Google Scholar PubMed

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, 806–811CrossRef Google Scholar PubMed

Gil, J. and Esteban, M. (2000). Induction of apoptosis by the dsRNA-dependent protein kinase (PKR): Mechanism of action. Apoptosis, 5, 107–114CrossRef Google Scholar PubMed

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, 414–417CrossRef Google Scholar PubMed

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, 531–537CrossRef Google Scholar PubMed

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 Scholar PubMed

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, 598–605CrossRef Google Scholar PubMed

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, 23–34CrossRef Google 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, 13–24CrossRef Google Scholar PubMed

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 Scholar PubMed

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, 5006–5010CrossRef Google Scholar PubMed

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, 1147–1153CrossRef Google Scholar PubMed

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, 227–230CrossRef Google Scholar PubMed

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, 3299–3303CrossRef Google Scholar PubMed

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, 396–400CrossRef Google Scholar PubMed

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 Scholar PubMed

Hunter, T. (1991). Cooperation between oncogenes. Cell, 64, 249–270CrossRef Google Scholar PubMed

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, 834–838CrossRef Google Scholar PubMed

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, 203–208CrossRef Google Scholar PubMed

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 Scholar PubMed

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–L1035CrossRef Google Scholar PubMed

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, 980–984CrossRef Google Scholar PubMed

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, 957–73CrossRef Google Scholar PubMed

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, 26563–26571CrossRef Google Scholar PubMed

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, 231–237CrossRef Google Scholar PubMed

Karin, M., Liu, Z. and Zandi, E. (1997). AP-1 function and regulation. Current Opinion in Cell Biology, 9, 240–246CrossRef Google Scholar PubMed

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, 713–716CrossRef Google Scholar PubMed

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, 2654–2659CrossRef Google Scholar PubMed

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, 133–141CrossRef Google Scholar PubMed

Ketting, R. F. and Plasterk, R. H. (2000). A genetic link between co-suppression and RNA interference in C. elegans. Nature, 404, 296–298CrossRef Google Scholar PubMed

Klein, G., Powers, A. and Croce, C. (2002). Association of SV40 with human tumors. Oncogene, 21, 1141–1149CrossRef Google Scholar PubMed

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>CrossRef Google Scholar PubMed

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, 2269–2271CrossRef Google Scholar PubMed

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, 963–976CrossRef Google Scholar PubMed

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, 860–921CrossRef Google Scholar PubMed

Lebedeva, I. and Stein, C. A. (2001). Antisenseoligonucleotides: Promise and reality. Annual Review of Pharmacology and Toxicology, 41, 403–419CrossRef Google 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, 500–505CrossRef Google Scholar PubMed

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, 843–850CrossRef Google Scholar PubMed

Li, Y. and Heldin, P. (2001). Hyaluronanproduction increases the malignant properties of mesothelioma cells. British Journal of Cancer, 85, 600–607CrossRef Google Scholar PubMed

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, 683–687CrossRef Google Scholar

Lloyd, A., Yancheva, N. and Wasylyk, B. (1991). Transformation suppressor activity of a Jun transcription factor lacking its activation domain. Nature, 352, 635–638CrossRef Google Scholar PubMed

Malumbres, M. and Pellicer, A. (1998). RAS pathways to cell cycle control and cell transformation. Frontiers of Bioscience, 3, 887–912Google Scholar PubMed

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, 966–970CrossRef Google Scholar PubMed

Marais, R., Wynne, J. and Treisman, R. (1993). The SRF accessory protein Elk-1 contains a growth factor-regulated transcriptional activation domain. Cell, 73, 381–393CrossRef Google Scholar PubMed

McCormick, F. (1999). Signalling networks that cause cancer. Trends in Cellular Biology, 9, M53–M56CrossRef Google Scholar PubMed

McDonald, J. and Wagner, A. (1996). The epidemiology of mesothelioma in historical context. European Respiratory Journal, 9, 1932–1942CrossRef Google Scholar PubMed

McManus, M. T. and Sharp, P. A. (2002). Gene silencing in mammals by small interfering RNAs. Nature Reviews Genetics, 3, 737–747CrossRef Google Scholar PubMed

Mechta, F., Lallemand, D., Pfarr, C. and Yaniv, M. (1997). Transformation by ras modifies AP-1 composition and activity. Oncogene, 14, 837–847CrossRef Google Scholar PubMed

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, 1381–1389CrossRef Google Scholar PubMed

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, 497–500CrossRef Google Scholar PubMed

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, 294–301CrossRef Google Scholar PubMed

Mossman, B. and Gee, J. (1989). Asbestosrelated disease. New England Journal of Medicine, 320, 1721–1730CrossRef Google 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, 167–170CrossRef Google Scholar PubMed

Mulloy, R., Salinas, S., Philips, A. and Hipskind, R. A. (2003). Activation of cyclin D1 expression by the ERK5 cascade. Oncogene, 22, 5387–5398CrossRef Google Scholar PubMed

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, 39–49CrossRef Google Scholar PubMed

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, 279–289CrossRef Google Scholar PubMed

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, 10802–10806CrossRef Google Scholar PubMed

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, 948–958CrossRef Google 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, 854–849CrossRef Google Scholar PubMed

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, 634–644CrossRef Google Scholar PubMed

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, 505–508CrossRef Google Scholar PubMed

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, 7927–7931CrossRef Google Scholar PubMed

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, 747–752CrossRef Google Scholar PubMed

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, 41–46CrossRef Google Scholar PubMed

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, 15149–15154CrossRef Google Scholar PubMed

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 Scholar PubMed

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, 111–118CrossRef Google Scholar PubMed

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–L1178CrossRef Google 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, 9248–9253CrossRef Google Scholar PubMed

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, 95–100CrossRef Google Scholar PubMed

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, 1328–1337CrossRef Google Scholar PubMed

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, 3057–3068CrossRef Google Scholar PubMed

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, 5958–5962CrossRef Google Scholar PubMed

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, 1023–1029CrossRef Google Scholar PubMed

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, 805–813CrossRef Google Scholar PubMed

Schaeffer, H. and , MJ W. (1999). Mitogen-activated protein kinases: Specific messages from ubiquitous messengers. Molecular and Cellular Biology, 19, 2435–2444CrossRef Google Scholar PubMed

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, 810–816CrossRef Google Scholar PubMed

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, 6347–6352CrossRef Google Scholar PubMed

Sharp, P. A. (2001). RNA interference – 2001. Genes & Development, 15, 485–490CrossRef Google Scholar PubMed

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 Scholar PubMed

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, 43344–43351CrossRef Google Scholar PubMed

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, 1863–1877CrossRef Google Scholar PubMed

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 Scholar PubMed

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, 115–120CrossRef Google Scholar PubMed

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, 88–97CrossRef Google Scholar PubMed

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, 291–296CrossRef Google Scholar PubMed

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, 321–329CrossRef Google Scholar PubMed

Tuschl, T. and Borkhardt, A. (2002). Small interfering RNAs a revolutionary tool for the analyiss of gene function and gene therapy. Molecular Interventions, 2, 158–167CrossRef Google 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, 91–96CrossRef Google Scholar PubMed

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, 291–299CrossRef Google Scholar PubMed

‘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, 530–536CrossRef Google Scholar PubMed

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, 1304–1351CrossRef Google Scholar PubMed

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–L225CrossRef Google Scholar PubMed

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, 3493–3498CrossRef Google Scholar PubMed

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, 4194–4203CrossRef Google Scholar PubMed

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, 1947–1958CrossRef Google Scholar PubMed

Williams, B. R. (1997). Role of the double-stranded RNA-activated protein kinase (PKR) in cell regulation. Biochemical Society Transactions, 25, 509–513CrossRef Google 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 Scholar PubMed

Wisdom, R. and Verma, I. (1993). Transformation by Fos proteins requires a c-terminal transactivation domain. Molecular and Cellular Biology, 13, 7429–7438CrossRef Google 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, 1159–1162CrossRef Google Scholar PubMed

Xia, H., Mao, Q., Paulson, H. L. and Davidson, B. L. (2002). siRNA-mediated gene silencing in vitro and in vivo. Nature Biotechnology, 20, 1006–1010CrossRef Google Scholar PubMed

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, 143–150CrossRef Google 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, 6047–6052CrossRef Google Scholar PubMed

Zamore, P. D. (2001). RNA interference: Listening to the sound of silence. Nature Structural Biology, 8, 746–750CrossRef Google Scholar PubMed

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 Scholar PubMed

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–L693CrossRef Google Scholar PubMed

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, 1169–1178CrossRef Google Scholar