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1.
Nucleic Acids Res ; 52(5): 2740-2757, 2024 Mar 21.
Artículo en Inglés | MEDLINE | ID: mdl-38321963

RESUMEN

Prime editors have high potential for disease modelling and regenerative medicine efforts including those directed at the muscle-wasting disorder Duchenne muscular dystrophy (DMD). However, the large size and multicomponent nature of prime editing systems pose substantial production and delivery issues. Here, we report that packaging optimized full-length prime editing constructs in adenovector particles (AdVPs) permits installing precise DMD edits in human myogenic cells, namely, myoblasts and mesenchymal stem cells (up to 80% and 64%, respectively). AdVP transductions identified optimized prime-editing reagents capable of correcting DMD reading frames of ∼14% of patient genotypes and restoring dystrophin synthesis and dystrophin-ß-dystroglycan linkages in unselected DMD muscle cell populations. AdVPs were equally suitable for correcting DMD iPSC-derived cardiomyocytes and delivering dual prime editors tailored for DMD repair through targeted exon 51 deletion. Moreover, by exploiting the cell cycle-independent AdVP transduction process, we report that 2- and 3-component prime-editing modalities are both most active in cycling than in post-mitotic cells. Finally, we establish that combining AdVP transduction with seamless prime editing allows for stacking chromosomal edits through successive delivery rounds. In conclusion, AdVPs permit versatile investigation of advanced prime editing systems independently of their size and component numbers, which should facilitate their screening and application.


Asunto(s)
Distrofina , Terapia Genética , Distrofia Muscular de Duchenne , Humanos , Sistemas CRISPR-Cas/genética , Distrofina/genética , Distrofina/metabolismo , Edición Génica , Distrofia Muscular de Duchenne/genética , Distrofia Muscular de Duchenne/terapia , Mioblastos/metabolismo , Miocitos Cardíacos/metabolismo
2.
Mol Ther ; 2024 Aug 22.
Artículo en Inglés | MEDLINE | ID: mdl-39169620

RESUMEN

The repurposing of RNA-programmable CRISPR systems from genome editing into epigenome editing tools is gaining pace, including in research and development efforts directed at tackling human disorders. This momentum stems from the increasing knowledge regarding the epigenetic factors and networks underlying cell physiology and disease etiology and from the growing realization that genome editing principles involving chromosomal breaks generated by programmable nucleases are prone to unpredictable genetic changes and outcomes. Hence, engineered CRISPR systems are serving as versatile DNA-targeting scaffolds for heterologous and synthetic effector domains that, via locally recruiting transcription factors and chromatin remodeling complexes, seek interfering with loss-of-function and gain-of-function processes underlying recessive and dominant disorders, respectively. Here, after providing an overview about epigenetic drugs and CRISPR-Cas-based activation and interference platforms, we cover the testing of these platforms in the context of molecular therapies for muscular dystrophies. Finally, we examine attributes, obstacles, and deployment opportunities for CRISPR-based epigenetic modulating technologies.

3.
Nucleic Acids Res ; 51(7): 3465-3484, 2023 04 24.
Artículo en Inglés | MEDLINE | ID: mdl-36928106

RESUMEN

Homology-directed recombination (HDR) between donor constructs and acceptor genomic sequences cleaved by programmable nucleases, permits installing large genomic edits in mammalian cells in a precise fashion. Yet, next to precise gene knock-ins, programmable nucleases yield unintended genomic modifications resulting from non-homologous end-joining processes. Alternatively, in trans paired nicking (ITPN) involving tandem single-strand DNA breaks at target loci and exogenous donor constructs by CRISPR-Cas9 nickases, fosters seamless and scarless genome editing. In the present study, we identified high-specificity CRISPR-Cas9 nucleases capable of outperforming parental CRISPR-Cas9 nucleases in directing genome editing through homologous recombination (HR) and homology-mediated end joining (HMEJ) with donor constructs having regular and 'double-cut' designs, respectively. Additionally, we explored the ITPN principle by demonstrating its compatibility with orthogonal and high-specificity CRISPR-Cas9 nickases and, importantly, report that in human induced pluripotent stem cells (iPSCs), in contrast to high-specificity CRISPR-Cas9 nucleases, neither regular nor high-specificity CRISPR-Cas9 nickases activate P53 signaling, a DNA damage-sensing response linked to the emergence of gene-edited cells with tumor-associated mutations. Finally, experiments in human iPSCs revealed that differently from HR and HMEJ genome editing based on high-specificity CRISPR-Cas9 nucleases, ITPN involving high-specificity CRISPR-Cas9 nickases permits editing allelic sequences associated with essentiality and recurrence in the genome.


Asunto(s)
Sistemas CRISPR-Cas , Edición Génica , Animales , Humanos , Sistemas CRISPR-Cas/genética , Roturas del ADN de Doble Cadena , Edición Génica/métodos , Genómica , Células Madre Pluripotentes Inducidas , Mamíferos
4.
Nucleic Acids Res ; 50(13): 7761-7782, 2022 07 22.
Artículo en Inglés | MEDLINE | ID: mdl-35776127

RESUMEN

Targeted chromosomal insertion of large genetic payloads in human cells leverages and broadens synthetic biology and genetic therapy efforts. Yet, obtaining large-scale gene knock-ins remains particularly challenging especially in hard-to-transfect stem and progenitor cells. Here, fully viral gene-deleted adenovector particles (AdVPs) are investigated as sources of optimized high-specificity CRISPR-Cas9 nucleases and donor DNA constructs tailored for targeted insertion of full-length dystrophin expression units (up to 14.8-kb) through homologous recombination (HR) or homology-mediated end joining (HMEJ). In muscle progenitor cells, donors prone to HMEJ yielded higher CRISPR-Cas9-dependent genome editing frequencies than HR donors, with values ranging between 6% and 34%. In contrast, AdVP transduction of HR and HMEJ substrates in induced pluripotent stem cells (iPSCs) resulted in similar CRISPR-Cas9-dependent genome editing levels. Notably, when compared to regular iPSCs, in p53 knockdown iPSCs, CRISPR-Cas9-dependent genome editing frequencies increased up to 6.7-fold specifically when transducing HMEJ donor constructs. Finally, single DNA molecule analysis by molecular combing confirmed that AdVP-based genome editing achieves long-term complementation of DMD-causing mutations through the site-specific insertion of full-length dystrophin expression units. In conclusion, AdVPs are a robust and flexible platform for installing large genomic edits in human cells and p53 inhibition fosters HMEJ-based genome editing in iPSCs.


Asunto(s)
Distrofina , Edición Génica , Distrofia Muscular de Duchenne/genética , Distrofia Muscular de Duchenne/terapia , Sistemas CRISPR-Cas/genética , Distrofina/genética , Distrofina/metabolismo , Endonucleasas/genética , Endonucleasas/metabolismo , Edición Génica/métodos , Humanos , Células Musculares/metabolismo , Distrofia Muscular de Duchenne/patología , Proteína p53 Supresora de Tumor/metabolismo
5.
Curr Cardiol Rep ; 2024 Sep 11.
Artículo en Inglés | MEDLINE | ID: mdl-39259489

RESUMEN

PURPOSE OF REVIEW: This review aims to evaluate the potential of CRISPR-based gene editing tools, particularly prime editors (PE), in treating genetic cardiac diseases. It seeks to answer how these tools can overcome current therapeutic limitations and explore the synergy between PE and induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) for personalized medicine. RECENT FINDINGS: Recent advancements in CRISPR technology, including CRISPR-Cas9, base editors, and PE, have demonstrated precise genome correction capabilities. Notably, PE has shown exceptional precision in correcting genetic mutations. Combining PE with iPSC-CMs has emerged as a robust platform for disease modeling and developing innovative treatments for genetic cardiac diseases. The review finds that PE, when combined with iPSC-CMs, holds significant promise for treating genetic cardiac diseases by addressing their root causes. This approach could revolutionize personalized medicine, offering more effective and precise treatments. Future research should focus on refining these technologies and their clinical applications.

6.
Nucleic Acids Res ; 49(20): 11986-12001, 2021 11 18.
Artículo en Inglés | MEDLINE | ID: mdl-34669958

RESUMEN

Prime editing is a recent precision genome editing modality whose versatility offers the prospect for a wide range of applications, including the development of targeted genetic therapies. Yet, an outstanding bottleneck for its optimization and use concerns the difficulty in delivering large prime editing complexes into cells. Here, we demonstrate that packaging prime editing constructs in adenoviral capsids overcomes this constrain resulting in robust genome editing in both transformed and non-transformed human cells with up to 90% efficiencies. Using this cell cycle-independent delivery platform, we found a direct correlation between prime editing activity and cellular replication and disclose that the proportions between accurate prime editing events and unwanted byproducts can be influenced by the target-cell context. Hence, adenovector particles permit the efficacious delivery and testing of prime editing reagents in human cells independently of their transformation and replication statuses. The herein integrated gene delivery and gene editing technologies are expected to aid investigating the potential and limitations of prime editing in numerous experimental settings and, eventually, in ex vivo or in vivo therapeutic contexts.


Asunto(s)
Adenoviridae/genética , Edición Génica/métodos , Técnicas de Transferencia de Gen , Vectores Genéticos/genética , Eliminación de Gen , Células HEK293 , Células HeLa , Humanos
7.
Nucleic Acids Res ; 49(2): 1173-1198, 2021 01 25.
Artículo en Inglés | MEDLINE | ID: mdl-33398349

RESUMEN

RNA-guided nucleases (RGNs) based on CRISPR systems permit installing short and large edits within eukaryotic genomes. However, precise genome editing is often hindered due to nuclease off-target activities and the multiple-copy character of the vast majority of chromosomal sequences. Dual nicking RGNs and high-specificity RGNs both exhibit low off-target activities. Here, we report that high-specificity Cas9 nucleases are convertible into nicking Cas9D10A variants whose precision is superior to that of the commonly used Cas9D10A nickase. Dual nicking RGNs based on a selected group of these Cas9D10A variants can yield gene knockouts and gene knock-ins at frequencies similar to or higher than those achieved by their conventional counterparts. Moreover, high-specificity dual nicking RGNs are capable of distinguishing highly similar sequences by 'tiptoeing' over pre-existing single base-pair polymorphisms. Finally, high-specificity RNA-guided nicking complexes generally preserve genomic integrity, as demonstrated by unbiased genome-wide high-throughput sequencing assays. Thus, in addition to substantially enlarging the Cas9 nickase toolkit, we demonstrate the feasibility in expanding the range and precision of DNA knockout and knock-in procedures. The herein introduced tools and multi-tier high-specificity genome editing strategies might be particularly beneficial whenever predictability and/or safety of genetic manipulations are paramount.


Asunto(s)
Proteínas Bacterianas/metabolismo , Proteína 9 Asociada a CRISPR/metabolismo , Sistemas CRISPR-Cas , Desoxirribonucleasa I/metabolismo , Edición Génica/métodos , Proteínas Bacterianas/genética , Secuencia de Bases , Proteína 9 Asociada a CRISPR/genética , Células Clonales , Desoxirribonucleasa I/genética , Técnicas de Sustitución del Gen , Técnicas de Inactivación de Genes , Genes Reporteros , Técnicas de Genotipaje , Células HEK293 , Células HeLa , Heterocromatina/genética , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Células Madre Pluripotentes Inducidas , Polimorfismo Genético , ARN Guía de Kinetoplastida/genética , Proteínas Recombinantes/metabolismo , Streptococcus pyogenes/enzimología , Especificidad por Sustrato , Transfección
8.
Nucleic Acids Res ; 48(2): 974-995, 2020 01 24.
Artículo en Inglés | MEDLINE | ID: mdl-31799604

RESUMEN

Genome editing typically involves recombination between donor nucleic acids and acceptor genomic sequences subjected to double-stranded DNA breaks (DSBs) made by programmable nucleases (e.g. CRISPR-Cas9). Yet, nucleases yield off-target mutations and, most pervasively, unpredictable target allele disruptions. Remarkably, to date, the untoward phenotypic consequences of disrupting allelic and non-allelic (e.g. pseudogene) sequences have received scant scrutiny and, crucially, remain to be addressed. Here, we demonstrate that gene-edited cells can lose fitness as a result of DSBs at allelic and non-allelic target sites and report that simultaneous single-stranded DNA break formation at donor and acceptor DNA by CRISPR-Cas9 nickases (in trans paired nicking) mostly overcomes such disruptive genotype-phenotype associations. Moreover, in trans paired nicking gene editing can efficiently and precisely add large DNA segments into essential and multiple-copy genomic sites. As shown herein by genotyping assays and high-throughput genome-wide sequencing of DNA translocations, this is achieved while circumventing most allelic and non-allelic mutations and chromosomal rearrangements characteristic of nuclease-dependent procedures. Our work demonstrates that in trans paired nicking retains target protein dosages in gene-edited cell populations and expands gene editing to chromosomal tracts previously not possible to modify seamlessly due to their recurrence in the genome or essentiality for cell function.


Asunto(s)
Sistemas CRISPR-Cas/genética , ADN/genética , Desoxirribonucleasa I/química , Edición Génica/métodos , Secuencia de Bases , ADN/química , Roturas del ADN de Doble Cadena , Roturas del ADN de Cadena Simple , Desoxirribonucleasa I/genética , Endonucleasas/química , Marcación de Gen/métodos , Genoma/genética , Humanos , Mutación/genética , ARN Guía de Kinetoplastida/química , ARN Guía de Kinetoplastida/genética
9.
J Inherit Metab Dis ; 44(1): 54-71, 2021 01.
Artículo en Inglés | MEDLINE | ID: mdl-32510617

RESUMEN

Genetic therapies based on gene addition have witnessed a variety of clinical successes and the first therapeutic products have been approved for clinical use. Moreover, innovative gene editing techniques are starting to offer new opportunities in which the mutations that underlie genetic diseases can be directly corrected in afflicted somatic cells. The toolboxes underpinning these DNA modifying technologies are expanding with great pace. Concerning the ongoing efforts for their implementation, viral vector-based gene delivery systems have acquired center-stage, providing new hopes for patients with inherited and acquired disorders. Specifically, the application of genetic therapies using viral vectors for the treatment of inborn metabolic disorders is growing and clinical applications are starting to appear. While the field has matured from the technology perspective and has yielded efficacious products, it is the perception of many stakeholders that from the regulatory side further developments are urgently needed. In this review, we summarize the features of state-of-the-art viral vector systems and the corresponding gene-centered therapies they seek to deliver. Moreover, a brief summary is also given on emerging gene editing approaches built on CRISPR-Cas9 nucleases and, more recently, nickases, including base editors and prime editors. Finally, we will point at some regulatory aspects that may deserve further attention for translating these technological developments into actual advanced therapy medicinal products (ATMPs).


Asunto(s)
Edición Génica/tendencias , Terapia Genética/tendencias , Animales , Sistemas CRISPR-Cas , Edición Génica/métodos , Técnicas de Transferencia de Gen , Enfermedades Genéticas Congénitas/terapia , Terapia Genética/métodos , Vectores Genéticos , Humanos , Virus/genética
10.
Gene Ther ; 27(5): 209-225, 2020 05.
Artículo en Inglés | MEDLINE | ID: mdl-31900423

RESUMEN

Enhancing the intracellular delivery and performance of RNA-guided CRISPR-Cas9 nucleases (RGNs) remains in demand. Here, we show that nuclear translocation of commonly used Streptococcus pyogenes Cas9 (SpCas9) proteins is suboptimal. Hence, we generated eCas9.4NLS by endowing the high-specificity eSpCas9(1.1) nuclease (eCas9.2NLS) with additional nuclear localization signals (NLSs). We demonstrate that eCas9.4NLS coupled to prototypic or optimized guide RNAs achieves efficient targeted DNA cleavage and probe the performance of SpCas9 proteins with different NLS compositions at target sequences embedded in heterochromatin versus euchromatin. Moreover, after adenoviral vector (AdV)-mediated transfer of SpCas9 expression units, unbiased quantitative immunofluorescence microscopy revealed 2.3-fold higher eCas9.4NLS nuclear enrichment levels than those observed for high-specificity eCas9.2NLS. This improved nuclear translocation yielded in turn robust gene editing after nonhomologous end joining repair of targeted double-stranded DNA breaks. In particular, AdV delivery of eCas9.4NLS into muscle progenitor cells resulted in significantly higher editing frequencies at defective DMD alleles causing Duchenne muscular dystrophy (DMD) than those achieved by AdVs encoding the parental, eCas9.2NLS, protein. In conclusion, this work provides a strong rationale for integrating viral vector and optimized gene-editing technologies to bring about enhanced RGN delivery and performance.


Asunto(s)
Sistemas CRISPR-Cas , Edición Génica , Terapia Genética , Vectores Genéticos/genética , ARN Guía de Kinetoplastida/genética
11.
J Med Genet ; 56(12): 828-837, 2019 12.
Artículo en Inglés | MEDLINE | ID: mdl-31676591

RESUMEN

BACKGROUND: Facioscapulohumeral dystrophy (FSHD) is associated with partial chromatin relaxation of the DUX4 retrogene containing D4Z4 macrosatellite repeats on chromosome 4, and transcriptional de-repression of DUX4 in skeletal muscle. The common form of FSHD, FSHD1, is caused by a D4Z4 repeat array contraction. The less common form, FSHD2, is generally caused by heterozygous variants in SMCHD1. METHODS: We employed whole exome sequencing combined with Sanger sequencing to screen uncharacterised FSHD2 patients for extra-exonic SMCHD1 mutations. We also used CRISPR-Cas9 genome editing to repair a pathogenic intronic SMCHD1 variant from patient myoblasts. RESULTS: We identified intronic SMCHD1 variants in two FSHD families. In the first family, an intronic variant resulted in partial intron retention and inclusion of the distal 14 nucleotides of intron 13 into the transcript. In the second family, a deep intronic variant in intron 34 resulted in exonisation of 53 nucleotides of intron 34. In both families, the aberrant transcripts are predicted to be non-functional. Deleting the pseudo-exon by CRISPR-Cas9 mediated genome editing in primary and immortalised myoblasts from the index case of the second family restored wild-type SMCHD1 expression to a level that resulted in efficient suppression of DUX4. CONCLUSIONS: The estimated intronic mutation frequency of almost 2% in FSHD2, as exemplified by the two novel intronic SMCHD1 variants identified here, emphasises the importance of screening for intronic variants in SMCHD1. Furthermore, the efficient suppression of DUX4 after restoring SMCHD1 levels by genome editing of the mutant allele provides further guidance for therapeutic strategies.


Asunto(s)
Proteínas Cromosómicas no Histona/genética , Proteínas de Homeodominio/genética , Distrofia Muscular Facioescapulohumeral/genética , Adulto , Anciano , Alelos , Sistemas CRISPR-Cas/genética , Cromatina/genética , Ensamble y Desensamble de Cromatina/genética , Cromosomas Humanos Par 4/genética , Metilación de ADN/genética , Femenino , Edición Génica/métodos , Expresión Génica/genética , Predisposición Genética a la Enfermedad , Humanos , Masculino , Persona de Mediana Edad , Músculo Esquelético/metabolismo , Músculo Esquelético/patología , Distrofia Muscular Facioescapulohumeral/fisiopatología , Distrofia Muscular Facioescapulohumeral/terapia , Mutación/genética
12.
Nucleic Acids Res ; 44(3): 1449-70, 2016 Feb 18.
Artículo en Inglés | MEDLINE | ID: mdl-26762977

RESUMEN

Duchenne muscular dystrophy (DMD) is a fatal X-linked muscle-wasting disorder caused by mutations in the 2.4 Mb dystrophin-encoding DMD gene. The integration of gene delivery and gene editing technologies based on viral vectors and sequence-specific designer nucleases, respectively, constitutes a potential therapeutic modality for permanently repairing defective DMD alleles in patient-derived myogenic cells. Therefore, we sought to investigate the feasibility of combining adenoviral vectors (AdVs) with CRISPR/Cas9 RNA-guided nucleases (RGNs) alone or together with transcriptional activator-like effector nucleases (TALENs), for endogenous DMD repair through non-homologous end-joining (NHEJ). The strategies tested involved; incorporating small insertions or deletions at out-of-frame sequences for reading frame resetting, splice acceptor knockout for DNA-level exon skipping, and RGN-RGN or RGN-TALEN multiplexing for targeted exon(s) removal. We demonstrate that genome editing based on the activation and recruitment of the NHEJ DNA repair pathway after AdV delivery of designer nuclease genes, is a versatile and robust approach for repairing DMD mutations in bulk populations of patient-derived muscle progenitor cells (up to 37% of corrected DMD templates). These results open up a DNA-level genetic medicine strategy in which viral vector-mediated transient designer nuclease expression leads to permanent and regulated dystrophin synthesis from corrected native DMD alleles.


Asunto(s)
Distrofina/metabolismo , Endonucleasas/metabolismo , Mioblastos/metabolismo , ARN Guía de Kinetoplastida/metabolismo , Adenoviridae/genética , Alelos , Secuencia de Bases , Western Blotting , Sistemas CRISPR-Cas , Línea Celular , Reparación del ADN por Unión de Extremidades , Distrofina/genética , Endonucleasas/genética , Terapia Genética/métodos , Vectores Genéticos/genética , Células HEK293 , Células HeLa , Humanos , Microscopía Fluorescente , Datos de Secuencia Molecular , Distrofia Muscular de Duchenne/genética , Distrofia Muscular de Duchenne/metabolismo , Distrofia Muscular de Duchenne/terapia , Mutación , ARN Guía de Kinetoplastida/genética , Transducción Genética
13.
Nucleic Acids Res ; 44(13): 6482-92, 2016 07 27.
Artículo en Inglés | MEDLINE | ID: mdl-27280977

RESUMEN

Transcription activator-like effector nucleases (TALENs) and RNA-guided nucleases derived from clustered, regularly interspaced, short palindromic repeats (CRISPR)-Cas9 systems have become ubiquitous genome editing tools. Despite this, the impact that distinct high-order chromatin conformations have on these sequence-specific designer nucleases is, presently, ill-defined. The same applies to the relative performance of TALENs and CRISPR/Cas9 nucleases at isogenic target sequences subjected to different epigenetic modifications. Here, to address these gaps in our knowledge, we have implemented quantitative cellular systems based on genetic reporters in which the euchromatic and heterochromatic statuses of designer nuclease target sites are stringently controlled by small-molecule drug availability. By using these systems, we demonstrate that TALENs and CRISPR/Cas9 nucleases are both significantly affected by the high-order epigenetic context of their target sequences. In addition, this outcome could also be ascertained for S. pyogenes CRISPR/Cas9 complexes harbouring Cas9 variants whose DNA cleaving specificities are superior to that of the wild-type Cas9 protein. Thus, the herein investigated cellular models will serve as valuable functional readouts for screening and assessing the role of chromatin on designer nucleases based on different platforms or with different architectures or compositions.


Asunto(s)
Sistemas CRISPR-Cas/genética , Cromatina/genética , Edición Génica , Nucleasas de los Efectores Tipo Activadores de la Transcripción/genética , Epigénesis Genética/genética , Ingeniería Genética , Genotipo , Humanos , Conformación Molecular , Streptococcus pyogenes/genética
14.
Nat Methods ; 11(10): 1051-7, 2014 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-25152084

RESUMEN

Engineered sequence-specific nucleases and donor DNA templates can be customized to edit mammalian genomes via the homologous recombination (HR) pathway. Here we report that the nature of the donor DNA greatly affects the specificity and accuracy of the editing process following site-specific genomic cleavage by transcription activator-like effector nucleases (TALENs) and clustered, regularly interspaced, short palindromic repeats (CRISPR)-Cas9 nucleases. By applying these designer nucleases together with donor DNA delivered as protein-capped adenoviral vector (AdV), free-ended integrase-defective lentiviral vector or nonviral vector templates, we found that the vast majority of AdV-modified human cells underwent scarless homology-directed genome editing. In contrast, a significant proportion of cells exposed to free-ended or to covalently closed HR substrates were subjected to random and illegitimate recombination events. These findings are particularly relevant for genome engineering approaches aiming at high-fidelity genetic modification of human cells.


Asunto(s)
Adenoviridae/genética , ADN Viral/genética , ADN/química , Desoxirribonucleasas/química , Ingeniería Genética/métodos , Línea Celular , Separación Celular , Marcación de Gen/métodos , Genoma , Células HEK293 , Células HeLa , Humanos , Reacción en Cadena de la Polimerasa , Recombinación Genética , Secuencias Repetitivas de Ácidos Nucleicos , Reproducibilidad de los Resultados
15.
Mol Ther ; 24(3): 447-57, 2016 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-26336974

RESUMEN

Genome editing based on sequence-specific designer nucleases, also known as programmable nucleases, seeks to modify in a targeted and precise manner the genetic information content of living cells. Delivering into cells designer nucleases alone or together with donor DNA templates, which serve as surrogate homologous recombination (HR) substrates, can result in gene knockouts or gene knock-ins, respectively. As engineered replication-defective viruses, viral vectors are having an increasingly important role as delivery vehicles for donor DNA templates and designer nucleases, namely, zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and clustered, regularly interspaced, short palindromic repeats (CRISPR)-associated Cas9 (CRISPR-Cas9) nucleases, also known as RNA-guided nucleases (RGNs). We review this dual role played by engineered viral particles on genome editing while focusing on their main scaffolds, consisting of lentiviruses, adeno-associated viruses, and adenoviruses. In addition, the coverage of the growing body of research on the repurposing of viral vectors as delivery systems for genome editing tools is complemented with information regarding their main characteristics, pros, and cons. Finally, this information is framed by a concise description of the chief principles, tools, and applications of the genome editing field as a whole.


Asunto(s)
Edición Génica , Ingeniería Genética , Vectores Genéticos/genética , Genoma , Virus/genética , Animales , Endonucleasas/genética , Endonucleasas/metabolismo , Edición Génica/métodos , Marcación de Gen , Ingeniería Genética/métodos , Humanos
16.
Methods ; 69(2): 179-87, 2014 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-24561826

RESUMEN

Transcription activator-like effector nucleases (TALENs) are designed to cut the genomic DNA at specific chromosomal positions. The resulting DNA double strand break activates cellular repair pathways that can be harnessed for targeted genome modifications. TALENs thus constitute a powerful tool to interrogate the function of DNA sequences within complex genomes. Moreover, their high DNA cleavage activity combined with a low cytotoxicity make them excellent candidates for applications in human gene therapy. Full exploitation of these large and repeat-bearing nucleases in human cell types will benefit largely from using the adenoviral vector (AdV) technology. The genetic stability and the episomal nature of AdV genomes in conjunction with the availability of a large number of AdV serotypes able to transduce various human cell types make it possible to achieve high-level and transient expression of TALENs in numerous target cells, regardless of their mitotic state. Here, we describe a set of protocols detailing the rescue, propagation and purification of TALEN-encoding AdVs. Moreover, we describe procedures for the characterization and quantification of recombinant viral DNA present in the resulting AdV preparations. The protocols are preceded by information about their underlying principles and applied in the context of second-generation capsid-modified AdVs expressing TALENs targeted to the AAVS1 "safe harbor" locus on human chromosome 19.


Asunto(s)
Adenoviridae/genética , ADN Viral/genética , Técnicas de Transferencia de Gen , Vectores Genéticos/genética , ADN Viral/administración & dosificación , Endonucleasas/genética , Vectores Genéticos/administración & dosificación , Células HEK293 , Células HeLa , Humanos
17.
Nucleic Acids Res ; 41(5): e63, 2013 Mar 01.
Artículo en Inglés | MEDLINE | ID: mdl-23275534

RESUMEN

The array of genome editing strategies based on targeted double-stranded DNA break formation have recently been enriched through the introduction of transcription activator-like type III effector (TALE) nucleases (TALENs). To advance the testing of TALE-based approaches, it will be crucial to deliver these custom-designed proteins not only into transformed cell types but also into more relevant, chromosomally stable, primary cells. Viral vectors are among the most effective gene transfer vehicles. Here, we investigated the capacity of human immunodeficiency virus type 1- and adenovirus-based vectors to package and deliver functional TALEN genes into various human cell types. To this end, we attempted to assemble particles of these two vector classes, each encoding a monomer of a TALEN pair targeted to a bipartite sequence within the AAVS1 'safe harbor' locus. Vector DNA analyses revealed that adenoviral vectors transferred intact TALEN genes, whereas lentiviral vectors failed to do so, as shown by their heterogeneously sized proviruses in target cells. Importantly, adenoviral vector-mediated TALEN gene delivery resulted in site-specific double-stranded DNA break formation at the intended AAVS1 target site at similarly high levels in both transformed and non-transformed cells. In conclusion, we demonstrate that adenoviral, but not lentiviral, vectors constitute a valuable TALEN gene delivery platform.


Asunto(s)
Adenoviridae/genética , Proteínas Bacterianas/genética , Desoxirribonucleasas/genética , VIH-1/genética , Cromosomas Humanos , Roturas del ADN de Doble Cadena , Sitios Genéticos , Vectores Genéticos , Células HEK293 , Células HeLa , Humanos , Transducción Genética
18.
Nucleic Acids Res ; 40(5): 1984-99, 2012 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-22080552

RESUMEN

DNA repeats constitute potential sites for the nucleation of secondary structures such as hairpins and cruciforms. Studies performed mostly in bacteria and yeast showed that these noncanonical DNA structures are breakage-prone, making them candidate targets for cellular DNA repair pathways. Possible culprits for fragility at repetitive DNA sequences include replication and transcription as well as the action of structure-specific nucleases. Despite their patent biological relevance, the parameters governing DNA repeat-associated chromosomal transactions remain ill-defined. Here, we established an episomal recombination system based on donor and acceptor complementary DNA templates to investigate the role of direct and inverted DNA repeats in homologous recombination (HR) in mammalian cells. This system allowed us also to ascertain in a stringent manner the impact of repetitive sequence replication on homology-directed gene repair. We found that nonspaced DNA repeats can, per se, engage the HR pathway of the cell and that this process is primarily dependent on their spacing and relative arrangement (i.e. parallel or antiparallel) rather than on their sequence. Indeed, our data demonstrate that contrary to direct and spaced inverted repeats, nonspaced inverted repeats are intrinsically recombinogenic motifs in mammalian cells lending experimental support to their role in genome dynamics in higher eukaryotes.


Asunto(s)
ADN/química , Secuencias Invertidas Repetidas , Reparación del ADN por Recombinación , Animales , Secuencia de Bases , Células COS , Línea Celular , Chlorocebus aethiops , ADN Cruciforme/química , Desoxirribonucleasas/metabolismo , Células HeLa , Humanos , Datos de Secuencia Molecular , Plásmidos/genética
19.
Nucleic Acids Res ; 40(8): 3443-55, 2012 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-22189101

RESUMEN

The exchange of genetic information between donor and acceptor DNA molecules by homologous recombination (HR) depends on the cleavage of phosphodiester bonds. Although double-stranded and single-stranded DNA breaks (SSBs) have both been invoked as triggers of HR, until very recently the focus has been primarily on the former type of DNA lesions mainly due to the paucity of SSB-based recombination models. Here, to investigate the role of nicked DNA molecules as HR-initiating substrates in human somatic cells, we devised a homology-directed gene targeting system based on exogenous donor and chromosomal target DNA containing recognition sequences for the adeno-associated virus sequence- and strand-specific endonucleases Rep78 and Rep68. We found that HR is greatly fostered if a SSB is not only introduced in the chromosomal acceptor but also in the donor DNA template. Our data are consistent with HR models postulating the occurrence of SSBs or single-stranded gaps in both donor and acceptor molecules during the genetic exchange process. These findings can guide the development of improved HR-based genome editing strategies in which sequence- and strand-specific endonucleolytic cleavage of the chromosomal target site is combined with that of the targeting vector.


Asunto(s)
Roturas del ADN de Cadena Simple , Marcación de Gen , Recombinación Homóloga , Línea Celular , ADN/metabolismo , Endodesoxirribonucleasas/metabolismo , Sitios Genéticos , Humanos
20.
J Gene Med ; 15(1): 1-11, 2013 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-23225636

RESUMEN

BACKGROUND: The AdEasy system has acquired preeminence amongst the various methods for producing first-generation, early region 1 (E1)-deleted human adenovirus (HAdV) vectors (AdVs) as a result of the fast and reproducible recovery of full-length AdV genomes via homologous recombination in Escherichia coli. METHODS: From the classical AdEasy system, a new production platform was derived to assemble first- and second-generation [i.e. E1- plus early region 2A (E2A)-deleted] AdVs displaying on their surface HAdV serotype 5 (HAdV5) fibers (F5) or chimeric fibers (F5/50) comprising the tail of F5 and the fiber shaft and knob of HAdV serotype 50 (HAdV50). The CD46-interacting chimeric fibers allow for the high-level transduction of various human primary cell types of clinical interest with low or no surface expression of the Coxsackievirus and adenovirus receptor. RESULTS: A new set of pAdEasy plasmid 'backbones' with or without E2A and encoding F5 or F5/50 was constructed and recombined in E. coli strain BJ5183 with a 'shuttle' plasmid coding for ß-galactosidase. The resulting clones yielded AdV preparations with similar high titers following their rescue and propagation in producer cells. The AdVs with F5/50 were superior to those carrying F5 with respect to transducing human skeletal myocytes and mesenchymal stem cells. CONCLUSIONS: In the present study, an AdEasy system tailored for the production of not only first-, but also second-generation AdVs equipped with the receptor-interacting fiber domains of the prototypic species C HAdV5 or of the species B member HAdV50 is presented. This system expands the range of applications for this robust and versatile AdV production platform.


Asunto(s)
Adenovirus Humanos/genética , Enterovirus/genética , Vectores Genéticos/genética , Proteína Cofactora de Membrana/genética , Tropismo Viral , Western Blotting , Línea Celular , Clonación Molecular , Escherichia coli/genética , Perfilación de la Expresión Génica , Células HeLa , Humanos , Células Madre Mesenquimatosas/metabolismo , Proteínas Recombinantes/genética , Reproducibilidad de los Resultados , Análisis de Secuencia de ADN , Transducción Genética , beta-Galactosidasa/genética
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