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Cell Cycle-Dependent Control and Roles of DNA Topoisomerase II. Genes (Basel) 2019; 10:genes10110859. [PMID: 31671531 PMCID: PMC6896119 DOI: 10.3390/genes10110859] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 10/25/2019] [Accepted: 10/28/2019] [Indexed: 12/13/2022] Open
Abstract
Type II topoisomerases are ubiquitous enzymes in all branches of life that can alter DNA superhelicity and unlink double-stranded DNA segments during processes such as replication and transcription. In cells, type II topoisomerases are particularly useful for their ability to disentangle newly-replicated sister chromosomes. Growing lines of evidence indicate that eukaryotic topoisomerase II (topo II) activity is monitored and regulated throughout the cell cycle. Here, we discuss the various roles of topo II throughout the cell cycle, as well as mechanisms that have been found to govern and/or respond to topo II function and dysfunction. Knowledge of how topo II activity is controlled during cell cycle progression is important for understanding how its misregulation can contribute to genetic instability and how modulatory pathways may be exploited to advance chemotherapeutic development.
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Ayala I, Crispino R, Colanzi A. GRASP65 controls Golgi position and structure during G2/M transition by regulating the stability of microtubules. Traffic 2019; 20:785-802. [DOI: 10.1111/tra.12682] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 07/17/2019] [Accepted: 07/19/2019] [Indexed: 12/29/2022]
Affiliation(s)
- Inmaculada Ayala
- Institute of Biochemistry and Cell Biology (IBBC)National Research Council (CNR) Naples Italy
| | - Roberta Crispino
- Telethon Institute of Genetics and Medicine (TIGEM) Pozzuoli Italy
| | - Antonino Colanzi
- Institute of Biochemistry and Cell Biology (IBBC)National Research Council (CNR) Naples Italy
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Pommier Y, Sun Y, Huang SYN, Nitiss JL. Roles of eukaryotic topoisomerases in transcription, replication and genomic stability. Nat Rev Mol Cell Biol 2016; 17:703-721. [DOI: 10.1038/nrm.2016.111] [Citation(s) in RCA: 540] [Impact Index Per Article: 67.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Wu WK, Sakamoto KM, Milani M, Aldana-Masankgay G, Fan D, Wu K, Lee CW, Cho CH, Yu J, Sung JJ. Macroautophagy modulates cellular response to proteasome inhibitors in cancer therapy. Drug Resist Updat 2010; 13:87-92. [DOI: 10.1016/j.drup.2010.04.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2010] [Revised: 04/20/2010] [Accepted: 04/20/2010] [Indexed: 12/09/2022]
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Dallmann HG, Fackelmayer OJ, Tomer G, Chen J, Wiktor-Becker A, Ferrara T, Pope C, Oliveira MT, Burgers PMJ, Kaguni LS, McHenry CS. Parallel multiplicative target screening against divergent bacterial replicases: identification of specific inhibitors with broad spectrum potential. Biochemistry 2010; 49:2551-62. [PMID: 20184361 DOI: 10.1021/bi9020764] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Typically, biochemical screens that employ pure macromolecular components focus on single targets or a small number of interacting components. Researches rely on whole cell screens for more complex systems. Bacterial DNA replicases contain multiple subunits that change interactions with each stage of a complex reaction. Thus, the actual number of targets is a multiple of the proteins involved. It is estimated that the overall replication reaction includes up to 100 essential targets, many suitable for discovery of antibacterial inhibitors. We have developed an assay, using purified protein components, in which inhibitors of any of the essential targets can be detected through a common readout. Use of purified components allows each protein to be set within the linear range where the readout is proportional to the extent of inhibition of the target. By performing assays against replicases from model Gram-negative and Gram-positive bacteria in parallel, we show that it is possible to distinguish compounds that inhibit only a single bacterial replicase from those that exhibit broad spectrum potential.
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Affiliation(s)
- H Garry Dallmann
- Department of Chemistry and Biochemistry, University of Colorado, Campus Box 215, Boulder, Colorado 80309, USA
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Furet P, Schoepfer J, Radimerski T, Chène P. Discovery of a new class of catalytic topoisomerase II inhibitors targeting the ATP-binding site by structure based design. Part I. Bioorg Med Chem Lett 2009; 19:4014-7. [PMID: 19560355 DOI: 10.1016/j.bmcl.2009.06.034] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2009] [Revised: 06/05/2009] [Accepted: 06/08/2009] [Indexed: 11/27/2022]
Abstract
Topoisomerase II is a validated target in oncology. Among the different ways of blocking the function of this enzyme, inhibiting its ATPase activity has been relatively less investigated. In an effort to identify topoisomerase II inhibitors of a novel type, exerting their action by this mechanism, we have designed a purine inhibitor scaffold targeting the ATP-binding site of the enzyme. Searching the Novartis compound collection for molecules containing this purine motif has allowed the identification of two micromolar hits providing access to a new class of catalytic topoisomerase II inhibitors.
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Affiliation(s)
- Pascal Furet
- Novartis Institutes for BioMedical Research, WKL-136.P.12, CH-4002 Basel, Switzerland.
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Abstract
DNA topoisomerases are enzymes that disentangle the topological problems that arise in double-stranded DNA. Many of these can be solved by the generation of either single or double strand breaks. However, where there is a clear requirement to alter DNA topology by introducing transient double strand breaks, only DNA topoisomerase II (TOP2) can carry out this reaction. Extensive biochemical and structural studies have provided detailed models of how TOP2 alters DNA structure, and recent molecular studies have greatly expanded knowledge of the biological contexts in which TOP2 functions, such as DNA replication, transcription and chromosome segregation -- processes that are essential for preventing tumorigenesis.
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Affiliation(s)
- John L Nitiss
- Molecular Pharmacology Department, St Jude Children's Research Hospital, Memphis, TN 38105, USA.
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Abstract
Recent molecular studies have expanded the biological contexts in which topoisomerase II (TOP2) has crucial functions, including DNA replication, transcription and chromosome segregation. Although the biological functions of TOP2 are important for ensuring genomic integrity, the ability to interfere with TOP2 and generate enzyme-mediated DNA damage is an effective strategy for cancer chemotherapy. The molecular tools that have allowed an understanding of the biological functions of TOP2 are also being applied to understanding the details of drug action. These studies promise refined targeting of TOP2 as an effective anticancer strategy.
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Affiliation(s)
- John L Nitiss
- Molecular Pharmacology Department, St Jude Children's Research Hospital, Memphis, TN 38105, USA.
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Abstract
Although the clinical manifestations of alcoholic liver disease are well-described, little is known about the molecular basis of liver injury. Recent studies have indicated that ethanol exposure induces global protein hyperacetylation. This reversible, post-translational modification on the epsilon-amino groups of lysine residues has been shown to modulate multiple, diverse cellular processes ranging from transcriptional activation to microtubule stability. Thus, alcohol-induced protein hyperacetylation likely leads to major physiological consequences that contribute to alcohol-induced hepatotoxicity. Lysine acetylation is controlled by the activities of two opposing enzymes, histone acetyltransferases and histone deacetylases. Currently, efforts are aimed at determining which enzymes are responsible for the increased acetylation of specific substrates. However, the greater challenge will be to determine the physiological ramifications of protein hyperacetylation and how they might contribute to the progression of liver disease. In this review, we will first list and discuss the proteins known to be hyperacetylated in the presence of ethanol. We will then describe what is known about the mechanisms leading to increased protein acetylation and how hyperacetylation may perturb hepatic function.
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Smith PJ, Khan IA, Errington RJ. Cytomics and cellular informatics – coping with asymmetry and heterogeneity in biological systems. Drug Discov Today 2009; 14:271-7. [DOI: 10.1016/j.drudis.2008.11.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2008] [Revised: 10/31/2008] [Accepted: 11/18/2008] [Indexed: 01/03/2023]
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Abstract
Her2 (ErbB2) protein is overexpressed in breast and other solid tumors, and its expression is associated with progressive disease. Current therapies directed toward Her2 either block dimerization of the receptor or inhibit tyrosine kinase activity to disrupt intracellular signaling. However, little is known about alternative mechanisms for suppressing Her2 expression, possibly by inducing degradation or blocking synthesis. Here, we describe a hybrid western-blotting and enzyme-linked immunosorbent assay (ELISA) designed to identify in low- to medium-throughput format noncytotoxic compounds that reduce expression of Her2 protein.
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Affiliation(s)
- Gabriela Chiosis
- Program in Molecular Pharmacology and Chemistry, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
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Affiliation(s)
- Alexander Varshavsky
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA.
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Joseph RA, Shepard BD, Kannarkat GT, Rutledge TM, Tuma DJ, Tuma PL. Microtubule acetylation and stability may explain alcohol-induced alterations in hepatic protein trafficking. Hepatology 2008; 47:1745-53. [PMID: 18161881 PMCID: PMC2957806 DOI: 10.1002/hep.22014] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Abstract
UNLABELLED We have been using polarized hepatic WIF-B cells to examine ethanol-induced liver injury. Previously, we determined microtubules were more highly acetylated and more stable in ethanol-treated WIF-B cells. We proposed that the ethanol-induced alterations in microtubule dynamics may explain the ethanol-induced defects in membrane trafficking that have been previously documented. To test this, we compared the trafficking of selected proteins in control cells and cells treated with ethanol or with the histone deacetylase 6 inhibitor trichostatin A (TSA). We determined that exposure to 50 nM TSA for 30 minutes induced microtubule acetylation ( approximately 3-fold increase) and stability to the same extent as did ethanol. As shown previously in situ, the endocytic trafficking of the asialoglycoprotein receptor (ASGP-R) was impaired in ethanol-treated WIF-B cells. This impairment required ethanol metabolism and was likely mediated by acetaldehyde. TSA also impaired ASGP-R endocytic trafficking, but to a lesser extent. Similarly, both ethanol and TSA impaired transcytosis of the single-spanning apical resident aminopeptidase N (APN). For both ASGP-R and APN and for both treatments, the block in trafficking was internalization from the basolateral membrane. Interestingly, no changes in transcytosis of the glycophosphatidylinositol-anchored protein, 5'-nucleotidase, were observed, suggesting that increased microtubule acetylation and stability differentially regulate internalization. We further determined that albumin secretion was impaired in both ethanol-treated and TSA-treated cells, indicating that increased microtubule acetylation and stability also disrupted this transport step. CONCLUSION These results indicate that altered microtubule dynamics explain in part alcohol-induced defects in membrane trafficking.
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Affiliation(s)
- Rohan A. Joseph
- Department of Biology, The Catholic University of America, Washington, DC
| | - Blythe D. Shepard
- Department of Biology, The Catholic University of America, Washington, DC
| | | | - Tara M. Rutledge
- Department of Biology, The Catholic University of America, Washington, DC
| | - Dean J. Tuma
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE
| | - Pamela L. Tuma
- Department of Biology, The Catholic University of America, Washington, DC
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Sturgeon CM, Cinel B, Díaz-Marrero AR, McHardy LM, Ngo M, Andersen RJ, Roberge M. Abrogation of ionizing radiation-induced G2 checkpoint and inhibition of nuclear export by Cryptocarya pyrones. Cancer Chemother Pharmacol 2008; 61:407-13. [PMID: 17440726 DOI: 10.1007/s00280-007-0483-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2006] [Accepted: 03/17/2007] [Indexed: 10/23/2022]
Abstract
G(2) checkpoint inhibitors can force cells arrested in G(2) phase by DNA damage to enter mitosis. In this manner, several G(2) checkpoint inhibitors can enhance killing of cancer cells by ionizing radiation and DNA-damaging chemotherapeutic agents, particularly in cells lacking p53 function. All G(2) checkpoint inhibitors identified to date target protein phosphorylation by inhibiting checkpoint kinases or phosphatases. Using a phenotypic cell-based assay for G(2) checkpoint inhibitors, we have screened a large collection of plant extracts and identified Z-Cryptofolione and Cryptomoscatone D2 as highly efficacious inhibitors of the G(2) checkpoint. These compounds and related pyrones also inhibit nuclear export. Leptomycin B, a potent inhibitor of Crm1-mediated nuclear export, is also a very potent G(2) checkpoint inhibitor. These compounds possess a reactive Michael acceptor site and do not appear promising as a radiosensitizing agents because they are toxic to unirradiated cells at checkpoint inhibitory concentrations. Nevertheless, the results show that inhibition of nuclear export is an alternative to checkpoint kinase inhibition for abrogating the G(2) checkpoint and they should stimulate the search for less toxic nuclear export inhibitors.
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Affiliation(s)
- Christopher M Sturgeon
- Department of Biochemistry and Molecular Biology, Life Sciences Centre, University of British Columbia, Vancouver, BC, Canada
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McCarthy JR, Kelly KA, Sun EY, Weissleder R. Targeted delivery of multifunctional magnetic nanoparticles. Nanomedicine (Lond) 2007; 2:153-67. [PMID: 17716118 DOI: 10.2217/17435889.2.2.153] [Citation(s) in RCA: 191] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Magnetic nanoparticles and their magnetofluorescent analogues have become important tools for in vivo imaging using magnetic resonance imaging and fluorescent optical methods. A number of monodisperse magnetic nanoparticle preparations have been developed over the last decade for angiogenesis imaging, cancer staging, tracking of immune cells (monocyte/macrophage, T cells) and for molecular and cellular targeting. Phage display and data mining have enabled the procurement of novel tissue- or receptor-specific peptides, while high-throughput screening of diversity-oriented synthesis libraries has identified small molecules that permit or prevent uptake by specific cell types. Next-generation magnetic nanoparticles are expected to be truly multifunctional, incorporating therapeutic functionalities and further enhancing an already diverse repertoire of capabilities.
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Affiliation(s)
- Jason R McCarthy
- Center for Molecular Imaging Research, Harvard Medical School and Massachusetts General Hospital, 149 13th St, Rm 5406, Charlestown, MA 02129, USA.
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Affiliation(s)
- Daniel P Walsh
- Department of Chemistry, New York University, New York, New York 10003, USA
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Abstract
The decatenation checkpoint delays entry into mitosis until the chromosomes have been disentangled. Deficiency in or bypass of the decatenation checkpoint can cause chromosome breakage and nondisjunction during mitosis, which results in aneuploidy and chromosome rearrangements in the daughter cells. A deficiency in the decatenation checkpoint has been reported in lung and bladder cancer cell lines and may contribute to the accumulation of chromosome aberrations that commonly occur during tumour progression. A checkpoint deficiency has also been documented in cultured stem and progenitor cells, and cancer stem cells are likely to be derived from stem and progenitor cells that lack an effective decatenation checkpoint. An inefficient decatenation checkpoint is likely to be a source of the chromosome aberrations that are common features of most tumours, but an inefficient decatenation checkpoint in cancer stem cells could also provide a potential target for chemotherapy.
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Affiliation(s)
- M Damelin
- Department of Genetics and Development, College of Physicians and Surgeons of Columbia University, 701 W. 168th St., New York, NY 10032, USA
| | - T H Bestor
- Department of Genetics and Development, College of Physicians and Surgeons of Columbia University, 701 W. 168th St., New York, NY 10032, USA
- E-mail:
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Park I, Avraham HK. Cell cycle-dependent DNA damage signaling induced by ICRF-193 involves ATM, ATR, CHK2, and BRCA1. Exp Cell Res 2006; 312:1996-2008. [PMID: 16630610 DOI: 10.1016/j.yexcr.2006.02.029] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2005] [Revised: 02/11/2006] [Accepted: 02/28/2006] [Indexed: 01/13/2023]
Abstract
Topoisomerase II is essential for cell proliferation and survival and has been a target of various anticancer drugs. ICRF-193 has long been used as a catalytic inhibitor to study the function of topoisomerase II. Here, we show that ICRF-193 treatment induces DNA damage signaling. Treatment with ICRF-193 induced G2 arrest and DNA damage signaling involving gamma-H2AX foci formation and CHK2 phosphorylation. DNA damage by ICRF-193 was further demonstrated by formation of the nuclear foci of 53BP1, NBS1, BRCA1, MDC1, and FANCD2 and increased comet tail moment. The DNA damage signaling induced by ICRF-193 was mediated by ATM and ATR and was restricted to cells in specific cell cycle stages such as S, G2, and mitosis including late and early G1 phases. Downstream signaling of ATM and ATR involved the phosphorylation of CHK2 and BRCA1. Altogether, our results demonstrate that ICRF-193 induces DNA damage signaling in a cell cycle-dependent manner and suggest that topoisomerase II might be essential for the progression of the cell cycle at several stages including DNA decondensation.
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Affiliation(s)
- Iha Park
- Division of Experimental Medicine, Beth Israel Deaconess Medical Center, Harvard Institutes of Medicine, 4 Blackfan Circle, 3rd Floor, Boston, MA 02115, USA
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19
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Abstract
Chemical genetics is an emerging approach for studying biological systems using chemical tools. This strategy aims to reveal the macromolecules responsible for regulating biological systems; thus, the approach shares much in common with genetics. In both strategies, one must (a) develop an assay that reports on a biological process of interest, (b) perturb this process systematically (with mutations or small molecules), and (c) determine the target of each perturbation to reveal macromolecules (i.e., proteins and genes) regulating the process of interest. In this review, we discuss advances and challenges in this field that have emerged over the past four years. Several technologies have converged, raising the hope that it may be possible to systematically apply chemical probes to biological processes.
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Affiliation(s)
- Inese Smukste
- Department of Biological Sciences and Department of Chemistry, Columbia University, Fairchild Center, New York, New York 10027, USA
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20
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Jarecki J, Chen X, Bernardino A, Coovert DD, Whitney M, Burghes A, Stack J, Pollok BA. Diverse small-molecule modulators of SMN expression found by high-throughput compound screening: early leads towards a therapeutic for spinal muscular atrophy. Hum Mol Genet 2005; 14:2003-18. [PMID: 15944201 DOI: 10.1093/hmg/ddi205] [Citation(s) in RCA: 126] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
We have exploited the existence of a second copy of the human SMN gene (SMN2) to develop a high-throughput screening strategy to identify potential small molecule therapeutics for the genetic disease spinal muscular atrophy (SMA), which is caused by the loss of the SMN1 gene. Our screening process was designed to identify synthetic compounds that increase the total amount of full-length SMN messenger RNA and protein arising from the SMN2 gene, thereby suppressing the deleterious effects of losing SMN1. A cell-based bioassay was generated that detects SMN2 promoter activity, on which greater than 550,000 compounds was tested. This resulted in the identification of 17 distinct compounds with confirmed biological activity on the cellular primary assay, belonging to nine different structural families. Six of the nine scaffolds were chosen on the basis of their drug-like features to be tested for their ability to modulate SMN gene expression in SMA patient-derived fibroblasts. Five of the six compound classes altered SMN mRNA levels or mRNA splicing patterns in SMA patient-derived fibroblasts. Two of the compound classes, a quinazoline compound series and an indole compound, also increased SMN protein levels and nuclear gem/Cajal body numbers in patient-derived cells. In addition, these two distinct scaffolds showed additive effects when used in combination, suggesting that they may act on different molecular targets. The work described here has provided the foundation for a successful medicinal chemistry effort to further advance these compounds as potential small molecule therapeutics for SMA.
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Affiliation(s)
- Jill Jarecki
- Vertex Pharmaceuticals, Inc., San Diego, CA 92121, USA.
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Haggarty SJ. The principle of complementarity: chemical versus biological space. Curr Opin Chem Biol 2005; 9:296-303. [PMID: 15939332 DOI: 10.1016/j.cbpa.2005.04.006] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2005] [Accepted: 04/15/2005] [Indexed: 02/07/2023]
Abstract
Chemical genomics aims to systematically explore the interactions between small molecules and biological systems. These efforts aim to annotate genomes using the language of chemistry, and to provide information-rich profiles of chemical and biological systems. Here, I describe recent conceptual and experimental advances toward the goal of mapping multidimensional chemical and biological descriptor spaces. In doing so, I will focus on the complementary nature of these efforts, the importance of recognizing the distinction between computed versus observed descriptors, and highlight recent 'landmark' examples of small molecules discovered using phenotypic screens. Future computation and experimental advances will be needed to fully realize the goals of chemical genomics. For those willing to consider both local and global properties of chemical and biological space, and to venture into uncharted territory, there promises to be new vistas and principles to be discovered.
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Affiliation(s)
- Stephen J Haggarty
- Eli & Edythe L Broad Institute, 320 Charles Street, Cambridge, MA 02141, USA.
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