1
|
Chiusano ML, Incerti G, Colantuono C, Termolino P, Palomba E, Monticolo F, Benvenuto G, Foscari A, Esposito A, Marti L, de Lorenzo G, Vega-Muñoz I, Heil M, Carteni F, Bonanomi G, Mazzoleni S. Arabidopsis thaliana Response to Extracellular DNA: Self Versus Nonself Exposure. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10081744. [PMID: 34451789 PMCID: PMC8400022 DOI: 10.3390/plants10081744] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/12/2021] [Accepted: 08/17/2021] [Indexed: 01/14/2023]
Abstract
The inhibitory effect of extracellular DNA (exDNA) on the growth of conspecific individuals was demonstrated in different kingdoms. In plants, the inhibition has been observed on root growth and seed germination, demonstrating its role in plant-soil negative feedback. Several hypotheses have been proposed to explain the early response to exDNA and the inhibitory effect of conspecific exDNA. We here contribute with a whole-plant transcriptome profiling in the model species Arabidopsis thaliana exposed to extracellular self- (conspecific) and nonself- (heterologous) DNA. The results highlight that cells distinguish self- from nonself-DNA. Moreover, confocal microscopy analyses reveal that nonself-DNA enters root tissues and cells, while self-DNA remains outside. Specifically, exposure to self-DNA limits cell permeability, affecting chloroplast functioning and reactive oxygen species (ROS) production, eventually causing cell cycle arrest, consistently with macroscopic observations of root apex necrosis, increased root hair density and leaf chlorosis. In contrast, nonself-DNA enters the cells triggering the activation of a hypersensitive response and evolving into systemic acquired resistance. Complex and different cascades of events emerge from exposure to extracellular self- or nonself-DNA and are discussed in the context of Damage- and Pathogen-Associated Molecular Patterns (DAMP and PAMP, respectively) responses.
Collapse
Affiliation(s)
- Maria Luisa Chiusano
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, Italy; (F.M.); (F.C.); (G.B.)
- Department of Research Infrastructures for Marine Biological Resources (RIMAR), Stazione Zoologica “Anton Dohrn”, 80121 Napoli, Italy;
- Correspondence: (M.L.C.); (S.M.)
| | - Guido Incerti
- Department of Agri-Food, Animal and Environmental Sciences, University of Udine, 33100 Udine, Italy;
| | - Chiara Colantuono
- Telethon Institute of Genetics and Medicine, via campi Flegrei, 34 Pozzuoli, 80078 Napoli, Italy;
| | - Pasquale Termolino
- Institute of Biosciences and Bioresources (IBBR), National Research Council of Italy (CNR), 80055 Portici, Italy;
| | - Emanuela Palomba
- Department of Research Infrastructures for Marine Biological Resources (RIMAR), Stazione Zoologica “Anton Dohrn”, 80121 Napoli, Italy;
| | - Francesco Monticolo
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, Italy; (F.M.); (F.C.); (G.B.)
| | - Giovanna Benvenuto
- Biology and Evolution of Marine Organisms Department (BEOM), Stazione Zoologica “Anton Dohrn”, 80121 Napoli, Italy;
| | - Alessandro Foscari
- Dipartimento di Scienze della Vita, University of Trieste, 34127 Trieste, Italy;
| | - Alfonso Esposito
- Department of Cellular, Computational and Integrative Biology—CIBIO, University of Trento, 38123 Trento, Italy;
| | - Lucia Marti
- Department of Biology and Biotechnology “C. Darwin”, Sapienza University of Rome, 00185 Rome, Italy; (L.M.); (G.d.L.)
| | - Giulia de Lorenzo
- Department of Biology and Biotechnology “C. Darwin”, Sapienza University of Rome, 00185 Rome, Italy; (L.M.); (G.d.L.)
| | - Isaac Vega-Muñoz
- Departemento de Ingeniería Genética, CINVESTAV-Irapuato, Guanajuato 36821, Mexico; (I.V.-M.); (M.H.)
| | - Martin Heil
- Departemento de Ingeniería Genética, CINVESTAV-Irapuato, Guanajuato 36821, Mexico; (I.V.-M.); (M.H.)
| | - Fabrizio Carteni
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, Italy; (F.M.); (F.C.); (G.B.)
| | - Giuliano Bonanomi
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, Italy; (F.M.); (F.C.); (G.B.)
| | - Stefano Mazzoleni
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, Italy; (F.M.); (F.C.); (G.B.)
- Correspondence: (M.L.C.); (S.M.)
| |
Collapse
|
2
|
Kawai H, Sato K, Shirahama W, Suzuki T, Kamiya H. Single-stranded DNA versus tailed duplex in sequence conversion of lacZα DNA. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2020; 39:1245-1250. [PMID: 32727258 DOI: 10.1080/15257770.2020.1790596] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Targeted DNA editing has great potential to cure some genetic diseases; however, the use of artificial nucleases such as CRISPR-Cas9 and TALEN in gene therapy can potentially cause severe side effects due to off-target DNA cleavages. Single-stranded (ss) DNAs and 5'-tailed duplexes (TDs) can achieve target base substitutions when introduced without artificial nucleases into cultured cells and mouse liver. In this study, ss DNA and TD were separately co-introduced into human U2OS cells, together with a target plasmid DNA bearing an inactivated lacZα gene, and the gene correction efficiencies were compared. Unlike the genes examined in previous studies, ss DNA and TD showed similar efficiencies. Therefore, ss DNAs might be as useful as TD for gene correction, depending on the target sequence.
Collapse
Affiliation(s)
- Hidehiko Kawai
- Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Kento Sato
- Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Wataru Shirahama
- Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Tetsuya Suzuki
- Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Hiroyuki Kamiya
- Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| |
Collapse
|
3
|
Cabrini G. Innovative Therapies for Cystic Fibrosis: The Road from Treatment to Cure. Mol Diagn Ther 2019; 23:263-279. [PMID: 30478715 DOI: 10.1007/s40291-018-0372-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Cystic fibrosis (CF), a life-threatening multiorgan genetic disease, is facing a new era of research and development using innovative gene-directed personalized therapies. The priority organ to cure is the lung, which suffers recurrent and chronic bacterial infection and inflammation since infancy, representing the main cause of morbidity and precocious mortality of these individuals. After the disappointing failure of gene-replacement approaches using gene therapy vectors, no single drug is presently available to repair all the CF gene defects. The impressive number of different CF gene mutations is now tackled with different chemical and biotechnological tools tailored to the specific molecular derangements, thanks to the extensive knowledge acquired over many years on the mechanisms of CF cell and organ pathology. This review provides an overview and recalls both the successes and limitations of the different experimental approaches, such as high-throughput screening on chemical libraries to discover CF gene correctors and potentiators, dual-acting compounds, read-through molecules, splicing defect repairing tools, cystic fibrosis transmembrane conductance regulator (CFTR) "amplifiers," CFTR interactome modulators and the first gene editing attempts.
Collapse
Affiliation(s)
- Giulio Cabrini
- Laboratory of Molecular Pathology, University Hospital, Verona, Italy. .,Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy.
| |
Collapse
|
4
|
Pankow S, Bamberger C, Yates JR. A posttranslational modification code for CFTR maturation is altered in cystic fibrosis. Sci Signal 2019; 12:12/562/eaan7984. [PMID: 30600261 DOI: 10.1126/scisignal.aan7984] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The multistep process regulating the maturation of membrane proteins in the endoplasmic reticulum (ER) and the secretory pathway is disrupted in many protein misfolding disorders. Mutations in the ion channel CFTR that impair its folding and subsequent localization to the plasma membrane cause cystic fibrosis (CF), an inherited and eventually lethal disease that impairs the function of multiple organs, mostly the lungs. Here, we found that proper maturation of CFTR is dependent on cross-talk between phosphorylation and methylation events in the regulatory insertion (RI) element of the protein. Manipulating these posttranslational modifications (PTMs) prevented the maturation of wild-type CFTR and instead induced its degradation by ER quality control systems. Deletion of Phe508 (ΔF508), the most prevalent mutation in CF, and other mutations in CFTR that impair its trafficking, such as N1303K, also led to quantitative and qualitative PTM changes that prevented the maturation of misfolded CFTR. Further analysis revealed that a wild-type CFTR-like PTM pattern and function was restored in ΔF508 CFTR when cells were cultured at 28°C but only in the presence of the kinase CK2α. Furthermore, the ability to replicate this PTM pattern predicted the efficacy of treatments in restoring ΔF508 CFTR activity. Accordingly, evaluation of patient information revealed that point mutations of several of the modification sites are associated with clinical CF. These findings identify a minimal quantitative and qualitative PTM code for CFTR maturation that distinguishes correctly folded from misfolded CFTR.
Collapse
Affiliation(s)
- Sandra Pankow
- Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
| | - Casimir Bamberger
- Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - John R Yates
- Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
| |
Collapse
|
5
|
Suzuki T, Yanai Y, Nishigaki N, Nakatsu Y, Tsuzuki T, Kamiya H. Effects of mismatches distant from the target position on gene correction with a 5′-tailed duplex. J Biosci Bioeng 2018; 125:619-623. [DOI: 10.1016/j.jbiosc.2017.12.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 12/14/2017] [Accepted: 12/17/2017] [Indexed: 11/16/2022]
|
6
|
Suzuki T, Imada T, Komatsu Y, Kamiya H. Comparison of DNA fragments as donor DNAs upon sequence conversion of cleaved target DNA. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2017; 36:428-434. [PMID: 28486036 DOI: 10.1080/15257770.2017.1310385] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Pinpoint sequence alteration (genome editing) by the combination of the site-specific cleavage of a target DNA and a donor nucleic acid has attracted much attention and the sequence of the target DNA is expected to be changed to that of a donor nucleic acid. In most cases, oligodeoxyribonucleotides (ODNs) and plasmid DNAs have been used as donors. However, a several hundred-base single-stranded (ss) DNA fragment and a 5'-tailed duplex (TD) accomplished the desired sequence changes without DNA cleavage, and might serve as better donors for the cleaved target DNA than ODNs and plasmid DNAs. In this study, sequence conversion efficiencies were compared with various donor DNAs in model sequence alteration experiments, using episomal DNA. The efficiencies with the ss and TD fragments were higher than those with the ODN and plasmid DNA. The sequence change by the TD seemed somewhat less efficient but slightly more accurate than that by the ss DNA fragment. These results suggested that the ss and TD fragments are better donors for targeted sequence alteration.
Collapse
Affiliation(s)
- Tetsuya Suzuki
- a Graduate School of Biomedical and Health Sciences , Hiroshima University , Kasumi, Minami-ku , Hiroshima , Japan
| | - Takashi Imada
- a Graduate School of Biomedical and Health Sciences , Hiroshima University , Kasumi, Minami-ku , Hiroshima , Japan
| | - Yasuo Komatsu
- b Bioproduction Research Institute , National Institute of Advanced Industrial Science and Technology (AIST) , Tsukisamu-Higashi, Toyohira-ku, Sapporo , Japan
| | - Hiroyuki Kamiya
- a Graduate School of Biomedical and Health Sciences , Hiroshima University , Kasumi, Minami-ku , Hiroshima , Japan
| |
Collapse
|
7
|
Kamiya H, Nishigaki N, Ikeda A, Yukawa S, Morita Y, Nakatsu Y, Tsuzuki T, Harashima H. Insertion and Deletion Mismatches Distant from the Target Position Improve Gene Correction with a Tailed Duplex. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2016; 35:379-88. [PMID: 27253876 DOI: 10.1080/15257770.2016.1163384] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
A 5'-tailed duplex (TD) DNA corrects a base-substitution mutation. In this study, the effects of insertion and deletion (indel) mismatches distant from the target position on the gene correction were examined. Three target plasmid DNAs with and without indel mismatches ∼330 bases distant from the correction target position were prepared, and introduced into HeLa cells together with the TD. The indel mismatches improved the gene correction efficiency and specificity without sequence conversions at the indel mismatch site. These results suggested that the gene correction efficiency and specificity are increased when an appropriate second mismatch is introduced into the TD fragment.
Collapse
Affiliation(s)
- Hiroyuki Kamiya
- a Graduate School of Science and Engineering, Ehime University , Matsuyama , Japan.,b Graduate School of Biomedical and Health Sciences, Hiroshima University , Minami-ku, Hiroshima , Japan.,c Faculty of Pharmaceutical Sciences, Hokkaido University , Sapporo , Japan
| | - Natsuki Nishigaki
- a Graduate School of Science and Engineering, Ehime University , Matsuyama , Japan.,b Graduate School of Biomedical and Health Sciences, Hiroshima University , Minami-ku, Hiroshima , Japan
| | - Akihiro Ikeda
- a Graduate School of Science and Engineering, Ehime University , Matsuyama , Japan
| | - Seiya Yukawa
- a Graduate School of Science and Engineering, Ehime University , Matsuyama , Japan
| | - Yukiko Morita
- c Faculty of Pharmaceutical Sciences, Hokkaido University , Sapporo , Japan
| | - Yoshimichi Nakatsu
- d Graduate School of Medical Sciences, Kyushu University , Higashi-ku, Fukuoka , Japan
| | - Teruhisa Tsuzuki
- d Graduate School of Medical Sciences, Kyushu University , Higashi-ku, Fukuoka , Japan
| | | |
Collapse
|
8
|
The Gene Targeting Approach of Small Fragment Homologous Replacement (SFHR) Alters the Expression Patterns of DNA Repair and Cell Cycle Control Genes. MOLECULAR THERAPY-NUCLEIC ACIDS 2016; 5:e304. [PMID: 27045208 PMCID: PMC5014528 DOI: 10.1038/mtna.2016.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 12/12/2015] [Indexed: 12/27/2022]
Abstract
Cellular responses and molecular mechanisms activated by exogenous DNA that
invades cells are only partially understood. This limits the practical use of
gene targeting strategies. Small fragment homologous replacement (SFHR) uses a
small exogenous wild-type DNA fragment to restore the endogenous wild-type
sequence; unfortunately, this mechanism has a low frequency of correction.
In this study, we used a mouse embryonic fibroblast cell line with a stably
integrated mutated gene for enhanced green fluorescence protein. The restoration
of a wild-type sequence can be detected by flow cytometry analysis. We
quantitatively analyzed the expression of 84 DNA repair genes and 84 cell cycle
control genes. Peculiar temporal gene expression patterns were observed for both
pathways. Different DNA repair pathways, not only homologous recombination, as
well as the three main cell cycle checkpoints appeared to mediate the cellular
response. Eighteen genes were selected as highly significant target/effectors of
SFHR. We identified a wide interconnection between SFHR, DNA repair, and cell
cycle control. Our results increase the knowledge of the molecular mechanisms
involved in cell invasion by exogenous DNA and SFHR. Specific molecular targets
of both the cell cycle and DNA repair machineries were selected for manipulation
to enhance the practical application of SFHR.
Collapse
|
9
|
|
10
|
Suzuki S, Sargent RG, Illek B, Fischer H, Esmaeili-Shandiz A, Yezzi MJ, Lee A, Yang Y, Kim S, Renz P, Qi Z, Yu J, Muench MO, Beyer AI, Guimarães AO, Ye L, Chang J, Fine EJ, Cradick TJ, Bao G, Rahdar M, Porteus MH, Shuto T, Kai H, Kan YW, Gruenert DC. TALENs Facilitate Single-step Seamless SDF Correction of F508del CFTR in Airway Epithelial Submucosal Gland Cell-derived CF-iPSCs. MOLECULAR THERAPY. NUCLEIC ACIDS 2016; 5:e273. [PMID: 26730810 PMCID: PMC5012545 DOI: 10.1038/mtna.2015.43] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Accepted: 10/17/2015] [Indexed: 12/22/2022]
Abstract
Cystic fibrosis (CF) is a recessive inherited disease associated with multiorgan damage that compromises epithelial and inflammatory cell function. Induced pluripotent stem cells (iPSCs) have significantly advanced the potential of developing a personalized cell-based therapy for diseases like CF by generating patient-specific stem cells that can be differentiated into cells that repair tissues damaged by disease pathology. The F508del mutation in airway epithelial cell-derived CF-iPSCs was corrected with small/short DNA fragments (SDFs) and sequence-specific TALENs. An allele-specific PCR, cyclic enrichment strategy gave ~100-fold enrichment of the corrected CF-iPSCs after six enrichment cycles that facilitated isolation of corrected clones. The seamless SDF-based gene modification strategy used to correct the CF-iPSCs resulted in pluripotent cells that, when differentiated into endoderm/airway-like epithelial cells showed wild-type (wt) airway epithelial cell cAMP-dependent Cl ion transport or showed the appropriate cell-type characteristics when differentiated along mesoderm/hematopoietic inflammatory cell lineage pathways.
Collapse
Affiliation(s)
- Shingo Suzuki
- Department of Otolaryngology - Head and Neck Surgery, University of California-San Francisco, San Francisco, California, USA.,Department of Molecular Medicine, Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
| | - R Geoffrey Sargent
- Department of Otolaryngology - Head and Neck Surgery, University of California-San Francisco, San Francisco, California, USA.,California Pacific Medical Center Research Institute, San Francisco, California, USA
| | - Beate Illek
- Childrens Hospital Oakland Research Institute, Oakland, California, USA
| | - Horst Fischer
- Childrens Hospital Oakland Research Institute, Oakland, California, USA
| | - Alaleh Esmaeili-Shandiz
- Department of Otolaryngology - Head and Neck Surgery, University of California-San Francisco, San Francisco, California, USA
| | - Michael J Yezzi
- Department of Otolaryngology - Head and Neck Surgery, University of California-San Francisco, San Francisco, California, USA.,California Pacific Medical Center Research Institute, San Francisco, California, USA
| | - Albert Lee
- Department of Otolaryngology - Head and Neck Surgery, University of California-San Francisco, San Francisco, California, USA.,Present address: Graduate Program in Biochemistry, Molecular, Cellular, and Developmental Biology, University of California-Davis, Davis, California, USA
| | - Yanu Yang
- California Pacific Medical Center Research Institute, San Francisco, California, USA.,Present address: Molecular Department, Hunter Laboratories, Campbell, California, USA
| | - Soya Kim
- Liver Center, University of California-San Francisco, San Francisco, California, USA.,Present address: Heinrich-Heine-Universität Düsseldorf, Institut für Genetik, Düsseldorf, Germany
| | - Peter Renz
- Department of Otolaryngology - Head and Neck Surgery, University of California-San Francisco, San Francisco, California, USA.,California Pacific Medical Center Research Institute, San Francisco, California, USA.,Present address: Graduate Program in the Department of Biosystems Science and Engineering, ETH, Zürich, Switzerland
| | - Zhongxia Qi
- Department of Laboratory Medicine, University of California-San Francisco, San Francisco, California, USA
| | - Jingwei Yu
- Department of Laboratory Medicine, University of California-San Francisco, San Francisco, California, USA
| | - Marcus O Muench
- Department of Laboratory Medicine, University of California-San Francisco, San Francisco, California, USA.,Liver Center, University of California-San Francisco, San Francisco, California, USA.,Blood Systems Research Institute, San Francisco, California, USA
| | - Ashley I Beyer
- Blood Systems Research Institute, San Francisco, California, USA
| | | | - Lin Ye
- Department of Medicine, University of California-San Francisco, San Francisco, California, USA
| | - Judy Chang
- Department of Medicine, University of California-San Francisco, San Francisco, California, USA
| | - Eli J Fine
- Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Thomas J Cradick
- Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Gang Bao
- Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Meghdad Rahdar
- Department of Pediatrics, Stanford University, Stanford, California, USA
| | - Matthew H Porteus
- Department of Pediatrics, Stanford University, Stanford, California, USA
| | - Tsuyoshi Shuto
- Department of Molecular Medicine, Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
| | - Hirofumi Kai
- Department of Molecular Medicine, Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
| | - Yuet W Kan
- Department of Medicine, University of California-San Francisco, San Francisco, California, USA.,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Helen Diller Family Comprehensive Cancer Center, Institute for Human Genetics, Cardiovascular Research Institute, University of California-San Francisco, San Francisco, California, USA
| | - Dieter C Gruenert
- Department of Otolaryngology - Head and Neck Surgery, University of California-San Francisco, San Francisco, California, USA.,California Pacific Medical Center Research Institute, San Francisco, California, USA.,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Helen Diller Family Comprehensive Cancer Center, Institute for Human Genetics, Cardiovascular Research Institute, University of California-San Francisco, San Francisco, California, USA.,Department of Pediatrics, University of Vermont College of Medicine, Burlington, Vermont, USA
| |
Collapse
|
11
|
Cartenì F, Bonanomi G, Giannino F, Incerti G, Vincenot CE, Chiusano ML, Mazzoleni S. Self-DNA inhibitory effects: Underlying mechanisms and ecological implications. PLANT SIGNALING & BEHAVIOR 2016; 11:e1158381. [PMID: 26950417 PMCID: PMC4883922 DOI: 10.1080/15592324.2016.1158381] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 02/22/2016] [Indexed: 05/22/2023]
Abstract
DNA is usually known as the molecule that carries the instructions necessary for cell functioning and genetic inheritance. A recent discovery reported a new functional role for extracellular DNA. After fragmentation, either by natural or artificial decomposition, small DNA molecules (between ∼50 and ∼2000 bp) exert a species specific inhibitory effect on individuals of the same species. Evidence shows that such effect occurs for a wide range of organisms, suggesting a general biological process. In this paper we explore the possible molecular mechanisms behind those findings and discuss the ecological implications, specifically those related to plant species coexistence.
Collapse
Affiliation(s)
- Fabrizio Cartenì
- Dipartimento di Agraria, University of Naples Federico II, via Università 100, Portici (NA), Italy
| | - Giuliano Bonanomi
- Dipartimento di Agraria, University of Naples Federico II, via Università 100, Portici (NA), Italy
| | - Francesco Giannino
- Dipartimento di Agraria, University of Naples Federico II, via Università 100, Portici (NA), Italy
| | - Guido Incerti
- Dipartimento di Agraria, University of Naples Federico II, via Università 100, Portici (NA), Italy
| | | | - Maria Luisa Chiusano
- Dipartimento di Agraria, University of Naples Federico II, via Università 100, Portici (NA), Italy
| | - Stefano Mazzoleni
- Dipartimento di Agraria, University of Naples Federico II, via Università 100, Portici (NA), Italy
| |
Collapse
|
12
|
Suzuki T, Imada T, Nishigaki N, Kobayashi M, Matsuoka I, Kamiya H. Cleavage of Target DNA Promotes Sequence Conversion with a Tailed Duplex. Biol Pharm Bull 2016; 39:1392-5. [DOI: 10.1248/bpb.b16-00325] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Tetsuya Suzuki
- Graduate School of Biomedical and Health Sciences, Hiroshima University
| | - Takashi Imada
- Graduate School of Biomedical and Health Sciences, Hiroshima University
| | - Natsuki Nishigaki
- Graduate School of Biomedical and Health Sciences, Hiroshima University
- Graduate School of Science and Engineering, Ehime University
| | | | | | - Hiroyuki Kamiya
- Graduate School of Biomedical and Health Sciences, Hiroshima University
- Graduate School of Science and Engineering, Ehime University
- College of Pharmaceutical Sciences, Matsuyama University
| |
Collapse
|
13
|
Mazzoleni S, Bonanomi G, Incerti G, Chiusano ML, Termolino P, Mingo A, Senatore M, Giannino F, Cartenì F, Rietkerk M, Lanzotti V. Inhibitory and toxic effects of extracellular self-DNA in litter: a mechanism for negative plant-soil feedbacks? THE NEW PHYTOLOGIST 2015; 205:1195-1210. [PMID: 25354164 DOI: 10.1111/nph.13121] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 09/23/2014] [Indexed: 05/20/2023]
Abstract
Plant-soil negative feedback (NF) is recognized as an important factor affecting plant communities. The objectives of this work were to assess the effects of litter phytotoxicity and autotoxicity on root proliferation, and to test the hypothesis that DNA is a driver of litter autotoxicity and plant-soil NF. The inhibitory effect of decomposed litter was studied in different bioassays. Litter biochemical changes were evaluated with nuclear magnetic resonance (NMR) spectroscopy. DNA accumulation in litter and soil was measured and DNA toxicity was assessed in laboratory experiments. Undecomposed litter caused nonspecific inhibition of root growth, while autotoxicity was produced by aged litter. The addition of activated carbon (AC) removed phytotoxicity, but was ineffective against autotoxicity. Phytotoxicity was related to known labile allelopathic compounds. Restricted (13) C NMR signals related to nucleic acids were the only ones negatively correlated with root growth on conspecific substrates. DNA accumulation was observed in both litter decomposition and soil history experiments. Extracted total DNA showed evident species-specific toxicity. Results indicate a general occurrence of litter autotoxicity related to the exposure to fragmented self-DNA. The evidence also suggests the involvement of accumulated extracellular DNA in plant-soil NF. Further studies are needed to further investigate this unexpected function of extracellular DNA at the ecosystem level and related cellular and molecular mechanisms.
Collapse
Affiliation(s)
- Stefano Mazzoleni
- Dipartimento di Agraria, University of Naples Federico II, via Università 100, 80055, Portici (NA), Italy
| | - Giuliano Bonanomi
- Dipartimento di Agraria, University of Naples Federico II, via Università 100, 80055, Portici (NA), Italy
| | - Guido Incerti
- Dipartimento di Agraria, University of Naples Federico II, via Università 100, 80055, Portici (NA), Italy
| | - Maria Luisa Chiusano
- Dipartimento di Agraria, University of Naples Federico II, via Università 100, 80055, Portici (NA), Italy
| | - Pasquale Termolino
- CNR-IGV, Istituto di Genetica Vegetale, via Università 133, 80055, Portici (NA), Italy
| | - Antonio Mingo
- Dipartimento di Agraria, University of Naples Federico II, via Università 100, 80055, Portici (NA), Italy
| | - Mauro Senatore
- Dipartimento di Agraria, University of Naples Federico II, via Università 100, 80055, Portici (NA), Italy
| | - Francesco Giannino
- Dipartimento di Agraria, University of Naples Federico II, via Università 100, 80055, Portici (NA), Italy
| | - Fabrizio Cartenì
- Dipartimento di Agraria, University of Naples Federico II, via Università 100, 80055, Portici (NA), Italy
| | - Max Rietkerk
- Department of Environmental Sciences, Copernicus Institute, Utrecht University, PO Box 80115, 3508, TC Utrecht, the Netherlands
| | - Virginia Lanzotti
- Dipartimento di Agraria, University of Naples Federico II, via Università 100, 80055, Portici (NA), Italy
| |
Collapse
|
14
|
Small Fragment Homologous Replacement (SFHR): sequence-specific modification of genomic DNA in eukaryotic cells by small DNA fragments. Methods Mol Biol 2014; 1114:85-101. [PMID: 24557898 DOI: 10.1007/978-1-62703-761-7_6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
The sequence-specific correction of a mutated gene (e.g., point mutation) by the Small Fragment Homologous Replacement (SFHR) method is a highly attractive approach for gene therapy. Small DNA fragments (SDFs) were used in SFHR to modify endogenous genomic DNA in both human and murine cells. The advantage of this gene targeting approach is to maintain the physiologic expression pattern of targeted genes without altering the regulatory sequences (e.g., promoter, enhancer), but the application of this technique requires the knowledge of the sequence to be targeted. In our recent study, an optimized SFHR protocol was used to replace the eGFP mutant sequence in SV-40-transformed mouse embryonic fibroblast (MEF-SV40), with the wild-type eGFP sequence. Nevertheless in the past, SFHR has been used to correct several mutant genes, each related to a specific genetic disease (e.g., spinal muscular atrophy, cystic fibrosis, severe combined immune deficiency). Several parameters can be modified to optimize the gene modification efficiency, as described in our recent study. In this chapter we describe the main guidelines that should be followed in SFHR application, in order to increase technique efficiency.
Collapse
|
15
|
Nuclease-mediated double-strand break (DSB) enhancement of small fragment homologous recombination (SFHR) gene modification in human-induced pluripotent stem cells (hiPSCs). Methods Mol Biol 2014; 1114:279-90. [PMID: 24557910 DOI: 10.1007/978-1-62703-761-7_18] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Recent developments in methods to specifically modify genomic DNA using sequence-specific endonucleases and donor DNA have opened the door to a new therapeutic paradigm for cell and gene therapy of inherited diseases. Sequence-specific endonucleases, in particular transcription activator-like (TAL) effector nucleases (TALENs), have been coupled with polynucleotide small/short DNA fragments (SDFs) to correct the most common mutation in the cystic fibrosis (CF) transmembrane conductance regulator (CFTR) gene, a 3-base-pair deletion at codon 508 (delF508), in induced pluripotent stem (iPS) cells. The studies presented here describe the generation of candidate TALENs and their co-transfection with wild-type (wt) CFTR-SDFs into CF-iPS cells homozygous for the delF508 mutation. Using an allele-specific PCR (AS-PCR)-based cyclic enrichment protocol, clonal populations of corrected CF-iPS cells were isolated and expanded.
Collapse
|
16
|
Small fragment homologous replacement: evaluation of factors influencing modification efficiency in an eukaryotic assay system. PLoS One 2012; 7:e30851. [PMID: 22359552 PMCID: PMC3281040 DOI: 10.1371/journal.pone.0030851] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Accepted: 12/26/2011] [Indexed: 02/07/2023] Open
Abstract
Homologous Replacement is used to modify specific gene sequences of chromosomal DNA in a process referred to as “Small Fragment Homologous Replacement”, where DNA fragments replace genomic target resulting in specific sequence changes. To optimize the efficiency of this process, we developed a reporter based assay system where the replacement frequency is quantified by cytofluorimetric analysis following restoration of a stably integrated mutated eGFP gene in the genome of SV-40 immortalized mouse embryonic fibroblasts (MEF-SV-40). To obtain the highest correction frequency with this system, several parameters were considered: fragment synthesis and concentration, cell cycle phase and methylation status of both fragment and recipient genome. In addition, different drugs were employed to test their ability to improve technique efficiency. SFHR-mediated genomic modification resulted to be stably transmitted for several cell generations and confirmed at transcript and genomic levels. Modification efficiency was estimated in a range of 0.01–0.5%, further increasing when PARP-1 repair pathway was inhibited. In this study, for the first time SFHR efficiency issue was systematically approached and in part addressed, therefore opening new potential therapeutic ex-vivo applications.
Collapse
|
17
|
Gruenert DC, Sargent RG. Virus-mediated Genetic Surgery: Homologous Recombination With a Little "Helper" From My Friends. MOLECULAR THERAPY. NUCLEIC ACIDS 2012; 1:e2. [PMID: 23344619 PMCID: PMC3381596 DOI: 10.1038/mtna.2011.7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Dieter C Gruenert
- 1] Department of Otolaryngology-Head and Neck Surgery, University of California, San Francisco, San Francisco, California, USA [2] Department of Laboratory Medicine, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Helen Diller Family Comprehensive Cancer Center, Institute for Human Genetics, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California, USA
| | | |
Collapse
|
18
|
Sargent RG, Kim S, Gruenert DC. Oligo/polynucleotide-based gene modification: strategies and therapeutic potential. Oligonucleotides 2011; 21:55-75. [PMID: 21417933 DOI: 10.1089/oli.2010.0273] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Oligonucleotide- and polynucleotide-based gene modification strategies were developed as an alternative to transgene-based and classical gene targeting-based gene therapy approaches for treatment of genetic disorders. Unlike the transgene-based strategies, oligo/polynucleotide gene targeting approaches maintain gene integrity and the relationship between the protein coding and gene-specific regulatory sequences. Oligo/polynucleotide-based gene modification also has several advantages over classical vector-based homologous recombination approaches. These include essentially complete homology to the target sequence and the potential to rapidly engineer patient-specific oligo/polynucleotide gene modification reagents. Several oligo/polynucleotide-based approaches have been shown to successfully mediate sequence-specific modification of genomic DNA in mammalian cells. The strategies involve the use of polynucleotide small DNA fragments, triplex-forming oligonucleotides, and single-stranded oligodeoxynucleotides to mediate homologous exchange. The primary focus of this review will be on the mechanistic aspects of the small fragment homologous replacement, triplex-forming oligonucleotide-mediated, and single-stranded oligodeoxynucleotide-mediated gene modification strategies as it relates to their therapeutic potential.
Collapse
Affiliation(s)
- R Geoffrey Sargent
- Department of Otolaryngology-Head and Neck Surgery, University of California , San Francisco, California 94115, USA
| | | | | |
Collapse
|
19
|
Jensen NM, Dalsgaard T, Jakobsen M, Nielsen RR, Sørensen CB, Bolund L, Jensen TG. An update on targeted gene repair in mammalian cells: methods and mechanisms. J Biomed Sci 2011; 18:10. [PMID: 21284895 PMCID: PMC3042377 DOI: 10.1186/1423-0127-18-10] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Accepted: 02/02/2011] [Indexed: 11/10/2022] Open
Abstract
Transfer of full-length genes including regulatory elements has been the preferred gene therapy strategy for clinical applications. However, with significant drawbacks emerging, targeted gene alteration (TGA) has recently become a promising alternative to this method. By means of TGA, endogenous DNA repair pathways of the cell are activated leading to specific genetic correction of single-base mutations in the genome. This strategy can be implemented using single-stranded oligodeoxyribonucleotides (ssODNs), small DNA fragments (SDFs), triplex-forming oligonucleotides (TFOs), adeno-associated virus vectors (AAVs) and zinc-finger nucleases (ZFNs). Despite difficulties in the use of TGA, including lack of knowledge on the repair mechanisms stimulated by the individual methods, the field holds great promise for the future. The objective of this review is to summarize and evaluate the different methods that exist within this particular area of human gene therapy research.
Collapse
Affiliation(s)
- Nanna M Jensen
- Institute of Human Genetics, The Bartholin Building, University of Aarhus, 8000 Aarhus C, Denmark
| | | | | | | | | | | | | |
Collapse
|
20
|
Silva G, Poirot L, Galetto R, Smith J, Montoya G, Duchateau P, Pâques F. Meganucleases and other tools for targeted genome engineering: perspectives and challenges for gene therapy. Curr Gene Ther 2011; 11:11-27. [PMID: 21182466 PMCID: PMC3267165 DOI: 10.2174/156652311794520111] [Citation(s) in RCA: 235] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Revised: 12/10/2010] [Accepted: 12/10/2010] [Indexed: 12/17/2022]
Abstract
The importance of safer approaches for gene therapy has been underscored by a series of severe adverse events (SAEs) observed in patients involved in clinical trials for Severe Combined Immune Deficiency Disease (SCID) and Chromic Granulomatous Disease (CGD). While a new generation of viral vectors is in the process of replacing the classical gamma-retrovirus-based approach, a number of strategies have emerged based on non-viral vectorization and/or targeted insertion aimed at achieving safer gene transfer. Currently, these methods display lower efficacies than viral transduction although many of them can yield more than 1% of engineered cells in vitro. Nuclease-based approaches, wherein an endonuclease is used to trigger site-specific genome editing, can significantly increase the percentage of targeted cells. These methods therefore provide a real alternative to classical gene transfer as well as gene editing. However, the first endonuclease to be in clinic today is not used for gene transfer, but to inactivate a gene (CCR5) required for HIV infection. Here, we review these alternative approaches, with a special emphasis on meganucleases, a family of naturally occurring rare-cutting endonucleases, and speculate on their current and future potential.
Collapse
Affiliation(s)
- George Silva
- Cellectis, 102 Avenue Gaston Roussel, 93 235 Romainville, Cedex, France
| | - Laurent Poirot
- Cellectis Genome Surgery, 102 Avenue Gaston Roussel, 93 235 Romainville, Cedex, France
| | - Roman Galetto
- Cellectis Genome Surgery, 102 Avenue Gaston Roussel, 93 235 Romainville, Cedex, France
| | - Julianne Smith
- Cellectis Genome Surgery, 102 Avenue Gaston Roussel, 93 235 Romainville, Cedex, France
| | - Guillermo Montoya
- Macromolecular Crystallography Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Centre (CNIO), Melchor Fdez. Almagro 3, 28029 Madrid, Spain
| | | | - Frédéric Pâques
- Cellectis Genome Surgery, 102 Avenue Gaston Roussel, 93 235 Romainville, Cedex, France
- Cellectis, 102 Avenue Gaston Roussel, 93 235 Romainville, Cedex, France
| |
Collapse
|
21
|
Illek B, Lei D, Fischer H, Gruenert DC. Sensitivity of chloride efflux vs. transepithelial measurements in mixed CF and normal airway epithelial cell populations. Cell Physiol Biochem 2011; 26:983-90. [PMID: 21220929 DOI: 10.1159/000324011] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/15/2010] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND/AIMS While the Cl(-) efflux assays are relatively straightforward, their ability to assess the efficacy of phenotypic correction in cystic fibrosis (CF) tissue or cells may be limited. Accurate assessment of therapeutic efficacy, i.e., correlating wild type CF transmembrane conductance regulator (CFTR) levels with phenotypic correction in tissue or individual cells, requires a sensitive assay. METHODS Radioactive chloride ((36)Cl) efflux was compared to Ussing chamber analysis for measuring cAMP-dependent Cl(-) transport in mixtures of human normal (16HBE14o-) and cystic fibrosis (CF) (CFTE29o- or CFBE41o-, respectively) airway epithelial cells. Cell mixtures with decreasing amounts of 16HBE14o- cells were evaluated. RESULTS Efflux and Ussing chamber studies on mixed populations of normal and CF airway epithelial cells showed that, as the number of CF cells within the population was progressively increased, the cAMP-dependent Cl(-) decreased. The (36)Cl efflux assay was effective for measuring Cl(-) transport when ≥ 25% of the cells were normal. If < 25% of the cells were phenotypically wild-type (wt), the (36)Cl efflux assay was no longer reliable. Polarized CFBE41o- cells, also homozygous for the ΔF508 mutation, were used in the Ussing chamber studies. Ussing analysis detected cAMP-dependent Cl(-) currents in mixtures with ≥1% wild-type cells indicating that Ussing analysis is more sensitive than (36)Cl efflux analysis for detection of functional CFTR. CONCLUSIONS Assessment of CFTR function by Ussing analysis is more sensitive than (36)Cl efflux analysis. Ussing analysis indicates that cell mixtures containing 10% 16HBE14o- cells showed 40-50% of normal cAMP-dependent Cl(-) transport that drops off exponentially between 10-1% wild-type cells.
Collapse
Affiliation(s)
- Beate Illek
- Children's Hospital Oakland Research Institute, Oakland, USA
| | | | | | | |
Collapse
|
22
|
Bedayat B, Abdolmohamadi A, Ye L, Maurisse R, Parsi H, Schwarz J, Emamekhoo H, Nicklas JA, O'Neill JP, Gruenert DC. Sequence-specific correction of genomic hypoxanthine-guanine phosphoribosyl transferase mutations in lymphoblasts by small fragment homologous replacement. Oligonucleotides 2010; 20:7-16. [PMID: 19995283 DOI: 10.1089/oli.2009.0205] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Oligo/polynucleotide-based gene targeting strategies provide new options for achieving sequence-specific modification of genomic DNA and have implications for the development of new therapies and transgenic animal models. One such gene modification strategy, small fragment homologous replacement (SFHR), was evaluated qualitatively and quantitatively in human lymphoblasts that contain a single base substitution in the hypoxanthine-guanine phosphoribosyl transferase (HPRT1) gene. Because HPRT1 mutant cells are readily discernable from those expressing the wild type (wt) gene through growth in selective media, it was possible to identify and isolate cells that have been corrected by SFHR. Transfection of HPRT1 mutant cells with polynucleotide small DNA fragments (SDFs) comprising wild type HPRT1 (wtHPRT1) sequences resulted in clones of cells that grew in hypoxanthine-aminopterin-thymidine (HAT) medium. Initial studies quantifying the efficiency of correction in 3 separate experiments indicate frequencies ranging from 0.1% to 2%. Sequence analysis of DNA and RNA showed correction of the HPRT1 mutation. Random integration was not indicated after transfection of the mutant cells with an SDF comprised of green fluorescent protein (GFP) sequences that are not found in human genomic DNA. Random integration was also not detected following Southern blot hybridization analysis of an individual corrected cell clone.
Collapse
Affiliation(s)
- Babak Bedayat
- California Pacific Medical Center Research Institute, San Francisco, California 94107, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
23
|
Kamiya H, Uchiyama M, Piao J, Nakatsu Y, Tsuzuki T, Harashima H. Targeted sequence alteration of a chromosomal locus in mouse liver. Int J Pharm 2010; 387:180-3. [DOI: 10.1016/j.ijpharm.2009.12.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2009] [Revised: 12/04/2009] [Accepted: 12/10/2009] [Indexed: 10/20/2022]
|
24
|
Galetto R, Duchateau P, Pâques F. Targeted approaches for gene therapy and the emergence of engineered meganucleases. Expert Opin Biol Ther 2009; 9:1289-303. [PMID: 19689185 DOI: 10.1517/14712590903213669] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND In spite of significant advances in gene transfer strategies in the field of gene therapy, there is a strong emphasis on the development of alternative methods, providing better control of transgene expression and insertion patterns. OBJECTIVE Several new approaches consist of targeting a desired transgene or gene modification in a well defined locus, and we collectively refer to them as 'targeted approaches'. The use of redesigned meganucleases is one of these emerging technologies. Here we try to define the potential of this method, in the larger scope of targeted strategies. METHODS We survey the different types of targeted strategies, presenting the achievements and the potential applications, with a special emphasis on the use of redesigned endonucleases. CONCLUSION redesigned endonucleases represent one of the most promising tools for targeted approaches, and the opening of a clinical trial for AIDS patients has recently shown the maturity of these strategies. However, there is still a 'quest' for the best reagents, that is the endonucleases providing the best efficacy:toxicity ratio. New advances in protein design have allowed the engineering of new scaffolds, such as meganucleases, and the landscape of existing methods is likely to change over the next few years.
Collapse
Affiliation(s)
- Roman Galetto
- Cellectis Genome Surgery, 102 Avenue Gaston Roussel, 93 340 Romainville Cedex, France
| | | | | |
Collapse
|
25
|
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.
Collapse
|
26
|
|
27
|
Tsuchiya H, Uchiyama M, Hara K, Nakatsu Y, Tsuzuki T, Inoue H, Harashima H, Kamiya H. Improved gene correction efficiency with a tailed duplex DNA fragment. Biochemistry 2008; 47:8754-9. [PMID: 18642931 DOI: 10.1021/bi800588k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A 606-base single-stranded (ss) DNA fragment, prepared by restriction enzyme digestion of ss phagemid DNA, corrects a hygromycin resistance and enhanced green fluorescent protein (Hyg-EGFP) fusion gene more efficiently than a PCR fragment, which is the conventional type of DNA fragment used in gene correction. Here, a tailed duplex, obtained by annealing an oligonucleotide to the ss DNA fragment, was used in the correction. The tailed duplex may be a good substrate for the RAD51 protein, an important enzyme in homologous recombination, which could be the gene correction pathway. The annealing of the oligonucleotides enhanced the correction efficiency of the Hyg-EGFP gene, especially when annealed in the 3'-region of the ss DNA fragment. Both the length and backbone structure of the oligonucleotides affected the gene correction efficiency. This type of gene correction device was also effective for another target gene, the rpsL gene. The results obtained in this study indicate that tailed duplex DNA fragments are effective nucleic acids for gene correction.
Collapse
Affiliation(s)
- Hiroyuki Tsuchiya
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | | | | | | | | | | | | | | |
Collapse
|
28
|
Sangiuolo F, Scaldaferri ML, Filareto A, Spitalieri P, Guerra L, Favia M, Caroppo R, Mango R, Bruscia E, Gruenert DC, Casavola V, De Felici M, Novelli G. Cftr gene targeting in mouse embryonic stem cells mediated by Small Fragment Homologous Replacement (SFHR). FRONTIERS IN BIOSCIENCE : A JOURNAL AND VIRTUAL LIBRARY 2008; 13:2989-99. [PMID: 17981772 PMCID: PMC3725395 DOI: 10.2741/2904] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Different gene targeting approaches have been developed to modify endogenous genomic DNA in both human and mouse cells. Briefly, the process involves the targeting of a specific mutation in situ leading to the gene correction and the restoration of a normal gene function. Most of these protocols with therapeutic potential are oligonucleotide based, and rely on endogenous enzymatic pathways. One gene targeting approach, "Small Fragment Homologous Replacement (SFHR)", has been found to be effective in modifying genomic DNA. This approach uses small DNA fragments (SDF) to target specific genomic loci and induce sequence and subsequent phenotypic alterations. This study shows that SFHR can stably introduce a 3-bp deletion (deltaF508, the most frequent cystic fibrosis (CF) mutation) into the Cftr (CF Transmembrane Conductance Regulator) locus in the mouse embryonic stem (ES) cell genome. After transfection of deltaF508-SDF into murine ES cells, SFHR-mediated modification was evaluated at the molecular levels on DNA and mRNA obtained from transfected ES cells. About 12% of transcript corresponding to deleted allele was detected, while 60% of the electroporated cells completely lost any measurable CFTR-dependent chloride efflux. The data indicate that the SFHR technique can be used to effectively target and modify genomic sequences in ES cells. Once the SFHR-modified ES cells differentiate into different cell lineages they can be useful for elucidating tissue-specific gene function and for the development of transplantation-based cellular and therapeutic protocols.
Collapse
Affiliation(s)
- Federica Sangiuolo
- Department of Biopathology and Diagnostic Imaging, Tor Vergata University, Rome, Italy.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Todaro M, Quigley A, Kita M, Chin J, Lowes K, Kornberg AJ, Cook MJ, Kapsa R. Effective detection of corrected dystrophin loci in mdx mouse myogenic precursors. Hum Mutat 2007; 28:816-23. [PMID: 17394239 DOI: 10.1002/humu.20494] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Targeted corrective gene conversion (TCGC) holds much promise as a future therapy for many hereditary diseases in humans. Mutation correction frequencies varying between 0.0001% and 40% have been reported using chimeraplasty, oligoplasty, triplex-forming oligonucleotides, and small corrective PCR amplicons (CPA). However, PCR technologies used to detect correction events risk either falsely indicating or greatly exaggerating the presence of corrected loci. This is a problem that is considerably exacerbated by attempted improvement of the TCGC system using high corrective nucleic acid (CNA) to nuclear ratios. Small fragment homologous replacement (SFHR)-mediated correction of the exon 23 dystrophin (DMD) gene mutation in the mdx mouse model of DMD has been used in this study to evaluate the effect of increasing CPA amounts. In these experiments, we detected extremely high levels of apparently corrected loci and determined that at higher CNA to nuclear ratios the extent of locus correction was highly exaggerated by residual CNA species in the nucleic acids extracted from the treated cells. This study describes a generic locus-specific detection protocol designed to eradicate residual CNA species and avoid the artifactual or exaggerated detection of gene correction.
Collapse
Affiliation(s)
- Marian Todaro
- National Muscular Dystrophy Research Centre, Howard Florey Institute, Fitzroy, Victoria, Australia
| | | | | | | | | | | | | | | |
Collapse
|
30
|
Affiliation(s)
- John F Engelhardt
- Department of Anatomy and Cell Biology, College of Medicine, University of Iowa, 51 Newton Road, Iowa City, IA 52242, USA.
| |
Collapse
|
31
|
Fichou Y, Férec C. The potential of oligonucleotides for therapeutic applications. Trends Biotechnol 2006; 24:563-70. [PMID: 17045686 DOI: 10.1016/j.tibtech.2006.10.003] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2006] [Revised: 08/21/2006] [Accepted: 10/03/2006] [Indexed: 12/15/2022]
Abstract
Viral-derived particles have been widely used and described in gene therapy clinical trials. Although substantial results have been achieved, major safety issues have also arisen. For more than a decade, oligonucleotides have been seen as an alternative to gene complementation by viral vectors or DNA plasmids, either to correct the genetic defect or to silence gene expression. The development of RNA interference has strengthened the potential of this approach. Recent clinical trials have also tested the ability of aptamer molecules and decoy oligonucleotides to sequestrate pathogenic proteins. Here, we review the potential of oligonucleotides in gene therapy, outline what has already been accomplished, and consider what remains to be done.
Collapse
Affiliation(s)
- Yann Fichou
- Inserm U613, Université de Bretagne Occidentale, 46 rue Félix Le Dantec, 29275 Brest Cedex, France
| | | |
Collapse
|
32
|
Khanahmad H, Noori Daloii MR, Shokrgozar MA, Azadmanesh K, Niavarani AR, Karimi M, Rabbani B, Khalili M, Bagheri R, Maryami F, Zeinali S. A novel single step double positive double negative selection strategy for β-globin gene replacement. Biochem Biophys Res Commun 2006; 345:14-20. [PMID: 16674923 DOI: 10.1016/j.bbrc.2006.04.060] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2006] [Accepted: 04/07/2006] [Indexed: 11/18/2022]
Abstract
beta-Thalassemias are a heterogeneous group of autosomal recessive disorders, characterized by reduced or absence of the beta-globin chain production by the affected alleles. Transplantation of genetically corrected autologous hematopoietic stem cell (HSC) is an attractive approach for treatment of these disorders. Gene targeting (homologous recombination) has many desirable features for gene therapy due to its ability to target the mutant genes and restore their normal expression. In the present study, a specific gene construct for beta-globin gene replacement was constructed consisting of: two homologous stems including, upstream and downstream regions of beta-globin gene, beta-globin gene lying between hygromycin and neomycin resistant genes as positive selection markers and thymidine kinase expression cassettes at both termini as negative selection marker. All segments were subcloned into pBGGT vector. The final plasmid was checked by sequencing and named as pFBGGT. Mammalian cell line COS-7 was transfected with linear plasmid by lipofection followed by positive and negative selection. DNA of the selected cells was analyzed by PCR and sequencing to confirm the occurrence of homologous recombination. In this novel strategy gene replacement was achieved in one step and by a single construct.
Collapse
Affiliation(s)
- H Khanahmad
- Biotechnology Research Centre, Pasteur Institute of Iran, Tehran, Iran
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Tsuchiya H, Sawamura T, Harashima H, Kamiya H. Correction of frameshift mutations with single-stranded and double-stranded DNA fragments prepared from phagemid/plasmid DNAs. Biol Pharm Bull 2006; 28:1958-62. [PMID: 16204954 DOI: 10.1248/bpb.28.1958] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We recently found that a heat-denatured, double-stranded DNA fragment, prepared from plasmid DNA (dsHES), and a sense single-stranded DNA fragment, prepared from single-stranded phagemid DNA (fSense), corrected an inactivated hygromycin-resistance and enhanced green fluorescence protein fusion (Hyg-EGFP) gene containing a base substitution (G:C to C:G) mutation 2-fold and more than 10-fold, respectively, more efficiently than the conventional PCR fragment (pcrHES), in the small fragment homologous replacement method. In this study, we tested the abilities of these new DNA fragments to correct Hyg-EGFP genes inactivated by one base insertion (+G) and deletion (-C) mutations. In contrast to its activity with the substitution mutation, the fSense fragment showed similar efficiencies to those of the dsHES fragment in the correction of frameshift mutations. For the correction of the insertion mutation, the efficiencies were in the order of dsHES (0.21%)>or=fSense (0.18%)>pcrHES (0.08%). In the case of the correction of the deletion mutation, the efficiencies were in the order of fSense (0.27%)>or=dsHES (0.19%)>pcrHES (0.12%). These results suggest that sense single- and double-stranded DNA fragments prepared from phagemid and plasmid DNAs, respectively, have the potential to correct frameshift mutations.
Collapse
Affiliation(s)
- Hiroyuki Tsuchiya
- Graduate School of Pharmaceutical Sciences, Hokkaido University; Kita-12, Nishi-6, Sapporo, 060-0812, Japan
| | | | | | | |
Collapse
|
34
|
Lewin AS, Glazer PM, Milstone LM. Gene therapy for autosomal dominant disorders of keratin. J Investig Dermatol Symp Proc 2005; 10:47-61. [PMID: 16250209 DOI: 10.1111/j.1087-0024.2005.10207.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Dominant mutations that interfere with the assembly of keratin filaments cause painful and disfiguring epidermal diseases like pachyonychia congenita and epidermolysis bullosa simplex. Genetic therapies for such diseases must either suppress the production of the toxic proteins or correct the genetic defect in the chromosome. Because epidermal skin cells may be genetically modified in tissue culture or in situ, gene correction is a legitimate goal for keratin diseases. In addition, recent innovations, such as RNA interference in animals, make an RNA knockdown approach plausible in the near future. Although agents of RNA reduction (small interfering RNA, ribozymes, triplex oligonucleotides, or antisense DNA) can be delivered as nucleotides, the impermeability of the skin to large charged molecules presents a serious impediment. Using viral vectors to deliver genes for selective inhibitors of gene expression presents an attractive alternative for long-term treatment of genetic disease in the skin.
Collapse
MESH Headings
- Animals
- Darier Disease/genetics
- Darier Disease/therapy
- Dependovirus/genetics
- Ectodermal Dysplasia/genetics
- Ectodermal Dysplasia/therapy
- Epidermolysis Bullosa Simplex/genetics
- Epidermolysis Bullosa Simplex/therapy
- Gene Silencing
- Gene Targeting
- Genes, Dominant
- Genetic Therapy
- Genetic Vectors
- Humans
- Keratins/genetics
- Keratoderma, Palmoplantar/genetics
- Keratoderma, Palmoplantar/therapy
- Mice
- Mutation
- Nails, Malformed/genetics
- Nails, Malformed/therapy
- Oligonucleotides, Antisense/genetics
- Oligonucleotides, Antisense/therapeutic use
- RNA Interference
- RNA, Catalytic/genetics
- RNA, Catalytic/therapeutic use
- RNA, Small Interfering/genetics
- RNA, Small Interfering/therapeutic use
Collapse
Affiliation(s)
- Alfred S Lewin
- Department of Molecular Genetics and Microbiology, University of Florida College of Medicine, Gainesville, Florida 32610-0266, USA.
| | | | | |
Collapse
|
35
|
Yin W, Kren B, Steer C. Site-specific base changes in the coding or promoter region of the human beta- and gamma-globin genes by single-stranded oligonucleotides. Biochem J 2005; 390:253-61. [PMID: 15828874 PMCID: PMC1184579 DOI: 10.1042/bj20050045] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
SSOs (single-stranded oligonucleotides) can mediate site-specific alteration of base-pairs in episomal and chromosomal target genes in mammalian cells. The TNE (targeted nucleotide exchange) can result in either repair or mutation of a gene sequence and is mediated through endogenous DNA repair pathway(s). Thus the approach provides a technique for the treatment of monogenic disorders associated with specific point mutations such as SCD (sickle cell disease). We studied the potential application of SSOs for SCD by introducing either an A to T substitution at the sixth codon of the human beta-globin gene (sickle locus) or a C to G mutation at -202 of the Ggamma-globin gene promoter region. The latter TNE is an alternative strategy to ameliorate the clinical manifestations of sickle cell anaemia by re-activating fetal haemoglobin gene expression in adult erythrocytes. A sensitive and valid PCR assay system was developed, which allows detection of point mutations as low as 0.01% at these sites. Using this system, TNE between 0.01 and 0.1% at the sickle locus or gamma-globin gene promoter region was detected after transfection with SSOs in cultured human cell lines. TNE in the Ggamma-globin promoter region exhibited varying degrees of strand bias that was dependent on SSO design and the cell's DNA mismatch repair activity. The results suggest that the endogenous DNA repair machinery may permit SSO correction of the sickle defect by modification of the beta- and/or gamma-globin genes.
Collapse
Affiliation(s)
- Wenxuan Yin
- *Department of Medicine, University of Minnesota Medical School, Minneapolis, MN 55455, U.S.A
| | - Betsy T. Kren
- *Department of Medicine, University of Minnesota Medical School, Minneapolis, MN 55455, U.S.A
| | - Clifford J. Steer
- *Department of Medicine, University of Minnesota Medical School, Minneapolis, MN 55455, U.S.A
- †Department of Genetics, Cell Biology and Development, University of Minnesota Medical School, Minneapolis, MN 55455, U.S.A
- To whom correspondence should be addressed (email )
| |
Collapse
|
36
|
Tsuchiya H, Harashima H, Kamiya H. Factors affecting SFHR gene correction efficiency with single-stranded DNA fragment. Biochem Biophys Res Commun 2005; 336:1194-200. [PMID: 16171787 DOI: 10.1016/j.bbrc.2005.08.258] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2005] [Accepted: 08/30/2005] [Indexed: 12/17/2022]
Abstract
A 606-nt single-stranded (ss) DNA fragment, prepared by restriction enzyme digestion of ss phagemid DNA, improves the gene correction efficiency by 12-fold as compared with a PCR fragment, which is the conventional type of fragment used in the small fragment homologous replacement method [H. Tsuchiya, H. Harashima, H. Kamiya, Increased SFHR gene correction efficiency with sense single-stranded DNA, J. Gene Med. 7 (2005) 486-493]. To reveal the characteristic features of this gene correction with the ss DNA fragment, the effects on the gene correction in CHO-K1 cells of the chain length, 5'-phosphate, adenine methylation, and transcription were studied. Moreover, the possibility that the ss DNA fragment is integrated into the target DNA was examined with a radioactively labeled ss DNA fragment. The presence of methylated adenine, but not the 5'-phosphate, enhanced the gene correction efficiency, and the optimal length of the ss DNA fragment (approximately 600 nt) was determined. Transcription of the target gene did not affect the gene correction efficiency. In addition, the target DNA recovered from the transfected CHO-K1 cells was radioactive. The results obtained in this study indicate that length and adenine methylation were important factors affecting the gene correction efficiency, and that the ss DNA fragment was integrated into the double-stranded target DNA.
Collapse
Affiliation(s)
- Hiroyuki Tsuchiya
- Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | | | | |
Collapse
|
37
|
Del Vecchio F, Filareto A, Spitalieri P, Sangiuolo F, Novelli G. Cellular genetic therapy. Transplant Proc 2005; 37:2657-61. [PMID: 16182776 DOI: 10.1016/j.transproceed.2005.06.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Cellular genetic therapy is the ultimate frontier for those pathologies that are consequent to a specific nonfunctional cellular type. A viable cure for there kinds of diseases is the replacement of sick cells with healthy ones, which can be obtained from the same patient or a different donor. In fact, structures can be corrected and strengthened with the introduction of undifferentiated cells within specific target tissues, where they will specialize into the desired cellular types. Furthermore, consequent to the recent results obtained with the transdifferentiation experiments, a process that allows the in vitro differentiation of embryonic and adult stem cells, it has also became clear that many advantages may be obtained from the use of stem cells to produce drugs, vaccines, and therapeutic molecules. Since stem cells can sustain lineage potentials, the capacity for differentiation, and better tolerance for the introduction of exogenous genes, they are also considered as feasible therapeutic vehicles for gene therapy. In fact, it is strongly believed that the combination of cellular genetic and gene therapy approaches will definitely allow the development of new therapeutic strategies as well as the production of totipotent cell lines to be used as experimental models for the cure of genetic disorders.
Collapse
Affiliation(s)
- F Del Vecchio
- Dipartimento di Biopatologia e Diagnostica per Immagini, Sezione di Genetica, Universita' di Tor Vergata, Rome, Italy
| | | | | | | | | |
Collapse
|
38
|
Tsuchiya H, Harashima H, Kamiya H. Increased SFHR gene correction efficiency with sense single-stranded DNA. J Gene Med 2005; 7:486-93. [PMID: 15521053 DOI: 10.1002/jgm.673] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND The correction of a mutated gene by the small fragment homologous replacement (SFHR) method is a highly attractive approach for gene therapy. However, the current SFHR method with a heat-denatured double-stranded PCR fragment yielded a low correction efficiency. METHODS Single-stranded (ss) DNA fragments were prepared from ss phagemid DNA and tested in a gene correction assay with an inactivated Hyg-EGFP fusion gene, as a model target. RESULTS A 606-nt sense, ss DNA fragment dramatically (12-fold) improved the gene correction efficiency, although the antisense strand showed only minimal correction efficiency. CONCLUSIONS These results suggest that the use of a sense, single-stranded DNA fragment is useful in the SFHR method for the correction of mutated genes.
Collapse
Affiliation(s)
- Hiroyuki Tsuchiya
- Laboratory for Molecular Design of Pharmaceutics and COE Program in the 21st Century, Graduate School of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Sapporo, Hokkaido 060-0812, Japan
| | | | | |
Collapse
|
39
|
Andrieu-Soler C, Casas M, Faussat AM, Gandolphe C, Doat M, Tempé D, Giovannangeli C, Behar-Cohen F, Concordet JP. Stable transmission of targeted gene modification using single-stranded oligonucleotides with flanking LNAs. Nucleic Acids Res 2005; 33:3733-42. [PMID: 16002788 PMCID: PMC1174897 DOI: 10.1093/nar/gki686] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Targeted mutagenesis directed by oligonucleotides (ONs) is a promising method for manipulating the genome in higher eukaryotes. In this study, we have compared gene editing by different ONs on two new target sequences, the eBFP and the rd1 mutant photoreceptor βPDE cDNAs, which were integrated as single copy transgenes at the same genomic site in 293T cells. Interestingly, antisense ONs were superior to sense ONs for one target only, showing that target sequence can by itself impart strand-bias in gene editing. The most efficient ONs were short 25 nt ONs with flanking locked nucleic acids (LNAs), a chemistry that had only been tested for targeted nucleotide mutagenesis in yeast, and 25 nt ONs with phosphorothioate linkages. We showed that LNA-modified ONs mediate dose-dependent target modification and analyzed the importance of LNA position and content. Importantly, when using ONs with flanking LNAs, targeted gene modification was stably transmitted during cell division, which allowed reliable cloning of modified cells, a feature essential for further applications in functional genomics and gene therapy. Finally, we showed that ONs with flanking LNAs aimed at correcting the rd1 stop mutation could promote survival of photoreceptors in retinas of rd1 mutant mice, suggesting that they are also active in vivo.
Collapse
Affiliation(s)
- Charlotte Andrieu-Soler
- INSERM U598, Institut Biomédical des Cordeliers15 rue de l'Ecole de Médecine, 75270 Paris Cedex 06, France
| | - Mariana Casas
- Département Génétique et Développement, Institut Cochin, INSERM U567, CNRS UMR810424 rue du Faubourg St-Jacques, 75014 Paris, France
| | - Anne-Marie Faussat
- INSERM U598, Institut Biomédical des Cordeliers15 rue de l'Ecole de Médecine, 75270 Paris Cedex 06, France
| | - Christelle Gandolphe
- INSERM U598, Institut Biomédical des Cordeliers15 rue de l'Ecole de Médecine, 75270 Paris Cedex 06, France
| | - Marc Doat
- INSERM U598, Institut Biomédical des Cordeliers15 rue de l'Ecole de Médecine, 75270 Paris Cedex 06, France
| | - Denis Tempé
- Département Génétique et Développement, Institut Cochin, INSERM U567, CNRS UMR810424 rue du Faubourg St-Jacques, 75014 Paris, France
| | - Carine Giovannangeli
- Laboratoire de Biophysique, Muséum National d'Histoire Naturelle, INSERM, U565, CNRS UMR 51537505 Paris, France
| | - Francine Behar-Cohen
- INSERM U598, Institut Biomédical des Cordeliers15 rue de l'Ecole de Médecine, 75270 Paris Cedex 06, France
- Fondation Ophtalmologique RothschildParis, France
| | - Jean-Paul Concordet
- Département Génétique et Développement, Institut Cochin, INSERM U567, CNRS UMR810424 rue du Faubourg St-Jacques, 75014 Paris, France
- To whom correspondence should be addressed. Tel: +33 1 44412436; Fax: +33 1 44412421;
| |
Collapse
|
40
|
Parekh-Olmedo H, Ferrara L, Brachman E, Kmiec EB. Gene therapy progress and prospects: targeted gene repair. Gene Ther 2005; 12:639-46. [PMID: 15815682 DOI: 10.1038/sj.gt.3302511] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The capacity to correct a mutant gene within the context of the chromosome holds great promise as a therapy for inherited disorders but fulfilling this promise has proven to be challenging. However, steady progress is being made and the development of gene repair as a viable and robust approach is underway. Here, we present some of the recent advances that are helping to shape our thinking about the feasibility and the limitations of this technique. For the most part, these advances center on understanding the regulation of the reaction and validating its application in animal models.
Collapse
Affiliation(s)
- H Parekh-Olmedo
- Department of Biological Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19716, USA
| | | | | | | |
Collapse
|
41
|
Volodin AA, Voloshin ON, Camerini-Otero RD. Homologous recombination and RecA protein: towards a new generation of tools for genome manipulations. Trends Biotechnol 2005; 23:97-102. [DOI: 10.1016/j.tibtech.2004.12.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
42
|
Abstract
RNA and DNA molecules can form complex, three-dimensional folded structures that have surprisingly sophisticated functions, including catalysing chemical reactions and controlling gene expression. Although natural nucleic acids make occasional use of these advanced functions, the true potential for sophisticated function by these biological polymers is far greater. An important challenge for biochemists is to take RNA and DNA beyond their proven use as polymers that form double-helical structures. Molecular engineers are beginning to harness the power of nucleic acids that form more complex three-dimensional structures, and apply them as tools for exploring biological systems and as therapeutics.
Collapse
Affiliation(s)
- Ronald R Breaker
- Department of Molecular, Cellular and Developmental Biology, Yale University, P. O. Box 208103, New Haven, Connecticut 06520-8103, USA.
| |
Collapse
|
43
|
Abstract
Alpha-1-antitrypsin (AT) deficiency was first described in the late 1960s in patients with severe pulmonary emphysema. The recognition of AT deficiency as a cause of emphysema then led to what is still the prevailing theory for the pathogenesis of emphysema, the protease-antiprotease theory. Soon it was found that AT deficiency accounted for a significant number of cases of neonatal liver disease that were previously categorized as idiopathic. We now know that AT deficiency is the most common genetic cause of neonatal liver disease and the most frequent diagnosis necessitating liver transplantation. It has also been shown to cause chronic liver disease, cryptogenic cirrhosis, and hepatocellular carcinoma in adults never previously known to have liver disease in infancy or childhood. Observations indicate that genetic traits unlinked to the AT gene or environmental factors predispose to or protect AT-deficient individuals from liver disease.
Collapse
|
44
|
Klink D, Schindelhauer D, Laner A, Tucker T, Bebok Z, Schwiebert EM, Boyd AC, Scholte BJ. Gene delivery systems—gene therapy vectors for cystic fibrosis. J Cyst Fibros 2004; 3 Suppl 2:203-12. [PMID: 15463959 DOI: 10.1016/j.jcf.2004.05.042] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Gene delivery systems (GDS) play a central role in the development of gene therapy strategies for Cystic Fibrosis (CF). Further, these systems are important tools in studies with cultured cells and in animal models. In this review, we describe the properties of several viral and synthetic gene delivery systems, and evaluate their possible application in gene therapy of CF. While many gene delivery systems give satisfactory results in cultured or animal studies, none of these systems has been shown to fulfil all the requirements of safety and efficacy for use in CF patients. The intact airway epithelium, the most important target in CF gene therapy, proves to be well protected against invading vector systems.
Collapse
Affiliation(s)
- Daniel Klink
- Department of Cell Biology, Erasmus MC, Erasmus University, P.O. Box 1738, Rotterdam DR 3000, The Netherlands
| | | | | | | | | | | | | | | |
Collapse
|
45
|
Sullenger BA. Targeted genetic repair: an emerging approach to genetic therapy. J Clin Invest 2003; 112:310-1. [PMID: 12897195 PMCID: PMC166306 DOI: 10.1172/jci19419] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Affiliation(s)
- Bruce A Sullenger
- Department of Surgeru, Duke University Medical Center, Durham, North Carolina 27710, USA.
| |
Collapse
|
46
|
Suzuki I, Im S, Tada A, Scott C, Akcali C, Davis MB, Barsh G, Hearing V, Abdel-Malek Z. Participation of the melanocortin-1 receptor in the UV control of pigmentation. J Investig Dermatol Symp Proc 1999; 4:29-34. [PMID: 10537004 DOI: 10.1038/sj.jidsp.5640177] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The cloning of the melanocortin-1 receptor (MC1R) gene from human melanocytes and the demonstration that these cells respond to the melanocortins alpha-melanocyte stimulating hormone (alpha-MSH) and adrenocorticotropic hormone (ACTH) with increased proliferation and melanogenesis have renewed the interest in investigation the physiological role of these hormones in regulating human pigmentation. Alpha-melanocyte stimulating hormone and ACTH are both synthesized in the human epidermis, and their synthesis is upregulated by exposure to ultraviolet radiation (UVR). Activation of the MC1R by ligand binding results in stimulation of cAMP formation, which is a principal mechanism for inducing melanogenesis. The increase in cAMP is required for the pigmentary response of human melanocytes to UVR, and for allowing them to overcome the UVR-induced G1 arrest. Treatment of human melanocytes with alpha-MSH increases eumelanin synthesis, an effect that is expected to enhance photoprotection of the skin. Population studies have revealed more than 20 allelic variants of the MC1R gene. Some of these variants are overexpressed in individuals with skin type I or II, red hair, and poor tanning ability. Future studies will aim at further exploration of the role of these variants in MC1R function, and in determining constitutive human pigmentation, the response to sun exposure, and possibly the susceptibility to skin cancer.
Collapse
Affiliation(s)
- I Suzuki
- Department of Dermatology, University of Cincinnati, Ohio 45267-0592, USA
| | | | | | | | | | | | | | | | | |
Collapse
|