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Kmiec EB. Genome editing before CRISPR: The gnostic bible. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 31:525-526. [PMID: 36873110 PMCID: PMC9978322 DOI: 10.1016/j.omtn.2023.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Affiliation(s)
- Eric B. Kmiec
- Gene Editing Institute, ChristianaCare, 550 S. College Avenue, Suite 208 2 Floor, Room 213, Newark, DE 19713, USA
- Corresponding author: Eric B. Kmiec, PhD Executive Director, 550 S. College Avenue, Suite 208 2 Floor, Room 213, Newark, DE 19713, USA.
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2
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Mishra AP, Hartford SA, Sahu S, Klarmann K, Chittela RK, Biswas K, Jeon AB, Martin BK, Burkett S, Southon E, Reid S, Albaugh ME, Karim B, Tessarollo L, Keller JR, Sharan SK. BRCA2-DSS1 interaction is dispensable for RAD51 recruitment at replication-induced and meiotic DNA double strand breaks. Nat Commun 2022; 13:1751. [PMID: 35365640 PMCID: PMC8975877 DOI: 10.1038/s41467-022-29409-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 03/14/2022] [Indexed: 12/31/2022] Open
Abstract
The interaction between tumor suppressor BRCA2 and DSS1 is essential for RAD51 recruitment and repair of DNA double stand breaks (DSBs) by homologous recombination (HR). We have generated mice with a leucine to proline substitution at position 2431 of BRCA2, which disrupts this interaction. Although a significant number of mutant mice die during embryogenesis, some homozygous and hemizygous mutant mice undergo normal postnatal development. Despite lack of radiation induced RAD51 foci formation and a severe HR defect in somatic cells, mutant mice are fertile and exhibit normal RAD51 recruitment during meiosis. We hypothesize that the presence of homologous chromosomes in close proximity during early prophase I may compensate for the defect in BRCA2-DSS1 interaction. We show the restoration of RAD51 foci in mutant cells when Topoisomerase I inhibitor-induced single strand breaks are converted into DSBs during DNA replication. We also partially rescue the HR defect by tethering the donor DNA to the site of DSBs using streptavidin-fused Cas9. Our findings demonstrate that the BRCA2-DSS1 complex is dispensable for RAD51 loading when the homologous DNA is close to the DSB. Mishra et al. have generated mice with a single amino acid substitution in BRCA2, which disrupts its interaction with DSS1 resulting in a severe HR defect. They show the interaction to be dispensable for HR at replication induced and meiotic DSBs.
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Affiliation(s)
- Arun Prakash Mishra
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Suzanne A Hartford
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA.,Regeneron Pharmaceuticals, Inc, Tarrytown, NY, USA
| | - Sounak Sahu
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Kimberly Klarmann
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA.,Developmental Therapeutics Program, Division of Cancer Treatment and Diagnosis, NCI, Frederick, MD, USA
| | - Rajani Kant Chittela
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA.,Applied Genomics Section, Bhabha Atomic Research Center, Trombay, Mumbai, India
| | - Kajal Biswas
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Albert B Jeon
- Molecular Histopathology Laboratory, Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Betty K Martin
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA.,Laboratory Animal Sciences Program, Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Sandra Burkett
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Eileen Southon
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Susan Reid
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Mary E Albaugh
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA.,Laboratory Animal Sciences Program, Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Baktiar Karim
- Molecular Histopathology Laboratory, Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Lino Tessarollo
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Jonathan R Keller
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA.,Basic Science Program, Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Shyam K Sharan
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA.
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3
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Kmiec EB, Bloh K. A toolmaker's perspective on CRISPR-directed gene editing as a therapeutic strategy for leukemia and beyond. Expert Rev Hematol 2021; 14:587-592. [PMID: 34047246 DOI: 10.1080/17474086.2021.1935853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Eric B Kmiec
- Gene Editing Institute, Helen F. Graham Cancer Center and Research Institute, Newark, USA
| | - Kevin Bloh
- Gene Editing Institute, Helen F. Graham Cancer Center and Research Institute, Newark, USA.,University of Delaware, Department of Medical and Molecular Sciences, College of Health Sciences, Newark, USA
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4
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Gualtieri C, Gianella M, Pagano A, Cadeddu T, Araújo S, Balestrazzi A, Macovei A. Exploring microRNA Signatures of DNA Damage Response Using an Innovative System of Genotoxic Stress in Medicago truncatula Seedlings. FRONTIERS IN PLANT SCIENCE 2021; 12:645323. [PMID: 33767724 PMCID: PMC7985446 DOI: 10.3389/fpls.2021.645323] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/15/2021] [Indexed: 05/08/2023]
Abstract
One of the challenges that living organisms face is to promptly respond to genotoxic stress to avoid DNA damage. To this purpose, all organisms, including plants, developed complex DNA damage response (DDR) mechanisms. These mechanisms are highly conserved among organisms and need to be finely regulated. In this scenario, microRNAs (miRNAs) are emerging as active players, thus attracting the attention of the research community. The involvement of miRNAs in DDR has been investigated prominently in human cells whereas studies in plants are still scarce. To experimentally investigate the involvement of plant miRNAs in the regulation of DDR-associated pathways, an ad hoc system was developed, using the model legume Medicago truncatula. Specific treatments with camptothecin (CPT) and/or NSC120686 (NSC), targeting distinct components of DDR, namely topoisomerase I (TopI) and tyrosyl-DNA phosphodiesterase 1 (TDP1), were used. Phenotypic (germination percentage and speed, seedling growth) and molecular (cell death, DNA damage, and gene expression profiles) analyses demonstrated that the imposed treatments impact DDR. Our results show that these treatments do not influence the germination process but rather inhibit seedling development, causing an increase in cell death and accumulation of DNA damage. Moreover, treatment-specific changes in the expression of suppressor of gamma response 1 (SOG1), master-regulator of plant DDR, were observed. Additionally, the expression of multiple genes playing important roles in different DNA repair pathways and cell cycle regulation were differentially expressed in a treatment-specific manner. Subsequently, specific miRNAs identified from our previous bioinformatics approaches as putatively targeting genes involved in DDR processes were investigated alongside their targets. The obtained results indicate that under most conditions when a miRNA is upregulated the corresponding candidate target gene is downregulated, providing an indirect evidence of miRNAs action over these targets. Hence, the present study extends the present knowledge on the information available regarding the roles played by miRNAs in the post-transcriptional regulation of DDR in plants.
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Affiliation(s)
- Carla Gualtieri
- Plant Biotechnology Laboratory, Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Maraeva Gianella
- Plant Biotechnology Laboratory, Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Andrea Pagano
- Plant Biotechnology Laboratory, Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Tiziano Cadeddu
- Plant Biotechnology Laboratory, Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Susana Araújo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Association BLC3, Technology and Innovation Campus, Centre BIO- R&D Unit, Lagares da Beira, Portugal
| | - Alma Balestrazzi
- Plant Biotechnology Laboratory, Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Anca Macovei
- Plant Biotechnology Laboratory, Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
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5
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Lau CH, Tin C, Suh Y. CRISPR-based strategies for targeted transgene knock-in and gene correction. Fac Rev 2020; 9:20. [PMID: 33659952 PMCID: PMC7886068 DOI: 10.12703/r/9-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The last few years have seen tremendous advances in CRISPR-mediated genome editing. Great efforts have been made to improve the efficiency, specificity, editing window, and targeting scope of CRISPR/Cas9-mediated transgene knock-in and gene correction. In this article, we comprehensively review recent progress in CRISPR-based strategies for targeted transgene knock-in and gene correction in both homology-dependent and homology-independent approaches. We cover homology-directed repair (HDR), synthesis-dependent strand annealing (SDSA), microhomology-mediated end joining (MMEJ), and homology-mediated end joining (HMEJ) pathways for a homology-dependent strategy and alternative DNA repair pathways such as non-homologous end joining (NHEJ), base excision repair (BER), and mismatch repair (MMR) for a homology-independent strategy. We also discuss base editing and prime editing that enable direct conversion of nucleotides in genomic DNA without damaging the DNA or requiring donor DNA. Notably, we illustrate the key mechanisms and design principles for each strategy, providing design guidelines for multiplex, flexible, scarless gene insertion and replacement at high efficiency and specificity. In addition, we highlight next-generation base editors that provide higher editing efficiency, fewer undesired by-products, and broader targeting scope.
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Affiliation(s)
- Cia-Hin Lau
- Department of Biomedical Engineering, Academic 1, 83 Tat Chee Avenue, City University of Hong Kong, Hong Kong
| | - Chung Tin
- Department of Biomedical Engineering, Academic 1, 83 Tat Chee Avenue, City University of Hong Kong, Hong Kong
| | - Yousin Suh
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA
- Department of Genetics and Development, Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA
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6
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Sun X, Wang Y, Ji K, Liu Y, Kong Y, Nie S, Li N, Hao J, Xie Y, Xu C, Du L, Liu Q. NRF2 preserves genomic integrity by facilitating ATR activation and G2 cell cycle arrest. Nucleic Acids Res 2020; 48:9109-9123. [PMID: 32729622 PMCID: PMC7498319 DOI: 10.1093/nar/gkaa631] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 06/21/2020] [Accepted: 07/27/2020] [Indexed: 01/02/2023] Open
Abstract
Nuclear factor erythroid 2-related factor 2 (NRF2) is a well-characterized transcription factor that protects cells against oxidative and electrophilic stresses. Emerging evidence has suggested that NRF2 protects cells against DNA damage by mechanisms other than antioxidation, yet the mechanism remains poorly understood. Here, we demonstrate that knockout of NRF2 in cells results in hypersensitivity to ionizing radiation (IR) in the presence or absence of reactive oxygen species (ROS). Under ROS scavenging conditions, induction of DNA double-strand breaks (DSBs) increases the NRF2 protein level and recruits NRF2 to DNA damage sites where it interacts with ATR, resulting in activation of the ATR-CHK1-CDC2 signaling pathway. In turn, this leads to G2 cell cycle arrest and the promotion of homologous recombination repair of DSBs, thereby preserving genome stability. The inhibition of NRF2 by brusatol increased the radiosensitivity of tumor cells in xenografts by perturbing ATR and CHK1 activation. Collectively, our results reveal a novel function of NRF2 as an ATR activator in the regulation of the cellular response to DSBs. This shift in perspective should help furnish a more complete understanding of the function of NRF2 and the DNA damage response.
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Affiliation(s)
- Xiaohui Sun
- Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Tianjin, China
| | - Yan Wang
- Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Tianjin, China
| | - Kaihua Ji
- Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Tianjin, China
| | - Yang Liu
- Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Tianjin, China
| | - Yangyang Kong
- Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Tianjin, China
| | - Shasha Nie
- Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Tianjin, China
| | - Na Li
- Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Tianjin, China
| | - Jianxiu Hao
- Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Tianjin, China
| | - Yi Xie
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Chang Xu
- Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Tianjin, China
| | - Liqing Du
- Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Tianjin, China
| | - Qiang Liu
- Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Tianjin, China
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7
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Hacker L, Dorn A, Puchta H. WITHDRAWN: DNA-protein crosslink repair in plants. DNA Repair (Amst) 2020; 88:102786. [PMID: 32057665 DOI: 10.1016/j.dnarep.2020.102786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 01/06/2020] [Indexed: 10/25/2022]
Affiliation(s)
- Leonie Hacker
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Annika Dorn
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Holger Puchta
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany.
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8
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Xiang C, Wu X, Zhao Z, Feng X, Bai X, Liu X, Zhao J, Takeda S, Qing Y. Nonhomologous end joining and homologous recombination involved in luteolin-induced DNA damage in DT40 cells. Toxicol In Vitro 2020; 65:104825. [PMID: 32169435 DOI: 10.1016/j.tiv.2020.104825] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 02/08/2020] [Accepted: 03/08/2020] [Indexed: 02/05/2023]
Abstract
Luteolin (3',4',5,7-tetrahydroxyflavone), a naturally occurring flavonoid, has been shown to have anticancer activity in many types of cancer cell lines. The anticancer capacity of luteolin may be related to its ability to induce DNA double-strand breaks (DSBs). Here, we used DT40 cells to determine whether nonhomologous end joining (NHEJ) and homologous recombination (HR) are involved in the repair mechanism of luteolin-induced DNA damage. Cells defective in Ku70 (an enzyme associated with NHEJ) or Rad54 (an enzyme essential for HR) were hypersensitive and presented more apoptosis in response to luteolin. Moreover, the sensitivity and apoptosis of Ku70-/- and Rad54-/- cells were associated with increased DNA damage when the numbers of γ-H2AX foci and chromosomal aberrations (CAs) were compared with those from WT cells. Additionally, after treatment with luteolin, Ku70-/- cells presented more Top2 covalent cleavage complexes (Top2cc). These results indicated that luteolin induced DSBs in DT40 cells and demonstrated that both NHEJ and HR participated in the repair of luteolin-induced DSBs, which might be related to the inhibition of topoisomerases. These results imply that simultaneous inhibition of NHEJ and HR with luteolin treatment would provide a powerful protocol in cancer chemotherapy.
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Affiliation(s)
- Cuifang Xiang
- Department of Pharmacology, Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan, China
| | - Xiaohua Wu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Zilu Zhao
- Department of Pharmacology, Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan, China
| | - Xiaoyu Feng
- Department of Pharmacology, Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan, China
| | - Xin Bai
- Department of Pharmacology, Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan, China
| | - Xin Liu
- Department of Pharmacology, Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan, China
| | - Jingxia Zhao
- Department of Pharmacology, Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan, China
| | - Shunichi Takeda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yong Qing
- Department of Pharmacology, Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan, China.
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9
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Stampone E, Bencivenga D, Barone C, Aulitto A, Verace F, Della Ragione F, Borriello A. High Dosage Lithium Treatment Induces DNA Damage and p57 Kip2 Decrease. Int J Mol Sci 2020; 21:ijms21031169. [PMID: 32050593 PMCID: PMC7038110 DOI: 10.3390/ijms21031169] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 02/06/2020] [Accepted: 02/07/2020] [Indexed: 12/22/2022] Open
Abstract
Lithium salt is the first-line therapeutic option for bipolar disorder and has been proposed as a potential antitumoral drug. The effects of LiCl treatment were investigated in SH-SY5Y, a human neuroblastoma cell line and an in vitro model of dopaminergic neuronal differentiation. LiCl, at the dosage used in psychiatric treatment, does not affect cell proliferation, while at higher doses it delays the SH-SY5Y cell division cycle and for prolonged usage reduces cell viability. Moreover, the ion treatment affects DNA integrity as demonstrated by accumulation of p53 and γH2AX (the phosphorylated form of H2AX histone), two important markers of genome damage. p57Kip2, a CIP/Kip protein, is required for proper neuronal maturation and represents a main factor of response to stress including genotoxicity. We evaluated the effect of lithium on p57Kip2 levels. Unexpectedly, we found that lithium downregulates the level of p57Kip2 in a dose-dependent manner, mainly acting at the transcriptional level. A number of different approaches, mostly based on p57Kip2 content handling, confirmed that the CKI/Kip reduction plays a key role in the DNA damage activated by lithium and suggests the unanticipated view that p57Kip2 might be involved in DNA double-strand break responses. In conclusion, our study identified novel roles for p57Kip2 in the molecular mechanism of lithium at high concentration and, more in general, in the process of DNA repair.
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Affiliation(s)
| | | | | | | | | | - Fulvio Della Ragione
- Correspondence: (A.B.); (F.D.R.); Tel.: +39-0815667554 (A.B.); +39-0815665812 (F.D.R.)
| | - Adriana Borriello
- Correspondence: (A.B.); (F.D.R.); Tel.: +39-0815667554 (A.B.); +39-0815665812 (F.D.R.)
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10
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Abstract
DNA-protein crosslinks represent a severe kind of DNA damage as they disturb essential processes, such as transcription and DNA replication, due to their bulkiness. To ensure the maintenance of genome integrity, it is necessary for all living organisms to repair these lesions in a timely manner. Over recent years, much knowledge has been obtained regarding the repair of DNA-protein crosslinks (DPC), but it was only recently that the first insights into the mechanisms of DPC repair in plants were obtained. The plant DPC repair network consists of at least three parallel pathways that resolve DPC by distinct biochemical mechanisms. The endonuclease MUS81 resolves the DPC by cleaving the DNA part of the crosslink, the protease WSS1A is able to degrade the protein part and the tyrosyl-DNA-phosphodiesterase TDP1 can hydrolyse the crosslink between a protein and the DNA. However, due to the variety of different DPC types and the evolutionary conservation of pathways between eukaryotes, we expect that future research will reveal additional factors involved in DPC repair in plants.
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Benyettou F, Prakasam T, Ramdas Nair A, Witzel II, Alhashimi M, Skorjanc T, Olsen JC, Sadler KC, Trabolsi A. Potent and selective in vitro and in vivo antiproliferative effects of metal-organic trefoil knots. Chem Sci 2019; 10:5884-5892. [PMID: 31360392 PMCID: PMC6582759 DOI: 10.1039/c9sc01218d] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 04/26/2019] [Indexed: 01/01/2023] Open
Abstract
A set of metal-organic trefoil knots (M-TKs) generated by metal-templated self-assembly of a simple pair of chelating ligands were well tolerated in vitro by non-cancer cells but were significantly more potent than cisplatin in both human cancer cells--including those resistant to cisplatin--and in zebrafish embryos. In cultured cells, M-TKs generated reactive oxygen species that triggered apoptosis via the mitochondrial pathway without directly disrupting the cell-membrane or damaging nuclear DNA. The cytotoxicity and wide scope for structural variation of M-TKs indicate the potential of synthetic metal-organic knots as a new field of chemical space for pharmaceutical design and development.
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Affiliation(s)
- Farah Benyettou
- Program in Chemistry , New York University Abu Dhabi , UAE .
| | | | | | | | - Marwa Alhashimi
- Program in Chemistry , New York University Abu Dhabi , UAE .
| | - Tina Skorjanc
- Program in Chemistry , New York University Abu Dhabi , UAE .
| | - John-Carl Olsen
- Department of Chemistry , University of Rochester , Rochester , New York , USA
| | | | - Ali Trabolsi
- Program in Chemistry , New York University Abu Dhabi , UAE .
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12
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Programmable Molecular Scissors: Applications of a New Tool for Genome Editing in Biotech. MOLECULAR THERAPY-NUCLEIC ACIDS 2018; 14:212-238. [PMID: 30641475 PMCID: PMC6330515 DOI: 10.1016/j.omtn.2018.11.016] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 11/23/2018] [Accepted: 11/23/2018] [Indexed: 01/04/2023]
Abstract
Targeted genome editing is an advanced technique that enables precise modification of the nucleic acid sequences in a genome. Genome editing is typically performed using tools, such as molecular scissors, to cut a defined location in a specific gene. Genome editing has impacted various fields of biotechnology, such as agriculture; biopharmaceutical production; studies on the structure, regulation, and function of the genome; and the creation of transgenic organisms and cell lines. Although genome editing is used frequently, it has several limitations. Here, we provide an overview of well-studied genome-editing nucleases, including single-stranded oligodeoxynucleotides (ssODNs), transcription activator-like effector nucleases (TALENs), zinc-finger nucleases (ZFNs), and CRISPR-Cas9 RNA-guided nucleases (CRISPR-Cas9). To this end, we describe the progress toward editable nuclease-based therapies and discuss the minimization of off-target mutagenesis. Future prospects of this challenging scientific field are also discussed.
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13
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Curcumin sensitizes lymphoma cells to DNA damage agents through regulating Rad51-dependent homologous recombination. Biomed Pharmacother 2017; 97:115-119. [PMID: 29080451 DOI: 10.1016/j.biopha.2017.09.078] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 09/13/2017] [Accepted: 09/18/2017] [Indexed: 12/21/2022] Open
Abstract
Curcumin is a natural compound isolated from the rhizome of Curcuma longa. It possesses anti-tumor activity through arresting cell cycles and promoting cell apoptosis. However, the effect of curcumin on DNA damage is not well defined. In this study, we investigated the effect of curcumin on inducing DNA damage and on sensitizing lymphoma cells to anti-tumoral DNA damage drugs. Western blot showed curcumin induced γ-H2AX foci in CH12F3 lymphoma cells, which suggests curcumin induces DNA breaks. In addition, curcumin decreased the expression of Rad51, which suggests curcumin induces DNA damage through regulating Rad51-dependant homologous recombination. Rad51-dependant homologous recombination is a vital DNA repair pathway for cancer cells to resist anti-tumoral DNA damage drugs, therefore, we studied the effect of curcumin on the sensitizing lymphoma cells to various chemotherapeutic drugs. We found low level of curcumin (5μM) sensitized lymphoma cells to anti-tumoral DNA damage agents including cisplatin, methyl methanesulfonate, hydroxyurea and camptothecin. We also found curcumin sensitized CH12F3 lymphoma cells to DNA-PK and PARP inhibitors. Flow cytometry analysis showed curcumin promoted apoptosis and western blot analysis confirmed curcumin activated caspase3-dependent apoptosis. Taken together, these results demonstrate that curcumin induces DNA damage through regulating Rad51-dependant homologous recombination and triggers caspase3-dependent apoptosis, more importantly, curcumin sensitizes lymphoma cells to various DNA damage drugs. Consequently, curcumin would be a potent agent for sensitizing lymphoma cells to anti-tumoral chemotherapeutic agents.
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14
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Josephs EA, Marszalek PE. A 'Semi-Protected Oligonucleotide Recombination' Assay for DNA Mismatch Repair in vivo Suggests Different Modes of Repair for Lagging Strand Mismatches. Nucleic Acids Res 2017; 45:e63. [PMID: 28053122 PMCID: PMC5416779 DOI: 10.1093/nar/gkw1339] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 12/20/2016] [Indexed: 12/18/2022] Open
Abstract
In Escherichia coli, a DNA mismatch repair (MMR) pathway corrects errors that occur during DNA replication by coordinating the excision and re-synthesis of a long tract of the newly-replicated DNA between an epigenetic signal (a hemi-methylated d(GATC) site or a single-stranded nick) and the replication error after the error is identified by protein MutS. Recent observations suggest that this 'long-patch repair' between these sites is coordinated in the same direction of replication by the replisome. Here, we have developed a new assay that uniquely allows us to introduce targeted 'mismatches' directly into the replication fork via oligonucleotide recombination, examine the directionality of MMR, and quantify the nucleotide-dependence, sequence context-dependence, and strand-dependence of their repair in vivo-something otherwise nearly impossible to achieve. We find that repair of genomic lagging strand mismatches occurs bi-directionally in E. coli and that, while all MutS-recognized mismatches had been thought to be repaired in a consistent manner, the directional bias of repair and the effects of mutations in MutS are dependent on the molecular species of the mismatch. Because oligonucleotide recombination is routinely performed in both prokaryotic and eukaryotic cells, we expect this assay will be broadly applicable for investigating mechanisms of MMR in vivo.
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Affiliation(s)
- Eric A Josephs
- Department of Mechanical Engineering and Materials Science, Edmund T. Pratt, Jr. School of Engineering, Duke University, Durham, NC, USA
| | - Piotr E Marszalek
- Department of Mechanical Engineering and Materials Science, Edmund T. Pratt, Jr. School of Engineering, Duke University, Durham, NC, USA
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Rivera-Torres N, Kmiec EB. A Standard Methodology to Examine On-site Mutagenicity As a Function of Point Mutation Repair Catalyzed by CRISPR/Cas9 and SsODN in Human Cells. J Vis Exp 2017. [PMID: 28872131 PMCID: PMC5614406 DOI: 10.3791/56195] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Combinatorial gene editing using CRISPR/Cas9 and single-stranded oligonucleotides is an effective strategy for the correction of single-base point mutations, which often are responsible for a variety of human inherited disorders. Using a well-established cell-based model system, the point mutation of a single-copy mutant eGFP gene integrated into HCT116 cells has been repaired using this combinatorial approach. The analysis of corrected and uncorrected cells reveals both the precision of gene editing and the development of genetic lesions, when indels are created in uncorrected cells in the DNA sequence surrounding the target site. Here, the specific methodology used to analyze this combinatorial approach to the gene editing of a point mutation, coupled with a detailed experimental strategy to measuring indel formation at the target site, is outlined. This protocol outlines a foundational approach and workflow for investigations aimed at developing CRISPR/Cas9-based gene editing for human therapy. The conclusion of this work is that on-site mutagenesis takes place as a result of CRISPR/Cas9 activity during the process of point mutation repair. This work puts in place a standardized methodology to identify the degree of mutagenesis, which should be an important and critical aspect of any approach destined for clinical implementation.
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Affiliation(s)
- Natalia Rivera-Torres
- Gene Editing Institute, Helen F. Graham Cancer Center and Research Institute, Christiana Care Health Services; Department of Medical Sciences, University of Delaware
| | - Eric B Kmiec
- Gene Editing Institute, Helen F. Graham Cancer Center and Research Institute, Christiana Care Health Services; Department of Medical Sciences, University of Delaware;
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Kan Y, Ruis B, Takasugi T, Hendrickson EA. Mechanisms of precise genome editing using oligonucleotide donors. Genome Res 2017; 27:1099-1111. [PMID: 28356322 PMCID: PMC5495063 DOI: 10.1101/gr.214775.116] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 03/24/2017] [Indexed: 12/26/2022]
Abstract
The use of programmable meganucleases is transforming genome editing and functional genomics. CRISPR/Cas9 was developed such that targeted genomic lesions could be introduced in vivo with unprecedented ease. In the presence of homology donors, these lesions facilitate high-efficiency precise genome editing (PGE) via homology-directed repair (HDR) pathways. However, the identity and hierarchy of the HDR (sub)pathways leading to the formation of PGE products remain elusive. Here, we established a green to blue fluorescent protein conversion system to systematically characterize oligodeoxynucleotide (ODN)-mediated PGE using Cas9 and its nickase variants in human cells. We demonstrate that, unlike double-stranded DNA (dsDNA) donors with central heterologies, ODNs generated short conversion tracts with Gaussian-like distributions. Interestingly, single-nick–induced PGE using ODN donors produced conversion tracts biased either mostly uni- or bidirectional depending on the relative strandedness of the ODNs and the nick. Moreover, the ODNs were physically incorporated into the genome only in the bidirectional, but not in the unidirectional, conversion pathway. In the presence of double-stranded genomic lesions, the unidirectional conversion pathway was preferentially utilized even though the knock-in mutation could theoretically have been converted by both pathways. Collectively, our results suggest that ODN-mediated PGE utilizes synthesis-dependent strand annealing and single-stranded DNA incorporation pathways. Both of these pathways generate short conversion tracts with Gaussian-like distributions. Although synthesis-dependent strand annealing is preferentially utilized, our work unequivocally establishes the existence of a single-stranded DNA incorporation pathway in human cells. This work extends the paradigms of HDR-mediated gene conversion and establishes guidelines for PGE in human cells.
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Affiliation(s)
- Yinan Kan
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, Minnesota 55455, USA
| | - Brian Ruis
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, Minnesota 55455, USA
| | - Taylor Takasugi
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, Minnesota 55455, USA
| | - Eric A Hendrickson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, Minnesota 55455, USA
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Rivera-Torres N, Banas K, Bialk P, Bloh KM, Kmiec EB. Insertional Mutagenesis by CRISPR/Cas9 Ribonucleoprotein Gene Editing in Cells Targeted for Point Mutation Repair Directed by Short Single-Stranded DNA Oligonucleotides. PLoS One 2017; 12:e0169350. [PMID: 28052104 PMCID: PMC5214427 DOI: 10.1371/journal.pone.0169350] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 12/15/2016] [Indexed: 11/18/2022] Open
Abstract
CRISPR/Cas9 and single-stranded DNA oligonucleotides (ssODNs) have been used to direct the repair of a single base mutation in human genes. Here, we examine a method designed to increase the precision of RNA guided genome editing in human cells by utilizing a CRISPR/Cas9 ribonucleoprotein (RNP) complex to initiate DNA cleavage. The RNP is assembled in vitro and induces a double stranded break at a specific site surrounding the mutant base designated for correction by the ssODN. We use an integrated mutant eGFP gene, bearing a single base change rendering the expressed protein nonfunctional, as a single copy target in HCT 116 cells. We observe significant gene correction activity of the mutant base, promoted by the RNP and single-stranded DNA oligonucleotide with validation through genotypic and phenotypic readout. We demonstrate that all individual components must be present to obtain successful gene editing. Importantly, we examine the genotype of individually sorted corrected and uncorrected clonally expanded cell populations for the mutagenic footprint left by the action of these gene editing tools. While the DNA sequence of the corrected population is exact with no adjacent sequence modification, the uncorrected population exhibits heterogeneous mutagenicity with a wide variety of deletions and insertions surrounding the target site. We designate this type of DNA aberration as on-site mutagenicity. Analyses of two clonal populations bearing specific DNA insertions surrounding the target site, indicate that point mutation repair has occurred at the level of the gene. The phenotype, however, is not rescued because a section of the single-stranded oligonucleotide has been inserted altering the reading frame and generating truncated proteins. These data illustrate the importance of analysing mutagenicity in uncorrected cells. Our results also form the basis of a simple model for point mutation repair directed by a short single-stranded DNA oligonucleotides and CRISPR/Cas9 ribonucleoprotein complex.
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Affiliation(s)
- Natalia Rivera-Torres
- Gene Editing Institute, Helen F. Graham Cancer Center and Research Institute, Newark, Delaware, United States of America
- Department of Medical Sciences University of Delaware, Newark, Delaware, United States of America
| | - Kelly Banas
- Gene Editing Institute, Helen F. Graham Cancer Center and Research Institute, Newark, Delaware, United States of America
- Department of Medical Sciences University of Delaware, Newark, Delaware, United States of America
| | - Pawel Bialk
- Gene Editing Institute, Helen F. Graham Cancer Center and Research Institute, Newark, Delaware, United States of America
| | - Kevin M. Bloh
- Gene Editing Institute, Helen F. Graham Cancer Center and Research Institute, Newark, Delaware, United States of America
- Nemours Center for Childhood Cancer Research, Alfred I. duPont Hospital for Children, Wilmington, Delaware, United States of America
| | - Eric B. Kmiec
- Gene Editing Institute, Helen F. Graham Cancer Center and Research Institute, Newark, Delaware, United States of America
- Department of Medical Sciences University of Delaware, Newark, Delaware, United States of America
- * E-mail:
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Wen X, Lu R, Xie S, Zheng H, Wang H, Wang Y, Sun J, Gao X, Guo L. APE1 overexpression promotes the progression of ovarian cancer and serves as a potential therapeutic target. Cancer Biomark 2016; 17:313-322. [DOI: 10.3233/cbm-160643] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Xuemei Wen
- Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Renquan Lu
- Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Suhong Xie
- Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Hui Zheng
- Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Hongling Wang
- Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Yanchun Wang
- Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Jiajun Sun
- Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Xiang Gao
- Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Lin Guo
- Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
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Rivera-Torres N, Kmiec EB. Genetic spell-checking: gene editing using single-stranded DNA oligonucleotides. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:463-470. [PMID: 26402400 DOI: 10.1111/pbi.12473] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Revised: 08/07/2015] [Accepted: 08/12/2015] [Indexed: 06/05/2023]
Abstract
Single-stranded oligonucleotides (ssODNs) can be used to direct the exchange of a single nucleotide or the repair of a single base within the coding region of a gene in a process that is known, generically, as gene editing. These molecules are composed of either all DNA residues or a mixture of RNA and DNA bases and utilize inherent metabolic functions to execute the genetic alteration within the context of a chromosome. The mechanism of action of gene editing is now being elucidated as well as an understanding of its regulatory circuitry, work that has been particularly important in establishing a foundation for designing effective gene editing strategies in plants. Double-strand DNA breakage and the activation of the DNA damage response pathway play key roles in determining the frequency with which gene editing activity takes place. Cellular regulators respond to such damage and their action impacts the success or failure of a particular nucleotide exchange reaction. A consequence of such activation is the natural slowing of replication fork progression, which naturally creates a more open chromatin configuration, thereby increasing access of the oligonucleotide to the DNA template. Herein, how critical reaction parameters influence the effectiveness of gene editing is discussed. Functional interrelationships between DNA damage, the activation of DNA response pathways and the stalling of replication forks are presented in detail as potential targets for increasing the frequency of gene editing by ssODNs in plants and plant cells.
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Affiliation(s)
- Natalia Rivera-Torres
- Gene Editing Institute, Center for Translational Cancer Research, Helen F. Graham Cancer Center & Research Institute, Christiana Care Health System, Newark, DE, USA
| | - Eric B Kmiec
- Gene Editing Institute, Center for Translational Cancer Research, Helen F. Graham Cancer Center & Research Institute, Christiana Care Health System, Newark, DE, USA
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20
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Bialk P, Rivera-Torres N, Strouse B, Kmiec EB. Regulation of Gene Editing Activity Directed by Single-Stranded Oligonucleotides and CRISPR/Cas9 Systems. PLoS One 2015; 10:e0129308. [PMID: 26053390 PMCID: PMC4459703 DOI: 10.1371/journal.pone.0129308] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 05/07/2015] [Indexed: 02/01/2023] Open
Abstract
Single-stranded DNA oligonucleotides (ssODNs) can direct the repair of a single base mutation in human genes. While the regulation of this gene editing reaction has been partially elucidated, the low frequency with which repair occurs has hampered development toward clinical application. In this work a CRISPR/Cas9 complex is employed to induce double strand DNA breakage at specific sites surrounding the nucleotide designated for exchange. The result is a significant elevation in ssODN-directed gene repair, validated by a phenotypic readout. By analysing reaction parameters, we have uncovered restrictions on gene editing activity involving CRISPR/Cas9 complexes. First, ssODNs that hybridize to the non-transcribed strand direct a higher level of gene repair than those that hybridize to the transcribed strand. Second, cleavage must be proximal to the targeted mutant base to enable higher levels of gene editing. Third, DNA cleavage enables a higher level of gene editing activity as compared to single-stranded DNA nicks, created by modified Cas9 (Nickases). Fourth, we calculated the hybridization potential and free energy levels of ssODNs that are complementary to the guide RNA sequences of CRISPRs used in this study. We find a correlation between free energy potential and the capacity of single-stranded oligonucleotides to inhibit specific DNA cleavage activity, thereby indirectly reducing gene editing activity. Our data provide novel information that might be taken into consideration in the design and usage of CRISPR/Cas9 systems with ssODNs for gene editing.
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Affiliation(s)
- Pawel Bialk
- Department of Chemistry, Delaware State University, Dover, Delaware, United States of America
- Gene Editing Institute, Helen F. Graham Cancer Center, Newark, Delaware, United States of America
| | - Natalia Rivera-Torres
- Department of Chemistry, Delaware State University, Dover, Delaware, United States of America
| | - Bryan Strouse
- Department of Chemistry, Delaware State University, Dover, Delaware, United States of America
| | - Eric B. Kmiec
- Department of Chemistry, Delaware State University, Dover, Delaware, United States of America
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21
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Kmiec EB. Is the age of genetic surgery finally upon us? Surg Oncol 2015; 24:95-9. [PMID: 25936245 DOI: 10.1016/j.suronc.2015.04.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 04/04/2015] [Indexed: 12/12/2022]
Abstract
This review discusses gene editing and its potential in oncology. Gene editing has not evolved faster towards clinical application because of its difficulty in implementation. There have been many limitations of the tools thought to be useful in therapeutic gene editing. However, recently the combinatorial use of multiple biological tools appears to have broken the barrier impending clinical development. This review gives a short primer on gene editing followed by some of the foundational work in gene editing and subsequently a discussion of programmable nucleases leading to a description of Zinc Finger Nuclease, TALENs and CRISPRs. Gene editing tools are now being used routinely to re-engineer the human genome. Theoretically, any gene or chromosomal sequence for which a targeting site can be identified could be rendered nonfunctional by the chromosomal breakage activity of Zinc Finger Nucleases, TALENs or a CRISPR/Cas9 system. Since the initial work started on the mechanism and regulation of gene editing, investigators have been searching for a way to develop these technologies as a treatment for cancer. The issue is finding a practical application of gene editing in oncology. However, progressive ideas are working their way through the research arena which may have an impact on cancer treatment.
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Affiliation(s)
- Eric B Kmiec
- Gene Editing Institute, Center for Translational Cancer Research, Helen F. Graham Cancer Center and Research Institute, 4701 Ogletown-Stanton Road, Suite 4300, Newark, DE, 19713, USA.
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Xu K, Stewart AF, Porter AC. Stimulation of oligonucleotide-directed gene correction by Redβ expression and MSH2 depletion in human HT1080 cells. Mol Cells 2015; 38:33-9. [PMID: 25431426 PMCID: PMC4314130 DOI: 10.14348/molcells.2015.2163] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 10/14/2014] [Accepted: 10/15/2014] [Indexed: 01/30/2023] Open
Abstract
The correction of disease-causing mutations by single-strand oligonucleotide-templated DNA repair (ssOR) is an attractive approach to gene therapy, but major improvements in ssOR efficiency and consistency are needed. The mechanism of ssOR is poorly understood but may involve annealing of oligonucleotides to transiently exposed single-stranded regions in the target duplex. In bacteria and yeast it has been shown that ssOR is promoted by expression of Redβ, a single-strand DNA annealing protein from bacteriophage lambda. Here we show that Redβ expression is well tolerated in a human cell line where it consistently promotes ssOR. By use of short interfering RNA, we also show that ssOR is stimulated by the transient depletion of the endogenous DNA mismatch repair protein MSH2. Furthermore, we find that the effects of Redβ expression and MSH2 depletion on ssOR can be combined with a degree of cooperativity. These results suggest that oligonucleotide annealing and mismatch recognition are distinct but interdependent events in ssOR that can be usefully modulated in gene correction strategies.
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Affiliation(s)
- Ke Xu
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenviroment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin 300052,
China
- Gene Targeting Group, Department of Hematology, Faculty of Medicine, Imperial College London, London W12 0NN,
UK
| | - A. Francis Stewart
- Genomics, Bio Innovations Zentrum, Technische Universitaet Dresden, 01307 Dresden,
Germany
| | - Andrew C.G. Porter
- Gene Targeting Group, Department of Hematology, Faculty of Medicine, Imperial College London, London W12 0NN,
UK
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23
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Wu Y, Wang KY, Li Z, Liu YP, Izumi H, Uramoto H, Nakayama Y, Ito KI, Kohno K. Y-box binding protein 1 enhances DNA topoisomerase 1 activity and sensitivity to camptothecin via direct interaction. J Exp Clin Cancer Res 2014; 33:112. [PMID: 25539742 PMCID: PMC4308875 DOI: 10.1186/s13046-014-0112-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 12/11/2014] [Indexed: 11/19/2022] Open
Abstract
Background The Y-box binding protein 1 (YB-1) possesses pleiotropic functions through its interactions with various cellular proteins, and its high expression levels make it a potential useful prognostic biomarker for cancer cells. Eukaryotic DNA topoisomerases, such as DNA topoisomerase 1 (TOPO1) and DNA topoisomerase 2 (TOPO2), are the essential DNA metabolism regulators that usually overexpressed in cancer cells, and multiple proteins have been reported to regulate the enzyme activity and the clinical efficacy of their inhibitors. The present study unraveled the interaction of YB-1 with TOPO1, and further investigated the related function and potential mechanisms during the interaction. Methods The direct association of TOPO1 with specific domain of YB-1 was explored by co-immunoprecipitation and GST pull-down assays. The interaction function was further clarified by DNA relaxation assays, co-immunoprecipitation and WST-8 assays with in vitro gain- and loss- of function models. Results We found that YB-1 interacts directly with TOPO1 (but not with TOPO2) and promotes TOPO1 catalytic activity. Interactions between YB-1 and TOPO1 increased when cancer cells were treated with the TOPO1 inhibitor, camptothecin (CPT), but not with the TOPO2 inhibitor, adriamycin (ADM). Furthermore, we found that the interaction is prevented by pretreatment with the antioxidant agent, N-acetyl cysteine, and that YB-1 downregulation renders cells resistant to CPT. Conclusions Our findings suggest that nuclear YB-1 serves as an intracellular promoter of TOPO1 catalytic activity that enhances CPT sensitivity through its direct interaction with TOPO1.
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Affiliation(s)
- Ying Wu
- Department of Medical Oncology, the First Hospital, China Medical University, Shenyang, China. .,The President Laboratory, University of Occupational and Environmental Health, Kitakyushu, Fukuoka, Japan.
| | - Ke-yong Wang
- Shared-Use Research Center, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Fukuoka, Japan.
| | - Zhi Li
- Department of Medical Oncology, the First Hospital, China Medical University, Shenyang, China.
| | - Yun-peng Liu
- Department of Medical Oncology, the First Hospital, China Medical University, Shenyang, China.
| | - Hiroto Izumi
- Department of Occupational Pneumology, Institute of Industrial Ecological Science, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Fukuoka, Japan.
| | - Hidetaka Uramoto
- Department of Surgery, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Fukuoka, Japan.
| | - Yoshifumi Nakayama
- Department of Surgery, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Fukuoka, Japan.
| | - Ken-ichi Ito
- Department of Surgery, School of Medicine, Shinshu University, Matsumoto, Nagano, Japan.
| | - Kimitoshi Kohno
- The President Laboratory, University of Occupational and Environmental Health, Kitakyushu, Fukuoka, Japan.
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Xylazine as a drug of abuse and its effects on the generation of reactive species and DNA damage on human umbilical vein endothelial cells. J Toxicol 2014; 2014:492609. [PMID: 25435874 PMCID: PMC4243599 DOI: 10.1155/2014/492609] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 10/05/2014] [Accepted: 10/15/2014] [Indexed: 01/14/2023] Open
Abstract
Human xylazine (XYL) abuse among addicts has received great interest due to its potential toxic effects upon addicts and the need to understand the mechanism of action associated with the potential health effects. XYL is an alpha-2 agonist restricted to veterinarian applications, without human medical applications. Our previous work demonstrated that XYL and its combination with cocaine (COC) and/or 6-monoacetylmorphine (6-MAM) induce cell death through an apoptotic mechanism. The aim of this study was to determine the effect of xylazine on the generation of reactive oxygen species (ROS) and reactive nitrogen species (RNS) as well as DNA damage on endothelial cell. Human umbilical vein endothelial cells (HUVEC) were treated with XYL (60 μM), COC (160 μM), 6-MAM (160 μM), camptothecin (positive control, 50 μM), XYL/COC (50 μM), XYL/6-MAM (50 μM), and XYL/COC/6-MAM (40 μM) for a period of 24 hours. Generation of intracellular ROS, RNS, and DNA fragmentation were analyzed using a fluorometric assay. Results reveal that XYL and 6-MAM increase levels of ROS; no induction of RNS production was observed. The combination of these drugs shows significant increase in DNA fragmentation in G2/M phase, while XYL, COC, and 6-MAM, without combination, present higher DNA fragmentation in G0/G1 phase. These findings support that these drugs and their combination alter important biochemical events aligned with an apoptotic mechanism of action in HUVEC.
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Esquissato GNM, De Sant'anna JR, Franco CCS, Rosada LJ, Dos Santos PASR, De Castro-Prado MAA. Gene homozygosis and mitotic recombination induced by camptothecin and irinotecan in Aspergillus nidulans diploid cells. AN ACAD BRAS CIENC 2014; 86:1703-10. [PMID: 25590709 DOI: 10.1590/0001-3765201420130106] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 02/17/2014] [Indexed: 11/22/2022] Open
Abstract
Mitotic recombination is a process involved in carcinogenesis which can lead to genetic loss through the loss of heterozygosity. The recombinogenic potentials of two anticancer drugs topoisomerase I inhibitors, camptothecin (CPT) and irinotecan (CPT-11), were evaluated in the present study. The homozygotization assay, which assess the induction of mitotic recombination and gene homozygosis, as well as the heterozygous A757//UT448 diploid strain of Aspergillus nidulans were employed. The three non-cytotoxic concentrations of CPT (3.5 ng mL-1, 10.5 ng mL-1 and 17.4 ng mL-1) were found to induce both mitotic recombination and gene homozygosis. CPT treatment produced three diploids homozygous, for nutritional and conidia color genes, and Homozygotization Indices (HI) significantly different from negative control. On the other hand, only the highest CPT-11 concentration tested (18 µg mL-1), corresponding to the maximal single chemotherapeutic dose, produced HI values higher than 2.0 and significantly different from negative control HI values. The recombinogenic effects of both topoisomerase I blockers were associated with the recombinational repair of DNA strand breaks induced by CPT and CPT-11. The anticancer drugs CPT and CPT-11 may be characterized as secondary malignancies promoters in cancer patients after chemotherapy treatment.
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Affiliation(s)
- Giovana N M Esquissato
- Genética e Biologia Celular, Departamento de Biotecnologia, Universidade Estadual de Maringá, Maringá, PR, Brasil
| | - Juliane R De Sant'anna
- Genética e Biologia Celular, Departamento de Biotecnologia, Universidade Estadual de Maringá, Maringá, PR, Brasil
| | - Claudinéia C S Franco
- Genética e Biologia Celular, Departamento de Biotecnologia, Universidade Estadual de Maringá, Maringá, PR, Brasil
| | - Lúcia J Rosada
- Genética e Biologia Celular, Departamento de Biotecnologia, Universidade Estadual de Maringá, Maringá, PR, Brasil
| | - Paula A S R Dos Santos
- Genética e Biologia Celular, Departamento de Biotecnologia, Universidade Estadual de Maringá, Maringá, PR, Brasil
| | - Marialba A A De Castro-Prado
- Genética e Biologia Celular, Departamento de Biotecnologia, Universidade Estadual de Maringá, Maringá, PR, Brasil
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26
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Dernigoghossian M, Krigel A, Behar-Cohen F, Andrieu-Soler C. Method for retinal gene repair in neonatal mouse. Methods Mol Biol 2014; 1114:387-98. [PMID: 24557917 DOI: 10.1007/978-1-62703-761-7_25] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Gene correction at the site of the mutation in the chromosome is the absolute way to really cure a genetic disease. The oligonucleotide (ODN)-mediated gene repair technology uses an ODN perfectly complementary to the genomic sequence except for a mismatch at the base that is mutated. The endogenous repair machinery of the targeted cell then mediates substitution of the desired base in the gene, resulting in a completely normal sequence. Theoretically, it avoids potential gene silencing or random integration associated with common viral gene augmentation approaches and allows an intact regulation of expression of the therapeutic protein. The eye is a particularly attractive target for gene repair because of its unique features (small organ, easily accessible, low diffusion into systemic circulation). Moreover therapeutic effects on visual impairment could be obtained with modest levels of repair. This chapter describes in details the optimized method to target active ODNs to the nuclei of photoreceptors in neonatal mouse using (1) an electric current application at the eye surface (saline transpalpebral iontophoresis), (2) combined with an intravitreous injection of ODNs, as well as the experimental methods for (3) the dissection of adult neural retinas, (4) their immuno-labelling, and (5) flat-mounting for direct observation of photoreceptor survival, a relevant criteria of treatment outcomes for retinal degeneration.
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Affiliation(s)
- Marilyn Dernigoghossian
- INSERM, Centre de Recherche des Cordeliers, Université René Descartes Sorbonne Paris Cité, Paris, France
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Sugahara R, Mon H, Lee JM, Shiotsuki T, Kusakabe T. Differential contribution of the Fanconi anemia-related proteins to repair of several types of DNA damage in cultured silkworm cells. FEBS Lett 2014; 588:3959-63. [DOI: 10.1016/j.febslet.2014.09.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 08/16/2014] [Accepted: 09/04/2014] [Indexed: 12/22/2022]
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Rivera-Torres N, Strouse B, Bialk P, Niamat RA, Kmiec EB. The position of DNA cleavage by TALENs and cell synchronization influences the frequency of gene editing directed by single-stranded oligonucleotides. PLoS One 2014; 9:e96483. [PMID: 24788536 PMCID: PMC4006861 DOI: 10.1371/journal.pone.0096483] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 04/08/2014] [Indexed: 11/21/2022] Open
Abstract
With recent technological advances that enable DNA cleavage at specific sites in the human genome, it may now be possible to reverse inborn errors, thereby correcting a mutation, at levels that could have an impact in a clinical setting. We have been developing gene editing, using single-stranded DNA oligonucleotides (ssODNs), as a tool to direct site specific single base changes. Successful application of this technique has been demonstrated in many systems ranging from bacteria to human (ES and somatic) cells. While the frequency of gene editing can vary widely, it is often at a level that does not enable clinical application. As such, a number of stimulatory factors such as double-stranded breaks are known to elevate the frequency significantly. The majority of these results have been discovered using a validated HCT116 mammalian cell model system where credible genetic and biochemical readouts are available. Here, we couple TAL-Effector Nucleases (TALENs) that execute specific ds DNA breaks with ssODNs, designed specifically to repair a missense mutation, in an integrated single copy eGFP gene. We find that proximal cleavage, relative to the mutant base, is key for enabling high frequencies of editing. A directionality of correction is also observed with TALEN activity upstream from the target base being more effective in promoting gene editing than activity downstream. We also find that cells progressing through S phase are more amenable to combinatorial gene editing activity. Thus, we identify novel aspects of gene editing that will help in the design of more effective protocols for genome modification and gene therapy in natural genes.
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Affiliation(s)
- Natalia Rivera-Torres
- Delaware State University, Department of Chemistry, Dover, Delaware, United States of America
| | - Bryan Strouse
- Delaware State University, Department of Chemistry, Dover, Delaware, United States of America
| | - Pawel Bialk
- Delaware State University, Department of Chemistry, Dover, Delaware, United States of America
| | - Rohina A. Niamat
- Delaware State University, Department of Chemistry, Dover, Delaware, United States of America
| | - Eric B. Kmiec
- Delaware State University, Department of Chemistry, Dover, Delaware, United States of America
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Bertoni C. Emerging gene editing strategies for Duchenne muscular dystrophy targeting stem cells. Front Physiol 2014; 5:148. [PMID: 24795643 PMCID: PMC4001063 DOI: 10.3389/fphys.2014.00148] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Accepted: 03/28/2014] [Indexed: 01/06/2023] Open
Abstract
The progressive loss of muscle mass characteristic of many muscular dystrophies impairs the efficacy of most of the gene and molecular therapies currently being pursued for the treatment of those disorders. It is becoming increasingly evident that a therapeutic application, to be effective, needs to target not only mature myofibers, but also muscle progenitors cells or muscle stem cells able to form new muscle tissue and to restore myofibers lost as the result of the diseases or during normal homeostasis so as to guarantee effective and lost lasting effects. Correction of the genetic defect using oligodeoxynucleotides (ODNs) or engineered nucleases holds great potential for the treatment of many of the musculoskeletal disorders. The encouraging results obtained by studying in vitro systems and model organisms have set the groundwork for what is likely to become an emerging field in the area of molecular and regenerative medicine. Furthermore, the ability to isolate and expand from patients various types of muscle progenitor cells capable of committing to the myogenic lineage provides the opportunity to establish cell lines that can be used for transplantation following ex vivo manipulation and expansion. The purpose of this article is to provide a perspective on approaches aimed at correcting the genetic defect using gene editing strategies and currently under development for the treatment of Duchenne muscular dystrophy (DMD), the most sever of the neuromuscular disorders. Emphasis will be placed on describing the potential of using the patient own stem cell as source of transplantation and the challenges that gene editing technologies face in the field of regenerative biology.
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Affiliation(s)
- Carmen Bertoni
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles CA, USA
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Strouse B, Bialk P, Niamat RA, Rivera-Torres N, Kmiec EB. Combinatorial gene editing in mammalian cells using ssODNs and TALENs. Sci Rep 2014; 4:3791. [PMID: 24445749 PMCID: PMC3896902 DOI: 10.1038/srep03791] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 12/24/2013] [Indexed: 11/09/2022] Open
Abstract
The regulation of gene editing is being elucidated in mammalian cells and its potential as well as its limitations are becoming evident. ssODNs carry out gene editing by annealing to their complimentary sequence at the target site and acting as primers for replication fork extension. To effect a genetic change, a large amount of ssODN molecules must be introduced into cells and as such induce a Reduced Proliferation Phenotype (RPP), a phenomenon in which corrected cells do not proliferate. To overcome this limitation, we have used TAL-Effector Nucleases (TALENs) to increase the frequency, while reducing the amount of ssODN required to direct gene correction. This strategy resolves the problem and averts the serious effects of RPP. The efficiency of gene editing can be increased significantly if cells are targeted while they progress through S phase. Our studies define new reaction parameters that will help guide experimental strategies of gene editing.
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Affiliation(s)
- Bryan Strouse
- Department of Chemistry, Delaware State University, 1200 N. DuPont Highway Dover, DE 19901
| | - Pawel Bialk
- Department of Chemistry, Delaware State University, 1200 N. DuPont Highway Dover, DE 19901
| | - Rohina A Niamat
- Department of Chemistry, Delaware State University, 1200 N. DuPont Highway Dover, DE 19901
| | - Natalia Rivera-Torres
- Department of Chemistry, Delaware State University, 1200 N. DuPont Highway Dover, DE 19901
| | - Eric B Kmiec
- Department of Chemistry, Delaware State University, 1200 N. DuPont Highway Dover, DE 19901
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Livingston P, Strouse B, Perry H, Borjigin M, Bialk P, Kmiec EB. Oligonucleotide delivery by nucleofection does not rescue the reduced proliferation phenotype of gene-edited cells. Nucleic Acid Ther 2012; 22:405-13. [PMID: 23072627 DOI: 10.1089/nat.2012.0374] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Gene editing using single-stranded oligonucleotides (ODNs) can be used to reverse or create a single base mutation in mammalian cells. This approach could be used to treat genetic diseases caused, at least in part, by a nucleotide substitution. The technique could also be used as a tool to establish single base polymorphisms at multiple sites and thus aid in creating cell lines that can be used to define the basis for drug resistance in human cells. A troubling outcome of the gene-editing reaction is the effect on normal growth of cells that have undergone nucleotide exchange. In this work, we attempt to overcome this reduced proliferation phenotype by changing the method by which the ODN is introduced into the target cell. Using a series of assays that measure gene editing, DNA damage response, and cell viability, we report that chemically modified ODNs, the most active form of ODN for gene editing, can be used successfully if introduced into the cell by the method of nucleofection. Unlike electroporation, which has been used as the standard mode of ODN delivery, one new result is that nucleofection does not induce a dramatic loss of viability within the first 24 hours after the start of gene editing. In addition, and importantly, ODNs introduced to the cell by nucleofection do not activate the DNA damage response pathway as dramatically as ODNs introduced by electroporation. These 2 novel findings are encouraging for the application of gene editing in other systems. However, reduced proliferation phenotype is still observed when the population of corrected cells is monitored out to 8 days, and thus, delivery by nucleofection does not solve the proliferation problem encountered by cells bearing an edited gene.
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Affiliation(s)
- Paula Livingston
- Marshall Institute for Interdisciplinary Research, Marshall University, Huntington, West Virginia, USA
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DNA damage response pathway and replication fork stress during oligonucleotide directed gene editing. MOLECULAR THERAPY. NUCLEIC ACIDS 2012; 1:e18. [PMID: 23343929 PMCID: PMC3381643 DOI: 10.1038/mtna.2012.9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Single-stranded DNA oligonucleotides (ODNs) can be used to direct the exchange of nucleotides in the genome of mammalian cells in a process known as gene editing. Once refined, gene editing should become a viable option for gene therapy and molecular medicine. Gene editing is regulated by a number of DNA recombination and repair pathways whose natural activities often lead to single- and double-stranded DNA breaks. It has been previously shown that introduction of a phosphorotioated ODN, designed to direct a gene-editing event, into cells results in the activation of γH2AX, a well-recognized protein biomarker for double-stranded DNA breakage. Using a single copy, integrated mutant enhanced green fluorescent protein (eGFP) gene as our target, we now demonstrate that several types of ODNs, capable of directing gene editing, also activate the DNA damage response and the post-translational modification of proliferating cell nuclear antigen (PCNA), a signature modification of replication stress. We find that the gene editing reaction itself leads to transient DNA breakage, perhaps through replication fork collapse. Unmodified specific ODNs elicit a lesser degree of replication stress than their chemically modified counterparts, but are also less active in gene editing. Modified phosphothioate oligonucleotides (PTOs) are detrimental irrespective of the DNA sequence. Such collateral damage may prove problematic for proliferation of human cells genetically modified by gene editing.
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The combination of hyperthermia or chemotherapy with gimeracil for effective radiosensitization. Strahlenther Onkol 2012; 188:255-61. [DOI: 10.1007/s00066-011-0043-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Accepted: 07/27/2011] [Indexed: 10/14/2022]
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Falgowski K, Falgowski C, York-Vickers C, Kmiec EB. Strand bias influences the mechanism of gene editing directed by single-stranded DNA oligonucleotides. Nucleic Acids Res 2011; 39:4783-94. [PMID: 21343181 PMCID: PMC3113578 DOI: 10.1093/nar/gkr061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Gene editing directed by modified single-stranded DNA oligonucleotides has been used to alter a single base pair in a variety of biological systems. It is likely that gene editing is facilitated by the direct incorporation of the oligonucleotides via replication and/or by direct conversion, most likely through the DNA mismatch repair pathway. The phenomenon of strand bias, however, as well as its importance to the gene editing reaction itself, has yet to be elucidated in terms of mechanism. We have taken a reductionist approach by using a genetic readout in Eschericha coli and a plasmid-based selectable system to evaluate the influence of strand bias on the mechanism of gene editing. We show that oligonucleotides (ODNs) designed to anneal to the lagging strand generate 100-fold greater 'editing' efficiency than 'those that anneal to' the leading strand. The majority of editing events (∼70%) occur by the incorporation of the ODN during replication within the lagging strand. Conversely, ODNs that anneal to the leading strand generate fewer editing events although this event may follow either the incorporation or direct conversion pathway. In general, the influence of DNA replication is independent of which ODN is used suggesting that the importance of strand bias is a reflection of the underlying mechanism used to carry out gene editing.
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Affiliation(s)
- Kerry Falgowski
- Marshall Institute for Interdisciplinary Research, Marshall University, Robert C. Byrd Biotechnology Science Center, 1700 Third Avenue, Suite 220, Huntington, WV 25755, USA
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35
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Falgowski KA, Kmiec EB. Gene editing activity on extrachromosomal arrays in C. elegans transgenics. Gene 2011; 475:87-93. [PMID: 21241788 DOI: 10.1016/j.gene.2010.12.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Accepted: 12/28/2010] [Indexed: 11/30/2022]
Abstract
Gene editing by modified single-stranded oligonucleotides is a strategy aimed at inducing single base changes into the genome, generating a permanent genetic change. The work presented here explores gene editing capabilities in the model organism Caenorhabditis elegans. Current approaches to gene mutagenesis in C. elegans have been plagued by non-specificity and thus the ability to induce precise, directed alterations within the genome of C. elegans would offer a platform upon which structure/function analyses can be carried out. As such, several in vivo assay systems were developed to evaluate gene editing capabilities in C. elegans. Fluorescence was chosen as the selectable endpoint as fluorescence can be easily detected through the transparent worm body even from minimal expression. Two tissue specific fluorescent expression vectors containing either a GFP or mCherry transgene were mutagenized to create a single nonsense mutation within the open reading frame of each respective fluorescent gene. These served as the target site to evaluate the frequency of gene editing on extrachromosomal array transgenic lines. Extrachromosomal arrays can carry hundreds of copies of the transgene, therefore low frequency events (like those in the gene editing reaction) may be detected. Delivery of the oligonucleotide was accomplished by microinjection into the gonads of young adult worms in an effort to induce repair of the mutated fluorescent gene in the F1 progeny. Despite many microinjections on the transgenic strains with varying concentrations of ODNs, no gene editing events were detected. This result is consistent with the previous research, demonstrating the difficulties encountered in targeting embryonic stem cells and the pronuclei of single-celled embryos.
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Affiliation(s)
- Kerry A Falgowski
- Marshall Institute for Interdisciplinary Research, Marshall University, Huntington, WV 25755, USA.
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36
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Aarts M, te Riele H. Progress and prospects: oligonucleotide-directed gene modification in mouse embryonic stem cells: a route to therapeutic application. Gene Ther 2010; 18:213-9. [PMID: 21160530 DOI: 10.1038/gt.2010.161] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Gene targeting by single-stranded oligodeoxyribonucleotides (ssODNs) is a promising technique for introducing site-specific sequence alterations without affecting the genomic organization of the target locus. Here, we discuss the significant progress that has been made over the last 5 years in unraveling the mechanisms and reaction parameters underlying ssODN-mediated gene targeting. We will specifically focus on ssODN-mediated gene targeting in murine embryonic stem cells (ESCs) and the impact of the DNA mismatch repair (MMR) system on the targeting process. Implications of novel findings for routine application of ssODN-mediated gene targeting and challenges that need to be overcome for future therapeutic applications are highlighted.
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Affiliation(s)
- M Aarts
- Division of Molecular Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
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37
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Kayali R, Bury F, Ballard M, Bertoni C. Site-directed gene repair of the dystrophin gene mediated by PNA-ssODNs. Hum Mol Genet 2010; 19:3266-81. [PMID: 20542988 DOI: 10.1093/hmg/ddq235] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Permanent correction of gene defects is an appealing approach to the treatment of genetic disorders. The use of single-stranded oligodeoxynucleotides (ssODNs) has been demonstrated to induce single-point mutations in the dystrophin gene and to restore dystrophin expression in the skeletal muscle of models of Duchenne muscular dystrophy (DMD). Here we show that ssODNs made of peptide nucleic acids (PNA-ssODNs) can achieve gene repair frequencies more than 10-fold higher than those obtained using an older generation of targeting oligonucleotides. Correction was demonstrated in muscles cells isolated from mdx(5cv) mice and was stably inherited over time. Direct intramuscular injection of PNA-ssODNs targeting the mdx(5cv) mutation resulted in a significant increase in dystrophin-positive fibers when compared with muscles that received the ssODNs designed to correct the dystrophin gene but made of unmodified bases. Correction was demonstrated at both the mRNA and the DNA levels using quantitative PCR and was confirmed by direct sequencing of amplification products. Analysis at the protein level demonstrated expression of full-length dystrophin in vitro as well as in vivo. These results demonstrate that oligonucleotides promoting strand invasion in the DNA double helix can significantly enhance gene repair frequencies of the dystrophin gene. The use of PNA-ssODNs has important implications in terms of both efficacy and duration of the repair process in muscles and may have a role in advancing the treatment of DMD.
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Affiliation(s)
- Refik Kayali
- Department of Neurology, David Geffen School of Medicine, University of California at Los Angeles, CA 90095, USA
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38
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Bertoni C, Rustagi A, Rando TA. Enhanced gene repair mediated by methyl-CpG-modified single-stranded oligonucleotides. Nucleic Acids Res 2010; 37:7468-82. [PMID: 19854937 PMCID: PMC2794159 DOI: 10.1093/nar/gkp757] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Gene editing mediated by oligonucleotides has been shown to induce stable single base alterations in genomic DNA in both prokaryotic and eukaryotic organisms. However, the low frequencies of gene repair have limited its applicability for both basic manipulation of genomic sequences and for the development of therapeutic approaches for genetic disorders. Here, we show that single-stranded oligodeoxynucleotides (ssODNs) containing a methyl-CpG modification and capable of binding to the methyl-CpG binding domain protein 4 (MBD4) are able to induce >10-fold higher levels of gene correction than ssODNs lacking the specific modification. Correction was stably inherited through cell division and was confirmed at the protein, transcript and genomic levels. Downregulation of MBD4 expression using RNAi prevented the enhancement of gene correction efficacy obtained using the methyl-CpG-modified ssODN, demonstrating the specificity of the repair mechanism being recruited. Our data demonstrate that efficient manipulation of genomic targets can be achieved and controlled by the type of ssODN used and by modulation of the repair mechanism involved in the correction process. This new generation of ssODNs represents an important technological advance that is likely to have an impact on multiple applications, especially for gene therapy where permanent correction of the genetic defect has clear advantages over viral and other nonviral approaches currently being tested.
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Affiliation(s)
- Carmen Bertoni
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA.
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39
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McLachlan J, Fernandez S, Helleday T, Bryant HE. Specific targeted gene repair using single-stranded DNA oligonucleotides at an endogenous locus in mammalian cells uses homologous recombination. DNA Repair (Amst) 2009; 8:1424-33. [PMID: 19854687 DOI: 10.1016/j.dnarep.2009.09.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2007] [Revised: 09/23/2009] [Accepted: 09/29/2009] [Indexed: 01/29/2023]
Abstract
The feasibility of introducing point mutations in vivo using single-stranded DNA oligonucleotides (ssON) has been demonstrated but the efficiency and mechanism remain elusive and potential side effects have not been fully evaluated. Understanding the mechanism behind this potential therapy may help its development. Here, we demonstrate the specific repair of an endogenous non-functional hprt gene by a ssON in mammalian cells, and show that the frequency of such an event is enhanced when cells are in S-phase of the cell cycle. A potential barrier in using ssONs as gene therapy could be non-targeted mutations or gene rearrangements triggered by the ssON. Both the non-specific mutation frequencies and the frequency of gene rearrangements were largely unaffected by ssONs. Furthermore, we find that the introduction of a mutation causing the loss of a functional endogenous hprt gene by a ssON occurred at a similarly low but statistically significant frequency in wild type cells and in cells deficient in single strand break repair, nucleotide excision repair and mismatch repair. However, this mutation was not induced in XRCC3 mutant cells deficient in homologous recombination. Thus, our data suggest ssON-mediated targeted gene repair is more efficient in S-phase and involves homologous recombination.
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Affiliation(s)
- Jennifer McLachlan
- The Institute for Cancer Studies, University of Sheffield, Sheffield S10 2RX, UK
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40
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Abstract
Gene targeting by single-stranded oligodeoxyribonucleotides (ssODNs) is emerging as a powerful tool for the introduction of subtle gene modifications in mouse embryonic stem (ES) cells and the generation of mutant mice. Here, we have studied the role of ssODN composition, transcription and replication of the target locus, and DNA repair pathways to gain more insight into the parameters governing ssODN-mediated gene targeting in mouse ES cells. We demonstrated that unmodified ssODNs of 35–40 nt were most efficient in correcting a chromosomally integrated mutant neomycin reporter gene. Addition of chemical modifications did not further enhance the efficacy of these ssODNs. The observed strand bias was not affected by transcriptional activity and may rather be caused by the different accessibility of the DNA strands during DNA replication. Consistently, targeting frequencies were enhanced when cells were treated with hydroxyurea to reduce the rate of replication fork progression. Transient down-regulation of various DNA repair genes by RNAi had no effect on the targeting frequency. Taken together, our data suggest that ssODN-mediated gene targeting occurs within the context of a replication fork. This implies that any given genomic sequence, irrespective of transcriptional status, should be amenable to ssODN-mediated gene targeting. The ability of ES cells to differentiate into various cell types after ssODN-mediated gene targeting may offer opportunities for future therapeutic applications.
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Affiliation(s)
- Marieke Aarts
- Division of Molecular Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
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41
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Bonner M, Kmiec EB. DNA breakage associated with targeted gene alteration directed by DNA oligonucleotides. Mutat Res 2009; 669:85-94. [PMID: 19463835 DOI: 10.1016/j.mrfmmm.2009.05.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2008] [Revised: 05/01/2009] [Accepted: 05/07/2009] [Indexed: 10/20/2022]
Abstract
Understanding the mechanism by which single-stranded oligonucleotides (ODNs) elicit targeted nucleotide exchange (TNE) is imperative to achieving optimal correction efficiencies and medical applicability. It has been previously shown that introduction of an ODN into cells results in the activation of DNA damage response pathways, but there has been no evaluation of the damage created at the level of the DNA. The activation of H2AX, a hallmark protein of DNA breakage, suggests that a double-strand break (DSB) could be occurring during the targeted gene alteration (TGA) reaction. Using the human HCT116 cell line with a single integrated mutant eGFP gene as our model system, we demonstrate that the DNA strand breakage occurs when a specific ODN, designed to direct TGA, is transfected into the cells. Both single- and double-stranded DNA cleavage is observed dependent on the level of ODN added to the reaction. Possible mechanisms of ODN-dependent DSB formation, as a function of TGA, are discussed herein.
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Affiliation(s)
- Melissa Bonner
- Department of Biological Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19716, USA
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42
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A comparison of synthetic oligodeoxynucleotides, DNA fragments and AAV-1 for targeted episomal and chromosomal gene repair. BMC Biotechnol 2009; 9:35. [PMID: 19379497 PMCID: PMC2676283 DOI: 10.1186/1472-6750-9-35] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2008] [Accepted: 04/20/2009] [Indexed: 12/14/2022] Open
Abstract
Background Current strategies for gene therapy of inherited diseases consist in adding functional copies of the gene that is defective. An attractive alternative to these approaches would be to correct the endogenous mutated gene in the affected individual. This study presents a quantitative comparison of the repair efficiency using different forms of donor nucleic acids, including synthetic DNA oligonucleotides, double stranded DNA fragments with sizes ranging from 200 to 2200 bp and sequences carried by a recombinant adeno-associated virus (rAAV-1). Evaluation of each gene repair strategy was carried out using two different reporter systems, a mutated eGFP gene or a dual construct with a functional eGFP and an inactive luciferase gene, in several different cell systems. Gene targeting events were scored either following transient co-transfection of reporter plasmids and donor DNAs, or in a system where a reporter construct was stably integrated into the chromosome. Results In both episomal and chromosomal assays, DNA fragments were more efficient at gene repair than oligonucleotides or rAAV-1. Furthermore, the gene targeting frequency could be significantly increased by using DNA repair stimulating drugs such as doxorubicin and phleomycin. Conclusion Our results show that it is possible to obtain repair frequencies of 1% of the transfected cell population under optimized transfection protocols when cells were pretreated with phleomycin using rAAV-1 and dsDNA fragments.
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43
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Illuzzi J, Yerkes S, Parekh-Olmedo H, Kmiec EB. DNA breakage and induction of DNA damage response proteins precede the appearance of visible mutant huntingtin aggregates. J Neurosci Res 2009; 87:733-47. [PMID: 18831068 DOI: 10.1002/jnr.21881] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Huntington's disease (HD) is a neurodegenerative disorder that follows an autosomal-dominant inheritance pattern. The pathogenesis of the disease depends on the degree of expansion of triplet (CAG) repeats located in the first exon on the gene. An expanded polyglutamine tract within the protein huntingtin (Htt) enables a gain-of-function phenotype that is often exhibited by a dysfunctional oligomerization process and the formation of protein aggregates. How this process leads to neurodegeneration remains undefined. We report that expression of a Htt-fragment containing an expanded glutamine tract induces DNA damage and activates the DNA damage response pathway. Both single-strand and double-strand breaks are observed as the mutant protein accumulates in the cell; these breaks precede the appearance of detectable protein aggregates containing mutant Htt. We also observe activation of H2AX, ATM, and p53 in cells expressing mutant Htt, a predictable response in cells containing chromosomal breakage. Expression of wild-type Htt does not affect the integrity of DNA, nor does it activate the same pathway. Furthermore, DNA damage and activated H2AX are present in HD transgenic mice before the formation of mutant Htt aggregates and HD pathogenesis. Taken together, our data suggest that the expression of mutant Htt causes an accumulation of DNA breaks that activates the DNA damage response pathway, a process that can disable cell function. Because these events can lead to apoptosis, it is possible that the DNA damage response pathway activated by single- and double-strand breaks that we found contributes to neurodegeneration.
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Affiliation(s)
- Jennifer Illuzzi
- Department of Biological Sciences, University of Delaware, Delaware Biotechnology Institute, Newark, Delaware 19711, USA
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44
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Engstrom JU, Suzuki T, Kmiec EB. Regulation of targeted gene repair by intrinsic cellular processes. Bioessays 2009; 31:159-68. [PMID: 19204988 DOI: 10.1002/bies.200800119] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Targeted gene alteration (TGA) is a strategy for correcting single base mutations in the DNA of human cells that cause inherited disorders. TGA aims to reverse a phenotype by repairing the mutant base within the chromosome itself, avoiding the introduction of exogenous genes. The process of how to accurately repair a genetic mutation is elucidated through the use of single-stranded DNA oligonucleotides (ODNs) that can enter the cell and migrate to the nucleus. These specifically designed ODNs hybridize to the target sequence and act as a beacon for nucleotide exchange. The key to this reaction is the frequency with which the base is corrected; this will determine whether the approach becomes clinically relevant or not. Over the course of the last five years, workers have been uncovering the role played by the cells in regulating the gene repair process. In this essay, we discuss how the impact of the cell on TGA has evolved through the years and illustrate ways that inherent cellular pathways could be used to enhance TGA activity. We also describe the cost to cell metabolism and survival when certain processes are altered to achieve a higher frequency of repair.
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Affiliation(s)
- Julia U Engstrom
- University of Delaware, Department of Biological Sciences, Newark, DE 19716, USA
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45
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Benton MG, Glasser NR, Palecek SP. Deletion of MAG1 and MRE11 enhances the sensitivity of the Saccharomyces cerevisiae HUG1P-GFP promoter-reporter construct to genotoxicity. Biosens Bioelectron 2008; 24:736-41. [PMID: 18693109 DOI: 10.1016/j.bios.2008.06.033] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2008] [Revised: 06/06/2008] [Accepted: 06/23/2008] [Indexed: 10/21/2022]
Abstract
Eukaryotic yeast-based DNA damage cellular sensors offer many advantages to traditional prokaryotic-based mutagenicity assays. The HUG1P-GFP promoter-reporter construct has proven to be an effective method to selectively screen for multiple types of DNA damage. To enhance the sensitivity and selectivity of the system to different types of DNA damage, two genes involved in distinct DNA damage responses were deleted. Deletion of MAG1, a gene encoding a DNA glycosylase and member of the base excision repair (BER) pathway, increased the biosensor's sensitivity to the alkylating agents methyl methanesulfonate (MMS) (lowering the sensitivity threshold to 0.0001% (v/v)) and ethyl methanesulfonate (EMS). Deletion of MRE11, part of the highly conserved RMX complex that aids in sensing and repairing double strand breaks in budding yeasts, enhanced sensitivity to gamma radiation (gamma-ray) (detection threshold of 50Gy) and camptothecin. The mre11Delta phenotype dominated in mag1Deltamre11Delta strains. Through the deletions, we were able to engineer increased selectivity to alkylating agents, gamma-ray, and camptothecin, since increased sensitivity to one type of damage did not alter the quantitative response to other genotoxins. The enhancements to the HUG1P-GFP system did not affect its ability to detect several other DNA damaging agents, including 1,2-dimethyl hydrazine (SDMH), phleomycin, and hydroxyurea (HU), or affect its lack of response to the potentially non-genotoxic carcinogen formaldehyde.
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Affiliation(s)
- Michael G Benton
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, USA
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Hegele H, Wuepping M, Ref C, Kenner O, Kaufmann D. Simultaneous targeted exchange of two nucleotides by single-stranded oligonucleotides clusters within a region of about fourteen nucleotides. BMC Mol Biol 2008; 9:14. [PMID: 18226192 PMCID: PMC2266939 DOI: 10.1186/1471-2199-9-14] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2007] [Accepted: 01/28/2008] [Indexed: 11/23/2022] Open
Abstract
Background Transfection of cells with gene-specific, single-stranded oligonucleotides can induce the targeted exchange of one or two nucleotides in the targeted gene. To characterize the features of the DNA-repair mechanisms involved, we examined the maximal distance for the simultaneous exchange of two nucleotides by a single-stranded oligonucleotide. The chosen experimental system was the correction of a hprt-point mutation in a hamster cell line, the generation of an additional nucleotide exchange at a variable distance from the first exchange position and the investigation of the rate of simultaneous nucleotide exchanges. Results The smaller the distance between the two exchange positions, the higher was the probability of a simultaneous exchange. The detected simultaneous nucleotide exchanges were found to cluster in a region of about fourteen nucleotides upstream and downstream from the first exchange position. Conclusion We suggest that the mechanism involved in the repair of the targeted DNA strand utilizes only a short sequence of the single-stranded oligonucleotide, which may be physically incorporated into the DNA or be used as a matrix for a repair process.
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Affiliation(s)
- Heike Hegele
- Institute of Human Genetics, University of Ulm, D 89070 Ulm, Germany.
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Ferrara L, Engstrom JU, Schwartz T, Parekh-Olmedo H, Kmiec EB. Recovery of cell cycle delay following targeted gene repair by oligonucleotides. DNA Repair (Amst) 2007; 6:1529-35. [PMID: 17560837 PMCID: PMC2083256 DOI: 10.1016/j.dnarep.2007.04.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2006] [Revised: 03/09/2007] [Indexed: 11/20/2022]
Abstract
We have previously shown that activation of the homologous recombinational repair pathway leads to a block of cell division in corrected cells, possibly through the activity of checkpoint proteins Chk1 and Chk2. In this study, we examine the long-term impact of this stalling on the growth of cells that have enabled gene repair events. Using a mutated eGFP gene as an episomal reporter, we show that corrected (eGFP-positive) cells contain only a few active replication templates 2 weeks after electroporation, yet do not display an apoptotic or senescent phenotype. By 6 weeks after electroporation, cells resume active replication with a cell cycle profile that is comparable to that of the non-corrected (eGFP-negative) population. These results indicate that the initial stalling is transient and eGFP-positive cells eventually resume a normal phenotypic growth pattern, allowing for passaging and expansion in vitro.
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Manipulation of cell cycle progression can counteract the apparent loss of correction frequency following oligonucleotide-directed gene repair. BMC Mol Biol 2007; 8:9. [PMID: 17284323 PMCID: PMC1797188 DOI: 10.1186/1471-2199-8-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2006] [Accepted: 02/06/2007] [Indexed: 11/10/2022] Open
Abstract
Background Single-stranded oligonucleotides (ssODN) are used routinely to direct specific base alterations within mammalian genomes that result in the restoration of a functional gene. Despite success with the technique, recent studies have revealed that following repair events, correction frequencies decrease as a function of time, possibly due to a sustained activation of damage response signals in corrected cells that lead to a selective stalling. In this study, we use thymidine to slow down the replication rate to enhance repair frequency and to maintain substantial levels of correction over time. Results First, we utilized thymidine to arrest cells in G1 and released the cells into S phase, at which point specific ssODNs direct the highest level of correction. Next, we devised a protocol in which cells are maintained in thymidine following the repair reaction, in which the replication is slowed in both corrected and non-corrected cells and the initial correction frequency is retained. We also present evidence that cells enter a senescence state upon prolonged treatment with thymidine but this passage can be avoided by removing thymidine at 48 hours. Conclusion Taken together, we believe that thymidine may be used in a therapeutic fashion to enable the maintenance of high levels of treated cells bearing repaired genes.
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Reduction of gene repair by selenomethionine with the use of single-stranded oligonucleotides. BMC Mol Biol 2007; 8:7. [PMID: 17257432 PMCID: PMC1797052 DOI: 10.1186/1471-2199-8-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2006] [Accepted: 01/26/2007] [Indexed: 12/02/2022] Open
Abstract
Background The repair of single base mutations in mammalian genes can be directed by single-stranded oligonucleotides in a process known as targeted gene repair. The mechanism of this reaction is currently being elucidated but likely involves a pairing step in which the oligonucleotide align in homologous register with its target sequence and a correction step in which the mutant base is replaced by endogenous repair pathways. This process is regulated by the activity of various factors and proteins that either elevate or depress the frequency at which gene repair takes place. Results In this report, we find that addition of selenomethionine reduces gene repair frequency in a dose-dependent fashion. A correlation between gene repair and altered cell cycle progression is observed. We also find that selenium induces expression of Ref-1 which, in turn, modifies the activity of p53 during the cell cycle. Conclusion We can conclude from the results that the suppression of gene repair by introduction of selenomethionine occurs through a p53-associated pathway. This result indicates that the successful application of gene repair for treatment of inherited disorders may be hampered by indirect activation of endogenous suppressor functions.
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Maguire KK, Kmiec EB. Multiple roles for MSH2 in the repair of a deletion mutation directed by modified single-stranded oligonucleotides. Gene 2007; 386:107-14. [PMID: 17113727 PMCID: PMC1847641 DOI: 10.1016/j.gene.2006.08.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2006] [Revised: 08/14/2006] [Accepted: 08/15/2006] [Indexed: 11/20/2022]
Abstract
The mechanism by which modified single-stranded oligonucleotides (MSSOs) direct base changes in genes is not completely understood, but there is evidence that DNA damage, repair and cell cycle checkpoint proteins are involved in the targeted nucleotide exchange (TNE) process. We are interested in the role of the mismatch repair protein, Msh2 in the correction of a frameshift mutation in both yeast and mammalian cells. We show that this protein exerts different and opposing influences on the TNE reaction in MSH2 deficient yeast compared to MSH2(-/-) mammalian cells and in wild-type cells that have RNAi silenced Msh2. Data from yeast show a 10-fold decrease in the targeting frequency whereas mammalian cells have an elevated correction frequency. These results show that in yeast this protein is required for efficient targeting and may play a role in mismatch recognition and repair. In mammalian cells, Msh2 plays a suppressive role in TNE reaction by either precluding the oligonucleotide annealing to the target gene or by maintenance of a cell cycle checkpoint induced by the MSSO itself. These results reveal that the mechanism of TNE between yeast and mammalian cells is not conserved, and demonstrate that the suppression of the TNE reaction can be bypassed using RNAi against MSH2 designed to knockdown its expression.
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Affiliation(s)
- Katie Kennedy Maguire
- Department of Biological Sciences, University of Delaware, Delaware Biotechnology Institute, 15 Innovation Way, Newark, DE 19711, USA
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