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Infante Lara L, Fenner S, Ratcliffe S, Isidro-Llobet A, Hann M, Bax B, Osheroff N. Coupling the core of the anticancer drug etoposide to an oligonucleotide induces topoisomerase II-mediated cleavage at specific DNA sequences. Nucleic Acids Res 2019; 46:2218-2233. [PMID: 29447373 PMCID: PMC5861436 DOI: 10.1093/nar/gky072] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 02/06/2018] [Indexed: 12/13/2022] Open
Abstract
Etoposide and other topoisomerase II-targeted drugs are important anticancer therapeutics. Unfortunately, the safe usage of these agents is limited by their indiscriminate induction of topoisomerase II-mediated DNA cleavage throughout the genome and by a lack of specificity toward cancer cells. Therefore, as a first step toward constraining the distribution of etoposide-induced DNA cleavage sites and developing sequence-specific topoisomerase II-targeted anticancer agents, we covalently coupled the core of etoposide to oligonucleotides centered on a topoisomerase II cleavage site in the PML gene. The initial sequence used for this ‘oligonucleotide-linked topoisomerase inhibitor’ (OTI) was identified as part of the translocation breakpoint of a patient with acute promyelocytic leukemia (APL). Subsequent OTI sequences were derived from the observed APL breakpoint between PML and RARA. Results indicate that OTIs can be used to direct the sites of etoposide-induced DNA cleavage mediated by topoisomerase IIα and topoisomerase IIβ. OTIs increased levels of enzyme-mediated cleavage by inhibiting DNA ligation, and cleavage complexes induced by OTIs were as stable as those induced by free etoposide. Finally, OTIs directed against the PML-RARA breakpoint displayed cleavage specificity for oligonucleotides with the translocation sequence over those with sequences matching either parental gene. These studies demonstrate the feasibility of using oligonucleotides to direct topoisomerase II-mediated DNA cleavage to specific sites in the genome.
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Affiliation(s)
- Lorena Infante Lara
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
| | - Sabine Fenner
- Platform Technology and Science, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK
| | - Steven Ratcliffe
- Platform Technology and Science, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK
| | - Albert Isidro-Llobet
- Platform Technology and Science, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK
| | - Michael Hann
- Platform Technology and Science, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK
| | - Ben Bax
- Platform Technology and Science, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK.,York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Neil Osheroff
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA.,Department of Medicine (Hematology/Oncology), Vanderbilt University School of Medicine, Nashville, TN 37232, USA.,VA Tennessee Valley Healthcare System, Nashville, TN 37212, USA
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2
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Geel TM, Ruiters MHJ, Cool RH, Halby L, Voshart DC, Andrade Ruiz L, Niezen-Koning KE, Arimondo PB, Rots MG. The past and presence of gene targeting: from chemicals and DNA via proteins to RNA. Philos Trans R Soc Lond B Biol Sci 2018; 373:20170077. [PMID: 29685979 PMCID: PMC5915719 DOI: 10.1098/rstb.2017.0077] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2017] [Indexed: 12/19/2022] Open
Abstract
The ability to target DNA specifically at any given position within the genome allows many intriguing possibilities and has inspired scientists for decades. Early gene-targeting efforts exploited chemicals or DNA oligonucleotides to interfere with the DNA at a given location in order to inactivate a gene or to correct mutations. We here describe an example towards correcting a genetic mutation underlying Pompe's disease using a nucleotide-fused nuclease (TFO-MunI). In addition to the promise of gene correction, scientists soon realized that genes could be inactivated or even re-activated without inducing potentially harmful DNA damage by targeting transcriptional modulators to a particular gene. However, it proved difficult to fuse protein effector domains to the first generation of programmable DNA-binding agents. The engineering of gene-targeting proteins (zinc finger proteins (ZFPs), transcription activator-like effectors (TALEs)) circumvented this problem. The disadvantage of protein-based gene targeting is that a fusion protein needs to be engineered for every locus. The recent introduction of CRISPR/Cas offers a flexible approach to target a (fusion) protein to the locus of interest using cheap designer RNA molecules. Many research groups now exploit this platform and the first human clinical trials have been initiated: CRISPR/Cas has kicked off a new era of gene targeting and is revolutionizing biomedical sciences.This article is part of a discussion meeting issue 'Frontiers in epigenetic chemical biology'.
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Affiliation(s)
- T M Geel
- Epigenetic Editing, Dept Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - M H J Ruiters
- Epigenetic Editing, Dept Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - R H Cool
- Chemical and Pharmaceutical Biology, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - L Halby
- CNRS FRE3600 ETaC, bât IBCG, 31062 Toulouse, France
| | - D C Voshart
- Epigenetic Editing, Dept Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - L Andrade Ruiz
- Epigenetic Editing, Dept Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - K E Niezen-Koning
- Laboratory of Metabolic Diseases, Dept Laboratory Medicine, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - P B Arimondo
- CNRS FRE3600 ETaC, bât IBCG, 31062 Toulouse, France
| | - M G Rots
- Epigenetic Editing, Dept Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
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Gasiunas G, Siksnys V. RNA-dependent DNA endonuclease Cas9 of the CRISPR system: Holy Grail of genome editing? Trends Microbiol 2013; 21:562-7. [DOI: 10.1016/j.tim.2013.09.001] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 09/02/2013] [Accepted: 09/04/2013] [Indexed: 12/23/2022]
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Seng HL, Wang WS, Kong SM, Alan Ong HK, Win YF, Raja Abd. Rahman RNZ, Chikira M, Leong WK, Ahmad M, Khoo ASB, Ng CH. Biological and cytoselective anticancer properties of copper(II)-polypyridyl complexes modulated by auxiliary methylated glycine ligand. Biometals 2012; 25:1061-81. [DOI: 10.1007/s10534-012-9572-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2012] [Accepted: 07/10/2012] [Indexed: 01/26/2023]
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5
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Chin L, Kong S, Seng H, Tiong Y, Neo K, Maah MJ, Khoo AS, Ahmad M, Hor TA, Lee H, San S, Chye S, Ng C. [Zn(phen)(O,N,O)(H2O)] and [Zn(phen)(O,N)(H2O)] with O,N,O is 2,6-dipicolinate and N,O is l-threoninate: synthesis, characterization, and biomedical properties. J Biol Inorg Chem 2012; 17:1093-105. [DOI: 10.1007/s00775-012-0923-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Accepted: 07/07/2012] [Indexed: 02/02/2023]
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6
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Silanskas A, Zaremba M, Sasnauskas G, Siksnys V. Catalytic activity control of restriction endonuclease--triplex forming oligonucleotide conjugates. Bioconjug Chem 2012; 23:203-11. [PMID: 22236287 DOI: 10.1021/bc200480m] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Targeting of individual genes in complex genomes requires endonucleases of extremely high specificity. To direct cleavage at the unique site(s) in the genome, both naturally occurring and artificial enzymes have been developed. These include homing endonucleases, zinc-finger nucleases, transcription activator-like effector nucleases, and restriction or chemical nucleases coupled to a triple-helix forming oligonucleotide (TFO). The desired cleavage has been demonstrated both in vivo and in vitro for several model systems. However, to limit cleavage strictly to unique sites and avoid undesired reactions, endonucleases with controlled activity are highly desirable. In this study we present a proof-of-concept demonstration of two strategies to generate restriction endonuclease-TFO conjugates with controllable activity. First, we combined the restriction endonuclease caging and TFO coupling procedures to produce a caged MunI-TFO conjugate, which can be activated by UV-light upon formation of a triple helix. Second, we coupled TFO to a subunit interface mutant of restriction endonuclease Bse634I which shows no activity due to impaired dimerization but is assembled into an active dimer when two Bse634I monomers are brought into close proximity by triple helix formation at the targeted site. Our results push the restriction endonuclease-TFO conjugate technology one step closer to potential in vivo applications.
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Affiliation(s)
- Arunas Silanskas
- Institute of Biotechnology, Vilnius University, Graiciuno 8, LT-02241 Vilnius, Lithuania
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Vekhoff P, Duca M, Guianvarc'h D, Benhida R, Arimondo PB. Sequence-specific base pair mimics are efficient topoisomerase IB inhibitors. Biochemistry 2011; 51:43-51. [PMID: 22124209 DOI: 10.1021/bi2012959] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Topoisomerase IB controls DNA topology by cleaving DNA transiently. This property is used by inhibitors, such as camptothecin, that stabilize, by inhibiting the religation step, the cleavage complex, in which the enzyme is covalently attached to the 3'-phosphate of the cleaved DNA strand. These drugs are used in clinics as antitumor agents. Because three-dimensional structural studies have shown that camptothecin derivatives act as base pair mimics and intercalate between two base pairs in the ternary DNA-topoisomerase-inhibitor complex, we hypothesized that base pairs mimics could act like campthotecin and inhibit the religation reaction after the formation of the topoisomerase I-DNA cleavage complex. We show here that three base pair mimics, nucleobases analogues of the aminophenyl-thiazole family, once targeted specifically to a DNA sequence were potent topoisomerase IB inhibitors. The targeting was achieved through covalent linkage to a sequence-specific DNA ligand, a triplex-forming oligonucleotide, and was necessary to position and keep the nucleobase analogue in the cleavage complex. In the absence of triplex formation, only a weak binding to the DNA and topoisomerase I-mediated DNA cleavage was observed. The three compounds were equally active once conjugated, implying that the intercalation of the nucleobase upon triplex formation is the essential feature for the inhibition activity.
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Affiliation(s)
- Pierre Vekhoff
- CNRS UMR7196, Muséum National d'Histoire Naturelle, 43 rue Cuvier, 75005 Paris, France
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Von ST, Seng HL, Lee HB, Ng SW, Kitamura Y, Chikira M, Ng CH. DNA molecular recognition and cellular selectivity of anticancer metal(II) complexes of ethylenediaminediacetate and phenanthroline: multiple targets. J Biol Inorg Chem 2011; 17:57-69. [DOI: 10.1007/s00775-011-0829-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2011] [Accepted: 07/16/2011] [Indexed: 01/29/2023]
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9
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Silva G, Poirot L, Galetto R, Smith J, Montoya G, Duchateau P, Pâques F. Meganucleases and other tools for targeted genome engineering: perspectives and challenges for gene therapy. Curr Gene Ther 2011; 11:11-27. [PMID: 21182466 PMCID: PMC3267165 DOI: 10.2174/156652311794520111] [Citation(s) in RCA: 223] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Revised: 12/10/2010] [Accepted: 12/10/2010] [Indexed: 12/17/2022]
Abstract
The importance of safer approaches for gene therapy has been underscored by a series of severe adverse events (SAEs) observed in patients involved in clinical trials for Severe Combined Immune Deficiency Disease (SCID) and Chromic Granulomatous Disease (CGD). While a new generation of viral vectors is in the process of replacing the classical gamma-retrovirus-based approach, a number of strategies have emerged based on non-viral vectorization and/or targeted insertion aimed at achieving safer gene transfer. Currently, these methods display lower efficacies than viral transduction although many of them can yield more than 1% of engineered cells in vitro. Nuclease-based approaches, wherein an endonuclease is used to trigger site-specific genome editing, can significantly increase the percentage of targeted cells. These methods therefore provide a real alternative to classical gene transfer as well as gene editing. However, the first endonuclease to be in clinic today is not used for gene transfer, but to inactivate a gene (CCR5) required for HIV infection. Here, we review these alternative approaches, with a special emphasis on meganucleases, a family of naturally occurring rare-cutting endonucleases, and speculate on their current and future potential.
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Affiliation(s)
- George Silva
- Cellectis, 102 Avenue Gaston Roussel, 93 235 Romainville, Cedex, France
| | - Laurent Poirot
- Cellectis Genome Surgery, 102 Avenue Gaston Roussel, 93 235 Romainville, Cedex, France
| | - Roman Galetto
- Cellectis Genome Surgery, 102 Avenue Gaston Roussel, 93 235 Romainville, Cedex, France
| | - Julianne Smith
- Cellectis Genome Surgery, 102 Avenue Gaston Roussel, 93 235 Romainville, Cedex, France
| | - Guillermo Montoya
- Macromolecular Crystallography Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Centre (CNIO), Melchor Fdez. Almagro 3, 28029 Madrid, Spain
| | | | - Frédéric Pâques
- Cellectis Genome Surgery, 102 Avenue Gaston Roussel, 93 235 Romainville, Cedex, France
- Cellectis, 102 Avenue Gaston Roussel, 93 235 Romainville, Cedex, France
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10
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Birkedal H, Nielsen PE. Targeted gene correction using psoralen, chlorambucil and camptothecin conjugates of triplex forming peptide nucleic acid (PNA). Artif DNA PNA XNA 2011; 2:23-32. [PMID: 21686249 PMCID: PMC3116579 DOI: 10.4161/adna.2.1.15553] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Revised: 03/18/2011] [Accepted: 03/22/2011] [Indexed: 05/30/2023]
Abstract
Gene correction activation effects of a small series of triplex forming peptide nucleic acid (PNA) covalently conjugated to the DNA interacting ligands psoralen, chlorambucil and camptothecin targeted proximal to a stop codon mutation in an EGFP reporter gene were studied. A 15-mer homopyrimidine PNA conjugated to the topoisomerase I inhibitor camptothecin was found to increase the frequency of repair domain mediated gene correctional events of the EGFP reporter in an in vitro HeLa cell nuclear extract assay, whereas PNA psoralen or chlorambucil conjugates both of which form covalent and also interstrand crosslinked adducts with dsDNA dramatically decreased the frequency of targeted repair/correction. The PNA conjugates were also studied in mammalian cell lines upon transfection of PNA bound EGFP reporter vector and scoring repair of the EGFP gene by FACS analysis of functional EGFP expression. Consistent with the extract experiments, treatment with adduct forming PNA conjugates (psoralen and chlorambucil) resulted in a decrease in background correction frequencies in transiently transfected cells, whereas unmodified PNA or the PNA-camptothecin conjugate had little or no effect. These results suggest that simple triplex forming PNAs have little effect on proximal gene correctional events whereas PNA conjugates capable of forming DNA adducts and interstrand crosslinks are strong inhibitors. Most interestingly the PNA conjugated to the topoisomerase inhibitor, camptothecin enhanced repair in nuclear extract. Thus the effects and use of camptothecin conjugates in gene targeted repair merit further studies.
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Affiliation(s)
- Henrik Birkedal
- Department of Cellular and Molecular Medicine; Faculty of Health Sciences; The Panum Institute; Copenhagen, Denmark
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11
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Jain AK, Bhattacharya S. Groove Binding Ligands for the Interaction with Parallel-Stranded ps-Duplex DNA and Triplex DNA. Bioconjug Chem 2010; 21:1389-403. [DOI: 10.1021/bc900247s] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Akash K. Jain
- Department of Organic Chemistry, Indian Institute of Science, Bangalore 560012, India, Chemical Biology Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560012, India
| | - Santanu Bhattacharya
- Department of Organic Chemistry, Indian Institute of Science, Bangalore 560012, India, Chemical Biology Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560012, India
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Oussedik K, François JC, Halby L, Senamaud-Beaufort C, Toutirais G, Dallavalle S, Pommier Y, Pisano C, Arimondo PB. Sequence-specific targeting of IGF-I and IGF-IR genes by camptothecins. FASEB J 2010; 24:2235-44. [PMID: 20179147 DOI: 10.1096/fj.09-132324] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We and others have clearly demonstrated that a topoisomerase I (Top1) inhibitor, such as camptothecin (CPT), coupled to a triplex-forming oligonucleotide (TFO) through a suitable linker can be used to cause site-specific cleavage of the targeted DNA sequence in in vitro models. Here we evaluated whether these molecular tools induce sequence-specific DNA damage in a genome context. We targeted the insulin-like growth factor (IGF)-I axis and in particular promoter 1 of IGF-I and intron 2 of type 1 insulin-like growth factor receptor (IGF-IR) in cancer cells. The IGF axis molecules represent important targets for anticancer strategies, because of their central role in oncogenic maintenance and metastasis processes. We chemically attached 2 CPT derivatives to 2 TFOs. Both conjugates efficiently blocked gene expression in cells, reducing the quantity of mRNA transcribed by 70-80%, as measured by quantitative RT-PCR. We confirmed that the inhibitory mechanism of these TFO conjugates was mediated by Top1-induced cleavage through the use of RNA interference experiments and a camptothecin-resistant cell line. In addition, induction of phospho-H2AX foci supports the DNA-damaging activity of TFO-CPT conjugates at specific sites. The evaluated conjugates induce a specific DNA damage at the target gene mediated by Top1.
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Affiliation(s)
- Kahina Oussedik
- Centre National de la Recherche, Scientifique, Unité Mixte de Recherche 7196, Muséum National d'Histoire Naturelle, Paris, France
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Zuco V, Benedetti V, Zunino F. ATM- and ATR-mediated response to DNA damage induced by a novel camptothecin, ST1968. Cancer Lett 2009; 292:186-96. [PMID: 20042274 DOI: 10.1016/j.canlet.2009.12.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Revised: 11/30/2009] [Accepted: 12/01/2009] [Indexed: 11/29/2022]
Abstract
DNA damage response and checkpoint activation are expected to influence the sensitivity to DNA-damaging agents. This study was designed to investigate the DNA damage response to the novel camptothecin, ST1968, in two tumor cell lines with a different biological background (A2780 and KB), which underwent distinct cell cycle perturbations and cell death modalities. Following treatment with the camptothecin or ionizing radiation, both inducing double-strand DNA breaks, the ovarian carcinoma A2780 cells exhibited activation of the ATM-Chk2 pathway and early induction of apoptosis. In contrast, the squamous carcinoma KB cells exhibited activation of ATR-Chk1 pathway, a persistent G(2)/M-phase arrest, cellular senescence, mitotic catastrophe and delayed apoptosis, suggesting a defective ATM pathway. The cellular response to UV-induced DNA damage, which activates ATR-Chk1 pathway, was similar in the two cell lines exhibiting early apoptosis induction. Inhibition of ATM in A2780 cells, resulting in reduced phosphorylation of Chk2, enhanced ST1968-induced apoptosis, but had no effect in KB cells. The susceptibility to camptothecin-induced apoptosis of A2780 cells was likely p53-dependent but not related to the activation of the ATM pathway. In contrast, the inhibition of Chk1 enhanced apoptosis response in KB cell but not in A2780. Thus, depending on the biological context, the camptothecin activated ATM-Chk2 or ATR-Chk1 pathways, both having a protective role. In conclusion, our results are consistent with the interpretation that the modality of cell death response is not the critical determinant of sensitivity to camptothecins, and support the interest of inhibition of checkpoint kinases to improve the efficacy of camptothecins.
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Affiliation(s)
- Valentina Zuco
- Fondazione IRCCS Istituto Nazionale dei Tumori, via Venezian 1, 20133 Milan, Italy
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Abstract
The development of methods for cell-mediated transgenesis, based on somatic cell nuclear transfer, provides a tremendous opportunity to shape the genetic make-up of livestock animals in a much more directed approach than traditional animal breeding and selection schemes. Progress in the site-directed modulation of livestock genomes is currently limited by the low efficiencies of gene targeting imposed by the low frequency of homologous recombination and limited proliferative capacity of primary somatic cells that are used to produce transgenic animals. Here we review the current state of the art in the field, discuss the crucial aspects of the methodology and provide an overview of emerging approaches to increase the efficiency of gene targeting in somatic cells.
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Affiliation(s)
- Götz Laible
- AgResearch, Ruakura Research Centre, Hamilton, New Zealand.
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15
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Abstract
BACKGROUND In spite of significant advances in gene transfer strategies in the field of gene therapy, there is a strong emphasis on the development of alternative methods, providing better control of transgene expression and insertion patterns. OBJECTIVE Several new approaches consist of targeting a desired transgene or gene modification in a well defined locus, and we collectively refer to them as 'targeted approaches'. The use of redesigned meganucleases is one of these emerging technologies. Here we try to define the potential of this method, in the larger scope of targeted strategies. METHODS We survey the different types of targeted strategies, presenting the achievements and the potential applications, with a special emphasis on the use of redesigned endonucleases. CONCLUSION redesigned endonucleases represent one of the most promising tools for targeted approaches, and the opening of a clinical trial for AIDS patients has recently shown the maturity of these strategies. However, there is still a 'quest' for the best reagents, that is the endonucleases providing the best efficacy:toxicity ratio. New advances in protein design have allowed the engineering of new scaffolds, such as meganucleases, and the landscape of existing methods is likely to change over the next few years.
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Affiliation(s)
- Roman Galetto
- Cellectis Genome Surgery, 102 Avenue Gaston Roussel, 93 340 Romainville Cedex, France
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16
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Vekhoff P, Halby L, Oussedik K, Dallavalle S, Merlini L, Mahieu C, Lansiaux A, Bailly C, Boutorine A, Pisano C, Giannini G, Alloatti D, Arimondo PB. Optimized Synthesis and Enhanced Efficacy of Novel Triplex-Forming Camptothecin Derivatives Based on Gimatecan. Bioconjug Chem 2009; 20:666-72. [DOI: 10.1021/bc800494y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Pierre Vekhoff
- CNRS UMR5153, Muséum National d’Histoire Naturelle USM0503, and INSERM U565, 43 rue Cuvier, 75231 Paris cedex 05, France, UPMC, Paris 75005, France, DISMA, Università di Milano, via Celoria 2, 20133 Milano, Italy, INSERM U-837, COL, IRCL, Place Verdun, 59045 Lille, France, and Sigma-tau Industrie Farmaceutiche Riunite SpA, Pomezia, Italy
| | - Ludovic Halby
- CNRS UMR5153, Muséum National d’Histoire Naturelle USM0503, and INSERM U565, 43 rue Cuvier, 75231 Paris cedex 05, France, UPMC, Paris 75005, France, DISMA, Università di Milano, via Celoria 2, 20133 Milano, Italy, INSERM U-837, COL, IRCL, Place Verdun, 59045 Lille, France, and Sigma-tau Industrie Farmaceutiche Riunite SpA, Pomezia, Italy
| | - Kahina Oussedik
- CNRS UMR5153, Muséum National d’Histoire Naturelle USM0503, and INSERM U565, 43 rue Cuvier, 75231 Paris cedex 05, France, UPMC, Paris 75005, France, DISMA, Università di Milano, via Celoria 2, 20133 Milano, Italy, INSERM U-837, COL, IRCL, Place Verdun, 59045 Lille, France, and Sigma-tau Industrie Farmaceutiche Riunite SpA, Pomezia, Italy
| | - Sabrina Dallavalle
- CNRS UMR5153, Muséum National d’Histoire Naturelle USM0503, and INSERM U565, 43 rue Cuvier, 75231 Paris cedex 05, France, UPMC, Paris 75005, France, DISMA, Università di Milano, via Celoria 2, 20133 Milano, Italy, INSERM U-837, COL, IRCL, Place Verdun, 59045 Lille, France, and Sigma-tau Industrie Farmaceutiche Riunite SpA, Pomezia, Italy
| | - Lucio Merlini
- CNRS UMR5153, Muséum National d’Histoire Naturelle USM0503, and INSERM U565, 43 rue Cuvier, 75231 Paris cedex 05, France, UPMC, Paris 75005, France, DISMA, Università di Milano, via Celoria 2, 20133 Milano, Italy, INSERM U-837, COL, IRCL, Place Verdun, 59045 Lille, France, and Sigma-tau Industrie Farmaceutiche Riunite SpA, Pomezia, Italy
| | - Christine Mahieu
- CNRS UMR5153, Muséum National d’Histoire Naturelle USM0503, and INSERM U565, 43 rue Cuvier, 75231 Paris cedex 05, France, UPMC, Paris 75005, France, DISMA, Università di Milano, via Celoria 2, 20133 Milano, Italy, INSERM U-837, COL, IRCL, Place Verdun, 59045 Lille, France, and Sigma-tau Industrie Farmaceutiche Riunite SpA, Pomezia, Italy
| | - Amélie Lansiaux
- CNRS UMR5153, Muséum National d’Histoire Naturelle USM0503, and INSERM U565, 43 rue Cuvier, 75231 Paris cedex 05, France, UPMC, Paris 75005, France, DISMA, Università di Milano, via Celoria 2, 20133 Milano, Italy, INSERM U-837, COL, IRCL, Place Verdun, 59045 Lille, France, and Sigma-tau Industrie Farmaceutiche Riunite SpA, Pomezia, Italy
| | - Christian Bailly
- CNRS UMR5153, Muséum National d’Histoire Naturelle USM0503, and INSERM U565, 43 rue Cuvier, 75231 Paris cedex 05, France, UPMC, Paris 75005, France, DISMA, Università di Milano, via Celoria 2, 20133 Milano, Italy, INSERM U-837, COL, IRCL, Place Verdun, 59045 Lille, France, and Sigma-tau Industrie Farmaceutiche Riunite SpA, Pomezia, Italy
| | - Alexandre Boutorine
- CNRS UMR5153, Muséum National d’Histoire Naturelle USM0503, and INSERM U565, 43 rue Cuvier, 75231 Paris cedex 05, France, UPMC, Paris 75005, France, DISMA, Università di Milano, via Celoria 2, 20133 Milano, Italy, INSERM U-837, COL, IRCL, Place Verdun, 59045 Lille, France, and Sigma-tau Industrie Farmaceutiche Riunite SpA, Pomezia, Italy
| | - Claudio Pisano
- CNRS UMR5153, Muséum National d’Histoire Naturelle USM0503, and INSERM U565, 43 rue Cuvier, 75231 Paris cedex 05, France, UPMC, Paris 75005, France, DISMA, Università di Milano, via Celoria 2, 20133 Milano, Italy, INSERM U-837, COL, IRCL, Place Verdun, 59045 Lille, France, and Sigma-tau Industrie Farmaceutiche Riunite SpA, Pomezia, Italy
| | - Giuseppe Giannini
- CNRS UMR5153, Muséum National d’Histoire Naturelle USM0503, and INSERM U565, 43 rue Cuvier, 75231 Paris cedex 05, France, UPMC, Paris 75005, France, DISMA, Università di Milano, via Celoria 2, 20133 Milano, Italy, INSERM U-837, COL, IRCL, Place Verdun, 59045 Lille, France, and Sigma-tau Industrie Farmaceutiche Riunite SpA, Pomezia, Italy
| | - Domenico Alloatti
- CNRS UMR5153, Muséum National d’Histoire Naturelle USM0503, and INSERM U565, 43 rue Cuvier, 75231 Paris cedex 05, France, UPMC, Paris 75005, France, DISMA, Università di Milano, via Celoria 2, 20133 Milano, Italy, INSERM U-837, COL, IRCL, Place Verdun, 59045 Lille, France, and Sigma-tau Industrie Farmaceutiche Riunite SpA, Pomezia, Italy
| | - Paola B. Arimondo
- CNRS UMR5153, Muséum National d’Histoire Naturelle USM0503, and INSERM U565, 43 rue Cuvier, 75231 Paris cedex 05, France, UPMC, Paris 75005, France, DISMA, Università di Milano, via Celoria 2, 20133 Milano, Italy, INSERM U-837, COL, IRCL, Place Verdun, 59045 Lille, France, and Sigma-tau Industrie Farmaceutiche Riunite SpA, Pomezia, Italy
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17
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Vekhoff P, Ceccaldi A, Polverari D, Pylouster J, Pisano C, Arimondo PB. Triplex formation on DNA targets: how to choose the oligonucleotide. Biochemistry 2009; 47:12277-89. [PMID: 18954091 DOI: 10.1021/bi801087g] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Triplex-forming oligonucleotides (TFOs) are sequence-specific DNA binders. TFOs provide a tool for controlling gene expression or, when attached to an appropriate chemical reagent, for directing DNA damage. Here, we report a set of rules for predicting the best out of five different triple-helical binding motifs (TM, UM, GA, GT, and GU, where M is 5-methyldeoxycytidine and U is deoxyuridine) by taking into consideration the sequence composition of the underlying duplex target. We tested 11 different triplex targets present in genes having an oncogenic role. The rules have predictive power and are very useful in the design of TFOs for antigene applications. Briefly, we retained motifs GU and TM, and when they do form a triplex, TFOs containing G and U are preferred over those containing T and M. In the case of the G-rich TFOs, triplex formation is principally dependent on the percentage of G and the length of the TFO. In the case of the pyrimidine motif, replacement of T with U is destabilizing; triplex formation is dependent on the percentage of T and destabilized by the presence of several contiguous M residues. An equation to choose between a GU and TM motif is given.
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Affiliation(s)
- Pierre Vekhoff
- UMR 5153 CNRS, Museum National d'Histoire Naturelle USM0503, 43 rue Cuvier, 75231 Paris cedex 05, France
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18
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Abstract
We have prepared triplex-forming oligonucleotides containing the nucleotide analogue 5-dimethylaminopropargyl deoxyuridine (DMAPdU) in place of thymidine and examined their ability to form intermolecular triple helices by thermal melting and DNase I footprinting studies. The results were compared with those for oligonucleotides containing 5-aminopropargyl-dU (APdU), 5-guanidinopropargyl-dU (GPdU) and 5-propynyl dU (PdU). We find that DMAPdU enhances triplex stability relative to T, though slightly less than the other analogues that bear positive charges (T << PdU < DMAPdU < APdU < GPdU). For oligonucleotides that contain multiple substitutions with DMAPdU dispersed residues are more effective than clustered combinations. DMAPdU will be especially useful as a nucleotide analogue as, unlike APdU and GPdU, the base does not require protection during oligonucleotide synthesis and it can therefore be used with other derivatives that require mild deprotection conditions.
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Affiliation(s)
- David A Rusling
- School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK
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19
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Abstract
In this paper, we review recent DNA-binding agents that are expected to influence the field of DNA-targeting. We restrict ourselves to binders for which the three-dimensional structure in complex with DNA or RNA has been determined by X-ray crystallography or NMR. Furthermore, we primarily focus on unprecedented ways of targeting peculiar DNA structures, such as junctions, quadruplexes, and duplex DNAs different from the B-form. Classical binding modes of small molecular weight compounds to DNA, i.e. groove binding, intercalation and covalent addition are discussed in those cases where the structures represent a novelty. In addition, we review 3D structures of triple-stranded DNA, of the so-called Peptide Nucleic Acids (PNAs), which are oligonucleotide bases linked by a polypeptide backbone, and of aptamers, which are DNA or RNA receptors that are designed combinatorially. A discussion on perspectives in the field of DNA-targeting and on sequence recognition is also provided.
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Affiliation(s)
- D Roeland Boer
- Institute for Research in Biomedicine and Institut de Biologia Molecular de Barcelona (CSIC), Barcelona Science Park, Barcelona, Spain
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20
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Abstract
Triplex-forming oligonucleotides constitute an interesting DNA sequence-specific tool that can be used to target cleaving or cross-linking agents, transcription factors or nucleases to a chosen site on the DNA. They are not only used as biotechnological tools but also to induce modifications on DNA with the aim to control gene expression, such as by site-directed mutagenesis or DNA recombination. Here, we report the state of art of the triplex-based anti-gene strategy 50 years after the discovery of such a structure, and we show the importance of the actual applications and the main challenges that we still have ahead of us.
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Affiliation(s)
- Maria Duca
- LCMBA CNRS UMR6001, University of Nice-Sophia Antipolis, Parc Valrose, 06108 NICE Cedex 2, France
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21
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Koster DA, Czerwinski F, Halby L, Crut A, Vekhoff P, Palle K, Arimondo PB, Dekker NH. Single-molecule observations of topotecan-mediated TopIB activity at a unique DNA sequence. Nucleic Acids Res 2008; 36:2301-10. [PMID: 18292117 PMCID: PMC2367732 DOI: 10.1093/nar/gkn035] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The rate of DNA supercoil removal by human topoisomerase IB (TopIB) is slowed down by the presence of the camptothecin class of antitumor drugs. By preventing religation, these drugs also prolong the lifetime of the covalent TopIB–DNA complex. Here, we use magnetic tweezers to measure the rate of supercoil removal by drug-bound TopIB at a single DNA sequence in real time. This is accomplished by covalently linking camptothecins to a triple helix-forming oligonucleotide that binds at one location on the DNA molecule monitored. Surprisingly, we find that the DNA dynamics with the TopIB–drug interaction restricted to a single DNA sequence are indistinguishable from the dynamics observed when the TopIB–drug interaction takes place at multiple sites. Specifically, the DNA sequence does not affect the instantaneous supercoil removal rate or the degree to which camptothecins increase the lifetime of the covalent complex. Our data suggest that sequence-dependent dynamics need not to be taken into account in efforts to develop novel camptothecins.
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Affiliation(s)
- Daniel A. Koster
- Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands, Department of Molecular Pharmacology, St. Jude Children's Research Hospital, 332 N. Lauderdale, Memphis, TN 38105, USA, BioQuant, Soft Matter and Biological Physics, University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany, Laboratoire ‘Régulation et dynamique des génomes’ UMR 5153 CNRS-Muséum National d’Histoire Naturelle USM0503 and INSERM UR565; 43 rue Cuvier, 75231 Paris cedex 05, France
| | - Fabian Czerwinski
- Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands, Department of Molecular Pharmacology, St. Jude Children's Research Hospital, 332 N. Lauderdale, Memphis, TN 38105, USA, BioQuant, Soft Matter and Biological Physics, University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany, Laboratoire ‘Régulation et dynamique des génomes’ UMR 5153 CNRS-Muséum National d’Histoire Naturelle USM0503 and INSERM UR565; 43 rue Cuvier, 75231 Paris cedex 05, France
| | - Ludovic Halby
- Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands, Department of Molecular Pharmacology, St. Jude Children's Research Hospital, 332 N. Lauderdale, Memphis, TN 38105, USA, BioQuant, Soft Matter and Biological Physics, University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany, Laboratoire ‘Régulation et dynamique des génomes’ UMR 5153 CNRS-Muséum National d’Histoire Naturelle USM0503 and INSERM UR565; 43 rue Cuvier, 75231 Paris cedex 05, France
| | - Aurélien Crut
- Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands, Department of Molecular Pharmacology, St. Jude Children's Research Hospital, 332 N. Lauderdale, Memphis, TN 38105, USA, BioQuant, Soft Matter and Biological Physics, University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany, Laboratoire ‘Régulation et dynamique des génomes’ UMR 5153 CNRS-Muséum National d’Histoire Naturelle USM0503 and INSERM UR565; 43 rue Cuvier, 75231 Paris cedex 05, France
| | - Pierre Vekhoff
- Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands, Department of Molecular Pharmacology, St. Jude Children's Research Hospital, 332 N. Lauderdale, Memphis, TN 38105, USA, BioQuant, Soft Matter and Biological Physics, University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany, Laboratoire ‘Régulation et dynamique des génomes’ UMR 5153 CNRS-Muséum National d’Histoire Naturelle USM0503 and INSERM UR565; 43 rue Cuvier, 75231 Paris cedex 05, France
| | - Komaraiah Palle
- Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands, Department of Molecular Pharmacology, St. Jude Children's Research Hospital, 332 N. Lauderdale, Memphis, TN 38105, USA, BioQuant, Soft Matter and Biological Physics, University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany, Laboratoire ‘Régulation et dynamique des génomes’ UMR 5153 CNRS-Muséum National d’Histoire Naturelle USM0503 and INSERM UR565; 43 rue Cuvier, 75231 Paris cedex 05, France
| | - Paola B. Arimondo
- Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands, Department of Molecular Pharmacology, St. Jude Children's Research Hospital, 332 N. Lauderdale, Memphis, TN 38105, USA, BioQuant, Soft Matter and Biological Physics, University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany, Laboratoire ‘Régulation et dynamique des génomes’ UMR 5153 CNRS-Muséum National d’Histoire Naturelle USM0503 and INSERM UR565; 43 rue Cuvier, 75231 Paris cedex 05, France
| | - Nynke H. Dekker
- Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands, Department of Molecular Pharmacology, St. Jude Children's Research Hospital, 332 N. Lauderdale, Memphis, TN 38105, USA, BioQuant, Soft Matter and Biological Physics, University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany, Laboratoire ‘Régulation et dynamique des génomes’ UMR 5153 CNRS-Muséum National d’Histoire Naturelle USM0503 and INSERM UR565; 43 rue Cuvier, 75231 Paris cedex 05, France
- * To whom correspondence should be addressed. +31 15 2783219+31 15 2781202
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