101
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Myers CL, Robson D, Wible A, Hibbs MA, Chiriac C, Theesfeld CL, Dolinski K, Troyanskaya OG. Discovery of biological networks from diverse functional genomic data. Genome Biol 2005; 6:R114. [PMID: 16420673 PMCID: PMC1414113 DOI: 10.1186/gb-2005-6-13-r114] [Citation(s) in RCA: 170] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2005] [Revised: 08/31/2005] [Accepted: 11/21/2005] [Indexed: 01/31/2023] Open
Abstract
BioPIXIE is a probabilistic system for query-based discovery of pathway-specific networks through integration of diverse genome-wide data. We have developed a general probabilistic system for query-based discovery of pathway-specific networks through integration of diverse genome-wide data. This framework was validated by accurately recovering known networks for 31 biological processes in Saccharomyces cerevisiae and experimentally verifying predictions for the process of chromosomal segregation. Our system, bioPIXIE, a public, comprehensive system for integration, analysis, and visualization of biological network predictions for S. cerevisiae, is freely accessible over the worldwide web.
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Affiliation(s)
- Chad L Myers
- Department of Computer Science, Princeton University, 35 Olden Street, Princeton, NJ 08544, USA
- Lewis-Sigler Institute for Integrative Genomics, Carl Icahn Laboratory, Princeton University, Princeton, NJ 08544, USA
| | - Drew Robson
- Department of Mathematics, Princeton University, Washington Road, Princeton, NJ 08540, USA
| | - Adam Wible
- Department of Computer Science, Princeton University, 35 Olden Street, Princeton, NJ 08544, USA
| | - Matthew A Hibbs
- Department of Computer Science, Princeton University, 35 Olden Street, Princeton, NJ 08544, USA
- Lewis-Sigler Institute for Integrative Genomics, Carl Icahn Laboratory, Princeton University, Princeton, NJ 08544, USA
| | - Camelia Chiriac
- Lewis-Sigler Institute for Integrative Genomics, Carl Icahn Laboratory, Princeton University, Princeton, NJ 08544, USA
| | - Chandra L Theesfeld
- Department of Genetics, School of Medicine, Mailstop-S120, Stanford University, Stanford, CA 94305-5120, USA
| | - Kara Dolinski
- Lewis-Sigler Institute for Integrative Genomics, Carl Icahn Laboratory, Princeton University, Princeton, NJ 08544, USA
| | - Olga G Troyanskaya
- Department of Computer Science, Princeton University, 35 Olden Street, Princeton, NJ 08544, USA
- Lewis-Sigler Institute for Integrative Genomics, Carl Icahn Laboratory, Princeton University, Princeton, NJ 08544, USA
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102
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Chen S, Hilcove S, Ding S. Exploring stem cell biology with small molecules. MOLECULAR BIOSYSTEMS 2005; 2:18-24. [PMID: 16880919 DOI: 10.1039/b512000b] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Stem cells hold promise for the treatment of a number of diseases. Small molecules serve as useful chemical tools to control stem cell fate and may ultimately contribute to development of effective medicines for tissue repair and regeneration.
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Affiliation(s)
- Shuibing Chen
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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103
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Abstract
Heat-shock protein 90 (Hsp90) is a molecular chaperone involved in three-dimensional folding, intracellular translocation and degradation of multiple key regulatory proteins. Accumulated evidence has indicated an important role of Hsp90 in several signal transduction pathways that are deregulated in carcinogenesis. 17-allylamino-17-demethoxygeldanamycin (17-AAG), a selective inhibitor of Hsp90, is currently under clinical investigation in advanced malignancies in which Hsp90 client proteins are implicated. This article discusses the mechanistic evidence underlying 17-AAG's cytostatic, proapoptotic, antiangiogenic and anti-invasive properties that provide the basis for its antitumour activity and underscores its unique therapeutic potential as a multi-targeted agent, as opposed to most of the current-generation molecular therapeutics.
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104
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Aoyagi S, Archer TK. Modulating molecular chaperone Hsp90 functions through reversible acetylation. Trends Cell Biol 2005; 15:565-7. [PMID: 16199163 DOI: 10.1016/j.tcb.2005.09.003] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2005] [Revised: 08/22/2005] [Accepted: 09/19/2005] [Indexed: 01/19/2023]
Abstract
The molecular chaperone protein Hsp90 is a key regulator of approximately 100 'client' proteins crucial for numerous cell signaling processes. Consequently, understanding the molecular underpinnings that regulate Hsp90 activity is an important biological endeavor. Exciting new results now suggest that, at least for nuclear receptor activity, Hsp90 function is directly regulated by histone deacetylase 6 (HDAC6). These observations have consequences for various biological processes and potentially important implications for the development of cancer therapeutics.
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Affiliation(s)
- Sayura Aoyagi
- Chromatin and Gene Expression Section, Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, National Institutes of Health, 111 Alexander Drive, P.O. Box 12233, Research Triangle Park, NC 27709, USA
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105
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Bali P, Pranpat M, Swaby R, Fiskus W, Yamaguchi H, Balasis M, Rocha K, Wang HG, Richon V, Bhalla K. Activity of suberoylanilide hydroxamic Acid against human breast cancer cells with amplification of her-2. Clin Cancer Res 2005; 11:6382-9. [PMID: 16144943 DOI: 10.1158/1078-0432.ccr-05-0344] [Citation(s) in RCA: 151] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE We determined the effects of suberoylanilide hydroxamic acid (SAHA), a histone deacetylase inhibitor, on hsp90 and its client proteins Her-2, AKT, and c-Raf, as well as evaluated the cytotoxic effects of co-treatment of SAHA with trastuzumab or docetaxel in human breast cancer BT-474 and SKBR-3 cells containing amplification of Her-2. EXPERIMENTAL DESIGN The cells were treated with SAHA (1.0-5.0 micromol/L) and/or trastuzumab (5-40 microg/mL) or docetaxel (5-20 nmol/L). Following this, apoptosis and the levels of p21(WAF1), p27(KIP1), AKT, c-Raf, and Her-2, as well as of the key regulators of apoptosis were determined. Synergistic interaction between drugs was evaluated by median dose-effect analysis. RESULTS Treatment with SAHA up-regulated p21(WAF1) and p27(KIP1) levels, increased the percentage of cells in G2-M phase of the cell cycle, as well as induced apoptosis in a dose-dependent manner. This was associated with up-regulation of the pro-death Bak and Bim, as well as with attenuation of the levels of Her-2 and XIAP, survivin, Bcl-2, and Bcl-x(L) proteins. SAHA treatment induced acetylation of hsp90. This reduced the chaperone association of Her-2 with hsp90, promoting polyubiquitylation and degradation of Her-2. SAHA also attenuated the levels of c-Raf and AKT. Co-treatment with SAHA significantly increased trastuzumab or docetaxel-induced apoptosis of BT-474 and SKBR-3 cells. Additionally, median dose-effect analysis revealed that co-treatment with SAHA and trastuzumab or docetaxel induced synergistic cytotoxic effects against the breast cancer cells. CONCLUSIONS These preclinical findings support the development of SAHA in combination with docetaxel and/or trastuzumab against Her-2-amplified breast cancer.
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Affiliation(s)
- Purva Bali
- Department of Interdisciplinary Oncology, Moffitt Cancer Center and Research Institute, University of South Florida, Tampa, Florida 33612, USA
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106
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Abstract
Small heat shock proteins (sHSPs) function as molecular chaperones, preventing stress induced aggregation of partially denatured proteins and promoting their return to native conformations when favorable conditions pertain. Sequence similarity between sHSPs resides predominately in an internal stretch of residues termed the alpha-crystallin domain, a region usually flanked by two extensions. The poorly conserved N-terminal extension influences oligomer construction and chaperone activity, whereas the flexible C-terminal extension stabilizes quaternary structure and enhances protein/substrate complex solubility. sHSP polypeptides assemble into dynamic oligomers which undergo subunit exchange and they bind a wide range of cellular substrates. As molecular chaperones, the sHSPs protect protein structure and activity, thereby preventing disease, but they may contribute to cell malfunction when perturbed. For example, sHSPs prevent cataract in the mammalian lens and guard against ischemic and reperfusion injury due to heart attack and stroke. On the other hand, mutated sHSPs are implicated in diseases such as desmin-related myopathy and they have an uncertain relationship to neurological disorders including Parkinson's and Alzheimer's disease. This review explores the involvement of sHSPs in disease and their potential for therapeutic intervention.
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Affiliation(s)
- Yu Sun
- Department of Biology, Dalhousie University, Halifax, Canada
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107
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Isaacs JS. Heat-shock protein 90 inhibitors in antineoplastic therapy: is it all wrapped up? Expert Opin Investig Drugs 2005; 14:569-89. [PMID: 16004589 DOI: 10.1517/13543784.14.6.569] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Heat-shock protein (Hsp)-90 belongs to the class of molecular chaperone proteins that are capable of sensing cellular stress. Although Hsp90 is essential for viability, the pharmacological inhibition of this chaperone has emerged as an attractive means to inhibit tumorigenesis. This phenomenon is due to a unique property of Hsp90; its 'client proteins' are universally involved in signal transduction pathways commonly dysregulated in, and contributing to, cancer. The natural product geldanamycin, a potent ansamycin Hsp90 inhibitor, has served as a lead compound for the development of several derivatives that are currently undergoing clinical trials. Inhibition of Hsp90 with geldanamycin simultaneously depletes Hsp90-associated clients and impairs numerous signalling cascades that depend on chaperone function. Importantly, tumour cells are exquisitely sensitive to Hsp90 inhibition, lending credence to the feasibility of selectively targeting cancer tissue via the pharmacological modulation of Hsp90 function. Even more remarkably, Hsp90 inhibitors sensitise tumour cells to the cytotoxic effects of a variety of standard therapeutics, and thus, they are likely to have broad utility in combination therapy. Although these are promising developments, much remains to be discovered about client-chaperone biology and the tumour-specific effects of Hsp90 blockade. This information is required to fully grasp the multi-faceted roles of Hsp90 in cancer biology towards the goal of optimising the use of these agents in the clinic. Elucidation of these nuances will undoubtedly lead to better targeting of relevant oncogenic pathways and translate into the development of more effective anticancer regimens.
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Affiliation(s)
- Jennifer S Isaacs
- Urologic Oncology Branch, Center for Cancer Research, NCI, National Institutes of Health, Rockville, MD, USA.
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108
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Prince T, Shao J, Matts RL, Hartson SD. Evidence for chaperone heterocomplexes containing both Hsp90 and VCP. Biochem Biophys Res Commun 2005; 331:1331-7. [PMID: 15883021 DOI: 10.1016/j.bbrc.2005.04.047] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2005] [Indexed: 12/27/2022]
Abstract
With assistance from co-chaperone partner proteins, Hsp90 plays an essential positive role in supporting the structure and function of numerous client proteins in vivo. Hsp90's co-chaperone partnerships are believed to regulate and/or target its function. Here we describe associations between Hsp90 chaperone machinery and another chaperone, the 97-kDa valosin-containing protein VCP. Coimmunoadsorption assays indicate that VCP occurs in one or more native heterocomplexes containing Hsp90 and the Hsp90 partner proteins Cdc37, FKBP52, and p23. Functional characterizations indicate that VCP is not an Hsp90 substrate, but rather demonstrate the biochemical hallmarks of an Hsp90 co-chaperone. Potential roles for a collaboration between for Hsp90 and VCP are discussed.
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Affiliation(s)
- Thomas Prince
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078-3035, USA
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109
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N/A, 戴 洁, 张 林, 金 春, 李 玉. N/A. Shijie Huaren Xiaohua Zazhi 2005; 13:567-569. [DOI: 10.11569/wcjd.v13.i4.567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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110
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Müller P, Ceskova P, Vojtesek B. Hsp90 Is Essential for Restoring Cellular Functions of Temperature-sensitive p53 Mutant Protein but Not for Stabilization and Activation of Wild-type p53. J Biol Chem 2005; 280:6682-91. [PMID: 15613472 DOI: 10.1074/jbc.m412767200] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Several signaling pathways that monitor the dynamic state of the cell converge on the tumor suppressor p53. The ability of p53 to process these signals and exert a dynamic downstream response in the form of cell cycle arrest and/or apoptosis is crucial for preventing tumor development. This p53 function is abrogated by p53 gene mutations leading to alteration of protein conformation. Hsp90 has been implicated in regulating both wild-type and mutant p53 conformations, and Hsp90 antagonists are effective for the therapy of some human tumors. Using cell lines that contain human tumor-derived temperature-sensitive p53 mutants we show that Hsp90 is required for both stabilization and reactivation of mutated p53 at the permissive temperature. A temperature decrease to 32 degrees C causes conversion to a protein conformation that is capable of inducing expression of MDM2, leading to reduction of reactivated p53 levels by negative feedback. Mutant reactivation is enhanced by simultaneous treatment with agents that stabilize the reactivated protein and is blocked by geldanamycin, a specific inhibitor of Hsp90 activity, indicating that Hsp90 antagonist therapy and therapies that act to reactivate mutant p53 will be incompatible. In contrast, Hsp90 is not required for maintaining wild-type p53 or for stabilizing wild-type p53 after treatment with chemotherapeutic agents, indicating that Hsp90 therapy might synergize with conventional therapies in patients with wild-type p53. Our data demonstrate the importance of the precise characterization of the interaction between p53 mutants and stress proteins, which may shed valuable information for fighting cancer via the p53 tumor suppressor pathway.
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Affiliation(s)
- Petr Müller
- Department of Experimental Oncology, Masaryk Memorial Cancer Institute, Zluty kopec 7, Brno 656 53, Czech Republic
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111
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Papaconstantinou AD, Shanmugam I, Shan L, Schroeder IS, Qiu C, Yu M, Snyderwine EG. Gene expression profiling in the mammary gland of rats treated with 7,12-dimethylbenz[a]anthracene. Int J Cancer 2005; 118:17-24. [PMID: 16003757 DOI: 10.1002/ijc.21247] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Identification of molecular markers of early-stage breast cancer development is important for the diagnosis and prevention of the disease. In the present study, we used microarray analysis to examine the differential expression of genes in the rat mammary gland soon after treatment with a known chemical carcinogen, 7,12-dimethylbenz[a]anthracene (DMBA), and prior to tumor development. Six weeks after DMBA, differential expression of multiple genes involved in cell growth, differentiation and microtubule dynamics were observed. Gene expression changes were further validated by a combination of techniques, including real-time PCR, RT-PCR, Western blotting and immunohistochemistry. An inhibition of differentiation in this early stage was suggested by the lower expression of beta-casein and transferrin and higher expression of hsp27 in glands from DMBA-treated rats. Possible cell cycle deregulation was indicated by an increased expression of cyclin D1 and hsp86, a heat shock protein associated with cyclin D1. Prior to tumor development, DMBA increased cellular proliferation as detected by Ki-67 and stathmin immunostaining in histologically normal mammary gland. Genes regulating microtubule function, including stathmin, Ran, alpha-tubulin and hsp27, were all overexpressed in the mammary gland of DMBA-treated rats, raising the possibility that disruption of microtubule dynamics and abnormal mitosis may be critical events preceding breast cancer development. Several of the altered proteins, including hsp27, hsp86 and stathmin, may ultimately serve as markers of early breast cancer development.
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Affiliation(s)
- Andriana D Papaconstantinou
- Chemical Carcinogenesis Section, Laboratory of Experimental Carcinogenesis, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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