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Rosenkranz AA, Slastnikova TA, Durymanov MO, Georgiev GP, Sobolev AS. Exploiting active nuclear import for efficient delivery of Auger electron emitters into the cell nucleus. Int J Radiat Biol 2023; 99:28-38. [PMID: 32856963 DOI: 10.1080/09553002.2020.1815889] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
BACKGROUND The most attractive features of Auger electrons (AEs) in cancer therapy are their extremely short range and sufficiently high linear energy transfer (LET) for a majority of them. The cytotoxic effects of AE emitters can be realized only in close vicinity to sensitive cellular targets and they are negligible if the emitters are located outside the cell. The nucleus is considered the compartment most sensitive to high LET particles. Therefore, the use of AE emitters could be most useful in specific recognition of a cancer cell and delivery of AE emitters into its nucleus. PURPOSE This review describes the studies aimed at developing effective anticancer agents for the delivery of AE emitters to the nuclei of target cancer cells. The use of peptide-based conjugates, nanoparticles, recombinant proteins, and other constructs for AE emitter targeted intranuclear delivery as well as their advantages and limitations are discussed. CONCLUSION Transport from the cytoplasm to the nucleus along with binding to the cancer cell is one of the key stages in the delivery of AE emitters; therefore, several constructs for exploitation of this transport have been developed. The transport is carried out through a nuclear pore complex (NPC) with the use of specific amino acid nuclear localization sequences (NLS) and carrier proteins named importins, which are located in the cytosol. Therefore, the effectiveness of NLS-containing delivery constructs designed to provide energy-dependent transport of AE emitter into the nuclei of cancer cells also depends on their efficient entry into the cytosol of the target cell.
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Affiliation(s)
- Andrey A Rosenkranz
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.,Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | | | | | | | - Alexander S Sobolev
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.,Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
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Jackson MR, Bavelaar BM, Waghorn PA, Gill MR, El-Sagheer AH, Brown T, Tarsounas M, Vallis KA. Radiolabeled Oligonucleotides Targeting the RNA Subunit of Telomerase Inhibit Telomerase and Induce DNA Damage in Telomerase-Positive Cancer Cells. Cancer Res 2019; 79:4627-4637. [PMID: 31311806 PMCID: PMC7611324 DOI: 10.1158/0008-5472.can-18-3594] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 05/01/2019] [Accepted: 07/12/2019] [Indexed: 12/17/2022]
Abstract
Telomerase is expressed in the majority (>85%) of tumors, but has restricted expression in normal tissues. Long-term telomerase inhibition in malignant cells results in progressive telomere shortening and reduction in cell proliferation. Here we report the synthesis and characterization of radiolabeled oligonucleotides that target the RNA subunit of telomerase, hTR, simultaneously inhibiting enzymatic activity and delivering radiation intracellularly. Oligonucleotides complementary (Match) and noncomplementary (Scramble or Mismatch) to hTR were conjugated to diethylenetriaminepentaacetic dianhydride (DTPA), allowing radiolabeling with the Auger electron-emitting radionuclide indium-111 (111In). Match oligonucleotides inhibited telomerase activity with high potency, which was not observed with Scramble or Mismatch oligonucleotides. DTPA-conjugation and 111In-labeling did not change telomerase inhibition. In telomerase-positive cancer cells, unlabeled Match oligonucleotides had no effect on survival, however, 111In-labeled Match oligonucleotides significantly reduced clonogenic survival and upregulated the DNA damage marker γH2AX. Minimal radiotoxicity and DNA damage was observed in telomerase-negative cells exposed to 111In-Match oligonucleotides. Match oligonucleotides localized in close proximity to nuclear Cajal bodies in telomerase-positive cells. In comparison with Match oligonucleotides, 111In-Scramble or 111In-Mismatch oligonucleotides demonstrated reduced retention and negligible impact on cell survival. This study indicates the therapeutic activity of radiolabeled oligonucleotides that specifically target hTR through potent telomerase inhibition and DNA damage induction in telomerase-expressing cancer cells and paves the way for the development of novel oligonucleotide radiotherapeutics targeting telomerase-positive cancers. SIGNIFICANCE: These findings present a novel radiolabeled oligonucleotide for targeting telomerase-positive cancer cells that exhibits dual activity by simultaneously inhibiting telomerase and promoting radiation-induced genomic DNA damage.
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Affiliation(s)
- Mark R Jackson
- Oxford Institute for Radiation Oncology, University of Oxford, Oxford, United Kingdom
| | - Bas M Bavelaar
- Oxford Institute for Radiation Oncology, University of Oxford, Oxford, United Kingdom
| | - Philip A Waghorn
- Oxford Institute for Radiation Oncology, University of Oxford, Oxford, United Kingdom
| | - Martin R Gill
- Oxford Institute for Radiation Oncology, University of Oxford, Oxford, United Kingdom
| | - Afaf H El-Sagheer
- Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Tom Brown
- Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Madalena Tarsounas
- Oxford Institute for Radiation Oncology, University of Oxford, Oxford, United Kingdom
| | - Katherine A Vallis
- Oxford Institute for Radiation Oncology, University of Oxford, Oxford, United Kingdom.
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3
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Kye M, Lim YB. Synthesis and purification of self-assembling peptide-oligonucleotide conjugates by solid-phase peptide fragment condensation. J Pept Sci 2018; 24:e3092. [PMID: 29920844 DOI: 10.1002/psc.3092] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 05/13/2018] [Accepted: 05/14/2018] [Indexed: 12/18/2022]
Abstract
Peptide-oligonucleotide conjugates (POCs) are interesting molecules as they covalently combine 2 of the most important biomacromolecules. Sometimes, the synthesis of POCs involves unexpected difficulties; however, POCs with self-assembling propensity are even harder to synthesize and purify. Here, we show that solid-phase peptide fragment condensation combined with thiol-maleimide or copper-catalyzed azide-alkyne cycloaddition click chemistries is useful for the syntheses of self-assembling POCs. We describe guidelines for the selection of reactive functional groups and their placement during the conjugation reaction and consider the cost-effectiveness of the reaction. Purification is another important challenge during the preparation of POCs. Our results show that polyacrylamide gel electrophoresis under denaturing conditions is most suitable to recover a high yield of self-assembling POCs. This report provides the first comprehensive study of the preparation of self-assembling POCs, which will lay a foundation for the development of elegant and sophisticated molecular assemblies.
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Affiliation(s)
- Mahnseok Kye
- Department of Materials Science and Engineering, Yonsei University, Seoul, 03722, South Korea
| | - Yong-Beom Lim
- Department of Materials Science and Engineering, Yonsei University, Seoul, 03722, South Korea
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4
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Dahmen V, Schmitz S, Kriehuber R. Induction of the chromosomal translocation t(14;18) by targeting the BCL-2 locus with specific binding I-125-labeled triplex-forming oligonucleotides. Mutat Res 2017; 823:58-64. [PMID: 28985947 DOI: 10.1016/j.mrgentox.2017.09.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 08/29/2017] [Accepted: 09/07/2017] [Indexed: 01/23/2023]
Abstract
Triplex-Forming oligonucleotides (TFO) bind sequence-specific to the DNA double helix in-vitro and in-vivo and are a promising tool to manipulate genes or gene regulatory elements. TFO as a carrier molecule for short-range particle emitter such as Auger-Electron-Emitters (AEE) bear the potential to introduce radiation-induced site-specific complex DNA lesions, which are known to induce chromosomal translocations. We studied gene expression, translocation frequency and protein expression in SCL-II cells after transfection with the AEE Iodine-125 (I-125) labeled TFO-BCL2 targeting the human BCL2 gene. The TFO-BCL2 binds to the BCL2 gene in close proximity to a known major-breakage-region (mbr). SCL-II cells were transfected with I-125 labeled TFO and stored for decay accumulation. Monitoring of BCL2 translocations was done with the Fluorescence-In-Situ-Hybridization (FISH) method. The utilized FISH probes were designed to detect a t(14;18) translocation of the BCL2 gene, which is a common translocation leading to an overexpression of BCL2 protein. Analysis of BCL2 gene expression levels was done via quantitative Real-Time PCR. Verification of gene expression on the protein level was analyzed by Western blotting. The relative gene expression of BCL2 in I-125-TFO-BCL2 transfected cells showed a significant up-regulation when compared to controls. Analysis of the BCL2 t(14;18) translocation frequency revealed a significant 1.8- to 2-fold increase when compared to control cells. This 2-fold increase was not reflected on the protein level. We conclude that I-125 decays within the BCL2 gene facilitate the t(14;18) chromosomal translocation in the SCL-II cells and that the increased frequency contributes to the observed overall enhanced BCL2 gene expression.
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Affiliation(s)
- Volker Dahmen
- Radiation Biology Unit, Department of Safety and Radiation Protection, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Sabine Schmitz
- Radiation Biology Unit, Department of Safety and Radiation Protection, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Ralf Kriehuber
- Radiation Biology Unit, Department of Safety and Radiation Protection, Forschungszentrum Jülich, 52425 Jülich, Germany.
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5
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Violet JA, Farrugia G, Skene C, White J, Lobachevsky P, Martin R. Triple targeting of Auger emitters using octreotate conjugated to a DNA-binding ligand and a nuclear localizing signal. Int J Radiat Biol 2016; 92:707-715. [DOI: 10.3109/09553002.2016.1157278] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- John A. Violet
- Division of Radiation Oncology and Cancer Imaging, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
| | - Gabriella Farrugia
- Molecular Radiation Biology Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Colin Skene
- School of Chemistry and Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Jonathan White
- School of Chemistry and Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Pavel Lobachevsky
- Molecular Radiation Biology Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Roger Martin
- Molecular Radiation Biology Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
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6
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Martin RF, Feinendegen LE. The quest to exploit the Auger effect in cancer radiotherapy - a reflective review. Int J Radiat Biol 2016; 92:617-632. [PMID: 26926313 DOI: 10.3109/09553002.2015.1136854] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
To identify the emergence of the recognition of the potential of the Auger effect for clinical application, and after tracing the salient milestones towards that goal, to evaluate the status quo and future prospects. It was not until 40 years after the discovery of Auger electrons, that the availability of radioactive DNA precursors enabled the biological power, and the clinical potential, of the Auger effect to be appreciated. Important milestones on the path to clinical translation have been identified and reached, but hurdles remain. Nevertheless the potential is still evident, and there is reasonable optimism that the goal of clinical translation is achievable.
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Affiliation(s)
- Roger F Martin
- a Molecular Radiation Biology Laboratory , Peter MacCallum Cancer Centre.,b The Sir Peter MacCallum Department of Oncology , The University of Melbourne.,c School of Chemistry and Bio-21 Molecular Science and Biotechnology Institute , University of Melbourne , Melbourne , Australia
| | - Ludwig E Feinendegen
- d Heinrich-Heine-University Düsseldorf , Germany.,e Brookhaven National Laboratory , Upton , NY , USA
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7
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Cai H, Singh AN, Sun X, Peng F. Synthesis and characterization of Her2-NLP peptide conjugates targeting circulating breast cancer cells: cellular uptake and localization by fluorescent microscopic imaging. J Fluoresc 2015; 25:113-7. [PMID: 25620472 DOI: 10.1007/s10895-014-1486-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 12/01/2014] [Indexed: 10/24/2022]
Abstract
To synthesize a fluorescent Her2-NLP peptide conjugate consisting of Her2/neu targeting peptide and nuclear localization sequence peptide (NLP) and assess its cellular uptake and intracellular localization for radionuclide cancer therapy targeting Her2/neu-positive circulating breast cancer cells (CBCC). Fluorescent Cy5.5 Her2-NLP peptide conjugate was synthesized by coupling a bivalent peptide sequence, which consisted of a Her2-binding peptide (NH2-GSGKCCYSL) and an NLP peptide (CGYGPKKKRKVGG) linked by a polyethylene glycol (PEG) chain with 6 repeating units, with an activated Cy5.5 ester. The conjugate was separated and purified by HPLC and then characterized by Maldi-MS. The intracellular localization of fluorescent Cy5.5 Her2-NLP peptide conjugate was assessed by fluorescent microscopic imaging using a confocal microscope after incubation of Cy5.5-Her2-NLP with Her2/neu positive breast cancer cells and Her2/neu negative control breast cancer cells, respectively. Fluorescent signals were detected in cytoplasm of Her2/neu positive breast cancer cells (SKBR-3 and BT474 cell lines), but not or little in cytoplasm of Her2/neu negative breast cancer cells (MDA-MB-231), after incubation of the breast cancer cells with Cy5.5-Her2-NLP conjugates in vitro. No fluorescent signals were detected within the nuclei of Her2/neu positive SKBR-3 and BT474 breast cancer cells, neither Her2/neu negative MDA-MB-231 cells, incubated with the Cy5.5-Her2-NLP peptide conjugates, suggesting poor nuclear localization of the Cy5.5-Her2-NLP conjugates localized within the cytoplasm after their cellular uptake and internalization by the Her2/neu positive breast cancer cells. Her2-binding peptide (KCCYSL) is a promising agent for radionuclide therapy of Her2/neu positive breast cancer using a β(-) or α emitting radionuclide, but poor nuclear localization of the Her2-NLP peptide conjugates may limit its use for eradication of Her2/neu-positive CBCC using I-125 or other Auger electron emitting radionuclide.
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Affiliation(s)
- Huawei Cai
- Department of Radiology, University of Texas Southwestern Medical Center, 2201 Inwood Road, Dallas, TX, 75390, USA
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8
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Fatthalla MI, Elkholy YM, Abbas NS, Mandour AH, Jørgensen PT, Bomholt N, Pedersen EB. Conjugation of a 3-(1H-phenanthro[9,10-d]imidazol-2-yl)-1H-indole intercalator to a triplex oligonucleotide and to a three-way junction. Bioorg Med Chem 2011; 20:207-14. [PMID: 22154560 DOI: 10.1016/j.bmc.2011.11.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Revised: 11/02/2011] [Accepted: 11/07/2011] [Indexed: 11/29/2022]
Abstract
A new intercalating nucleic acid monomer M comprising a 4-(1-indole)-butane-1,2-diol moiety was synthesized via a classical alkylation reaction of indole-3-carboxaldehyde followed by a condensation reaction with phenanthrene-9,10-dione in the presence of ammonium acetate to form a phenanthroimidazole moiety linked to the indole ring. Insertion of the new intercalator as a bulge into a Triplex Forming Oligonucleotide resulted in good thermal stability of the corresponding Hoogsteen-type triplexes. Molecular modeling supports the possible intercalating ability of M. Hybridisation properties of DNA/DNA and RNA/DNA three-way junctions (TWJ) with M in the branching point were also evaluated by their thermal stability at pH 7. DNA/DNA TWJ showed increase in thermal stability compared to wild type oligonucleotides whereas this was not the case for RNA/DNA TWJ.
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Affiliation(s)
- Maha I Fatthalla
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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9
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Carter JD, Labean TH. Coupling strategies for the synthesis of Peptide-oligonucleotide conjugates for patterned synthetic biomineralization. J Nucleic Acids 2011; 2011:926595. [PMID: 22007290 PMCID: PMC3191822 DOI: 10.4061/2011/926595] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Accepted: 06/25/2011] [Indexed: 11/27/2022] Open
Abstract
This work describes preparation strategies for peptide-oligonucleotide conjugates that combine the self-assembling behavior of DNA oligonucleotides with the molecular recognition capabilities of peptides. The syntheses include a solution-phase fragment coupling reaction and a solid-phase fragment coupling strategy where the oligonucleotide has been immobilized on DEAE Sepharose. The yield of four coupling reagents is evaluated, two reagents in water, EDC (1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride) and DMTMM (4-(4,6-dimethoxy[1,3,5]triazin-2-yl)-4-methyl-morpholinium chloride), and two in dimethylformamide (DMF), PyBOP ((Benzotriazol-1-yloxy) tripyrrolidinophosphonium hexafluorophosphate) and HBTU (O-benzotriazole-N,N,N′,N′-tetramethyluronium hexafluorophosphate), while the oligonucleotide fragment is either in solution or immobilized on DEAE. These coupling strategies rely on an unprotected 5′ amino linker on the oligonucleotide reacting with the peptide C-terminus. The peptide, selected from a combinatorial library for its gold-binding behavior, was 12 amino acids long with an N-terminus acetyl cap. Formation of the conjugates was confirmed by gel electrophoresis and mass spectrometry while molecular recognition functionality of the peptide portion was verified using atomic force microscopy. Solution-phase yields were superior to their solid-phase counterparts. EDC resulted in the highest yield for both solution-phase (95%) and solid-phase strategies (24%), while the DMF-based reagents, PyBOP and HBTU, resulted in low yields with reduced recovery. All recoverable conjugates demonstrated gold nanoparticle templating capability.
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Affiliation(s)
- Joshua D Carter
- Departments of Computer Science and Chemistry, Duke University, Durham, NC 27708, USA
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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] [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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11
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Accumulation of DSBs in γ-H2AX domains fuel chromosomal aberrations. Biochem Biophys Res Commun 2008; 371:694-7. [DOI: 10.1016/j.bbrc.2008.04.127] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2008] [Accepted: 04/18/2008] [Indexed: 11/18/2022]
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12
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Costantini DL, Hu M, Reilly RM. Update:Peptide Motifs for Insertion of Radiolabeled Biomolecules into Cells and Routing to the Nucleus for Cancer Imaging or Radiotherapeutic Applications. Cancer Biother Radiopharm 2008; 23:3-24. [DOI: 10.1089/cbr.2007.0430] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Affiliation(s)
- Danny L. Costantini
- Leslie Dan Faculty of Pharmacy, Department of Pharmaceutical Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Meiduo Hu
- Leslie Dan Faculty of Pharmacy, Department of Pharmaceutical Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Raymond M. Reilly
- Leslie Dan Faculty of Pharmacy, Department of Pharmaceutical Sciences, University of Toronto, Toronto, Ontario, Canada
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13
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Venkatesan N, Kim BH. Peptide conjugates of oligonucleotides: synthesis and applications. Chem Rev 2007; 106:3712-61. [PMID: 16967918 DOI: 10.1021/cr0502448] [Citation(s) in RCA: 131] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Natarajan Venkatesan
- Laboratory for Modified Nucleic Acid Systems, Department of Chemistry, Pohang University of Science and Technology, Pohang 790-784, Korea
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Brunet E, Corgnali M, Cannata F, Perrouault L, Giovannangeli C. Targeting chromosomal sites with locked nucleic acid-modified triplex-forming oligonucleotides: study of efficiency dependence on DNA nuclear environment. Nucleic Acids Res 2006; 34:4546-53. [PMID: 16951289 PMCID: PMC1636373 DOI: 10.1093/nar/gkl630] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Triplex-forming oligonucleotides (TFOs) are synthetic DNA code-reading molecules that have been demonstrated to function to some extent in chromatin within cell nuclei. Here we have investigated the impact of DNA nuclear environment on the efficiency of TFO binding. For this study we have used locked nucleic acid-containing TFOs (TFO/LNAs) and we report the development of a rapid PCR-based method to quantify triplex formation. We have first compared triplex formation on genes located at different genomic sites and containing the same oligopyrimidine•oligopurine sequence. We have shown that efficient TFO binding is possible on both types of genes, expressed and silent. Then we have further investigated when gene transcription may influence triplex formation in chromatin. We have identified situations where for a given gene, increase of transcriptional activity leads to enhanced TFO binding: this was observed for silent or weakly expressed genes that are not or are only slightly accessible to TFO. Such a transcriptional dependence was observed for integrated and endogenous loci, and chemical and biological activations of transcription. Finally, we provide evidence that TFO binding is sequence-specific as measured on mutated target sequences and that up to 50% of chromosomal targets can be covered by the TFO/LNA in living cells.
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Affiliation(s)
- Erika Brunet
- CNRS, UMR5153Paris, F-75005, France
- Inserm, U565Paris, F-75005, France
- Museum National d'Histoire Naturelle, USM503Paris, F-75005, France
| | - Maddalena Corgnali
- Dipartimento di Scienze e Tecnologie Biomediche, Universita degli Studi di Udine33100 Udine, Italy
| | - Fabio Cannata
- CNRS, UMR5153Paris, F-75005, France
- Inserm, U565Paris, F-75005, France
- Museum National d'Histoire Naturelle, USM503Paris, F-75005, France
| | - Loïc Perrouault
- CNRS, UMR5153Paris, F-75005, France
- Inserm, U565Paris, F-75005, France
- Museum National d'Histoire Naturelle, USM503Paris, F-75005, France
| | - Carine Giovannangeli
- CNRS, UMR5153Paris, F-75005, France
- Inserm, U565Paris, F-75005, France
- Museum National d'Histoire Naturelle, USM503Paris, F-75005, France
- To whom correspondence should be addressed. Tel: +33 1 40793711; Fax: + 33 1 40793705;
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Abstract
Living organisms are constantly exposed to detrimental agents both from the environment (e.g. ionizing radiation, ultraviolet light, natural and synthetic chemicals) and from endogenous metabolic processes (e.g. oxidative and hydrolytic reactions), resulting in modifications of proteins, lipids and DNA. Proteins and lipids are degraded and resynthesized, but the DNA is replicated only during cell division, when DNA damage may result in mutation fixation. Thus the DNA damage generated has the potential to lead to carcinogenesis, cell death, or other genetic disorders in the absence of efficient error-free repair. Because modifications in DNA sequence or structure may be incompatible with its essential role in preservation and transmission of genetic information from generation to generation, exquisitely sensitive DNA repair pathways have evolved to maintain genomic stability and cell viability. This review focuses on the repair and processing of genome destabilizing lesions and helical distortions that differ significantly from the canonical B-form DNA in mammalian cells. In particular, we discuss the introduction and processing of site-specific lesions in mammalian cells with an emphasis on psoralen interstrand crosslinks.
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Affiliation(s)
- Madhava C Reddy
- Department of Carcinogenesis, The University of Texas M. D. Anderson Cancer Center, Science Park-Research Division, Smithville, Texas 78957, USA
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16
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Panyutin IG, Neumann RD. The potential for gene-targeted radiation therapy of cancers. Trends Biotechnol 2005; 23:492-6. [PMID: 16125814 DOI: 10.1016/j.tibtech.2005.08.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2005] [Revised: 05/23/2005] [Accepted: 08/11/2005] [Indexed: 01/08/2023]
Abstract
Targeted cancer therapy is the mantra now chanted by oncologists of all types. Everyone hopes that the rapid expansion in the knowledge of cancer cell genetics, signaling, regulatory factors and other changes that underlie malignant transformation and metastasis will lead to innovative approaches for the treatment of cancers. To date, successful targeted therapies have been derived from pharmaceutical chemistry - designing chemical compounds intended to disrupt a crucial pathway for malignant cells to survive, grow and metastasize. Radiotherapy also has a goal of more-selective targeting of therapeutic radiation effects to only tumor cells. In this review, we describe our efforts to create a form of gene-targeted radiation therapy by using the unique radiation effects of radionuclides that decay by the Auger process attached to oligonucleotide carrier-molecules that are capable of forming triplex DNA structures with target sequences in the genome of the human cancer cell.
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Affiliation(s)
- Igor G Panyutin
- Nuclear Medicine Department, Clinical Center, NIH, Bethesda, MD 20892-1180, USA.
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Ziemba AJ, Zhilina ZV, Krotova-Khan Y, Stankova L, Ebbinghaus SW. Targeting and regulation of the HER-2/neu oncogene promoter with bis-peptide nucleic acids. Oligonucleotides 2005; 15:36-50. [PMID: 15788899 DOI: 10.1089/oli.2005.15.36] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Antigene oligonucleotides have the potential to regulate gene expression through site-specific DNA binding. However, in vivo applications have been hindered by inefficient cellular uptake, degradation, and strand displacement. Peptide nucleic acids (PNAs) address several of these problems, as they are resistant to degradation and bind DNA with high affinity. We designed two cationic pyrimidine bis-PNAs (cpy-PNAs) to target the polypurine tract of the HER-2/neu promoter and compared them to an unmodified phosphodiester triplex-forming oligonucleotide (TFO1) and a TFO-nitrogen mustard conjugate (TFO2). PNA1 contains a + 2 charge and bound two adjacent 9-bp target sequences with high affinity and specificity, but only at low pH. PNA2 contains a +5 charge and bound one 11-bp target with high affinity up to pH 7.4, but with lower specificity. The PNA:DNA:PNA triplex formed by these cpy-bis-PNAs presented a stable barrier to DNA polymerase extension. The cpy-bis-PNAs and the TFO-alkylator conjugate prevented HER-2/neu transcription in a reporter gene assay (TFO2 = PNA1 > PNA2 >> TFO1). Both PNAs and TFOs were effective at binding the target sequence in naked genomic DNA, but only the TFO-alkylator (TFO2) and the more cationic PNA (PNA2) were detected at the endogenous HER-2/neu promoter in permeabilized cells. This work demonstrates the potential for preventing HER-2/neu gene expression with cpy-bis-PNAs in tumor cells.
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Rogers FA, Manoharan M, Rabinovitch P, Ward DC, Glazer PM. Peptide conjugates for chromosomal gene targeting by triplex-forming oligonucleotides. Nucleic Acids Res 2004; 32:6595-604. [PMID: 15602001 PMCID: PMC545466 DOI: 10.1093/nar/gkh998] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Triplex-forming oligonucleotides (TFOs) are DNA-binding molecules, which offer the potential to selectively modulate gene expression. However, the biological activity of TFOs as potential antigene compounds has been limited by cellular uptake. Here, we investigate the effect of cell-penetrating peptides on the biological activity of TFOs as measured in an assay for gene-targeted mutagenesis. Using the transport peptide derived from the third helix of the homeodomain of antennapedia (Antp), we tested TFO-peptide conjugates compared with unmodified TFOs. TFOs covalently linked to Antp resulted in a 20-fold increase in mutation frequency when compared with 'naked' oligonucleotides. There was no increase above background in mutation frequency when Antp by itself was added to the cells or when Antp was linked to mixed or scrambled sequence control oligonucleotides. In addition, the TFO-peptide conjugates increased the mutation frequency of the target gene, and not the control gene, in a dose-responsive manner. Confocal microscopy using labeled oligonucleotides indicated increased cellular uptake of TFOs when linked to Antp, consistent with the gene-targeting data. These results suggest that peptide conjugation may enhance intranuclear delivery of reagents designed to bind to chromosomal DNA.
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Affiliation(s)
- Faye A Rogers
- Department of Therapeutic Radiology, Yale University School of Medicine, 295 Congress Avenue, New Haven, CT 068520, USA
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19
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Panyutin IG, Sedelnikova OA, Karamychev VN, Neumann RD. Antigene radiotherapy: targeted radiodamage with 125i-labeled triplex-forming oligonucleotides. Ann N Y Acad Sci 2004; 1002:134-40. [PMID: 14751831 DOI: 10.1196/annals.1281.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Antigene radiotherapy is based upon damaging selected genes by a high dose of radiation from radionuclides delivered to this gene by a sequence-specific DNA-binding molecule. Here we describe our recent trials of antigene radiotherapy using the human mdr1 gene over-expressed in KB-V1 cells as a model. As a delivery molecule, we used a triplex-forming oligonucleotide (TFO) with a binding site in intron 14 of mdr1. This TFO was labeled with an Auger-electron-emitting radionuclide 125I. Decay of 125I releases a shower of low energy electrons that produce DNA strand breaks mostly within 10 bp from the decay site. Targeting in situ was assessed by restriction enzyme digestion of the DNA recovered from the TFO-treated cells followed by Southern hybridization with DNA probes flanking the target sequence. Double-strand breaks in the target sequence were detected in purified nuclei and digitonin-permeabilized cells, but not in the intact cells when TFO were delivered with liposomes. On the basis of these observations we hypothesized that there are cytoplasmic factors that bind such TFO and deliver them into the nucleus, but do not release them inside the nucleus, thus preventing TFO from binding their genomic targets. To test this hypothesis we (i) delivered TFO along with an excess of unlabeled oligonucleotide with an arbitrary sequence ("ballast") and (ii) conjugated TFO with a nuclear localization sequence peptide (NLS). We have found that TFO/NLS conjugates cleaved the target in a concentration-dependent manner regardless of the presence of the "ballast" oligonucleotide. In contrast, TFO without NLS cleaved the target only in the presence of an excess of the "ballast." These results may provide a new insight into the mechanism of intracellular transport of oligonucleotides.
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Affiliation(s)
- I G Panyutin
- Department of Nuclear Medicine, Warren G. Magnuson Clinical Center, National Institutes of Health, Bethesda, Maryland 20892, USA.
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He Y, Panyutin IG, Karavanov A, Demidov VV, Neumann RD. Sequence-specific DNA strand cleavage by 111In-labeled peptide nucleic acids. Eur J Nucl Med Mol Imaging 2004; 31:837-45. [PMID: 14762696 DOI: 10.1007/s00259-003-1446-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2003] [Accepted: 12/09/2003] [Indexed: 10/26/2022]
Abstract
Peptide nucleic acids (PNAs) bind tightly and sequence-specifically to single- and double-stranded nucleic acids, and are hence of interest in the design of gene-targeted radiotherapeutics that could deliver the radiodamage to designated DNA and/or RNA sites. As a first step towards this goal, we developed a procedure for incorporation of Auger electron-emitting radionuclide (indium-111) into PNA oligomers and studied the efficiency of PNA-directed cleavage of single-stranded DNA targets. Accordingly, diethylene triamine penta-acetic acid (DTPA) was conjugated to the lysine-appended mixed-base PNAs and sequence-homologous DNA oligomer with a proper linker for comparative studies. By chelation of PNA-DTPA and DNA-DTPA conjugates with (111)In(3+) in acidic aqueous solutions, (111)In-labeled PNA and DNA oligomers were obtained. Targeting of single-stranded DNA with PNA-DTPA-[(111)In] conjugates yielded highly localized DNA strand cleavage; the distribution of breaks along the target DNA strand has two maxima corresponding to both termini of PNA oligomer. After 10-14 days, the overall yield of breaks thus generated within the PNA-targeted DNA by (111)In decay was 5-7% versus < or =2% in the case of control oligonucleotide DNA-DTPA-[(111)In]. The estimated yield of DNA strand breaks per nuclear decay is ~0.1 for the PNA-directed delivery of (111)In, which is three times more than for the DNA-directed delivery of this radionuclide. This in vitro study shows that (111)In-labeled PNAs are much more effective than radiolabeled DNA oligonucleotides for site-specific damaging of DNA targets. Accordingly, we believe that PNA oligomers are promising radionuclide delivery tools for future antisense/antigene radiotherapy trials.
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Affiliation(s)
- Yujian He
- Department of Nuclear Medicine, Warren G. Magnuson Clinical Center, National Institutes of Health, Bethesda, MD 20892-1180, USA
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21
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Uil TG, Haisma HJ, Rots MG. Therapeutic modulation of endogenous gene function by agents with designed DNA-sequence specificities. Nucleic Acids Res 2003; 31:6064-78. [PMID: 14576293 PMCID: PMC275457 DOI: 10.1093/nar/gkg815] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Designer molecules that can specifically target pre-determined DNA sequences provide a means to modulate endogenous gene function. Different classes of sequence-specific DNA-binding agents have been developed, including triplex-forming molecules, synthetic polyamides and designer zinc finger proteins. These different types of designer molecules with their different principles of engineered sequence specificity are reviewed in this paper. Furthermore, we explore and discuss the potential of these molecules as therapeutic modulators of endogenous gene function, focusing on modulation by stable gene modification and by regulation of gene transcription.
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Affiliation(s)
- Taco G Uil
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
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22
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Affiliation(s)
- Scot W Ebbinghaus
- Arizona Cancer Center, 1515 North Campbell Avenue, Tucson, AZ 85724, USA
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Potaman VN. Applications of triple-stranded nucleic acid structures to DNA purification, detection and analysis. Expert Rev Mol Diagn 2003; 3:481-96. [PMID: 12877387 DOI: 10.1586/14737159.3.4.481] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Regions of double-stranded (duplex) DNA with purine bases predominantly in one strand and pyrimidine bases in the other may bind oligonucleotides of an appropriate sequence to form triple-stranded (triplex) structures. Oligonucleotide analogs and mimics, such as peptide nucleic acid, may also form stable complexes with duplex DNA. Triplex formation enables the specific targeting of duplex domains. The principles of triplex structures and recent developments in the gene therapeutic and biotechnological applications are briefly reviewed. Adaptations of triplex methodology to molecular diagnostics (DNA purification, detection and analysis) are reviewed in greater detail.
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Affiliation(s)
- Vladimir N Potaman
- Institute of Biosciences & Technology, Texas A&M University Health Sciences Center, Houston 77030-3303, USA.
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Majumdar A, Puri N, Cuenoud B, Natt F, Martin P, Khorlin A, Dyatkina N, George AJ, Miller PS, Seidman MM. Cell cycle modulation of gene targeting by a triple helix-forming oligonucleotide. J Biol Chem 2003; 278:11072-7. [PMID: 12538585 DOI: 10.1074/jbc.m211837200] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Successful gene-targeting reagents must be functional under physiological conditions and must bind chromosomal target sequences embedded in chromatin. Triple helix-forming oligonucleotides (TFOs) recognize and bind specific sequences via the major groove of duplex DNA and may have potential for gene targeting in vivo. We have constructed chemically modified, psoralen-linked TFOs that mediate site-specific mutagenesis of a chromosomal gene in living cells. Here we show that targeting efficiency is sensitive to the biology of the cell, specifically, cell cycle status. Targeted mutagenesis was variable across the cycle with the greatest activity in S phase. This was the result of differential TFO binding as measured by cross-link formation. Targeted cross-linking was low in quiescent cells but substantially enhanced in S phase cells with adducts in approximately 20-30% of target sequences. 75-80% of adducts were repaired faithfully, whereas the remaining adducts were converted into mutations (>5% mutation frequency). Clones with mutations could be recovered by direct screening of colonies chosen at random. These results demonstrate high frequency target binding and target mutagenesis by TFOs in living cells. Successful protocols for TFO-mediated manipulation of chromosomal sequences are likely to reflect a combination of appropriate oligonucleotide chemistry and manipulation of the cell biology.
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Affiliation(s)
- Alokes Majumdar
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224, USA
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