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Mudde ACA, Kuo CY, Kohn DB, Booth C. What a Clinician Needs to Know About Genome Editing: Status and Opportunities for Inborn Errors of Immunity. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. IN PRACTICE 2024; 12:1139-1149. [PMID: 38246560 DOI: 10.1016/j.jaip.2024.01.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 12/08/2023] [Accepted: 01/05/2024] [Indexed: 01/23/2024]
Abstract
During the past 20 years, gene editing has emerged as a novel form of gene therapy. Since the publication of the first potentially therapeutic gene editing platform for genetic disorders, increasingly sophisticated editing technologies have been developed. As with viral vector-mediated gene addition, inborn errors of immunity are excellent candidate diseases for a corrective autologous hematopoietic stem cell gene editing strategy. Research on gene editing for inborn errors of immunity is still entirely preclinical, with no trials yet underway. However, with editing techniques maturing, scientists are investigating this novel form of gene therapy in context of an increasing number of inborn errors of immunity. Here, we present an overview of these studies and the recent progress moving these technologies closer to clinical benefit.
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Affiliation(s)
- Anne C A Mudde
- UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Caroline Y Kuo
- Department of Pediatrics, UCLA David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, Calif
| | - Donald B Kohn
- Department of Pediatrics, UCLA David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, Calif; Department of Microbiology, Immunology & Molecular Genetics, UCLA David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, Calif
| | - Claire Booth
- UCL Great Ormond Street Institute of Child Health, London, United Kingdom; Department of Paediatric Immunology and Gene Therapy, Great Ormond Street Hospital NHS Foundation Trust, London, United Kingdom.
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Challenges in Gene Therapy for Somatic Reverted Mosaicism in X-Linked Combined Immunodeficiency by CRISPR/Cas9 and Prime Editing. Genes (Basel) 2022; 13:genes13122348. [PMID: 36553615 PMCID: PMC9777626 DOI: 10.3390/genes13122348] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/02/2022] [Accepted: 12/10/2022] [Indexed: 12/15/2022] Open
Abstract
X-linked severe combined immunodeficiency (X-SCID) is a primary immunodeficiency that is caused by mutations in the interleukin-2 receptor gamma (IL2RG) gene. Some patients present atypical X-SCID with mild clinical symptoms due to somatic revertant mosaicism. CRISPR/Cas9 and prime editing are two advanced genome editing tools that paved the way for treating immune deficiency diseases. Prime editing overcomes the limitations of the CRISPR/Cas9 system, as it does not need to induce double-strand breaks (DSBs) or exogenous donor DNA templates to modify the genome. Here, we applied CRISPR/Cas9 with single-stranded oligodeoxynucleotides (ssODNs) and prime editing methods to generate an in vitro model of the disease in K-562 cells and healthy donors' T cells for the c. 458T>C point mutation in the IL2RG gene, which also resulted in a useful way to optimize the gene correction approach for subsequent experiments in patients' cells. Both methods proved to be successful and were able to induce the mutation of up to 31% of treated K-562 cells and 26% of treated T cells. We also applied similar strategies to correct the IL2RG c. 458T>C mutation in patient T cells that carry the mutation with revertant somatic mosaicism. However, both methods failed to increase the frequency of the wild-type sequence in the mosaic T cells of patients due to limited in vitro proliferation of mutant cells and the presence of somatic reversion. To the best of our knowledge, this is the first attempt to treat mosaic cells from atypical X-SCID patients employing CRISPR/Cas9 and prime editing. We showed that prime editing can be applied to the formation of specific-point IL2RG mutations without inducing nonspecific on-target modifications. We hypothesize that the feasibility of the nucleotide substitution of the IL2RG gene using gene therapy, especially prime editing, could provide an alternative strategy to treat X-SCID patients without revertant mutations, and further technological improvements need to be developed to correct somatic mosaicism mutations.
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Li R, Wang Q, She K, Lu F, Yang Y. CRISPR/Cas systems usher in a new era of disease treatment and diagnosis. MOLECULAR BIOMEDICINE 2022; 3:31. [PMID: 36239875 PMCID: PMC9560888 DOI: 10.1186/s43556-022-00095-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 09/27/2022] [Indexed: 11/21/2022] Open
Abstract
The discovery and development of the CRISPR/Cas system is a milestone in precise medicine. CRISPR/Cas nucleases, base-editing (BE) and prime-editing (PE) are three genome editing technologies derived from CRISPR/Cas. In recent years, CRISPR-based genome editing technologies have created immense therapeutic potential with safe and efficient viral or non-viral delivery systems. Significant progress has been made in applying genome editing strategies to modify T cells and hematopoietic stem cells (HSCs) ex vivo and to treat a wide variety of diseases and disorders in vivo. Nevertheless, the clinical translation of this unique technology still faces many challenges, especially targeting, safety and delivery issues, which require further improvement and optimization. In addition, with the outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), CRISPR-based molecular diagnosis has attracted extensive attention. Growing from the specific set of molecular biological discoveries to several active clinical trials, CRISPR/Cas systems offer the opportunity to create a cost-effective, portable and point-of-care diagnosis through nucleic acid screening of diseases. In this review, we describe the development, mechanisms and delivery systems of CRISPR-based genome editing and focus on clinical and preclinical studies of therapeutic CRISPR genome editing in disease treatment as well as its application prospects in therapeutics and molecular detection.
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Affiliation(s)
- Ruiting Li
- grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Ke-yuan Road 4, No. 1, Gao-peng Street, Chengdu, 610041 Sichuan China
| | - Qin Wang
- grid.412723.10000 0004 0604 889XSchool of Pharmacy, Southwest Minzu University, Chengdu, 610225 Sichuan China
| | - Kaiqin She
- grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Ke-yuan Road 4, No. 1, Gao-peng Street, Chengdu, 610041 Sichuan China ,grid.412901.f0000 0004 1770 1022Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Fang Lu
- grid.412901.f0000 0004 1770 1022Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Yang Yang
- grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Ke-yuan Road 4, No. 1, Gao-peng Street, Chengdu, 610041 Sichuan China ,grid.412901.f0000 0004 1770 1022Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, Sichuan China
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Bijlani S, Pang KM, Sivanandam V, Singh A, Chatterjee S. The Role of Recombinant AAV in Precise Genome Editing. Front Genome Ed 2022; 3:799722. [PMID: 35098210 PMCID: PMC8793687 DOI: 10.3389/fgeed.2021.799722] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 12/14/2021] [Indexed: 12/14/2022] Open
Abstract
The replication-defective, non-pathogenic, nearly ubiquitous single-stranded adeno-associated viruses (AAVs) have gained importance since their discovery about 50 years ago. Their unique life cycle and virus-cell interactions have led to the development of recombinant AAVs as ideal genetic medicine tools that have evolved into effective commercialized gene therapies. A distinctive property of AAVs is their ability to edit the genome precisely. In contrast to all current genome editing platforms, AAV exclusively utilizes the high-fidelity homologous recombination (HR) pathway and does not require exogenous nucleases for prior cleavage of genomic DNA. Together, this leads to a highly precise editing outcome that preserves genomic integrity without incorporation of indel mutations or viral sequences at the target site while also obviating the possibility of off-target genotoxicity. The stem cell-derived AAV (AAVHSCs) were found to mediate precise and efficient HR with high on-target accuracy and at high efficiencies. AAVHSC editing occurs efficiently in post-mitotic cells and tissues in vivo. Additionally, AAV also has the advantage of an intrinsic delivery mechanism. Thus, this distinctive genome editing platform holds tremendous promise for the correction of disease-associated mutations without adding to the mutational burden. This review will focus on the unique properties of direct AAV-mediated genome editing and their potential mechanisms of action.
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Byambaa S, Uosaki H, Ohmori T, Hara H, Endo H, Nureki O, Hanazono Y. Non-viral ex vivo genome-editing in mouse bona fide hematopoietic stem cells with CRISPR/Cas9. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2021; 20:451-462. [PMID: 33614821 PMCID: PMC7873578 DOI: 10.1016/j.omtm.2021.01.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 01/06/2021] [Indexed: 12/26/2022]
Abstract
We conducted two lines of genome-editing experiments of mouse hematopoietic stem cells (HSCs) with the clustered regularly interspaced short palindromic repeat (CRISPR) and CRISPR-associated protein 9 (Cas9). First, to evaluate the genome-editing efficiency in mouse bona fide HSCs, we knocked out integrin alpha 2b (Itga2b) with Cas9 ribonucleoprotein (Cas9/RNP) and performed serial transplantation in mice. The knockout efficiency was estimated at approximately 15%. Second, giving an example of X-linked severe combined immunodeficiency (X-SCID) as a target genetic disease, we showed a proof-of-concept of universal gene correction, allowing rescue of most of X-SCID mutations, in a completely non-viral setting. We inserted partial cDNA of interleukin-2 receptor gamma chain (Il2rg) into intron 1 of Il2rg via non-homologous end-joining (NHEJ) with Cas9/RNP and a homology-independent targeted integration (HITI)-based construct. Repaired HSCs reconstituted T lymphocytes and thymuses in SCID mice. Our results show that a non-viral genome-editing of HSCs with CRISPR/Cas9 will help cure genetic diseases.
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Affiliation(s)
- Suvd Byambaa
- Division of Regenerative Medicine, Center for Molecular Medicine, Jichi Medical University, Tochigi 329-0498, Japan
| | - Hideki Uosaki
- Division of Regenerative Medicine, Center for Molecular Medicine, Jichi Medical University, Tochigi 329-0498, Japan
| | - Tsukasa Ohmori
- Division of Medical Biochemistry, Department of Biochemistry, School of Medicine, Jichi Medical University, Tochigi 329-0498, Japan
| | - Hiromasa Hara
- Division of Regenerative Medicine, Center for Molecular Medicine, Jichi Medical University, Tochigi 329-0498, Japan
| | - Hitoshi Endo
- Division of Functional Biochemistry, Department of Biochemistry, School of Medicine, Jichi Medical University, Tochigi 329-0498, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Yutaka Hanazono
- Division of Regenerative Medicine, Center for Molecular Medicine, Jichi Medical University, Tochigi 329-0498, Japan
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Blanco E, Izotova N, Booth C, Thrasher AJ. Immune Reconstitution After Gene Therapy Approaches in Patients With X-Linked Severe Combined Immunodeficiency Disease. Front Immunol 2020; 11:608653. [PMID: 33329605 PMCID: PMC7729079 DOI: 10.3389/fimmu.2020.608653] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 11/02/2020] [Indexed: 12/21/2022] Open
Abstract
X-linked severe immunodeficiency disease (SCID-X1) is an inherited, rare, and life-threating disease. The genetic origin is a defect in the interleukin 2 receptor γ chain (IL2RG) gene and patients are classically characterized by absence of T and NK cells, as well as presence of partially-functional B cells. Without any treatment the disease is usually lethal during the first year of life. The treatment of choice for these patients is hematopoietic stem cell transplantation, with an excellent survival rate (>90%) if an HLA-matched sibling donor is available. However, when alternative donors are used, the success and survival rates are often lower. Gene therapy has been developed as an alternative treatment initially using γ-retroviral vectors to correct the defective γ chain in the absence of pre-conditioning treatment. The results were highly promising in SCID-X1 infants, showing long-term T-cell recovery and clinical benefit, although NK and B cell recovery was less robust. However, some infants developed T-cell acute lymphoblastic leukemia after the gene therapy, due to vector-mediated insertional mutagenesis. Consequently, considerable efforts have been made to develop safer vectors. The most recent clinical trials using lentiviral vectors together with a low-dose pre-conditioning regimen have demonstrated excellent sustained T cell recovery, but also B and NK cells, in both children and adults. This review provides an overview about the different gene therapy approaches used over the last 20 years to treat SCID-X1 patients, particularly focusing on lymphoid immune reconstitution, as well as the developments that have improved the process and outcomes.
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Affiliation(s)
- Elena Blanco
- Molecular and Cellular Immunology, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Natalia Izotova
- Molecular and Cellular Immunology, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Claire Booth
- Molecular and Cellular Immunology, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
- Department of Paediatric Immunology, Great Ormond Street Hospital NHS Trust, London, United Kingdom
| | - Adrian James Thrasher
- Molecular and Cellular Immunology, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
- Department of Paediatric Immunology, Great Ormond Street Hospital NHS Trust, London, United Kingdom
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Identification of potential mRNA panels for severe acute respiratory syndrome coronavirus 2 (COVID-19) diagnosis and treatment using microarray dataset and bioinformatics methods. 3 Biotech 2020; 10:422. [PMID: 33251083 PMCID: PMC7679428 DOI: 10.1007/s13205-020-02406-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 08/20/2020] [Indexed: 12/15/2022] Open
Abstract
The goal of the present investigation is to identify the differentially expressed genes (DEGs) between SARS-CoV-2 infected and normal control samples to investigate the molecular mechanisms of infection with SARS-CoV-2. The microarray data of the dataset E-MTAB-8871 were retrieved from the ArrayExpress database. Pathway and Gene Ontology (GO) enrichment study, protein–protein interaction (PPI) network, modules, target gene–miRNA regulatory network, and target gene–TF regulatory network have been performed. Subsequently, the key genes were validated using an analysis of the receiver operating characteristic (ROC) curve. In SARS-CoV-2 infection, a total of 324 DEGs (76 up- and 248 down-regulated genes) were identified and enriched in a number of associated SARS-CoV-2 infection pathways and GO terms. Hub and target genes such as TP53, HRAS, MAPK11, RELA, IKZF3, IFNAR2, SKI, TNFRSF13C, JAK1, TRAF6, KLRF2, CD1A were identified from PPI network, target gene–miRNA regulatory network, and target gene–TF regulatory network. Study of the ROC showed that ten genes (CCL5, IFNAR2, JAK2, MX1, STAT1, BID, CD55, CD80, HAL-B, and HLA-DMA) were substantially involved in SARS-CoV-2 patients. The present investigation identified key genes and pathways that deepen our understanding of the molecular mechanisms of SARS-CoV-2 infection, and could be used for SARS-CoV-2 infection as diagnostic and therapeutic biomarkers.
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Chen S, Sun S, Moonen D, Lee C, Lee AYF, Schaffer DV, He L. CRISPR-READI: Efficient Generation of Knockin Mice by CRISPR RNP Electroporation and AAV Donor Infection. Cell Rep 2020; 27:3780-3789.e4. [PMID: 31242412 DOI: 10.1016/j.celrep.2019.05.103] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 04/01/2019] [Accepted: 05/29/2019] [Indexed: 01/08/2023] Open
Abstract
Genetically engineered mouse models harboring large sequence insertions or modifications are critical for a wide range of applications including endogenous gene tagging, conditional knockout, site-specific transgene insertion, and gene replacement; however, existing methods to generate such animals remain laborious and costly. To address this, we developed an approach called CRISPR-READI (CRISPR RNP electroporation and AAV donor infection), combining adeno-associated virus (AAV)-mediated HDR donor delivery with Cas9/sgRNA RNP electroporation to engineer large site-specific modifications in the mouse genome with high efficiency and throughput. We successfully targeted a 774 bp fluorescent reporter, a 2.1 kb CreERT2 driver, and a 3.3 kb expression cassette into endogenous loci in both embryos and live mice. CRISPR-READI is applicable to most widely used knockin schemes requiring donor lengths within the 4.9 kb AAV packaging capacity. Altogether, CRISPR-READI is an efficient, high-throughput, microinjection-free approach for sophisticated mouse genome engineering with potential applications in other mammalian species.
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Affiliation(s)
- Sean Chen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Sabrina Sun
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
| | - Dewi Moonen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Clancy Lee
- Department of Environmental Science and Policy Management, University of California, Berkeley, Berkeley, CA, USA
| | - Angus Yiu-Fai Lee
- Cancer Research Laboratory, University of California, Berkeley, Berkeley, CA, USA
| | - David V Schaffer
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA; Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA; Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA; The Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, USA.
| | - Lin He
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
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Kouchaki R, Abd-Nikfarjam B, Maali AH, Abroun S, Foroughi F, Ghaffari S, Azad M. Induced Pluripotent Stem Cell Meets Severe Combined Immunodeficiency. CELL JOURNAL 2020; 22:1-10. [PMID: 32779449 PMCID: PMC7481889 DOI: 10.22074/cellj.2020.6849] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Accepted: 08/27/2019] [Indexed: 12/14/2022]
Abstract
Severe combined immunodeficiency (SCID) is classified as a primary immunodeficiency, which is characterized by impaired
T-lymphocytes differentiation. IL2RG, IL7Ralpha, JAK3, ADA, RAG1/RAG2, and DCLE1C (Artemis) are the most defective
genes in SCID. The most recent SCID therapies are based on gene therapy (GT) of hematopoietic stem cells (HSC), which
are faced with many challenges. The new studies in the field of stem cells have made great progress in overcoming the
challenges ahead. In 2006, Yamanaka et al. achieved "reprogramming" technology by introducing four transcription factors
known as Yamanaka factors, which generate induced pluripotent stem cells (iPSC) from somatic cells. It is possible to apply
iPSC-derived HSC for transplantation in patients with abnormality or loss of function in specific cells or damaged tissue, such
as T-cells and NK-cells in the context of SCID. The iPSC-based HSC transplantation in SCID and other hereditary disorders
needs gene correction before transplantation. Furthermore, iPSC technology has been introduced as a promising tool in
cellular-molecular disease modeling and drug discovery. In this article, we review iPSC-based GT and modeling for SCID
disease and novel approaches of iPSC application in SCID.
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Affiliation(s)
- Reza Kouchaki
- Faculty of Allied Medicine, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Bahareh Abd-Nikfarjam
- Department of Immunology, School of Medicine, Qazvin University of Medical Sciences, Qazvin, Iran
| | | | - Saeid Abroun
- Department of Hematology and Blood Banking, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Farshad Foroughi
- Department of Immunology, School of Medicine, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Sasan Ghaffari
- Hematology Department, School of Allied Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mehdi Azad
- Faculty of Allied Medicine, Qazvin University of Medical Sciences, Qazvin, Iran. Electronic Address:
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van Haasteren J, Li J, Scheideler OJ, Murthy N, Schaffer DV. The delivery challenge: fulfilling the promise of therapeutic genome editing. Nat Biotechnol 2020; 38:845-855. [PMID: 32601435 DOI: 10.1038/s41587-020-0565-5] [Citation(s) in RCA: 126] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 05/19/2020] [Indexed: 12/15/2022]
Abstract
Genome editing has the potential to treat an extensive range of incurable monogenic and complex diseases. In particular, advances in sequence-specific nuclease technologies have dramatically accelerated the development of therapeutic genome editing strategies that are based on either the knockout of disease-causing genes or the repair of endogenous mutated genes. These technologies are progressing into human clinical trials. However, challenges remain before the therapeutic potential of genome editing can be fully realized. Delivery technologies that have serendipitously been developed over the past couple decades in the protein and nucleic acid delivery fields have been crucial to genome editing success to date, including adeno-associated viral and lentiviral vectors for gene therapy and lipid nanoparticle and other non-viral vectors for nucleic acid and protein delivery. However, the efficiency and tissue targeting capabilities of these vehicles must be further improved. In addition, the genome editing enzymes themselves need to be optimized, and challenges regarding their editing efficiency, specificity and immunogenicity must be addressed. Emerging protein engineering and synthetic chemistry approaches can offer solutions and enable the development of safe and efficacious clinical genome editing.
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Affiliation(s)
- Joost van Haasteren
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
| | - Jie Li
- Department of Bioengineering, University of California, Berkeley, CA, USA.,Innovative Genomics Institute (IGI), University of California, Berkeley, CA, USA
| | | | - Niren Murthy
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA. .,Department of Bioengineering, University of California, Berkeley, CA, USA. .,Innovative Genomics Institute (IGI), University of California, Berkeley, CA, USA.
| | - David V Schaffer
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA. .,Department of Bioengineering, University of California, Berkeley, CA, USA. .,Innovative Genomics Institute (IGI), University of California, Berkeley, CA, USA. .,Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA. .,Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA. .,Helen Wills Neuroscience Institute, University of California, Berkeley, CA, USA.
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Nemirovich-Danchenko NM, Khodanovich MY. Telomerase Gene Editing in the Neural Stem Cells in vivo as a Possible New Approach against Brain Aging. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795420040092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Dudek AM, Porteus MH. AAV6 Is Superior to Clade F AAVs in Stimulating Homologous Recombination-Based Genome Editing in Human HSPCs. Mol Ther 2019; 27:1701-1705. [PMID: 31537456 DOI: 10.1016/j.ymthe.2019.09.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Amanda M Dudek
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Matthew H Porteus
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA.
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Rogers GL, Chen HY, Morales H, Cannon PM. Homologous Recombination-Based Genome Editing by Clade F AAVs Is Inefficient in the Absence of a Targeted DNA Break. Mol Ther 2019; 27:1726-1736. [PMID: 31540849 DOI: 10.1016/j.ymthe.2019.08.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 08/30/2019] [Accepted: 08/31/2019] [Indexed: 12/26/2022] Open
Abstract
Adeno-associated virus (AAV) vectors are frequently used as donor templates for genome editing by homologous recombination. Although modification rates are typically under 1%, they are greatly enhanced by targeted double-stranded DNA breaks (DSBs). A recent report described clade F AAVs mediating high-efficiency homologous recombination-based editing in the absence of DSBs. The clade F vectors included AAV9 and a series isolated from human hematopoietic stem and progenitor cells (HSPCs). We evaluated these vectors by packaging homology donors into AAV9 and an AAVHSC capsid and examining their ability to insert GFP at the CCR5 and AAVS1 loci in human HSPCs and cell lines. As a control, we used AAV6, which effectively edits HSPCs but only when combined with a targeted DSB. Each AAV vector promoted GFP insertion in the presence of matched CCR5 or AAVS1 zinc-finger nucleases (ZFNs), but none supported detectable editing in the absence of the nucleases. Rates of editing with ZFNs correlated with transduction efficiencies for each vector, implying no differences in the ability of donor sequences delivered by the different vectors to direct genome editing. Our results, therefore, do not support that clade F AAVs can perform high-efficiency genome editing in the absence of a DSB.
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Affiliation(s)
- Geoffrey L Rogers
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Hsu-Yu Chen
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Heidy Morales
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Paula M Cannon
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.
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