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Dale GA, Wilkins DJ, Bohannon CD, Dilernia D, Hunter E, Bedford T, Antia R, Sanz I, Jacob J. Clustered Mutations at the Murine and Human IgH Locus Exhibit Significant Linkage Consistent with Templated Mutagenesis. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2019; 203:1252-1264. [PMID: 31375545 PMCID: PMC6702052 DOI: 10.4049/jimmunol.1801615] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 06/18/2019] [Indexed: 01/21/2023]
Abstract
Somatic hypermutation generates a myriad of Ab mutants in Ag-specific B cells, from which high-affinity mutants are selected. Chickens, sheep, and rabbits use nontemplated point mutations and templated mutations via gene conversion to diversify their expressed Ig loci, whereas mice and humans rely solely on untemplated somatic point mutations. In this study, we demonstrate that, in addition to untemplated point mutations, templated mutagenesis readily occurs at the murine and human Ig loci. We provide two distinct lines of evidence that are not explained by the Neuberger model of somatic hypermutation: 1) across multiple data sets there is significant linkage disequilibrium between individual mutations, especially among close mutations, and 2) among those mutations, those <8 bp apart are significantly more likely to match microhomologous regions in the IgHV repertoire than predicted by the mutation profiles of somatic hypermutation. Together, this supports the role of templated mutagenesis during somatic diversification of Ag-activated B cells.
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Affiliation(s)
- Gordon A Dale
- Emory Vaccine Center, Yerkes National Primate Center, Emory University, Atlanta, GA 30329
| | - Daniel J Wilkins
- Emory Vaccine Center, Yerkes National Primate Center, Emory University, Atlanta, GA 30329
| | - Caitlin D Bohannon
- Emory Vaccine Center, Yerkes National Primate Center, Emory University, Atlanta, GA 30329
| | - Dario Dilernia
- Emory Vaccine Center, Yerkes National Primate Center, Emory University, Atlanta, GA 30329
| | - Eric Hunter
- Emory Vaccine Center, Yerkes National Primate Center, Emory University, Atlanta, GA 30329
| | - Trevor Bedford
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA 98195
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, GA 30322; and
| | - Ignacio Sanz
- Lowance Center for Human Immunology, Department of Medicine, Emory University, Atlanta, GA 30322
| | - Joshy Jacob
- Emory Vaccine Center, Yerkes National Primate Center, Emory University, Atlanta, GA 30329;
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Watanabe K, Breier U, Hensel G, Kumlehn J, Schubert I, Reiss B. Stable gene replacement in barley by targeted double-strand break induction. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:1433-45. [PMID: 26712824 PMCID: PMC4762383 DOI: 10.1093/jxb/erv537] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Gene targeting is becoming an important tool for precision genome engineering in plants. During gene replacement, a variant of gene targeting, transformed DNA integrates into the genome by homologous recombination (HR) to replace resident sequences. We have analysed gene targeting in barley (Hordeum vulgare) using a model system based on double-strand break (DSB) induction by the meganuclease I-SceI and a transgenic, artificial target locus. In the plants we obtained, the donor construct was inserted at the target locus by homology-directed DNA integration in at least two transformants obtained in a single experiment and was stably inherited as a single Mendelian trait. Both events were produced by one-sided integration. Our data suggest that gene replacement can be achieved in barley with a frequency suitable for routine application. The use of a codon-optimized nuclease and co-transfer of the nuclease gene together with the donor construct are probably the components important for efficient gene targeting. Such an approach, employing the recently developed synthetic nucleases/nickases that allow DSB induction at almost any sequence of a genome of interest, sets the stage for precision genome engineering as a routine tool even for important crops such as barley.
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Affiliation(s)
- Koichi Watanabe
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466 Gatersleben, Stadt Seeland, Germany
| | - Ulrike Breier
- Max-Planck-Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, D-50829 Cologne, Germany
| | - Götz Hensel
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466 Gatersleben, Stadt Seeland, Germany
| | - Jochen Kumlehn
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466 Gatersleben, Stadt Seeland, Germany
| | - Ingo Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466 Gatersleben, Stadt Seeland, Germany Faculty of Science and Central European Institute of Technology, Masaryk University, 61137 Brno, Czech Republic
| | - Bernd Reiss
- Max-Planck-Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, D-50829 Cologne, Germany
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Byrne SM, Church GM. Crispr-mediated Gene Targeting of Human Induced Pluripotent Stem Cells. ACTA ACUST UNITED AC 2015; 35:5A.8.1-5A.8.22. [PMID: 26949444 DOI: 10.1002/9780470151808.sc05a08s35] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
CRISPR/Cas9 nuclease systems can create double-stranded DNA breaks at specific sequences to efficiently and precisely disrupt, excise, mutate, insert, or replace genes. However, human embryonic stem or induced pluripotent stem cells (iPSCs) are more difficult to transfect and less resilient to DNA damage than immortalized tumor cell lines. Here, we describe an optimized protocol for genome engineering of human iPSCs using a simple transient transfection of plasmids and/or single-stranded oligonucleotides. With this protocol, we achieve transfection efficiencies greater than 60%, with gene disruption efficiencies from 1-25% and gene insertion/replacement efficiencies from 0.5-10% without any further selection or enrichment steps. We also describe how to design and assess optimal sgRNA target sites and donor targeting vectors; cloning individual iPSC by single cell FACS sorting, and genotyping successfully edited cells.
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Affiliation(s)
- Susan M Byrne
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
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Abstract
The use of custom-engineered sequence-specific nucleases (including CRISPR/Cas9, ZFN, and TALEN) allows genetic changes in human cells to be easily made with much greater efficiency and precision than before. Engineered double-stranded DNA breaks can efficiently disrupt genes, or, with the right donor vector, engineer point mutations and gene insertions. However, a number of design considerations should be taken into account to ensure maximum gene targeting efficiency and specificity. This is especially true when engineering human embryonic stem or induced pluripotent stem cells (iPSCs), which are more difficult to transfect and less resilient to DNA damage than immortalized tumor cell lines. Here, we describe a protocol for easily engineering genetic changes in human iPSCs, through which we typically achieve targeting efficiencies between 1% and 10% without any subsequent selection steps. Since this protocol only uses the simple transient transfection of plasmids and/or single-stranded oligonucleotides, most labs will easily be able to perform it. We also describe strategies for identifying, cloning, and genotyping successfully edited cells, and how to design the optimal sgRNA target sites and donor vectors. Finally, we discuss alternative methods for gene editing including viral delivery vectors, Cas9 nickases, and orthogonal Cas9 systems.
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5
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Abstract
The use of custom-engineered sequence-specific nucleases (including CRISPR/Cas9, ZFN, and TALEN) allows genetic changes in human cells to be easily made with much greater efficiency and precision than before. Engineered double-stranded DNA breaks can efficiently disrupt genes, or, with the right donor vector, engineer point mutations and gene insertions. However, a number of design considerations should be taken into account to ensure maximum gene targeting efficiency and specificity. This is especially true when engineering human embryonic stem or induced pluripotent stem cells (iPSCs), which are more difficult to transfect and less resilient to DNA damage than immortalized tumor cell lines. Here, we describe a protocol for easily engineering genetic changes in human iPSCs, through which we typically achieve targeting efficiencies between 1% and 10% without any subsequent selection steps. Since this protocol only uses the simple transient transfection of plasmids and/or single-stranded oligonucleotides, most labs will easily be able to perform it. We also describe strategies for identifying, cloning, and genotyping successfully edited cells, and how to design the optimal sgRNA target sites and donor vectors. Finally, we discuss alternative methods for gene editing including viral delivery vectors, Cas9 nickases, and orthogonal Cas9 systems.
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Affiliation(s)
- Susan M Byrne
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Prashant Mali
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.
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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.
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Affiliation(s)
- R Geoffrey Sargent
- Department of Otolaryngology-Head and Neck Surgery, University of California , San Francisco, California 94115, USA
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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.
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Affiliation(s)
- Nanna M Jensen
- Institute of Human Genetics, The Bartholin Building, University of Aarhus, 8000 Aarhus C, Denmark
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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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Abstract
Several independent groups have reported targeted genomic editing in mammalian cells mediated by synthetic oligonucleotides. Nevertheless, the validity of data has been disputed because of experimental artefacts, inconsistent findings and low reproducibility. Here, we describe experiments designed to meet stringent criteria and completely eliminate artefactual results. In particular, by targeting cells expressing mutated enhanced green fluorescence protein (EGFP), which allow editing measurements at the protein level, and analyzing corrected clones by Southern blotting, we rigorously excluded spontaneous reversion, contamination artefacts, false-positives, or overestimation. Our findings provide unequivocal authentication that oligonucleotide-mediated gene editing is a real, not artefactual, phenomenon--a vital starting point from which to develop the technology into practical applications.
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Majumdar A, Muniandy PA, Liu J, Liu JL, Liu ST, Cuenoud B, Seidman MM. Targeted gene knock in and sequence modulation mediated by a psoralen-linked triplex-forming oligonucleotide. J Biol Chem 2008; 283:11244-52. [PMID: 18303025 DOI: 10.1074/jbc.m800607200] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Information from exogenous donor DNA can be introduced into the genome via homology-directed repair (HDR) pathways. These pathways are stimulated by double strand breaks and by DNA damage such as interstrand cross-links. We have employed triple helix-forming oligonucleotides linked to psoralen (pso-TFO) to introduce a DNA interstrand cross-link at a specific site in the genome of living mammalian cells. Co-introduction of duplex DNA with target region homology resulted in precise knock in of the donor at frequencies 2-3 orders of magnitude greater than with donor alone. Knock-in was eliminated in cells deficient in ERCC1-XPF, which is involved in recombinational pathways as well as cross-link repair. Separately, single strand oligonucleotide donors (SSO) were co-introduced with the pso-TFO. These were 10-fold more active than the duplex knock-in donor. SSO efficacy was further elevated in cells deficient in ERCC1-XPF, in contrast to the duplex donor. Resected single strand ends have been implicated as critical intermediates in sequence modulation by SSO, as well as duplex donor knock in. We asked whether there would be a competition between the donor species for these ends if both were present with the pso-TFO. The frequency of duplex donor knock in was unaffected by a 100-fold molar excess of the SSO. The same result was obtained when the homing endonuclease I-SceI was used to initiate HDR at the target site. We conclude that the entry of double strand breaks into distinct HDR pathways is controlled by factors other than the nucleic acid partners in those pathways.
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Affiliation(s)
- Alokes Majumdar
- Laboratory of Molecular Gerontology, NIA, National Institutes of Health, Baltimore, Maryland 21224, USA
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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.
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Affiliation(s)
- Federica Sangiuolo
- Department of Biopathology and Diagnostic Imaging, Tor Vergata University, Rome, Italy.
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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.
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Affiliation(s)
- Marian Todaro
- National Muscular Dystrophy Research Centre, Howard Florey Institute, Fitzroy, Victoria, Australia
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Srivastava N, Raman MJ. Homologous recombination-mediated double-strand break repair in mouse testicular extracts and comparison with different germ cell stages. Cell Biochem Funct 2007; 25:75-86. [PMID: 16989005 DOI: 10.1002/cbf.1375] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Homologous recombination (HR) is established as a significant contributor to double-strand break (DSB) repair in mammalian somatic cells; however, its role in mammalian germ cells has not been characterized, although being conservative in nature it is anticipated to be the major pathway in germ cells. The germ cell system has inherent limitations by which intact cell approaches are not feasible. The present study, therefore, investigates HR-mediated DSB repair in mouse germ cell extracts by using an in vitro plasmid recombination assay based on functional rescue of a neomycin (neo) gene. A significantly high-fold increase in neo+ (Kan(R)) colonies following incubation of two plasmid substrates (neo delta1 and neo delta2) with testicular extracts demonstrated the extracts' ability to catalyze intermolecular recombination. A significant enhancement in recombinants upon linearization of one of the plasmids suggested the existence of an HR-mediated DSB repair activity. Comparison of the activity at sequential developmental stages, spermatogonia, spermatocytes and spermatids revealed its presence at all the stages; spermatocyte being the most proficient stage. Further, restriction analysis of recombinant plasmids indicated the predominance of gene conversion in enriched spermatocytes (mostly pachytenes), in contrast to gonial and spermatid extracts that showed higher reciprocal exchange. In conclusion, this study demonstrates HR repair activity at all stages of male germ cells, suggesting an important role of HR-mediated DSB repair during mammalian spermatogenesis. Further, the observed preference of gene conversion over reciprocal exchange at spermatocyte stage correlates with the close association of gene conversion with the meiotic recombination program.
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Affiliation(s)
- Niloo Srivastava
- Cytogenetics Laboratory, Department of Zoology, Centre of Advanced Study, Banaras Hindu University, Varanasi, India
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Maurisse R, Fichou Y, De Semir D, Cheung J, Ferec C, Gruenert DC. Gel purification of genomic DNA removes contaminating small DNA fragments interfering with polymerase chain reaction analysis of small fragment homologous replacement. Oligonucleotides 2007; 16:375-86. [PMID: 17155912 DOI: 10.1089/oli.2006.16.375] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Oligonucleotides can mediate sequence-specific gene modification that results in the correction and/or alteration of genomic DNA. There is evidence to suggest that the polymerase chain reaction (PCR)-based analytical methods usually used to analyze oligonucleotide-mediated modification can generate artifacts. To investigate the conditions under which a PCR artifact can be generated and eliminated when analyzing small fragment homologous replacement (SHFR)-mediated modification, cells homozygous for the DeltaF508 mutation (CFBE41o-) were mixed with small DNA fragments (SDFs) containing the wild-type CFTR (wt-CFTR) sequence. An artifact could be generated after wild-type allele-specific PCR (wtAS-PCR) if the genomic DNA was not gel purified. Without gel purification, the amount of SDF/cell required to generate the artifact was dependent to the AS primer pairs used. When the genomic DNA was gel purified, no artifact could be detected with any of the wtAS-PCR primers whether the SDF was mixed with the cells or transfected into the cells. Furthermore, treatment of cellular mRNA with DNase was sufficient to eliminate potential artifacts in the reverse transcriptase-polymerase chain reaction (RT-PCR) analysis. Thus, it is critical to gel purify genomic DNA and DNase treat mRNA when analyzing SFHR-mediated modification by PCR.
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Affiliation(s)
- Rosalie Maurisse
- Research Institute, California Pacific Medical Center, San Francisco, CA 94107, USA
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15
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Goncz KK, Prokopishyn NL, Abdolmohammadi A, Bedayat B, Maurisse R, Davis BR, Gruenert DC. Small fragment homologous replacement-mediated modification of genomic beta-globin sequences in human hematopoietic stem/progenitor cells. Oligonucleotides 2006; 16:213-24. [PMID: 16978085 DOI: 10.1089/oli.2006.16.213] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
An ultimate goal of gene therapy is the development of a means to correct mutant genomic sequences in the cells that give rise to pathology. A number of oligonucleotide-based gene-targeting strategies have been developed to achieve this goal. One approach, small fragment homologous replacement (SFHR), has previously demonstrated disease-specific genotypic and phenotypic modification after introduction of small DNA fragments (SDFs) into somatic cells. To validate whether the gene responsible for sickle cell anemia (beta-globin) can be modified by SFHR, a series of studies were undertaken to introduce sickle globin sequences at the appropriate locus of human hematopoietic stem/progenitor cells (HSPCs). The characteristic A two head right arrow T transversion in codon 6 of the beta-globin gene was indicated by restriction fragment length polymorphic (RFLP) analysis of polymerase chain reaction (PCR) products generated by amplification of DNA and RNA. At the time of harvest, it was determined that the cells generally contained </=1 fragment per cell. Control studies mixing genomic DNA from nontransfected cells with varying amounts of the targeting SDFs did not indicate any PCR amplification artifacts due to the presence of residual SDF during amplification. RNA was analyzed after DNase treatment, thus eliminating the potential for SDF contamination. Stable SFHRmediated conversion of normal (beta (A)) to sickle (beta (S)) globin was detected at frequencies up to 13% in cells harvested 30-45 days posttransfection. The minimum conversion efficiency ranged from 0.2 to 3%, assuming modification of at least one cell per experiment showing conversion. Conversion of sickle (beta (S)) to normal (beta (A)) globin was detected up to 10 days posttransfection in lymphoblastoid cells from a sickle cell patient. These studies suggest that SFHR may be effective for ex vivo gene therapy of sickle cells in a patient's HSPCs before autologous transplantation.
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Affiliation(s)
- Kaarin K Goncz
- Department of Medicine, University of Vermont, Burlington, VT 05405, USA
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Gruenert DC, Kunzelmann K, Novelli G, Colosimo A, Kapsa R, Bruscia E. Oligonucleotide-based gene targeting approaches. Oligonucleotides 2005; 14:157-8; author reply 158-60. [PMID: 15294078 DOI: 10.1089/1545457041526272] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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17
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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.
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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;
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Sangiuolo F, Filareto A, Spitalieri P, Scaldaferri ML, Mango R, Bruscia E, Citro G, Brunetti E, De Felici M, Novelli G. In VitroRestoration of Functional SMN Protein in Human Trophoblast Cells Affected by Spinal Muscular Atrophy by Small Fragment Homologous Replacement. Hum Gene Ther 2005; 16:869-80. [PMID: 16000068 DOI: 10.1089/hum.2005.16.869] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The majority of patients affected by spinal muscular atrophy (SMA) have deletion of the survival of motor neuron 1 (SMN1) gene, but they retain a "nonfunctional" copy of the duplicate gene (SMN2) in their genome. SMN2 produces defective SMN protein because of a C --> T transition in exon 7, which causes the skipping of exon 7 during SMN mRNA maturation. Many attempts have been made to correct altered SMN gene expression and to increase the level of normal SMN protein, but to date an effective treatment for this disease has not been established. Small Fragment Homologous Replacement (SFHR) is a site-specific gene modification approach that has the potential to maintain the genomic organization necessary for expression. The target modification in the genome is mediated by small DNA fragments (SDFs) 400-800 bp in length. In this study we used SFHR to induce a T --> C transition at codon 280 in exon 7 of the SMN2 gene in order to produce an increase in functional SMN protein. SDFs were transfected in vitro into cells obtained from five human fetal chorionic villi of embryos, homozygous for the SMN1 deletion, by either electroporation or microinjection. Transfected SMA cells showed an increase of up to 53% in full-length SMN mRNA compared with untransfected controls, as detected by real-time polymerase chain reaction. Consistent with the RNA data, immunocytochemistry and immunoblotting revealed a significant 2-fold increase in wild-type SMN protein. Furthermore, genotype and phenotype of transfected cells remained stable after several in vitro passages, demonstrating the stability of the correction over time.
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Affiliation(s)
- Federica Sangiuolo
- Human Genetics Section, Department of Biopathology, Tor Vergata University, 00133 Rome, Italy.
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Sangiuolo F, Filareto A, Spitalieri P, Scaldaferri ML, Mango R, Bruscia E, Citro G, Brunetti E, De Felici M, Novelli G. In Vitro Restoration of Functional SMN Protein in Human Trophoblast Cells Affected by Spinal Muscular Atrophy by Small Fragment Homologous Replacement. Hum Gene Ther 2005. [DOI: 10.1089/hum.2005.16.ft-84] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Affiliation(s)
- Josep M. Aran
- Institut de Recerca Oncològica, Hospital Duran i Reynals, Gran Via, Km. 2.7, L'Hospitalet de Llobregat, 08907 Barcelona, Spain
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