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Siow KM, Güngör M, Wrona D, Raimondi F, Pastukhov O, Tsapogas P, Menzi T, Schmitz M, Kulcsár PI, Schwank G, Schulz A, Jinek M, Modlich U, Siler U, Reichenbach J. Targeted knock-in of NCF1 cDNA into the NCF2 locus leads to myeloid phenotypic correction of p47 phox -deficient chronic granulomatous disease. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102229. [PMID: 38952440 PMCID: PMC11215332 DOI: 10.1016/j.omtn.2024.102229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 05/22/2024] [Indexed: 07/03/2024]
Abstract
p47 phox -deficient chronic granulomatous disease (p47-CGD) is a primary immunodeficiency caused by mutations in the neutrophil cytosolic factor 1 (NCF1) gene, resulting in defective NADPH oxidase function in phagocytes. Due to its complex genomic context, the NCF1 locus is not suited for safe gene editing with current genome editing technologies. Therefore, we developed a targeted NCF1 coding sequence knock-in by CRISPR-Cas9 ribonucleoprotein and viral vector template delivery, to restore p47 phox expression under the control of the endogenous NCF2 locus. NCF2 encodes for p67 phox , an NADPH oxidase subunit that closely interacts with p47 phox and is predominantly expressed in myeloid cells. This approach restored p47 phox expression and NADPH oxidase function in p47-CGD patient hematopoietic stem and progenitor cells (HSPCs) and in p47 phox -deficient mouse HSPCs, with the transgene expression following a myeloid differentiation pattern. Adeno-associated viral vectors performed favorably over integration-deficient lentiviral vectors for template delivery, with fewer off-target integrations and higher correction efficacy in HSPCs. Such myeloid-directed gene editing is promising for clinical CGD gene therapy, as it leads to the co-expression of p47 phox and p67 phox , ensuring spatiotemporal and near-physiological transgene expression in myeloid cells.
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Affiliation(s)
- Kah Mun Siow
- Division of Gene and Cell Therapy, Institute for Regenerative Medicine, University of Zurich, Schlieren, 8952 Zurich, Switzerland
| | - Merve Güngör
- Division of Gene and Cell Therapy, Institute for Regenerative Medicine, University of Zurich, Schlieren, 8952 Zurich, Switzerland
| | - Dominik Wrona
- Division of Gene and Cell Therapy, Institute for Regenerative Medicine, University of Zurich, Schlieren, 8952 Zurich, Switzerland
| | - Federica Raimondi
- Division of Gene and Cell Therapy, Institute for Regenerative Medicine, University of Zurich, Schlieren, 8952 Zurich, Switzerland
| | - Oleksandr Pastukhov
- Division of Gene and Cell Therapy, Institute for Regenerative Medicine, University of Zurich, Schlieren, 8952 Zurich, Switzerland
| | - Panagiotis Tsapogas
- Division of Gene and Cell Therapy, Institute for Regenerative Medicine, University of Zurich, Schlieren, 8952 Zurich, Switzerland
| | - Timon Menzi
- Division of Gene and Cell Therapy, Institute for Regenerative Medicine, University of Zurich, Schlieren, 8952 Zurich, Switzerland
| | - Michael Schmitz
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Péter István Kulcsár
- Institute of Pharmacology and Toxicology, University of Zurich, 8057 Zurich, Switzerland
| | - Gerald Schwank
- Institute of Pharmacology and Toxicology, University of Zurich, 8057 Zurich, Switzerland
| | - Ansgar Schulz
- Department of Pediatrics, University Medical Center Ulm, 89075 Ulm, Germany
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Ute Modlich
- Division of Gene and Cell Therapy, Institute for Regenerative Medicine, University of Zurich, Schlieren, 8952 Zurich, Switzerland
| | - Ulrich Siler
- Division of Gene and Cell Therapy, Institute for Regenerative Medicine, University of Zurich, Schlieren, 8952 Zurich, Switzerland
- School of Life Sciences, Institute for Pharma Technology, University of Applied Sciences and Arts Northwestern Switzerland, 4132 Muttenz, Switzerland
| | - Janine Reichenbach
- Division of Gene and Cell Therapy, Institute for Regenerative Medicine, University of Zurich, Schlieren, 8952 Zurich, Switzerland
- Department of Somatic Gene Therapy, University Children’s Hospital Zurich, 8032 Zurich, Switzerland
- Center for Applied Biotechnology and Molecular Medicine (CABMM), University of Zurich, 8057 Zurich, Switzerland
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2
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Neumayer G, Torkelson JL, Li S, McCarthy K, Zhen HH, Vangipuram M, Mader MM, Gebeyehu G, Jaouni TM, Jacków-Malinowska J, Rami A, Hansen C, Guo Z, Gaddam S, Tate KM, Pappalardo A, Li L, Chow GM, Roy KR, Nguyen TM, Tanabe K, McGrath PS, Cramer A, Bruckner A, Bilousova G, Roop D, Tang JY, Christiano A, Steinmetz LM, Wernig M, Oro AE. A scalable and cGMP-compatible autologous organotypic cell therapy for Dystrophic Epidermolysis Bullosa. Nat Commun 2024; 15:5834. [PMID: 38992003 DOI: 10.1038/s41467-024-49400-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 05/25/2024] [Indexed: 07/13/2024] Open
Abstract
We present Dystrophic Epidermolysis Bullosa Cell Therapy (DEBCT), a scalable platform producing autologous organotypic iPS cell-derived induced skin composite (iSC) grafts for definitive treatment. Clinical-grade manufacturing integrates CRISPR-mediated genetic correction with reprogramming into one step, accelerating derivation of COL7A1-edited iPS cells from patients. Differentiation into epidermal, dermal and melanocyte progenitors is followed by CD49f-enrichment, minimizing maturation heterogeneity. Mouse xenografting of iSCs from four patients with different mutations demonstrates disease modifying activity at 1 month. Next-generation sequencing, biodistribution and tumorigenicity assays establish a favorable safety profile at 1-9 months. Single cell transcriptomics reveals that iSCs are composed of the major skin cell lineages and include prominent holoclone stem cell-like signatures of keratinocytes, and the recently described Gibbin-dependent signature of fibroblasts. The latter correlates with enhanced graftability of iSCs. In conclusion, DEBCT overcomes manufacturing and safety roadblocks and establishes a reproducible, safe, and cGMP-compatible therapeutic approach to heal lesions of DEB patients.
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Affiliation(s)
- Gernot Neumayer
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University, School of Medicine, Stanford, CA, USA
| | - Jessica L Torkelson
- Department of Dermatology-Program in Epithelial Biology, Stanford University, School of Medicine, Stanford, CA, USA
- Center for Definitive and Curative Medicine, Stanford University, School of Medicine, Stanford, CA, USA
| | - Shengdi Li
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Kelly McCarthy
- Department of Dermatology-Program in Epithelial Biology, Stanford University, School of Medicine, Stanford, CA, USA
- Center for Definitive and Curative Medicine, Stanford University, School of Medicine, Stanford, CA, USA
| | - Hanson H Zhen
- Department of Dermatology-Program in Epithelial Biology, Stanford University, School of Medicine, Stanford, CA, USA
- Center for Definitive and Curative Medicine, Stanford University, School of Medicine, Stanford, CA, USA
| | - Madhuri Vangipuram
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University, School of Medicine, Stanford, CA, USA
| | - Marius M Mader
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University, School of Medicine, Stanford, CA, USA
| | - Gulilat Gebeyehu
- Thermo Fisher Scientific, Life Sciences Solutions Group, Cell Biology, Research and Development, Frederick, MD, USA
| | - Taysir M Jaouni
- Thermo Fisher Scientific, Life Sciences Solutions Group, Cell Biology, Research and Development, Frederick, MD, USA
| | - Joanna Jacków-Malinowska
- Department of Dermatology, Columbia University, New York, NY, USA
- St. John's Institute of Dermatology, King's College London, London, UK
| | - Avina Rami
- Department of Dermatology, Columbia University, New York, NY, USA
| | - Corey Hansen
- Department of Dermatology, Columbia University, New York, NY, USA
| | - Zongyou Guo
- Department of Dermatology, Columbia University, New York, NY, USA
| | - Sadhana Gaddam
- Department of Dermatology-Program in Epithelial Biology, Stanford University, School of Medicine, Stanford, CA, USA
| | - Keri M Tate
- Center for Definitive and Curative Medicine, Stanford University, School of Medicine, Stanford, CA, USA
| | | | - Lingjie Li
- Department of Dermatology-Program in Epithelial Biology, Stanford University, School of Medicine, Stanford, CA, USA
| | - Grace M Chow
- Department of Dermatology-Program in Epithelial Biology, Stanford University, School of Medicine, Stanford, CA, USA
| | - Kevin R Roy
- Department of Genetics, Stanford University, School of Medicine, Stanford, CA, USA
- Stanford Genome Technology Center, Stanford University, School of Medicine, Stanford, CA, USA
| | - Thuylinh Michelle Nguyen
- Department of Genetics, Stanford University, School of Medicine, Stanford, CA, USA
- Stanford Genome Technology Center, Stanford University, School of Medicine, Stanford, CA, USA
| | | | - Patrick S McGrath
- Department of Dermatology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, CO, USA
| | - Amber Cramer
- Department of Dermatology-Program in Epithelial Biology, Stanford University, School of Medicine, Stanford, CA, USA
- Center for Definitive and Curative Medicine, Stanford University, School of Medicine, Stanford, CA, USA
| | - Anna Bruckner
- Department of Dermatology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, CO, USA
| | - Ganna Bilousova
- Department of Dermatology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, CO, USA
| | - Dennis Roop
- Department of Dermatology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, CO, USA
| | - Jean Y Tang
- Department of Dermatology-Program in Epithelial Biology, Stanford University, School of Medicine, Stanford, CA, USA
- Center for Definitive and Curative Medicine, Stanford University, School of Medicine, Stanford, CA, USA
| | | | - Lars M Steinmetz
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
- Department of Genetics, Stanford University, School of Medicine, Stanford, CA, USA
- Stanford Genome Technology Center, Stanford University, School of Medicine, Stanford, CA, USA
| | - Marius Wernig
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, School of Medicine, Stanford, CA, USA.
- Department of Pathology, Stanford University, School of Medicine, Stanford, CA, USA.
- Department of Chemical and Systems Biology, Stanford University, School of Medicine, Stanford, CA, USA.
| | - Anthony E Oro
- Department of Dermatology-Program in Epithelial Biology, Stanford University, School of Medicine, Stanford, CA, USA
- Center for Definitive and Curative Medicine, Stanford University, School of Medicine, Stanford, CA, USA
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Rossi M, Breman E. Engineering strategies to safely drive CAR T-cells into the future. Front Immunol 2024; 15:1411393. [PMID: 38962002 PMCID: PMC11219585 DOI: 10.3389/fimmu.2024.1411393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 05/27/2024] [Indexed: 07/05/2024] Open
Abstract
Chimeric antigen receptor (CAR) T-cell therapy has proven a breakthrough in cancer treatment in the last decade, giving unprecedented results against hematological malignancies. All approved CAR T-cell products, as well as many being assessed in clinical trials, are generated using viral vectors to deploy the exogenous genetic material into T-cells. Viral vectors have a long-standing clinical history in gene delivery, and thus underwent iterations of optimization to improve their efficiency and safety. Nonetheless, their capacity to integrate semi-randomly into the host genome makes them potentially oncogenic via insertional mutagenesis and dysregulation of key cellular genes. Secondary cancers following CAR T-cell administration appear to be a rare adverse event. However several cases documented in the last few years put the spotlight on this issue, which might have been underestimated so far, given the relatively recent deployment of CAR T-cell therapies. Furthermore, the initial successes obtained in hematological malignancies have not yet been replicated in solid tumors. It is now clear that further enhancements are needed to allow CAR T-cells to increase long-term persistence, overcome exhaustion and cope with the immunosuppressive tumor microenvironment. To this aim, a variety of genomic engineering strategies are under evaluation, most relying on CRISPR/Cas9 or other gene editing technologies. These approaches are liable to introduce unintended, irreversible genomic alterations in the product cells. In the first part of this review, we will discuss the viral and non-viral approaches used for the generation of CAR T-cells, whereas in the second part we will focus on gene editing and non-gene editing T-cell engineering, with particular regard to advantages, limitations, and safety. Finally, we will critically analyze the different gene deployment and genomic engineering combinations, delineating strategies with a superior safety profile for the production of next-generation CAR T-cell.
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Zhu H, Wang L, Wang Y, Jiang X, Qin Q, Song M, Huang Q. Directed-evolution mutations enhance DNA-binding affinity and protein stability of the adenine base editor ABE8e. Cell Mol Life Sci 2024; 81:257. [PMID: 38874784 DOI: 10.1007/s00018-024-05263-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/28/2024] [Accepted: 05/02/2024] [Indexed: 06/15/2024]
Abstract
Adenine base editors (ABEs), consisting of CRISPR Cas nickase and deaminase, can chemically convert the A:T base pair to G:C. ABE8e, an evolved variant of the base editor ABE7.10, contains eight directed evolution mutations in its deaminase TadA8e that significantly increase its base editing activity. However, the functional implications of these mutations remain unclear. Here, we combined molecular dynamics (MD) simulations and experimental measurements to investigate the role of the directed-evolution mutations in the base editing catalysis. MD simulations showed that the DNA-binding affinity of TadA8e is higher than that of the original deaminase TadA7.10 in ABE7.10 and is mainly driven by electrostatic interactions. The directed-evolution mutations increase the positive charge density in the DNA-binding region, thereby enhancing the electrostatic attraction of TadA8e to DNA. We identified R111, N119 and N167 as the key mutations for the enhanced DNA binding and confirmed them by microscale thermophoresis (MST) and in vivo reversion mutation experiments. Unexpectedly, we also found that the directed mutations improved the thermal stability of TadA8e by ~ 12 °C (Tm, melting temperature) and that of ABE8e by ~ 9 °C, respectively. Our results demonstrate that the directed-evolution mutations improve the substrate-binding ability and protein stability of ABE8e, thus providing a rational basis for further editing optimisation of the system.
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Affiliation(s)
- Haixia Zhu
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Lei Wang
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Ying Wang
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Xinyi Jiang
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Qin Qin
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Menghua Song
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Qiang Huang
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China.
- Multiscale Research Institute of Complex Systems, Fudan University, Shanghai, 201203, China.
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5
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Jin M, Lin J, Li H, Li Z, Yang D, Wang Y, Yu Y, Shao Z, Chen L, Wang Z, Zhang Y, Zhang X, Wang N, Xu C, Yang H, Chen WJ, Li G. Correction of human nonsense mutation via adenine base editing for Duchenne muscular dystrophy treatment in mouse. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102165. [PMID: 38571746 PMCID: PMC10988125 DOI: 10.1016/j.omtn.2024.102165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 03/04/2024] [Indexed: 04/05/2024]
Abstract
Duchenne muscular dystrophy (DMD) is the most prevalent herediatry disease in men, characterized by dystrophin deficiency, progressive muscle wasting, cardiac insufficiency, and premature mortality, with no effective therapeutic options. Here, we investigated whether adenine base editing can correct pathological nonsense point mutations leading to premature stop codons in the dystrophin gene. We identified 27 causative nonsense mutations in our DMD patient cohort. Treatment with adenine base editor (ABE) could restore dystrophin expression by direct A-to-G editing of pathological nonsense mutations in cardiomyocytes generated from DMD patient-derived induced pluripotent stem cells. We also generated two humanized mouse models of DMD expressing mutation-bearing exons 23 or 30 of human dystrophin gene. Intramuscular administration of ABE, driven by ubiquitous or muscle-specific promoters could correct these nonsense mutations in vivo, albeit with higher efficiency in exon 30, restoring dystrophin expression in skeletal fibers of humanized DMD mice. Moreover, a single systemic delivery of ABE with human single guide RNA (sgRNA) could induce body-wide dystrophin expression and improve muscle function in rotarod tests of humanized DMD mice. These findings demonstrate that ABE with human sgRNAs can confer therapeutic alleviation of DMD in mice, providing a basis for development of adenine base editing therapies in monogenic diseases.
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Affiliation(s)
- Ming Jin
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350004, China
| | - Jiajia Lin
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350004, China
| | - Haisen Li
- HuidaGene Therapeutics Co., Ltd, Shanghai 200131, China
- School of Medicine, Wayne State University, Detroit, MI 48201, USA
| | - Zhifang Li
- Lingang Laboratory, Shanghai 200031, China
| | - Dong Yang
- HuidaGene Therapeutics Co., Ltd, Shanghai 200131, China
| | - Yin Wang
- HuidaGene Therapeutics Co., Ltd, Shanghai 200131, China
| | - Yuyang Yu
- HuidaGene Therapeutics Co., Ltd, Shanghai 200131, China
| | - Zhurui Shao
- HuidaGene Therapeutics Co., Ltd, Shanghai 200131, China
| | - Long Chen
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350004, China
| | - Zhiqiang Wang
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350004, China
| | - Yu Zhang
- HuidaGene Therapeutics Co., Ltd, Shanghai 200131, China
| | - Xiumei Zhang
- HuidaGene Therapeutics Co., Ltd, Shanghai 200131, China
| | - Ning Wang
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350004, China
| | - Chunlong Xu
- Lingang Laboratory, Shanghai 200031, China
- Shanghai Center for Brain Science and Brain-Inspired Technology, Shanghai 201602, China
| | - Hui Yang
- HuidaGene Therapeutics Co., Ltd, Shanghai 200131, China
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- Shanghai Center for Brain Science and Brain-Inspired Technology, Shanghai 201602, China
| | - Wan-Jin Chen
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350004, China
| | - Guoling Li
- HuidaGene Therapeutics Co., Ltd, Shanghai 200131, China
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6
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Villiger L, Joung J, Koblan L, Weissman J, Abudayyeh OO, Gootenberg JS. CRISPR technologies for genome, epigenome and transcriptome editing. Nat Rev Mol Cell Biol 2024; 25:464-487. [PMID: 38308006 DOI: 10.1038/s41580-023-00697-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/18/2023] [Indexed: 02/04/2024]
Abstract
Our ability to edit genomes lags behind our capacity to sequence them, but the growing understanding of CRISPR biology and its application to genome, epigenome and transcriptome engineering is narrowing this gap. In this Review, we discuss recent developments of various CRISPR-based systems that can transiently or permanently modify the genome and the transcriptome. The discovery of further CRISPR enzymes and systems through functional metagenomics has meaningfully broadened the applicability of CRISPR-based editing. Engineered Cas variants offer diverse capabilities such as base editing, prime editing, gene insertion and gene regulation, thereby providing a panoply of tools for the scientific community. We highlight the strengths and weaknesses of current CRISPR tools, considering their efficiency, precision, specificity, reliance on cellular DNA repair mechanisms and their applications in both fundamental biology and therapeutics. Finally, we discuss ongoing clinical trials that illustrate the potential impact of CRISPR systems on human health.
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Affiliation(s)
- Lukas Villiger
- McGovern Institute for Brain Research, Massachusetts Institute of Technology Cambridge, Cambridge, MA, USA
| | - Julia Joung
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Luke Koblan
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jonathan Weissman
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Omar O Abudayyeh
- McGovern Institute for Brain Research, Massachusetts Institute of Technology Cambridge, Cambridge, MA, USA.
| | - Jonathan S Gootenberg
- McGovern Institute for Brain Research, Massachusetts Institute of Technology Cambridge, Cambridge, MA, USA.
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Bekaert B, Boel A, Rybouchkin A, Cosemans G, Declercq S, Chuva de Sousa Lopes SM, Parrington J, Stoop D, Coucke P, Menten B, Heindryckx B. Various repair events following CRISPR/Cas9-based mutational correction of an infertility-related mutation in mouse embryos. J Assist Reprod Genet 2024; 41:1605-1617. [PMID: 38557805 PMCID: PMC11224219 DOI: 10.1007/s10815-024-03095-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 03/12/2024] [Indexed: 04/04/2024] Open
Abstract
PURPOSE Unpredictable genetic modifications and chromosomal aberrations following CRISPR/Cas9 administration hamper the efficacy of germline editing. Repair events triggered by double-strand DNA breaks (DSBs) besides non-homologous end joining and repair template-driven homology-directed repair have been insufficiently investigated in mouse. In this work, we are the first to investigate the precise repair mechanisms triggered by parental-specific DSB induction in mouse for paternal mutational correction in the context of an infertility-related mutation. METHODS We aimed to correct a paternal 22-nucleotide deletion in Plcz1, associated with lack of fertilisation in vitro, by administrating CRISPR/Cas9 components during intracytoplasmic injection of Plcz1-null sperm in wild-type oocytes combined with assisted oocyte activation. Through targeted next-generation sequencing, 77 injected embryos and 26 blastomeres from seven injected embryos were investigated. In addition, low-pass whole genome sequencing was successfully performed on 17 injected embryo samples. RESULTS Repair mechanisms induced by two different CRISPR/Cas9 guide RNA (gRNA) designs were investigated. In 13.73% (7/51; gRNA 1) and 19.05% (4/21; gRNA 2) of the targeted embryos, only the wild-type allele was observed, of which the majority (85.71%; 6/7) showed integrity of the targeted chromosome. Remarkably, for both designs, only in one of these embryos (1/7; gRNA 1 and 1/4; gRNA2) could repair template use be detected. This suggests that alternative repair events have occurred. Next, various genetic events within the same embryo were detected after single-cell analysis of four embryos. CONCLUSION Our results suggest the occurrence of mosaicism and complex repair events after CRISPR/Cas9 DSB induction where chromosomal integrity is predominantly contained.
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Affiliation(s)
- B Bekaert
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - A Boel
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - A Rybouchkin
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - G Cosemans
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - S Declercq
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - S M Chuva de Sousa Lopes
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium
- Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, 2333 ZA, the Netherlands
| | - J Parrington
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK
| | - D Stoop
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - P Coucke
- Center for Medical Genetics Ghent, Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - B Menten
- Center for Medical Genetics Ghent, Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - B Heindryckx
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium.
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8
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Fiumara M, Ferrari S, Omer-Javed A, Beretta S, Albano L, Canarutto D, Varesi A, Gaddoni C, Brombin C, Cugnata F, Zonari E, Naldini MM, Barcella M, Gentner B, Merelli I, Naldini L. Genotoxic effects of base and prime editing in human hematopoietic stem cells. Nat Biotechnol 2024; 42:877-891. [PMID: 37679541 PMCID: PMC11180610 DOI: 10.1038/s41587-023-01915-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 07/26/2023] [Indexed: 09/09/2023]
Abstract
Base and prime editors (BEs and PEs) may provide more precise genetic engineering than nuclease-based approaches because they bypass the dependence on DNA double-strand breaks. However, little is known about their cellular responses and genotoxicity. Here, we compared state-of-the-art BEs and PEs and Cas9 in human hematopoietic stem and progenitor cells with respect to editing efficiency, cytotoxicity, transcriptomic changes and on-target and genome-wide genotoxicity. BEs and PEs induced detrimental transcriptional responses that reduced editing efficiency and hematopoietic repopulation in xenotransplants and also generated DNA double-strand breaks and genotoxic byproducts, including deletions and translocations, at a lower frequency than Cas9. These effects were strongest for cytidine BEs due to suboptimal inhibition of base excision repair and were mitigated by tailoring delivery timing and editor expression through optimized mRNA design. However, BEs altered the mutational landscape of hematopoietic stem and progenitor cells across the genome by increasing the load and relative proportions of nucleotide variants. These findings raise concerns about the genotoxicity of BEs and PEs and warrant further investigation in view of their clinical application.
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Affiliation(s)
- Martina Fiumara
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Samuele Ferrari
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy.
- Vita-Salute San Raffaele University, Milan, Italy.
| | - Attya Omer-Javed
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Stefano Beretta
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Luisa Albano
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Daniele Canarutto
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
- Pediatric Immunohematology Unit and BMT Program, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Angelica Varesi
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Chiara Gaddoni
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Chiara Brombin
- University Center for Statistics in the Biomedical Sciences, Vita-Salute San Raffaele University, Milan, Italy
| | - Federica Cugnata
- University Center for Statistics in the Biomedical Sciences, Vita-Salute San Raffaele University, Milan, Italy
| | - Erika Zonari
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Matteo Maria Naldini
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Matteo Barcella
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Bernhard Gentner
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Ivan Merelli
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
- National Research Council, Institute for Biomedical Technologies, Segrate, Italy
| | - Luigi Naldini
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy.
- Vita-Salute San Raffaele University, Milan, Italy.
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9
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Lazar NH, Celik S, Chen L, Fay MM, Irish JC, Jensen J, Tillinghast CA, Urbanik J, Bone WP, Gibson CC, Haque IS. High-resolution genome-wide mapping of chromosome-arm-scale truncations induced by CRISPR-Cas9 editing. Nat Genet 2024:10.1038/s41588-024-01758-y. [PMID: 38811841 DOI: 10.1038/s41588-024-01758-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 04/18/2024] [Indexed: 05/31/2024]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) is a powerful tool for introducing targeted mutations in DNA, but recent studies have shown that it can have unintended effects such as structural changes. However, these studies have not yet looked genome wide or across data types. Here we performed a phenotypic CRISPR-Cas9 scan targeting 17,065 genes in primary human cells, revealing a 'proximity bias' in which CRISPR knockouts show unexpected similarities to unrelated genes on the same chromosome arm. This bias was found to be consistent across cell types, laboratories, Cas9 delivery methods and assay modalities, and the data suggest that it is caused by telomeric truncations of chromosome arms, with cell cycle and apoptotic pathways playing a mediating role. Additionally, a simple correction is demonstrated to mitigate this pervasive bias while preserving biological relationships. This previously uncharacterized effect has implications for functional genomic studies using CRISPR-Cas9, with applications in discovery biology, drug-target identification, cell therapies and genetic therapeutics.
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Affiliation(s)
| | | | - Lu Chen
- Recursion, Salt Lake City, UT, USA
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10
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Bhattacharya S, Agarwal A, Muniyappa K. Deciphering the Substrate Specificity Reveals that CRISPR-Cas12a Is a Bifunctional Enzyme with Both Endo- and Exonuclease Activities. J Mol Biol 2024; 436:168550. [PMID: 38575054 DOI: 10.1016/j.jmb.2024.168550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 04/06/2024]
Abstract
The class 2 CRISPR-Cas9 and CRISPR-Cas12a systems, originally described as adaptive immune systems of bacteria and archaea, have emerged as versatile tools for genome-editing, with applications in biotechnology and medicine. However, significantly less is known about their substrate specificity, but such knowledge may provide instructive insights into their off-target cleavage and previously unrecognized mechanism of action. Here, we document that the Acidaminococcus sp. Cas12a (AsCas12a) binds preferentially, and independently of crRNA, to a suite of branched DNA structures, such as the Holliday junction (HJ), replication fork and D-loops, compared with single- or double-stranded DNA, and promotes their degradation. Further, our study revealed that AsCas12a binds to the HJ, specifically at the crossover region, protects it from DNase I cleavage and renders a pair of thymine residues in the HJ homologous core hypersensitive to KMnO4 oxidation, suggesting DNA melting and/or distortion. Notably, these structural changes enabled AsCas12a to resolve HJ into nonligatable intermediates, and subsequently their complete degradation. We further demonstrate that crRNA impedes HJ cleavage by AsCas12a, and that of Lachnospiraceae bacterium Cas12a, without affecting their DNA-binding ability. We identified a separation-of-function variant, which uncouples DNA-binding and DNA cleavage activities of AsCas12a. Importantly, we found robust evidence that AsCas12a endonuclease also has 3'-to-5' and 5'-to-3' exonuclease activity, and that these two activities synergistically promote degradation of DNA, yielding di- and mononucleotides. Collectively, this study significantly advances knowledge about the substrate specificity of AsCas12a and provides important insights into the degradation of different types of DNA substrates.
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Affiliation(s)
- Supreet Bhattacharya
- Department of Biochemistry, Indian Institute of Science, Bengaluru 560012, India
| | - Ankit Agarwal
- Department of Biochemistry, Indian Institute of Science, Bengaluru 560012, India
| | - Kalappa Muniyappa
- Department of Biochemistry, Indian Institute of Science, Bengaluru 560012, India.
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11
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Park JC, Kim YJ, Hwang GH, Kang CY, Bae S, Cha HJ. Enhancing genome editing in hPSCs through dual inhibition of DNA damage response and repair pathways. Nat Commun 2024; 15:4002. [PMID: 38734692 PMCID: PMC11088699 DOI: 10.1038/s41467-024-48111-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 04/22/2024] [Indexed: 05/13/2024] Open
Abstract
Precise genome editing is crucial for establishing isogenic human disease models and ex vivo stem cell therapy from the patient-derived hPSCs. Unlike Cas9-mediated knock-in, cytosine base editor and prime editor achieve the desirable gene correction without inducing DNA double strand breaks. However, hPSCs possess highly active DNA repair pathways and are particularly susceptible to p53-dependent cell death. These unique characteristics impede the efficiency of gene editing in hPSCs. Here, we demonstrate that dual inhibition of p53-mediated cell death and distinct activation of the DNA damage repair system upon DNA damage by cytosine base editor or prime editor additively enhanced editing efficiency in hPSCs. The BE4stem system comprised of p53DD, a dominant negative p53, and three UNG inhibitor, engineered to specifically diminish base excision repair, improves cytosine base editor efficiency in hPSCs. Addition of dominant negative MLH1 to inhibit mismatch repair activity and p53DD in the conventional prime editor system also significantly enhances prime editor efficiency in hPSCs. Thus, combined inhibition of the distinct cellular cascades engaged in hPSCs upon gene editing could significantly enhance precise genome editing in these cells.
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Affiliation(s)
- Ju-Chan Park
- College of Pharmacy, Seoul National University, Seoul, Republic of Korea
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea
| | - Yun-Jeong Kim
- College of Pharmacy, Seoul National University, Seoul, Republic of Korea
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea
| | - Gue-Ho Hwang
- Genomic Medicine Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Chan Young Kang
- Genomic Medicine Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sangsu Bae
- Genomic Medicine Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hyuk-Jin Cha
- College of Pharmacy, Seoul National University, Seoul, Republic of Korea.
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12
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Liu Y, Kong J, Liu G, Li Z, Xiao Y. Precise Gene Knock-In Tools with Minimized Risk of DSBs: A Trend for Gene Manipulation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2401797. [PMID: 38728624 DOI: 10.1002/advs.202401797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/29/2024] [Indexed: 05/12/2024]
Abstract
Gene knock-in refers to the insertion of exogenous functional genes into a target genome to achieve continuous expression. Currently, most knock-in tools are based on site-directed nucleases, which can induce double-strand breaks (DSBs) at the target, following which the designed donors carrying functional genes can be inserted via the endogenous gene repair pathway. The size of donor genes is limited by the characteristics of gene repair, and the DSBs induce risks like genotoxicity. New generation tools, such as prime editing, transposase, and integrase, can insert larger gene fragments while minimizing or eliminating the risk of DSBs, opening new avenues in the development of animal models and gene therapy. However, the elimination of off-target events and the production of delivery carriers with precise requirements remain challenging, restricting the application of the current knock-in treatments to mainly in vitro settings. Here, a comprehensive review of the knock-in tools that do not/minimally rely on DSBs and use other mechanisms is provided. Moreover, the challenges and recent advances of in vivo knock-in treatments in terms of the therapeutic process is discussed. Collectively, the new generation of DSBs-minimizing and large-fragment knock-in tools has revolutionized the field of gene editing, from basic research to clinical treatment.
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Affiliation(s)
- Yongfeng Liu
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
- Mudi Meng Honors College, China Pharmaceutical University, Nanjing, 210009, China
| | - Jianping Kong
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
| | - Gongyu Liu
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
| | - Zhaoxing Li
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
- Chongqing Innovation Institute of China Pharmaceutical University, Chongqing, 401135, China
| | - Yibei Xiao
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
- Chongqing Innovation Institute of China Pharmaceutical University, Chongqing, 401135, China
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13
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Puzzo F, Crossley MP, Goswami A, Zhang F, Pekrun K, Garzon JL, Cimprich KA, Kay MA. AAV-mediated genome editing is influenced by the formation of R-loops. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.07.592855. [PMID: 38766176 PMCID: PMC11100726 DOI: 10.1101/2024.05.07.592855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Recombinant adeno-associated viral vectors (rAAV) hold an intrinsic ability to stimulate homologous recombination (AAV-HR) and are the most used in clinical settings for in vivo gene therapy. However, rAAVs also integrate throughout the genome. Here, we describe DNA-RNA immunoprecipitation sequencing (DRIP-seq) in murine HEPA1-6 hepatoma cells and whole murine liver to establish the similarities and differences in genomic R-loop formation in a transformed cell line and intact tissue. We show enhanced AAV-HR in mice upon genetic and pharmacological upregulation of R-loops. Selecting the highly expressed Albumin gene as a model locus for genome editing in both in vitro and in vivo experiments showed that the R-loop prone, 3' end of Albumin was efficiently edited by AAV-HR, whereas the upstream R-loop-deficient region did not result in detectable vector integration. In addition, we found a positive correlation between previously reported off-target rAAV integration sites and R-loop enriched genomic regions. Thus, we conclude that high levels of R-loops, present in highly transcribed genes, promote rAAV vector genome integration. These findings may shed light on potential mechanisms for improving the safety and efficacy of genome editing by modulating R-loops and may enhance our ability to predict regions most susceptible to off-target insertional mutagenesis by rAAV vectors.
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Affiliation(s)
- Francesco Puzzo
- Department of Genetics, Stanford University, Stanford, CA
- Department of Pediatrics, Stanford University, Stanford, CA
| | | | - Aranyak Goswami
- Department of Genetics, Stanford University, Stanford, CA
- Department of Pediatrics, Stanford University, Stanford, CA
| | - Feijie Zhang
- Department of Genetics, Stanford University, Stanford, CA
- Department of Pediatrics, Stanford University, Stanford, CA
| | - Katja Pekrun
- Department of Genetics, Stanford University, Stanford, CA
- Department of Pediatrics, Stanford University, Stanford, CA
| | - Jada L Garzon
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA
| | - Karlene A Cimprich
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA
| | - Mark A Kay
- Department of Genetics, Stanford University, Stanford, CA
- Department of Pediatrics, Stanford University, Stanford, CA
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14
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Yuan B, Bi C, Tian Y, Wang J, Jin Y, Alsayegh K, Tehseen M, Yi G, Zhou X, Shao Y, Romero FV, Fischle W, Izpisua Belmonte JC, Hamdan S, Huang Y, Li M. Modulation of the microhomology-mediated end joining pathway suppresses large deletions and enhances homology-directed repair following CRISPR-Cas9-induced DNA breaks. BMC Biol 2024; 22:101. [PMID: 38685010 PMCID: PMC11059712 DOI: 10.1186/s12915-024-01896-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 04/18/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND CRISPR-Cas9 genome editing often induces unintended, large genomic rearrangements, posing potential safety risks. However, there are no methods for mitigating these risks. RESULTS Using long-read individual-molecule sequencing (IDMseq), we found the microhomology-mediated end joining (MMEJ) DNA repair pathway plays a predominant role in Cas9-induced large deletions (LDs). We targeted MMEJ-associated genes genetically and/or pharmacologically and analyzed Cas9-induced LDs at multiple gene loci using flow cytometry and long-read sequencing. Reducing POLQ levels or activity significantly decreases LDs, while depleting or overexpressing RPA increases or reduces LD frequency, respectively. Interestingly, small-molecule inhibition of POLQ and delivery of recombinant RPA proteins also dramatically promote homology-directed repair (HDR) at multiple disease-relevant gene loci in human pluripotent stem cells and hematopoietic progenitor cells. CONCLUSIONS Our findings reveal the contrasting roles of RPA and POLQ in Cas9-induced LD and HDR, suggesting new strategies for safer and more precise genome editing.
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Affiliation(s)
- Baolei Yuan
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Chongwei Bi
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Yeteng Tian
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Jincheng Wang
- Beijing Advanced Innovation Center for Genomics (ICG), Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, College of Chemistry, College of Engineering, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Yiqing Jin
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Khaled Alsayegh
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Present address: King Abdullah International Medical Research Center (KAIMRC), King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard Health Affairs (MNG-HA), Jeddah, Saudi Arabia
| | - Muhammad Tehseen
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Gang Yi
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Xuan Zhou
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | | | - Fernanda Vargas Romero
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Wolfgang Fischle
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Juan Carlos Izpisua Belmonte
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Altos Labs, Inc, San Diego, CA, 92121, USA
| | - Samir Hamdan
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Yanyi Huang
- Beijing Advanced Innovation Center for Genomics (ICG), Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, College of Chemistry, College of Engineering, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
- Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen, China
| | - Mo Li
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia.
- Bioengineering Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia.
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15
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Miskalis A, Shirguppe S, Winter J, Elias G, Swami D, Nambiar A, Stilger M, Woods WS, Gosstola N, Gapinske M, Zeballos A, Moore H, Maslov S, Gaj T, Perez-Pinera P. SPLICER: A Highly Efficient Base Editing Toolbox That Enables In Vivo Therapeutic Exon Skipping. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.01.587650. [PMID: 38883727 PMCID: PMC11178003 DOI: 10.1101/2024.04.01.587650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Exon skipping technologies enable exclusion of targeted exons from mature mRNA transcripts, which has broad applications in molecular biology, medicine, and biotechnology. Existing exon skipping techniques include antisense oligonucleotides, targetable nucleases, and base editors, which, while effective for specific applications at some target exons, remain hindered by shortcomings, including transient effects for oligonucleotides, genotoxicity for nucleases and inconsistent exon skipping for base editors. To overcome these limitations, we created SPLICER, a toolbox of next-generation base editors consisting of near-PAMless Cas9 nickase variants fused to adenosine or cytosine deaminases for the simultaneous editing of splice acceptor (SA) and splice donor (SD) sequences. Synchronized SA and SD editing with SPLICER improves exon skipping, reduces aberrant outcomes, including cryptic splicing and intron retention, and enables skipping of exons refractory to single splice-site editing. To demonstrate the therapeutic potential of SPLICER, we targeted APP exon 17, which encodes the amino acid residues that are cleaved to form the Aβ plaques in Alzheimer's disease. SPLICER reduced the formation of Aβ42 peptides in vitro and enabled efficient exon skipping in a mouse model of Alzheimer's disease. Overall, SPLICER is a widely applicable and efficient toolbox for exon skipping with broad therapeutic applications.
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16
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Chrzanowski S, Batra R. CRISPR-Based Gene Editing Techniques in Pediatric Neurological Disorders. Pediatr Neurol 2024; 153:166-174. [PMID: 38394831 DOI: 10.1016/j.pediatrneurol.2024.01.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 01/15/2024] [Accepted: 01/25/2024] [Indexed: 02/25/2024]
Abstract
The emergence of gene editing technologies offers a unique opportunity to develop mutation-specific treatments for pediatric neurological disorders. Gene editing systems can potentially alter disease trajectory by correcting dysfunctional mutations or therapeutically altering gene expression. Clustered regularly interspaced short palindromic repeats (CRISPR)-based approaches are attractive gene therapy platforms to personalize treatments because of their specificity, ease of design, versatility, and cost. However, many such approaches remain in the early stages of development, with ongoing efforts to optimize editing efficiency, minimize unintended off-target effects, and mitigate pathologic immune responses. Given the rapid evolution of CRISPR-based therapies, it is prudent for the clinically based child neurologist to have a conceptual understanding of what such therapies may entail, including both benefits and risks and how such therapies may be clinically applied. In this review, we describe the fundamentals of CRISPR-based therapies, discuss the opportunities and challenges that have arisen, and highlight preclinical work in several pediatric neurological diseases.
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Affiliation(s)
- Stephen Chrzanowski
- Department of Neurology, Boston Children's Hospital, Boston, Massachusetts; Division of Neuromuscular Medicine, Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts; Division of Neuromuscular Medicine, Department of Neurology, Brigham and Women's Hospital, Boston, Massachusetts.
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17
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Wang L, Wang J, Feng D, Wang B, Jahan-Mihan Y, Wang Y, Bi Y, Lim D, Ji B. A simple and effective genotyping workflow for rapid detection of CRISPR genome editing. Am J Physiol Gastrointest Liver Physiol 2024; 326:G473-G481. [PMID: 38410866 PMCID: PMC11216750 DOI: 10.1152/ajpgi.00013.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 02/15/2024] [Accepted: 02/17/2024] [Indexed: 02/28/2024]
Abstract
Genetically engineered mouse models play a pivotal role in the modeling of diseases, exploration of gene functions, and the development of novel therapies. In recent years, clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9)-mediated genome editing technology has revolutionized the process of developing such models by enabling precise genome modifications of the multiple interested genes simultaneously. Following genome editing, an efficient genotyping methodology is crucial for subsequent characterization. However, current genotyping methods are laborious, time-consuming, and costly. Here, using targeting the mouse trypsinogen genes as an example, we introduced common applications of CRISPR-Cas9 editing and a streamlined cost-effective genotyping workflow for CRISPR-edited mouse models, in which Sanger sequencing is required only at the initial steps. In the F0 mice, we focused on identifying the presence of positive editing by PCR followed by Sanger sequencing without the need to know the exact sequences, simplifying the initial screening. In the F1 mice, Sanger sequencing and algorithms decoding were used to identify the precise editing. Once the edited sequence was established, a simple and effective genotyping strategy was established to distinguish homozygous and heterozygous status by PCR from tail DNA. The genotyping workflow applies to deletions as small as one nucleotide, multiple-gene knockout, and knockin studies. This simplified, efficient, and cost-effective genotyping shall be instructive to new investigators who are unfamiliar with characterizing CRISPR-Cas9-edited mouse strains.NEW & NOTEWORTHY This study presents a streamlined, cost-effective genotyping workflow for clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) edited mouse models, focusing on trypsinogen genes. It simplifies initial F0 mouse screening using PCR and Sanger sequencing without needing exact sequences. For F1 mice, precise editing is identified through Sanger sequencing and algorithm decoding. The workflow includes a novel PCR strategy for distinguishing homozygous and heterozygous statuses in subsequent generations, effective for small deletions, multiple-gene knockouts, and knockins.
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Affiliation(s)
- Lingxiang Wang
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States
- Department of General Surgery, Second Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Jiale Wang
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States
| | - Dongfeng Feng
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States
| | - Bin Wang
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States
| | - Yasmin Jahan-Mihan
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States
| | - Ying Wang
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota, United States
| | - Yan Bi
- Department of Gastroenterology and Hepatology, Mayo Clinic, Jacksonville, Florida, United States
| | - DoYoung Lim
- The Transgenic and Knockout Core, Mayo Clinic, Rochester, Minnesota, United States
| | - Baoan Ji
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States
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18
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Hermantara R, Richmond L, Taqi AF, Chilaka S, Jeantet V, Guerrini I, West K, West A. Improving CRISPR-Cas9 directed faithful transgene integration outcomes by reducing unwanted random DNA integration. J Biomed Sci 2024; 31:32. [PMID: 38532479 DOI: 10.1186/s12929-024-01020-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 03/09/2024] [Indexed: 03/28/2024] Open
Abstract
BACKGROUND The field of genome editing has been revolutionized by the development of an easily programmable editing tool, the CRISPR-Cas9. Despite its promise, off-target activity of Cas9 posed a great disadvantage for genome editing purposes by causing DNA double strand breaks at off-target locations and causing unwanted editing outcomes. Furthermore, for gene integration applications, which introduce transgene sequences, integration of transgenes to off-target sites could be harmful, hard to detect, and reduce faithful genome editing efficiency. METHOD Here we report the development of a multicolour fluorescence assay for studying CRISPR-Cas9-directed gene integration at an endogenous locus in human cell lines. We examine genetic integration of reporter genes in transiently transfected cells as well as puromycin-selected stable cell lines to determine the fidelity of multiple CRISPR-Cas9 strategies. RESULT We found that there is a high occurrence of unwanted DNA integration which tarnished faithful knock-in efficiency. Integration outcomes are influenced by the type of DNA DSBs, donor design, the use of enhanced specificity Cas9 variants, with S-phase regulated Cas9 activity. Moreover, restricting Cas9 expression with a self-cleaving system greatly improves knock-in outcomes by substantially reducing the percentage of cells with unwanted DNA integration. CONCLUSION Our results highlight the need for a more stringent assessment of CRISPR-Cas9-mediated knock-in outcomes, and the importance of careful strategy design to maximise efficient and faithful transgene integration.
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Affiliation(s)
- Rio Hermantara
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.
- Department of Biomedicine, School of Life Sciences, Indonesia International Institute for Life Sciences, Jakarta, Indonesia.
| | - Laura Richmond
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Aqeel Faisal Taqi
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Sabari Chilaka
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Valentine Jeantet
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Ileana Guerrini
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Katherine West
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Adam West
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
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19
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Chang CW, Truong VA, Pham NN, Hu YC. RNA-guided genome engineering: paradigm shift towards transposons. Trends Biotechnol 2024:S0167-7799(24)00035-0. [PMID: 38443218 DOI: 10.1016/j.tibtech.2024.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 03/07/2024]
Abstract
CRISPR-Cas systems revolutionized the genome engineering field but need to induce double-strand breaks (DSBs) and may be difficult to deliver due to their large protein size. Tn7-like transposons such as CRISPR-associated transposons (CASTs) can be repurposed for RNA-guided DSB-free integration, and obligate mobile element guided activity (OMEGA) proteins of the IS200/IS605 transposon family have been developed as hypercompact RNA-guided genome editing tools. CASTs and OMEGA are exciting, innovative genome engineering tools that can improve the precision and efficiency of editing. This review explores the recent developments and uses of CASTs and OMEGA in genome editing across prokaryotic and eukaryotic cells. The pros and cons of these transposon-based systems are deliberated in comparison to other CRISPR systems.
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Affiliation(s)
- Chin-Wei Chang
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Vy Anh Truong
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Nam Ngoc Pham
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Yu-Chen Hu
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu 300, Taiwan; Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu 300, Taiwan.
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20
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Jung WJ, Park SJ, Cha S, Kim K. Factors affecting the cleavage efficiency of the CRISPR-Cas9 system. Anim Cells Syst (Seoul) 2024; 28:75-83. [PMID: 38440123 PMCID: PMC10911232 DOI: 10.1080/19768354.2024.2322054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 02/17/2024] [Indexed: 03/06/2024] Open
Abstract
The CRISPR-Cas system stands out as a promising genome editing tool due to its cost-effectiveness and time efficiency compared to other methods. This system has tremendous potential for treating various diseases, including genetic disorders and cancer, and promotes therapeutic research for a wide range of genetic diseases. Additionally, the CRISPR-Cas system simplifies the generation of animal models, offering a more accessible alternative to traditional methods. The CRISPR-Cas9 system can be used to cleave target DNA strands that need to be corrected, causing double-strand breaks (DSBs). DNA with DSBs can then be recovered by the DNA repair pathway that the CRISPR-Cas9 system uses to edit target gene sequences. High cleavage efficiency of the CRISPR-Cas9 system is thus imperative for effective gene editing. Herein, we explore several factors affecting the cleavage efficiency of the CRISPR-Cas9 system. These factors include the GC content of the protospacer-adjacent motif (PAM) proximal and distal regions, single-guide RNA (sgRNA) properties, and chromatin state. These considerations contribute to the efficiency of genome editing.
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Affiliation(s)
- Won Jun Jung
- Department of Physiology, Korea University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Soo-Ji Park
- Department of Physiology, Korea University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Seongkwang Cha
- Department of Physiology, Korea University College of Medicine, Seoul, Republic of Korea
- Neuroscience Research Institute, Korea University College of Medicine, Seoul, Republic of Korea
| | - Kyoungmi Kim
- Department of Physiology, Korea University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
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21
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Bijlani S, Pang KM, Bugga LV, Rangasamy S, Narayanan V, Chatterjee S. Nuclease-free precise genome editing corrects MECP2 mutations associated with Rett syndrome. Front Genome Ed 2024; 6:1346781. [PMID: 38495533 PMCID: PMC10940404 DOI: 10.3389/fgeed.2024.1346781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 02/12/2024] [Indexed: 03/19/2024] Open
Abstract
Rett syndrome is an acquired progressive neurodevelopmental disorder caused by de novo mutations in the X-linked MECP2 gene which encodes a pleiotropic protein that functions as a global transcriptional regulator and a chromatin modifier. Rett syndrome predominantly affects heterozygous females while affected male hemizygotes rarely survive. Gene therapy of Rett syndrome has proven challenging due to a requirement for stringent regulation of expression with either over- or under-expression being toxic. Ectopic expression of MECP2 in conjunction with regulatory miRNA target sequences has achieved some success, but the durability of this approach remains unknown. Here we evaluated a nuclease-free homologous recombination (HR)-based genome editing strategy to correct mutations in the MECP2 gene. The stem cell-derived AAVHSCs have previously been shown to mediate seamless and precise HR-based genome editing. We tested the ability of HR-based genome editing to correct pathogenic mutations in Exons 3 and 4 of the MECP2 gene and restore the wild type sequence while preserving all native genomic regulatory elements associated with MECP2 expression, thus potentially addressing a significant issue in gene therapy for Rett syndrome. Moreover, since the mutations are edited directly at the level of the genome, the corrections are expected to be durable with progeny cells inheriting the edited gene. The AAVHSC MECP2 editing vector was designed to be fully homologous to the target MECP2 region and to insert a promoterless Venus reporter at the end of Exon 4. Evaluation of AAVHSC editing in a panel of Rett cell lines bearing mutations in Exons 3 and 4 demonstrated successful correction and rescue of expression of the edited MECP2 gene. Sequence analysis of edited Rett cells revealed successful and accurate correction of mutations in both Exons 3 and 4 and permitted mapping of HR crossover events. Successful correction was observed only when the mutations were flanked at both the 5' and 3' ends by crossover events, but not when both crossovers occurred either exclusively upstream or downstream of the mutation. Importantly, we concluded that pathogenic mutations were successfully corrected in every Rett line analyzed, demonstrating the therapeutic potential of HR-based genome editing.
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Affiliation(s)
- Swati Bijlani
- Department of Surgery, Beckman Research Institute of the City of Hope, Duarte, CA, United States
| | - Ka Ming Pang
- Department of Surgery, Beckman Research Institute of the City of Hope, Duarte, CA, United States
| | - Lakshmi V. Bugga
- Department of Surgery, Beckman Research Institute of the City of Hope, Duarte, CA, United States
| | - Sampath Rangasamy
- Center for Rare Childhood Disorders (C4RCD), Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ, United States
| | - Vinodh Narayanan
- Center for Rare Childhood Disorders (C4RCD), Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ, United States
| | - Saswati Chatterjee
- Department of Surgery, Beckman Research Institute of the City of Hope, Duarte, CA, United States
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22
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Castiello MC, Brandas C, Ferrari S, Porcellini S, Sacchetti N, Canarutto D, Draghici E, Merelli I, Barcella M, Pelosi G, Vavassori V, Varesi A, Jacob A, Scala S, Basso Ricci L, Paulis M, Strina D, Di Verniere M, Sergi Sergi L, Serafini M, Holland SM, Bergerson JRE, De Ravin SS, Malech HL, Pala F, Bosticardo M, Brombin C, Cugnata F, Calzoni E, Crooks GM, Notarangelo LD, Genovese P, Naldini L, Villa A. Exonic knockout and knockin gene editing in hematopoietic stem and progenitor cells rescues RAG1 immunodeficiency. Sci Transl Med 2024; 16:eadh8162. [PMID: 38324638 PMCID: PMC11149094 DOI: 10.1126/scitranslmed.adh8162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 01/17/2024] [Indexed: 02/09/2024]
Abstract
Recombination activating genes (RAGs) are tightly regulated during lymphoid differentiation, and their mutations cause a spectrum of severe immunological disorders. Hematopoietic stem and progenitor cell (HSPC) transplantation is the treatment of choice but is limited by donor availability and toxicity. To overcome these issues, we developed gene editing strategies targeting a corrective sequence into the human RAG1 gene by homology-directed repair (HDR) and validated them by tailored two-dimensional, three-dimensional, and in vivo xenotransplant platforms to assess rescue of expression and function. Whereas integration into intron 1 of RAG1 achieved suboptimal correction, in-frame insertion into exon 2 drove physiologic human RAG1 expression and activity, allowing disruption of the dominant-negative effects of unrepaired hypomorphic alleles. Enhanced HDR-mediated gene editing enabled the correction of human RAG1 in HSPCs from patients with hypomorphic RAG1 mutations to overcome T and B cell differentiation blocks. Gene correction efficiency exceeded the minimal proportion of functional HSPCs required to rescue immunodeficiency in Rag1-/- mice, supporting the clinical translation of HSPC gene editing for the treatment of RAG1 deficiency.
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Affiliation(s)
- Maria Carmina Castiello
- San Raffaele-Telethon Institute for Gene Therapy (SR-Tiget), IRCSS San Raffaele Scientific Institute, Milan 20132, Italy
- Milan Unit, Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Rozzano (MI) 20089, Italy
| | - Chiara Brandas
- San Raffaele-Telethon Institute for Gene Therapy (SR-Tiget), IRCSS San Raffaele Scientific Institute, Milan 20132, Italy
- Translational and Molecular Medicine (DIMET), University of Milano-Bicocca, Monza 20900, Italy
| | - Samuele Ferrari
- San Raffaele-Telethon Institute for Gene Therapy (SR-Tiget), IRCSS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Simona Porcellini
- San Raffaele-Telethon Institute for Gene Therapy (SR-Tiget), IRCSS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Nicolò Sacchetti
- San Raffaele-Telethon Institute for Gene Therapy (SR-Tiget), IRCSS San Raffaele Scientific Institute, Milan 20132, Italy
- Vita-Salute San Raffaele University, Milan 20132, Italy
| | - Daniele Canarutto
- San Raffaele-Telethon Institute for Gene Therapy (SR-Tiget), IRCSS San Raffaele Scientific Institute, Milan 20132, Italy
- Vita-Salute San Raffaele University, Milan 20132, Italy
- Pediatric Immunohematology Unit and BMT Program, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Elena Draghici
- San Raffaele-Telethon Institute for Gene Therapy (SR-Tiget), IRCSS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Ivan Merelli
- San Raffaele-Telethon Institute for Gene Therapy (SR-Tiget), IRCSS San Raffaele Scientific Institute, Milan 20132, Italy
- National Research Council (CNR), Institute for Biomedical Technologies, Segrate (MI) 20054, Italy
| | - Matteo Barcella
- San Raffaele-Telethon Institute for Gene Therapy (SR-Tiget), IRCSS San Raffaele Scientific Institute, Milan 20132, Italy
- National Research Council (CNR), Institute for Biomedical Technologies, Segrate (MI) 20054, Italy
| | - Gabriele Pelosi
- San Raffaele-Telethon Institute for Gene Therapy (SR-Tiget), IRCSS San Raffaele Scientific Institute, Milan 20132, Italy
- Vita-Salute San Raffaele University, Milan 20132, Italy
| | - Valentina Vavassori
- San Raffaele-Telethon Institute for Gene Therapy (SR-Tiget), IRCSS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Angelica Varesi
- San Raffaele-Telethon Institute for Gene Therapy (SR-Tiget), IRCSS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Aurelien Jacob
- San Raffaele-Telethon Institute for Gene Therapy (SR-Tiget), IRCSS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Serena Scala
- San Raffaele-Telethon Institute for Gene Therapy (SR-Tiget), IRCSS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Luca Basso Ricci
- San Raffaele-Telethon Institute for Gene Therapy (SR-Tiget), IRCSS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Marianna Paulis
- Milan Unit, Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Rozzano (MI) 20089, Italy
- Humanitas Clinical and Research Center IRCCS, Rozzano (MI) 20089, Italy
| | - Dario Strina
- Milan Unit, Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Rozzano (MI) 20089, Italy
- Humanitas Clinical and Research Center IRCCS, Rozzano (MI) 20089, Italy
| | - Martina Di Verniere
- San Raffaele-Telethon Institute for Gene Therapy (SR-Tiget), IRCSS San Raffaele Scientific Institute, Milan 20132, Italy
- Milan Unit, Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Rozzano (MI) 20089, Italy
| | - Lucia Sergi Sergi
- San Raffaele-Telethon Institute for Gene Therapy (SR-Tiget), IRCSS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Marta Serafini
- Translational and Molecular Medicine (DIMET), University of Milano-Bicocca, Monza 20900, Italy
- Tettamanti Center, Fondazione IRCCS San Gerardo dei Tintori, Monza (MI) 20900, Italy
| | - Steven M Holland
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Jenna R E Bergerson
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Suk See De Ravin
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Harry L Malech
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Francesca Pala
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Marita Bosticardo
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Chiara Brombin
- University Center for Statistics in the Biomedical Sciences, Vita-Salute San Raffaele University, Milan 20132, Italy
| | - Federica Cugnata
- University Center for Statistics in the Biomedical Sciences, Vita-Salute San Raffaele University, Milan 20132, Italy
| | - Enrica Calzoni
- San Raffaele-Telethon Institute for Gene Therapy (SR-Tiget), IRCSS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Gay M Crooks
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Pietro Genovese
- San Raffaele-Telethon Institute for Gene Therapy (SR-Tiget), IRCSS San Raffaele Scientific Institute, Milan 20132, Italy
- Gene Therapy Program, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA 02115, USA
| | - Luigi Naldini
- San Raffaele-Telethon Institute for Gene Therapy (SR-Tiget), IRCSS San Raffaele Scientific Institute, Milan 20132, Italy
- Vita-Salute San Raffaele University, Milan 20132, Italy
| | - Anna Villa
- San Raffaele-Telethon Institute for Gene Therapy (SR-Tiget), IRCSS San Raffaele Scientific Institute, Milan 20132, Italy
- Milan Unit, Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Rozzano (MI) 20089, Italy
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23
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Kim-Yip RP, McNulty R, Joyce B, Mollica A, Chen PJ, Ravisankar P, Law BK, Liu DR, Toettcher JE, Ivakine EA, Posfai E, Adamson B. Efficient prime editing in two-cell mouse embryos using PEmbryo. Nat Biotechnol 2024:10.1038/s41587-023-02106-x. [PMID: 38321114 DOI: 10.1038/s41587-023-02106-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 12/14/2023] [Indexed: 02/08/2024]
Abstract
Using transient inhibition of DNA mismatch repair during a permissive stage of development, we demonstrate highly efficient prime editing of mouse embryos with few unwanted, local byproducts (average 58% precise edit frequency, 0.5% on-target error frequency across 13 substitution edits at 8 sites), enabling same-generation phenotyping of founders. Whole-genome sequencing reveals that mismatch repair inhibition increases off-target indels at low-complexity regions in the genome without any obvious phenotype in mice.
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Affiliation(s)
- Rebecca P Kim-Yip
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Ryan McNulty
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Bradley Joyce
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Antonio Mollica
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Peter J Chen
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Prime Medicine, Inc., Cambridge, MA, USA
| | - Purnima Ravisankar
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Benjamin K Law
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Jared E Toettcher
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Evgueni A Ivakine
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Physiology, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Eszter Posfai
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
| | - Britt Adamson
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
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24
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Li Z, Lan J, Shi X, Lu T, Hu X, Liu X, Chen Y, He Z. Whole-Genome Sequencing Reveals Rare Off-Target Mutations in MC1R-Edited Pigs Generated by Using CRISPR-Cas9 and Somatic Cell Nuclear Transfer. CRISPR J 2024; 7:29-40. [PMID: 38353621 DOI: 10.1089/crispr.2023.0034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 system has been widely used to create animal models for biomedical and agricultural use owing to its low cost and easy handling. However, the occurrence of erroneous cleavage (off-targeting) may raise certain concerns for the practical application of the CRISPR-Cas9 system. In this study, we created a melanocortin 1 receptor (MC1R)-edited pig model through somatic cell nuclear transfer (SCNT) by using porcine kidney cells modified by the CRISPR-Cas9 system. We then carried out whole-genome sequencing of two MC1R-edited pigs and two cloned wild-type siblings, together with the donor cells, to assess the genome-wide presence of single-nucleotide variants and small insertions and deletions (indels) and found only one candidate off-target indel in both MC1R-edited pigs. In summary, our study indicates that the minimal off-targeting effect induced by CRISPR-Cas9 may not be a major concern in gene-edited pigs created by SCNT.
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Affiliation(s)
- Zhenyang Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Jin Lan
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Xuan Shi
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Tong Lu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Xiaoli Hu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Xiaohong Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Yaosheng Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Zuyong He
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
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25
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Chen Y, Luo X, Kang R, Cui K, Ou J, Zhang X, Liang P. Current therapies for osteoarthritis and prospects of CRISPR-based genome, epigenome, and RNA editing in osteoarthritis treatment. J Genet Genomics 2024; 51:159-183. [PMID: 37516348 DOI: 10.1016/j.jgg.2023.07.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 07/13/2023] [Accepted: 07/15/2023] [Indexed: 07/31/2023]
Abstract
Osteoarthritis (OA) is one of the most common degenerative joint diseases worldwide, causing pain, disability, and decreased quality of life. The balance between regeneration and inflammation-induced degradation results in multiple etiologies and complex pathogenesis of OA. Currently, there is a lack of effective therapeutic strategies for OA treatment. With the development of CRISPR-based genome, epigenome, and RNA editing tools, OA treatment has been improved by targeting genetic risk factors, activating chondrogenic elements, and modulating inflammatory regulators. Supported by cell therapy and in vivo delivery vectors, genome, epigenome, and RNA editing tools may provide a promising approach for personalized OA therapy. This review summarizes CRISPR-based genome, epigenome, and RNA editing tools that can be applied to the treatment of OA and provides insights into the development of CRISPR-based therapeutics for OA treatment. Moreover, in-depth evaluations of the efficacy and safety of these tools in human OA treatment are needed.
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Affiliation(s)
- Yuxi Chen
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Xiao Luo
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Rui Kang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Kaixin Cui
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Jianping Ou
- Center for Reproductive Medicine, The Third Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Xiya Zhang
- Center for Reproductive Medicine, The Third Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong 510630, China.
| | - Puping Liang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China.
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26
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Xu S, Neupane S, Wang H, Pham TP, Snyman M, Huynh TV, Wang L. Efficient CRISPR genome editing and integrative genomic analyses reveal the mosaicism of Cas-induced mutations and pleiotropic effects of scarlet gene in an emerging model system. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.29.577787. [PMID: 38352317 PMCID: PMC10862705 DOI: 10.1101/2024.01.29.577787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Despite the revolutionary impacts of CRISPR-Cas gene editing systems, the effective and widespread use of CRISPR technologies in emerging model organisms still faces significant challenges. These include the inefficiency in generating heritable mutations at the organismal level, limited knowledge about the genomic consequences of gene editing, and an inadequate understanding of the inheritance patterns of CRISPR-Cas-induced mutations. This study addresses these issues by 1) developing an efficient microinjection delivery method for CRISPR editing in the microcrustacean Daphnia pulex; 2) assessing the editing efficiency of Cas9 and Cas12a nucleases, examining mutation inheritance patterns, and analyzing the local and global mutation spectrum in the scarlet mutants; and 3) investigating the transcriptomes of scarlet mutants to understand the pleiotropic effects of scarlet underlying their swimming behavior changes. Our reengineered CRISPR microinjection method results in efficient biallelic editing with both nucleases. While indels are dominant in Cas-induced mutations, a few on-site large deletions (>1kb) are observed, most likely caused by microhomology-mediated end joining repair. Knock-in of a stop codon cassette to the scarlet locus was successful, despite complex induced mutations surrounding the target site. Moreover, extensive germline mosaicism exists in some mutants, which unexpectedly produce different phenotypes/genotypes in their asexual progenies. Lastly, our transcriptomic analyses unveil significant gene expression changes associated with scarlet knock-out and altered swimming behavior in mutants, including several genes (e.g., NMDA1, ABAT, CNTNAP2) involved in human neurodegenerative diseases. This study expands our understanding of the dynamics of gene editing in the tractable model organism Daphnia and highlights its promising potential as a neurological disease model.
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Affiliation(s)
- Sen Xu
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, 65211, USA
| | - Swatantra Neupane
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, 65211, USA
| | - Hongjun Wang
- Department of Biology, University of Texas at Arlington, Arlington, Texas, 76019, USA
| | - Thinh Phu Pham
- Department of Biology, University of Texas at Arlington, Arlington, Texas, 76019, USA
| | - Marelize Snyman
- Department of Biology, University of Texas at Arlington, Arlington, Texas, 76019, USA
| | - Trung V. Huynh
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, 65211, USA
| | - Li Wang
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, 65211, USA
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27
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Tendolkar A, Mazo-Vargas A, Livraghi L, Hanly JJ, Van Horne KC, Gilbert LE, Martin A. Cis-regulatory modes of Ultrabithorax inactivation in butterfly forewings. eLife 2024; 12:RP90846. [PMID: 38261357 PMCID: PMC10945631 DOI: 10.7554/elife.90846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024] Open
Abstract
Hox gene clusters encode transcription factors that drive regional specialization during animal development: for example the Hox factor Ubx is expressed in the insect metathoracic (T3) wing appendages and differentiates them from T2 mesothoracic identities. Hox transcriptional regulation requires silencing activities that prevent spurious activation and regulatory crosstalks in the wrong tissues, but this has seldom been studied in insects other than Drosophila, which shows a derived Hox dislocation into two genomic clusters that disjoined Antennapedia (Antp) and Ultrabithorax (Ubx). Here, we investigated how Ubx is restricted to the hindwing in butterflies, amidst a contiguous Hox cluster. By analysing Hi-C and ATAC-seq data in the butterfly Junonia coenia, we show that a Topologically Associated Domain (TAD) maintains a hindwing-enriched profile of chromatin opening around Ubx. This TAD is bordered by a Boundary Element (BE) that separates it from a region of joined wing activity around the Antp locus. CRISPR mutational perturbation of this BE releases ectopic Ubx expression in forewings, inducing homeotic clones with hindwing identities. Further mutational interrogation of two non-coding RNA encoding regions and one putative cis-regulatory module within the Ubx TAD cause rare homeotic transformations in both directions, indicating the presence of both activating and repressing chromatin features. We also describe a series of spontaneous forewing homeotic phenotypes obtained in Heliconius butterflies, and discuss their possible mutational basis. By leveraging the extensive wing specialization found in butterflies, our initial exploration of Ubx regulation demonstrates the existence of silencing and insulating sequences that prevent its spurious expression in forewings.
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Affiliation(s)
- Amruta Tendolkar
- Department of Biological Sciences, The George Washington UniversityWashington, DCUnited States
| | - Anyi Mazo-Vargas
- Department of Biological Sciences, The George Washington UniversityWashington, DCUnited States
| | - Luca Livraghi
- Department of Biological Sciences, The George Washington UniversityWashington, DCUnited States
| | - Joseph J Hanly
- Department of Biological Sciences, The George Washington UniversityWashington, DCUnited States
- Smithsonian Tropical Research InstitutePanama CityPanama
| | - Kelsey C Van Horne
- Department of Biological Sciences, The George Washington UniversityWashington, DCUnited States
| | - Lawrence E Gilbert
- Department of Integrative Biology, University of Texas – AustinAustinUnited States
| | - Arnaud Martin
- Department of Biological Sciences, The George Washington UniversityWashington, DCUnited States
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Bailey SM, Cross EM, Kinner-Bibeau L, Sebesta HC, Bedford JS, Tompkins CJ. Monitoring Genomic Structural Rearrangements Resulting from Gene Editing. J Pers Med 2024; 14:110. [PMID: 38276232 PMCID: PMC10817574 DOI: 10.3390/jpm14010110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/04/2024] [Accepted: 01/13/2024] [Indexed: 01/27/2024] Open
Abstract
The cytogenomics-based methodology of directional genomic hybridization (dGH) enables the detection and quantification of a more comprehensive spectrum of genomic structural variants than any other approach currently available, and importantly, does so on a single-cell basis. Thus, dGH is well-suited for testing and/or validating new advancements in CRISPR-Cas9 gene editing systems. In addition to aberrations detected by traditional cytogenetic approaches, the strand specificity of dGH facilitates detection of otherwise cryptic intra-chromosomal rearrangements, specifically small inversions. As such, dGH represents a powerful, high-resolution approach for the quantitative monitoring of potentially detrimental genomic structural rearrangements resulting from exposure to agents that induce DNA double-strand breaks (DSBs), including restriction endonucleases and ionizing radiations. For intentional genome editing strategies, it is critical that any undesired effects of DSBs induced either by the editing system itself or by mis-repair with other endogenous DSBs are recognized and minimized. In this paper, we discuss the application of dGH for assessing gene editing-associated structural variants and the potential heterogeneity of such rearrangements among cells within an edited population, highlighting its relevance to personalized medicine strategies.
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Affiliation(s)
- Susan M. Bailey
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, USA;
- KromaTiD, Inc., Longmont, CO 80501, USA; (E.M.C.); (L.K.-B.); (H.C.S.)
| | - Erin M. Cross
- KromaTiD, Inc., Longmont, CO 80501, USA; (E.M.C.); (L.K.-B.); (H.C.S.)
| | | | - Henry C. Sebesta
- KromaTiD, Inc., Longmont, CO 80501, USA; (E.M.C.); (L.K.-B.); (H.C.S.)
| | - Joel S. Bedford
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, USA;
- KromaTiD, Inc., Longmont, CO 80501, USA; (E.M.C.); (L.K.-B.); (H.C.S.)
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29
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Poot M. Methods of Detection and Mechanisms of Origin of Complex Structural Genome Variations. Methods Mol Biol 2024; 2825:39-65. [PMID: 38913302 DOI: 10.1007/978-1-0716-3946-7_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
Based on classical karyotyping, structural genome variations (SVs) have generally been considered to be either "simple" (with one or two breakpoints) or "complex" (with more than two breakpoints). Studying the breakpoints of SVs at nucleotide resolution revealed additional, subtle structural variations, such that even "simple" SVs turned out to be "complex." Genome-wide sequencing methods, such as fosmid and paired-end mapping, short-read and long-read whole genome sequencing, and single-molecule optical mapping, also indicated that the number of SVs per individual was considerably larger than expected from karyotyping and high-resolution chromosomal array-based studies. Interestingly, SVs were detected in studies of cohorts of individuals without clinical phenotypes. The common denominator of all SVs appears to be a failure to accurately repair DNA double-strand breaks (DSBs) or to halt cell cycle progression if DSBs persist. This review discusses the various DSB response mechanisms during the mitotic cell cycle and during meiosis and their regulation. Emphasis is given to the molecular mechanisms involved in the formation of translocations, deletions, duplications, and inversions during or shortly after meiosis I. Recently, CRISPR-Cas9 studies have provided unexpected insights into the formation of translocations and chromothripsis by both breakage-fusion-bridge and micronucleus-dependent mechanisms.
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Affiliation(s)
- Martin Poot
- Department of Human Genetics, University of Wuerzburg, Wuerzburg, Germany
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Lampe GD, King RT, Halpin-Healy TS, Klompe SE, Hogan MI, Vo PLH, Tang S, Chavez A, Sternberg SH. Targeted DNA integration in human cells without double-strand breaks using CRISPR-associated transposases. Nat Biotechnol 2024; 42:87-98. [PMID: 36991112 PMCID: PMC10620015 DOI: 10.1038/s41587-023-01748-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 03/13/2023] [Indexed: 03/31/2023]
Abstract
Conventional genome engineering with CRISPR-Cas9 creates double-strand breaks (DSBs) that lead to undesirable byproducts and reduce product purity. Here we report an approach for programmable integration of large DNA sequences in human cells that avoids the generation of DSBs by using Type I-F CRISPR-associated transposases (CASTs). We optimized DNA targeting by the QCascade complex through protein design and developed potent transcriptional activators by exploiting the multi-valent recruitment of the AAA+ ATPase TnsC to genomic sites targeted by QCascade. After initial detection of plasmid-based integration, we screened 15 additional CAST systems from a wide range of bacterial hosts, identified a homolog from Pseudoalteromonas that exhibits improved activity and further increased integration efficiencies. Finally, we discovered that bacterial ClpX enhances genomic integration by multiple orders of magnitude, likely by promoting active disassembly of the post-integration CAST complex, akin to its known role in Mu transposition. Our work highlights the ability to reconstitute complex, multi-component machineries in human cells and establishes a strong foundation to exploit CRISPR-associated transposases for eukaryotic genome engineering.
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Affiliation(s)
- George D Lampe
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Rebeca T King
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Tyler S Halpin-Healy
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA
| | - Sanne E Klompe
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Department of Genomes and Genetics, Institut Pasteur, Paris, France
| | - Marcus I Hogan
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Phuc Leo H Vo
- Department of Molecular Pharmacology and Therapeutics, Columbia University, New York, NY, USA
- Vertex Pharmaceuticals, Inc., Boston, MA, USA
| | - Stephen Tang
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Alejandro Chavez
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Samuel H Sternberg
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
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31
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Schmitz M, Querques I. DNA on the move: mechanisms, functions and applications of transposable elements. FEBS Open Bio 2024; 14:13-22. [PMID: 38041553 PMCID: PMC10761935 DOI: 10.1002/2211-5463.13743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 10/24/2023] [Accepted: 11/30/2023] [Indexed: 12/03/2023] Open
Abstract
Transposons are mobile genetic elements that have invaded all domains of life by moving between and within their host genomes. Due to their mobility (or transposition), transposons facilitate horizontal gene transfer in bacteria and foster the evolution of new molecular functions in prokaryotes and eukaryotes. As transposition can lead to detrimental genomic rearrangements, organisms have evolved a multitude of molecular strategies to control transposons, including genome defense mechanisms provided by CRISPR-Cas systems. Apart from their biological impacts on genomes, DNA transposons have been leveraged as efficient gene insertion vectors in basic research, transgenesis and gene therapy. However, the close to random insertion profile of transposon-based tools limits their programmability and safety. Despite recent advances brought by the development of CRISPR-associated genome editing nucleases, a strategy for efficient insertion of large, multi-kilobase transgenes at user-defined genomic sites is currently challenging. The discovery and experimental characterization of bacterial CRISPR-associated transposons (CASTs) led to the attractive hypothesis that these systems could be repurposed as programmable, site-specific gene integration technologies. Here, we provide a broad overview of the molecular mechanisms underpinning DNA transposition and of its biological and technological impact. The second focus of the article is to describe recent mechanistic and functional analyses of CAST transposition. Finally, current challenges and desired future advances of CAST-based genome engineering applications are briefly discussed.
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Affiliation(s)
| | - Irma Querques
- Department of BiochemistryUniversity of ZurichSwitzerland
- Max Perutz Labs, Vienna Biocenter Campus (VBC)Austria
- Department of Structural and Computational Biology, Center for Molecular BiologyUniversity of ViennaAustria
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32
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Liu Y, Binda CS, Berkhout B, Das AT. CRISPR-Cas attack of HIV-1 proviral DNA can cause unintended deletion of surrounding cellular DNA. J Virol 2023; 97:e0133423. [PMID: 37982648 PMCID: PMC10734527 DOI: 10.1128/jvi.01334-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 10/23/2023] [Indexed: 11/21/2023] Open
Abstract
IMPORTANCE Although HIV replication can be effectively inhibited by antiretroviral therapy, this does not result in a cure as the available drugs do not inactivate the integrated HIV-1 DNA in infected cells. Consequently, HIV-infected individuals need lifelong therapy to prevent viral rebound. Several preclinical studies indicate that CRISPR-Cas gene-editing systems can be used to achieve permanent inactivation of the viral DNA. It was previously shown that this inactivation was due to small inactivating mutations at the targeted sites in the HIV genome and to excision or inversion of the viral DNA fragment between two target sites. We, here, demonstrate that CRISPR-Cas treatment also causes large unintended deletions, which can include surrounding chromosomal sequences. As the loss of chromosomal sequences may cause oncogenic transformation of the cell, such unintended large deletions form a potential safety risk in clinical application of this antiviral application and possibly all CRISPR-Cas gene-editing approaches.
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Affiliation(s)
- Ye Liu
- Amsterdam UMC, location University of Amsterdam, Laboratory of Experimental Virology, Medical Microbiology and Infection Prevention, Amsterdam, The Netherlands
- Amsterdam institute for Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
| | - Caroline S. Binda
- Amsterdam UMC, location University of Amsterdam, Laboratory of Experimental Virology, Medical Microbiology and Infection Prevention, Amsterdam, The Netherlands
- Amsterdam institute for Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
| | - Ben Berkhout
- Amsterdam UMC, location University of Amsterdam, Laboratory of Experimental Virology, Medical Microbiology and Infection Prevention, Amsterdam, The Netherlands
- Amsterdam institute for Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
| | - Atze T. Das
- Amsterdam UMC, location University of Amsterdam, Laboratory of Experimental Virology, Medical Microbiology and Infection Prevention, Amsterdam, The Netherlands
- Amsterdam institute for Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
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33
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Rossi M, Steklov M, Huberty F, Nguyen T, Marijsse J, Jacques-Hespel C, Najm P, Lonez C, Breman E. Efficient shRNA-based knockdown of multiple target genes for cell therapy using a chimeric miRNA cluster platform. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 34:102038. [PMID: 37799328 PMCID: PMC10548280 DOI: 10.1016/j.omtn.2023.102038] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 09/15/2023] [Indexed: 10/07/2023]
Abstract
Genome engineering technologies are powerful tools in cell-based immunotherapy to optimize or fine-tune cell functionalities. However, their use for multiple gene edits poses relevant biological and technical challenges. Short hairpin RNA (shRNA)-based cell engineering bypasses these criticalities and represents a valid alternative to CRISPR-based gene editing. Here, we describe a microRNA (miRNA)-based multiplex shRNA platform obtained by combining highly efficient miRNA scaffolds into a chimeric cluster, to deliver up to four shRNA-like sequences. Thanks to its limited size, our cassette could be deployed in a one-step process along with all the CAR components, streamlining the generation of engineered CAR T cells. The plug-and-play design of the shRNA platform allowed us to swap each shRNA-derived guide sequence without affecting the system performance. Appropriately choosing the target sequences, we were able to either achieve a functional KO, or fine-tune the expression levels of the target genes, all without the need for gene editing. Through our strategy we achieved easy, safe, efficient, and tunable modulation of multiple target genes simultaneously. This approach allows for the effective introduction of multiple functionally relevant tweaks in the transcriptome of the engineered cells, which may lead to increased performance in challenging environments, e.g., solid tumors.
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Affiliation(s)
- Matteo Rossi
- Celyad Oncology, 1435 Mont-Saint-Guibert, Belgium
| | | | | | - Thuy Nguyen
- Celyad Oncology, 1435 Mont-Saint-Guibert, Belgium
| | | | | | - Paul Najm
- Celyad Oncology, 1435 Mont-Saint-Guibert, Belgium
| | | | - Eytan Breman
- Celyad Oncology, 1435 Mont-Saint-Guibert, Belgium
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Canarutto D, Asperti C, Vavassori V, Porcellini S, Rovelli E, Paulis M, Ferrari S, Varesi A, Fiumara M, Jacob A, Sergi Sergi L, Visigalli I, Ferrua F, González‐Granado LI, Lougaris V, Finocchi A, Villa A, Radrizzani M, Naldini L. Unbiased assessment of genome integrity and purging of adverse outcomes at the target locus upon editing of CD4 + T-cells for the treatment of Hyper IgM1. EMBO J 2023; 42:e114188. [PMID: 37916874 PMCID: PMC10690452 DOI: 10.15252/embj.2023114188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 09/15/2023] [Accepted: 09/25/2023] [Indexed: 11/03/2023] Open
Abstract
Hyper IgM1 is an X-linked combined immunodeficiency caused by CD40LG mutations, potentially treatable with CD4+ T-cell gene editing with Cas9 and a "one-size-fits-most" corrective template. Contrary to established gene therapies, there is limited data on the genomic alterations following long-range gene editing, and no consensus on the relevant assays. We developed drop-off digital PCR assays for unbiased detection of large on-target deletions and found them at high frequency upon editing. Large deletions were also common upon editing different loci and cell types and using alternative Cas9 and template delivery methods. In CD40LG edited T cells, on-target deletions were counter-selected in culture and further purged by enrichment for edited cells using a selector coupled to gene correction. We then validated the sensitivity of optical genome mapping for unbiased detection of genome wide rearrangements and uncovered on-target trapping of one or more vector copies, which do not compromise functionality, upon editing using an integrase defective lentiviral donor template. No other recurring events were detected. Edited patient cells showed faithful reconstitution of CD40LG regulated expression and function with a satisfactory safety profile. Large deletions and donor template integrations should be anticipated and accounted for when designing and testing similar gene editing strategies.
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Affiliation(s)
- Daniele Canarutto
- San Raffaele Telethon Institute for Gene TherapyIRCCS San Raffaele Scientific InstituteMilanItaly
- Università Vita‐Salute San RaffaeleMilanItaly
- Pediatric Immunohematology Unit and BMT ProgramIRCCS San Raffaele Scientific InstituteMilanItaly
| | - Claudia Asperti
- San Raffaele Telethon Institute for Gene TherapyIRCCS San Raffaele Scientific InstituteMilanItaly
| | - Valentina Vavassori
- San Raffaele Telethon Institute for Gene TherapyIRCCS San Raffaele Scientific InstituteMilanItaly
| | - Simona Porcellini
- San Raffaele Telethon Institute for Gene TherapyIRCCS San Raffaele Scientific InstituteMilanItaly
| | - Elisabetta Rovelli
- San Raffaele Telethon Institute for Gene TherapyIRCCS San Raffaele Scientific InstituteMilanItaly
| | - Marianna Paulis
- Humanitas Clinical and Research Center IRCCSMilanItaly
- UOS Milan UnitIstituto di Ricerca Genetica e Biomedica (IRGB), CNRMilanItaly
| | - Samuele Ferrari
- San Raffaele Telethon Institute for Gene TherapyIRCCS San Raffaele Scientific InstituteMilanItaly
| | - Angelica Varesi
- San Raffaele Telethon Institute for Gene TherapyIRCCS San Raffaele Scientific InstituteMilanItaly
| | - Martina Fiumara
- San Raffaele Telethon Institute for Gene TherapyIRCCS San Raffaele Scientific InstituteMilanItaly
| | - Aurelien Jacob
- San Raffaele Telethon Institute for Gene TherapyIRCCS San Raffaele Scientific InstituteMilanItaly
| | - Lucia Sergi Sergi
- San Raffaele Telethon Institute for Gene TherapyIRCCS San Raffaele Scientific InstituteMilanItaly
| | - Ilaria Visigalli
- San Raffaele Telethon Institute for Gene TherapyIRCCS San Raffaele Scientific InstituteMilanItaly
| | - Francesca Ferrua
- San Raffaele Telethon Institute for Gene TherapyIRCCS San Raffaele Scientific InstituteMilanItaly
- Pediatric Immunohematology Unit and BMT ProgramIRCCS San Raffaele Scientific InstituteMilanItaly
| | - Luis Ignacio González‐Granado
- Unidad de Immunodeficiencias Primarias y la Unidad de Hematología y Oncología PediátricaInstituto de Investigacíon Hospital 12 de OctubreMadridSpain
| | | | - Andrea Finocchi
- Academic Department of Pediatrics (DPUO), Research Unit of Clinical Immunology and Vaccinology, Bambino Gesú Children's HospitalIstituto di Ricovero e Cura a Carattere ScientificoRomeItaly
| | - Anna Villa
- San Raffaele Telethon Institute for Gene TherapyIRCCS San Raffaele Scientific InstituteMilanItaly
- UOS Milan UnitIstituto di Ricerca Genetica e Biomedica (IRGB), CNRMilanItaly
| | - Marina Radrizzani
- San Raffaele Telethon Institute for Gene TherapyIRCCS San Raffaele Scientific InstituteMilanItaly
| | - Luigi Naldini
- San Raffaele Telethon Institute for Gene TherapyIRCCS San Raffaele Scientific InstituteMilanItaly
- Università Vita‐Salute San RaffaeleMilanItaly
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Quan ZJ, Li SA, Yang ZX, Zhao JJ, Li GH, Zhang F, Wen W, Cheng T, Zhang XB. GREPore-seq: A Robust Workflow to Detect Changes After Gene Editing Through Long-range PCR and Nanopore Sequencing. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:1221-1236. [PMID: 35752289 PMCID: PMC11082256 DOI: 10.1016/j.gpb.2022.06.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 05/19/2022] [Accepted: 06/13/2022] [Indexed: 05/09/2023]
Abstract
To achieve the enormous potential of gene-editing technology in clinical therapies, one needs to evaluate both the on-target efficiency and unintended editing consequences comprehensively. However, there is a lack of a pipelined, large-scale, and economical workflow for detecting genome editing outcomes, in particular insertion or deletion of a large fragment. Here, we describe an approach for efficient and accurate detection of multiple genetic changes after CRISPR/Cas9 editing by pooled nanopore sequencing of barcoded long-range PCR products. Recognizing the high error rates of Oxford nanopore sequencing, we developed a novel pipeline to capture the barcoded sequences by grepping reads of nanopore amplicon sequencing (GREPore-seq). GREPore-seq can assess nonhomologous end-joining (NHEJ)-mediated double-stranded oligodeoxynucleotide (dsODN) insertions with comparable accuracy to Illumina next-generation sequencing (NGS). GREPore-seq also reveals a full spectrum of homology-directed repair (HDR)-mediated large gene knock-in, correlating well with the fluorescence-activated cell sorting (FACS) analysis results. Of note, we discovered low-level fragmented and full-length plasmid backbone insertion at the CRISPR cutting site. Therefore, we have established a practical workflow to evaluate various genetic changes, including quantifying insertions of short dsODNs, knock-ins of long pieces, plasmid insertions, and large fragment deletions after CRISPR/Cas9-mediated editing. GREPore-seq is freely available at GitHub (https://github.com/lisiang/GREPore-seq) and the National Genomics Data Center (NGDC) BioCode (https://ngdc.cncb.ac.cn/biocode/tools/BT007293).
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Affiliation(s)
- Zi-Jun Quan
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Si-Ang Li
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Zhi-Xue Yang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Juan-Juan Zhao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Guo-Hua Li
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Feng Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Wei Wen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China.
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Tianjin 300020, China; Department of Stem Cell & Regenerative Medicine, Peking Union Medical College, Tianjin 300020, China.
| | - Xiao-Bing Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China.
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Liu J, Chen Y, Nong B, Luo X, Cui K, Li Z, Zhang P, Tan W, Yang Y, Ma W, Liang P, Songyang Z. CRISPR-assisted transcription activation by phase-separation proteins. Protein Cell 2023; 14:874-887. [PMID: 36905356 PMCID: PMC10691850 DOI: 10.1093/procel/pwad013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 01/11/2023] [Indexed: 03/12/2023] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 system has been widely used for genome engineering and transcriptional regulation in many different organisms. Current CRISPR-activation (CRISPRa) platforms often require multiple components because of inefficient transcriptional activation. Here, we fused different phase-separation proteins to dCas9-VPR (dCas9-VP64-P65-RTA) and observed robust increases in transcriptional activation efficiency. Notably, human NUP98 (nucleoporin 98) and FUS (fused in sarcoma) IDR domains were best at enhancing dCas9-VPR activity, with dCas9-VPR-FUS IDR (VPRF) outperforming the other CRISPRa systems tested in this study in both activation efficiency and system simplicity. dCas9-VPRF overcomes the target strand bias and widens gRNA designing windows without affecting the off-target effect of dCas9-VPR. These findings demonstrate the feasibility of using phase-separation proteins to assist in the regulation of gene expression and support the broad appeal of the dCas9-VPRF system in basic and clinical applications.
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Affiliation(s)
- Jiaqi Liu
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yuxi Chen
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Baoting Nong
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
- Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
| | - Xiao Luo
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Kaixin Cui
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Zhan Li
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Pengfei Zhang
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | | | - Yue Yang
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Wenbin Ma
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Puping Liang
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Zhou Songyang
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
- Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
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Qiu H, Li G, Yuan J, Yang D, Ma Y, Wang F, Dai Y, Chang X. Efficient exon skipping by base-editor-mediated abrogation of exonic splicing enhancers. Cell Rep 2023; 42:113340. [PMID: 37906593 DOI: 10.1016/j.celrep.2023.113340] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 08/31/2023] [Accepted: 10/09/2023] [Indexed: 11/02/2023] Open
Abstract
Duchenne muscular dystrophy (DMD) is a severe genetic disease caused by the loss of the dystrophin protein. Exon skipping is a promising strategy to treat DMD by restoring truncated dystrophin. Here, we demonstrate that base editors (e.g., targeted AID-mediated mutagenesis [TAM]) are able to efficiently induce exon skipping by disrupting functional redundant exonic splicing enhancers (ESEs). By developing an unbiased and high-throughput screening to interrogate exonic sequences, we successfully identify novel ESEs in DMD exons 51 and 53. TAM-CBE (cytidine base editor) induces near-complete skipping of the respective exons by targeting these ESEs in patients' induced pluripotent stem cell (iPSC)-derived cardiomyocytes. Combined with strategies to disrupt splice sites, we identify suitable single guide RNAs (sgRNAs) with TAM-CBE to efficiently skip most DMD hotspot exons without substantial double-stranded breaks. Our study thus expands the repertoire of potential targets for CBE-mediated exon skipping in treating DMD and other RNA mis-splicing diseases.
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Affiliation(s)
- Han Qiu
- Research Center for Industries of the Future, Westlake University, Hangzhou 310024, Zhejiang, China; Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, Zhejiang, China; Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang, China; Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Geng Li
- Research Center for Industries of the Future, Westlake University, Hangzhou 310024, Zhejiang, China; Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, Zhejiang, China; Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang, China
| | - Juanjuan Yuan
- Shunde Hospital, Southern Medical University, Foshan 528308, Guangdong, China
| | - Dian Yang
- Research Center for Industries of the Future, Westlake University, Hangzhou 310024, Zhejiang, China; Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, Zhejiang, China; Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang, China
| | - Yunqing Ma
- Research Center for Industries of the Future, Westlake University, Hangzhou 310024, Zhejiang, China; Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, Zhejiang, China; Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang, China
| | - Feng Wang
- Department of Laboratory Medicine, Ningbo Medical Center Lihuili Hospital, Ningbo 315040, Zhejiang, China
| | - Yi Dai
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100730, China
| | - Xing Chang
- Research Center for Industries of the Future, Westlake University, Hangzhou 310024, Zhejiang, China; Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, Zhejiang, China; Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang, China.
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Ceglie G, Lecis M, Canciani G, Algeri M, Frati G. Genome editing for sickle cell disease: still time to correct? Front Pediatr 2023; 11:1249275. [PMID: 38027257 PMCID: PMC10652763 DOI: 10.3389/fped.2023.1249275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 10/10/2023] [Indexed: 12/01/2023] Open
Abstract
Sickle cell disease (SCD) is an inherited blood disorder, due to a single point mutation in the β-globin gene (HBB) leading to multisystemic manifestations and it affects millions of people worldwide. The monogenic nature of the disease and the availability of autologous hematopoietic stem cells (HSCs) make this disorder an ideal candidate for gene modification strategies. Notably, significant advances in the field of gene therapy and genome editing that took place in the last decade enabled the possibility to develop several strategies for the treatment of SCD. These curative approaches were firstly based on the correction of disease-causing mutations holding the promise for a specific, effective and safe option for patients. Specifically, gene-editing approaches exploiting the homology directed repair pathway were investigated, but soon their limited efficacy in quiescent HSC has curbed their wider development. On the other hand, a number of studies on globin gene regulation, led to the development of several genome editing strategies based on the reactivation of the fetal γ-globin gene (HBG) by nuclease-mediated targeting of HBG-repressor elements. Although the efficiency of these strategies seems to be confirmed in preclinical and clinical studies, very little is known about the long-term consequences of these modifications. Moreover, the potential genotoxicity of these nuclease-based strategies must be taken into account, especially when associated with high targeting rates. The recent introduction of nuclease-free genome editing technologies brought along the potential for safer strategies for SCD gene correction, which may also harbor significant advantages over HBG-reactivating ones. In this Review, we discuss the recent advances in genome editing strategies for the correction of SCD-causing mutations trying to recapitulate the promising strategies currently available and their relative strengths and weaknesses.
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Affiliation(s)
- Giulia Ceglie
- Cell and Gene Therapy for Hematological Disorders Unit, Department of Oncology-Hematology, Ospedale Pediatrico Bambino Gesù, Rome, Italy
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Marco Lecis
- Cell and Gene Therapy for Hematological Disorders Unit, Department of Oncology-Hematology, Ospedale Pediatrico Bambino Gesù, Rome, Italy
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
- Pediatric Unit, Modena University Hospital, Modena, Italy
| | - Gabriele Canciani
- Cell and Gene Therapy for Hematological Disorders Unit, Department of Oncology-Hematology, Ospedale Pediatrico Bambino Gesù, Rome, Italy
- Residency School of Pediatrics, University of Rome Tor Vergata, Rome, Italy
| | - Mattia Algeri
- Cell and Gene Therapy for Hematological Disorders Unit, Department of Oncology-Hematology, Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Giacomo Frati
- Cell and Gene Therapy for Hematological Disorders Unit, Department of Oncology-Hematology, Ospedale Pediatrico Bambino Gesù, Rome, Italy
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Zhou X, Renauer PA, Zhou L, Fang SY, Chen S. Applications of CRISPR technology in cellular immunotherapy. Immunol Rev 2023; 320:199-216. [PMID: 37449673 PMCID: PMC10787818 DOI: 10.1111/imr.13241] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 06/07/2023] [Indexed: 07/18/2023]
Abstract
CRISPR technology has transformed multiple fields, including cancer and immunology. CRISPR-based gene editing and screening empowers direct genomic manipulation of immune cells, opening doors to unbiased functional genetic screens. These screens aid in the discovery of novel factors that regulate and reprogram immune responses, offering novel drug targets. The engineering of immune cells using CRISPR has sparked a transformation in the cellular immunotherapy field, resulting in a multitude of ongoing clinical trials. In this review, we discuss the development and applications of CRISPR and related gene editing technologies in immune cells, focusing on functional genomics screening, gene editing-based cell therapies, as well as future directions in this rapidly advancing field.
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Affiliation(s)
- Xiaoyu Zhou
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
| | - Paul A. Renauer
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
| | - Liqun Zhou
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
- Immunobiology Program, Yale University, New Haven, CT, USA
| | - Shao-Yu Fang
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
| | - Sidi Chen
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
- Immunobiology Program, Yale University, New Haven, CT, USA
- Department of Immunobiology, Yale University, New Haven, CT, USA
- Molecular Cell Biology, Genetics, and Development Program, Yale University, New Haven, CT, USA
- Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
- Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA
- Center for Biomedical Data Science, Yale University School of Medicine, New Haven, CT, USA
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40
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Tang J, Zhao X. Chimeric antigen receptor T cells march into T cell malignancies. J Cancer Res Clin Oncol 2023; 149:13459-13475. [PMID: 37468610 DOI: 10.1007/s00432-023-05148-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 07/09/2023] [Indexed: 07/21/2023]
Abstract
T cell malignancies represent a diverse collection of leukemia/lymphoma conditions in humans arising from aberrant T cells. Such malignancies are often associated with poor clinical prognoses, cancer relapse, as well as progressive resistance to anti-cancer treatments. While chimeric antigen receptor (CAR) T cell immunotherapy has emerged as a revolutionary treatment strategy that is highly effective for treating B cell malignancies, its application as a treatment for T cell malignancies remains to be better explored. Furthermore, the effectiveness of CAR-T treatment in T cell malignancies is significantly influenced by the quality of contamination-free CAR-T cells during the manufacturing process, as well as by multiple characteristics of such malignancies, including the sharing of antigens across normal and malignant T cells, fratricide, and T cell aplasia. In this review, we provide a detailed account of the current developments in the clinical application of CAR-T therapy to treat T cell malignancies, offer strategies for addressing current challenges, and outline a roadmap toward its effective implementation as a broad treatment option for this condition.
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Affiliation(s)
- Jie Tang
- Department of Targeting Therapy & Immunology and Laboratory of Animal Tumor Models, Cancer Center and National Clinical Research Center for Geriatrics and Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xudong Zhao
- Department of Targeting Therapy & Immunology and Laboratory of Animal Tumor Models, Cancer Center and National Clinical Research Center for Geriatrics and Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
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41
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Zhang YR, Yin TL, Zhou LQ. CRISPR/Cas9 technology: applications in oocytes and early embryos. J Transl Med 2023; 21:746. [PMID: 37875936 PMCID: PMC10594749 DOI: 10.1186/s12967-023-04610-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 10/09/2023] [Indexed: 10/26/2023] Open
Abstract
CRISPR/Cas9, a highly versatile genome-editing tool, has garnered significant attention in recent years. Despite the unique characteristics of oocytes and early embryos compared to other cell types, this technology has been increasing used in mammalian reproduction. In this comprehensive review, we elucidate the fundamental principles of CRISPR/Cas9-related methodologies and explore their wide-ranging applications in deciphering molecular intricacies during oocyte and early embryo development as well as in addressing associated diseases. However, it is imperative to acknowledge the limitations inherent to these technologies, including the potential for off-target effects, as well as the ethical concerns surrounding the manipulation of human embryos. Thus, a judicious and thoughtful approach is warranted. Regardless of these challenges, CRISPR/Cas9 technology undeniably represents a formidable tool for genome and epigenome manipulation within oocytes and early embryos. Continuous refinements in this field are poised to fortify its future prospects and applications.
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Affiliation(s)
- Yi-Ran Zhang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Tai-Lang Yin
- Reproductive Medical Center, Renmin Hospital of Wuhan University & Hubei Clinic Research Center for Assisted Reproductive Technology and Embryonic Development, Wuhan, China.
| | - Li-Quan Zhou
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
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Tsuchida CA, Brandes N, Bueno R, Trinidad M, Mazumder T, Yu B, Hwang B, Chang C, Liu J, Sun Y, Hopkins CR, Parker KR, Qi Y, Hofman L, Satpathy AT, Stadtmauer EA, Cate JHD, Eyquem J, Fraietta JA, June CH, Chang HY, Ye CJ, Doudna JA. Mitigation of chromosome loss in clinical CRISPR-Cas9-engineered T cells. Cell 2023; 186:4567-4582.e20. [PMID: 37794590 PMCID: PMC10664023 DOI: 10.1016/j.cell.2023.08.041] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 05/11/2023] [Accepted: 08/31/2023] [Indexed: 10/06/2023]
Abstract
CRISPR-Cas9 genome editing has enabled advanced T cell therapies, but occasional loss of the targeted chromosome remains a safety concern. To investigate whether Cas9-induced chromosome loss is a universal phenomenon and evaluate its clinical significance, we conducted a systematic analysis in primary human T cells. Arrayed and pooled CRISPR screens revealed that chromosome loss was generalizable across the genome and resulted in partial and entire loss of the targeted chromosome, including in preclinical chimeric antigen receptor T cells. T cells with chromosome loss persisted for weeks in culture, implying the potential to interfere with clinical use. A modified cell manufacturing process, employed in our first-in-human clinical trial of Cas9-engineered T cells (NCT03399448), reduced chromosome loss while largely preserving genome editing efficacy. Expression of p53 correlated with protection from chromosome loss observed in this protocol, suggesting both a mechanism and strategy for T cell engineering that mitigates this genotoxicity in the clinic.
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Affiliation(s)
- Connor A Tsuchida
- University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Nadav Brandes
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Raymund Bueno
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Marena Trinidad
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Thomas Mazumder
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Bingfei Yu
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA; Parker Institute for Cancer Immunotherapy, Stanford University School of Medicine, Stanford, CA, USA
| | - Byungjin Hwang
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Christopher Chang
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA; Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Parker Institute for Cancer Immunotherapy, University of California, San Francisco, San Francisco, CA, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Jamin Liu
- University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Yang Sun
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Caitlin R Hopkins
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kevin R Parker
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Yanyan Qi
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Laura Hofman
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA; Graduate School of Life Sciences, Utrecht University, Utrecht, the Netherlands
| | - Ansuman T Satpathy
- Parker Institute for Cancer Immunotherapy, Stanford University School of Medicine, Stanford, CA, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Edward A Stadtmauer
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jamie H D Cate
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Justin Eyquem
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Parker Institute for Cancer Immunotherapy, University of California, San Francisco, San Francisco, CA, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Joseph A Fraietta
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Carl H June
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA; Parker Institute for Cancer Immunotherapy, Stanford University School of Medicine, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Chun Jimmie Ye
- University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, USA; Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Parker Institute for Cancer Immunotherapy, University of California, San Francisco, San Francisco, CA, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA; Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, CA, USA; Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA.
| | - Jennifer A Doudna
- University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA; Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Department of Chemistry, University of California Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA, USA.
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Kubikova N, Keefe DL, Wells D, Oktay KH, Feinberg EC. Should we use CRISPR gene editing in human embryos? Fertil Steril 2023; 120:737-744. [PMID: 37656090 DOI: 10.1016/j.fertnstert.2023.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 08/07/2023] [Indexed: 09/02/2023]
Affiliation(s)
- Nada Kubikova
- Jesus College, University of Oxford, Oxford, United Kingdom; Nuffield Department of Women's and Reproductive Health, University of Oxford, Oxford, United Kingdom
| | - David L Keefe
- NYU Grossman School of Medicine, New York, New York; NYU Langone Fertility Center, New York, New York
| | - Dagan Wells
- John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom; Juno Genetics, Oxford, United Kingdom
| | - Kutluk H Oktay
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale University School of Medicine, New Haven, Connecticut; Innovation Institute for Fertility Preservation, New York, New York; Innovation Institute for Fertility Preservation, New Haven, Connecticut
| | - Eve C Feinberg
- Division of Reproductive Endocrinology and Infertility, Northwestern University Feinberg School of Medicine, Chicago, Illinois
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Yu M, Hu S, Tang B, Yang H, Sun D. Engineering Escherichia coli Nissle 1917 as a microbial chassis for therapeutic and industrial applications. Biotechnol Adv 2023; 67:108202. [PMID: 37343690 DOI: 10.1016/j.biotechadv.2023.108202] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 05/19/2023] [Accepted: 06/17/2023] [Indexed: 06/23/2023]
Abstract
Genetically engineered microbes, especially Escherichia coli, have been widely used in the biosynthesis of proteins and metabolites for medical and industrial applications. As a traditional probiotic with a well-established safety record, E. coli Nissle 1917 (EcN) has recently emerged as a microbial chassis for generating living therapeutics, drug delivery vehicles, and microbial platforms for industrial production. Despite the availability of genetic tools for engineering laboratory E. coli K-12 and B strains, new genetic engineering systems are still greatly needed to expand the application range of EcN. In this review, we have summarized the latest progress in the development of genetic engineering systems in EcN, as well as their applications in the biosynthesis and delivery of valuable small molecules and biomacromolecules of medical and/or industrial interest, followed by a glimpse of how this rapidly growing field will evolve in the future.
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Affiliation(s)
- Mingjing Yu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
| | - Shilong Hu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
| | - Biao Tang
- Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, Zhejiang, China
| | - Hua Yang
- Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, Zhejiang, China
| | - Dongchang Sun
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China.
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45
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Xie D, Gu B, Liu Y, Ye P, Ma Y, Wen T, Song X, Zhao Z. Efficient targeted recombination with CRISPR/Cas9 in hybrids of Caenorhabditis nematodes with suppressed recombination. BMC Biol 2023; 21:203. [PMID: 37775783 PMCID: PMC10542263 DOI: 10.1186/s12915-023-01704-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 09/18/2023] [Indexed: 10/01/2023] Open
Abstract
BACKGROUND Homology-based recombination (HR) is the cornerstone of genetic mapping. However, a lack of sufficient sequence homology or the presence of a genomic rearrangement prevents HR through crossing, which inhibits genetic mapping in relevant genomic regions. This is particularly true in species hybrids whose genomic sequences are highly divergent along with various genome arrangements, making the mapping of genetic loci, such as hybrid incompatibility (HI) loci, through crossing impractical. We previously mapped tens of HI loci between two nematodes, Caenorhabditis briggsae and C. nigoni, through the repeated backcrossing of GFP-linked C. briggsae fragments into C. nigoni. However, the median introgression size was over 7 Mb, indicating apparent HR suppression and preventing the subsequent cloning of the causative gene underlying a given HI phenotype. Therefore, a robust method that permits recombination independent of sequence homology is desperately desired. RESULTS Here, we report a method of highly efficient targeted recombination (TR) induced by CRISPR/Cas9 with dual guide RNAs (gRNAs), which circumvents the HR suppression in hybrids between the two species. We demonstrated that a single gRNA was able to induce efficient TR between highly homologous sequences only in the F1 hybrids but not in the hybrids that carry a GFP-linked C. briggsae fragment in an otherwise C. nigoni background. We achieved highly efficient TR, regardless of sequence homology or genetic background, when dual gRNAs were used that each specifically targeted one parental chromosome. We further showed that dual gRNAs were able to induce efficient TR within genomic regions that had undergone inversion, in which HR-based recombination was expected to be suppressed, supporting the idea that dual-gRNA-induced TR can be achieved through nonhomology-based end joining between two parental chromosomes. CONCLUSIONS Recombination suppression can be circumvented through CRISPR/Cas9 with dual gRNAs, regardless of sequence homology or the genetic background of the species hybrid. This method is expected to be applicable to other situations in which recombination is suppressed in interspecies or intrapopulation hybrids.
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Affiliation(s)
- Dongying Xie
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Bida Gu
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, USA
| | - Yiqing Liu
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Pohao Ye
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Yiming Ma
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Tongshu Wen
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Xiaoyuan Song
- MOE Key Laboratory of Cellular Dynamics, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, 230026, Anhui, China
| | - Zhongying Zhao
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China.
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Gapinske M, Winter J, Swami D, Gapinske L, Woods WS, Shirguppe S, Miskalis A, Busza A, Joulani D, Kao CJ, Kostan K, Bigot A, Bashir R, Perez-Pinera P. Targeting Duchenne muscular dystrophy by skipping DMD exon 45 with base editors. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:572-586. [PMID: 37637209 PMCID: PMC10448430 DOI: 10.1016/j.omtn.2023.07.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 07/25/2023] [Indexed: 08/29/2023]
Abstract
Duchenne muscular dystrophy is an X-linked monogenic disease caused by mutations in the dystrophin gene (DMD) characterized by progressive muscle weakness, leading to loss of ambulation and decreased life expectancy. Since the current standard of care for Duchenne muscular dystrophy is to merely treat symptoms, there is a dire need for treatment modalities that can correct the underlying genetic mutations. While several gene replacement therapies are being explored in clinical trials, one emerging approach that can directly correct mutations in genomic DNA is base editing. We have recently developed CRISPR-SKIP, a base editing strategy to induce permanent exon skipping by introducing C > T or A > G mutations at splice acceptors in genomic DNA, which can be used therapeutically to recover dystrophin expression when a genomic deletion leads to an out-of-frame DMD transcript. We now demonstrate that CRISPR-SKIP can be adapted to correct some forms of Duchenne muscular dystrophy by disrupting the splice acceptor in human DMD exon 45 with high efficiency, which enables open reading frame recovery and restoration of dystrophin expression. We also demonstrate that AAV-delivered split-intein base editors edit the splice acceptor of DMD exon 45 in cultured human cells and in vivo, highlighting the therapeutic potential of this strategy.
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Affiliation(s)
- Michael Gapinske
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jackson Winter
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Devyani Swami
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Lauren Gapinske
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Nick J. Holonyak Micro and Nano Technology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Wendy S. Woods
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Shraddha Shirguppe
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Angelo Miskalis
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Anna Busza
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Dana Joulani
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Collin J. Kao
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Kurt Kostan
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Anne Bigot
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, 75013 Paris, France
| | - Rashid Bashir
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Nick J. Holonyak Micro and Nano Technology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carle Illinois College of Medicine, Champaign, IL 61820, USA
| | - Pablo Perez-Pinera
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carle Illinois College of Medicine, Champaign, IL 61820, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Molecular and Integrative Physiology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
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47
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Bestas B, Wimberger S, Degtev D, Madsen A, Rottner AK, Karlsson F, Naumenko S, Callahan M, Touza JL, Francescatto M, Möller CI, Badertscher L, Li S, Cerboni S, Selfjord N, Ericson E, Gordon E, Firth M, Chylinski K, Taheri-Ghahfarokhi A, Bohlooly-Y M, Snowden M, Pangalos M, Nuttall B, Akcakaya P, Sienski G, Maresca M. A Type II-B Cas9 nuclease with minimized off-targets and reduced chromosomal translocations in vivo. Nat Commun 2023; 14:5474. [PMID: 37673883 PMCID: PMC10482872 DOI: 10.1038/s41467-023-41240-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 08/25/2023] [Indexed: 09/08/2023] Open
Abstract
Streptococcus pyogenes Cas9 (SpCas9) and derived enzymes are widely used as genome editors, but their promiscuous nuclease activity often induces undesired mutations and chromosomal rearrangements. Several strategies for mapping off-target effects have emerged, but they suffer from limited sensitivity. To increase the detection sensitivity, we develop an off-target assessment workflow that uses Duplex Sequencing. The strategy increases sensitivity by one order of magnitude, identifying previously unknown SpCas9's off-target mutations in the humanized PCSK9 mouse model. To reduce off-target risks, we perform a bioinformatic search and identify a high-fidelity Cas9 variant of the II-B subfamily from Parasutterella secunda (PsCas9). PsCas9 shows improved specificity as compared to SpCas9 across multiple tested sites, both in vitro and in vivo, including the PCSK9 site. In the future, while PsCas9 will offer an alternative to SpCas9 for research and clinical use, the Duplex Sequencing workflow will enable a more sensitive assessment of Cas9 editing outcomes.
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Affiliation(s)
- Burcu Bestas
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Sandra Wimberger
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
- Department of Chemistry & Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Dmitrii Degtev
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Alexandra Madsen
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Antje K Rottner
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Fredrik Karlsson
- Data Sciences and Quantitative Biology, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Cambridge, UK
| | - Sergey Naumenko
- Department of Biostatistics, Harvard Chan School of Public Health, Boston, MA, USA
| | - Megan Callahan
- Translational Genomics, Translational Medicine, R&D Oncology, AstraZeneca, Waltham, MA, USA
| | - Julia Liz Touza
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Margherita Francescatto
- Data Sciences and Quantitative Biology, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Cambridge, UK
| | - Carl Ivar Möller
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Lukas Badertscher
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Songyuan Li
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Silvia Cerboni
- Translational Science and Experimental Medicine, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Niklas Selfjord
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Elke Ericson
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Euan Gordon
- Discovery Biology, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Mike Firth
- Data Sciences and Quantitative Biology, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Cambridge, UK
| | | | - Amir Taheri-Ghahfarokhi
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Mohammad Bohlooly-Y
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Mike Snowden
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | | | - Barrett Nuttall
- Translational Genomics, Translational Medicine, R&D Oncology, AstraZeneca, Waltham, MA, USA
| | - Pinar Akcakaya
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Grzegorz Sienski
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden.
| | - Marcello Maresca
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden.
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48
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Ryu J, Adashi EY, Hennebold JD. The history, use, and challenges of therapeutic somatic cell and germline gene editing. Fertil Steril 2023; 120:528-538. [PMID: 36878350 PMCID: PMC10477338 DOI: 10.1016/j.fertnstert.2023.02.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 02/24/2023] [Accepted: 02/28/2023] [Indexed: 03/08/2023]
Abstract
The advent of directed gene-editing technologies now over 10 years ago ushered in a new era of precision medicine wherein specific disease-causing mutations can be corrected. In parallel with developing new gene-editing platforms, optimizing their efficiency and delivery has been remarkable. With their development, there has been interest in using gene-editing systems for correcting disease mutations in differentiated somatic cells ex vivo or in vivo or for germline gene editing in gametes or 1-cell embryos to potentially limit genetic diseases in the offspring and in future generations. This review details the development and history of the current gene-editing systems and the advantages and challenges in their use for somatic cell and germline gene editing.
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Affiliation(s)
- Junghyun Ryu
- Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon
| | - Eli Y Adashi
- Department of Medical Science, The Warren Alpert Medical School, Brown University, Providence, Rhode Island
| | - Jon D Hennebold
- Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon; Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, Oregon.
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49
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Lidonnici MR, Scaramuzza S, Ferrari G. Gene Therapy for Hemoglobinopathies. Hum Gene Ther 2023; 34:793-807. [PMID: 37675899 DOI: 10.1089/hum.2023.138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2023] Open
Abstract
β-Thalassemia and sickle cell disease are autosomal recessive disorders of red blood cells due to mutations in the adult β-globin gene, with a worldwide diffusion. The severe forms of hemoglobinopathies are fatal if untreated, and allogeneic bone marrow transplantation can be offered to a limited proportion of patients. The unmet clinical need and the disease incidence have promoted the development of new genetic therapies based on the engineering of autologous hematopoietic stem cells. Here, the steps of ex vivo gene therapy development are reviewed along with results from clinical trials and recent new approaches employing cutting edge gene editing tools.
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Affiliation(s)
- Maria Rosa Lidonnici
- San Raffaele-Telethon Institute for Gene Therapy (SR-TIGET), San Raffaele Scientific Institute, Milan, Italy; and
| | - Samantha Scaramuzza
- San Raffaele-Telethon Institute for Gene Therapy (SR-TIGET), San Raffaele Scientific Institute, Milan, Italy; and
| | - Giuliana Ferrari
- San Raffaele-Telethon Institute for Gene Therapy (SR-TIGET), San Raffaele Scientific Institute, Milan, Italy; and
- University Vita-Salute San Raffaele, Milan, Italy
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50
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Riesenberg S, Kanis P, Macak D, Wollny D, Düsterhöft D, Kowalewski J, Helmbrecht N, Maricic T, Pääbo S. Efficient high-precision homology-directed repair-dependent genome editing by HDRobust. Nat Methods 2023; 20:1388-1399. [PMID: 37474806 PMCID: PMC10482697 DOI: 10.1038/s41592-023-01949-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 06/12/2023] [Indexed: 07/22/2023]
Abstract
Homology-directed repair (HDR), a method for repair of DNA double-stranded breaks can be leveraged for the precise introduction of mutations supplied by synthetic DNA donors, but remains limited by low efficiency and off-target effects. In this study, we report HDRobust, a high-precision method that, via the combined transient inhibition of nonhomologous end joining and microhomology-mediated end joining, resulted in the induction of point mutations by HDR in up to 93% (median 60%, s.e.m. 3) of chromosomes in populations of cells. We found that, using this method, insertions, deletions and rearrangements at the target site, as well as unintended changes at other genomic sites, were largely abolished. We validated this approach for 58 different target sites and showed that it allows efficient correction of pathogenic mutations in cells derived from patients suffering from anemia, sickle cell disease and thrombophilia.
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Affiliation(s)
- Stephan Riesenberg
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Philipp Kanis
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Dominik Macak
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Damian Wollny
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Dorothee Düsterhöft
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Johannes Kowalewski
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Nelly Helmbrecht
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Tomislav Maricic
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Svante Pääbo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Human Evolutionary Genomics Unit, Okinawa Institute of Science and Technology, Onna-son, Japan
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