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Zheng Y, Li Y, Zhou K, Li T, VanDusen NJ, Hua Y. Precise genome-editing in human diseases: mechanisms, strategies and applications. Signal Transduct Target Ther 2024; 9:47. [PMID: 38409199 PMCID: PMC10897424 DOI: 10.1038/s41392-024-01750-2] [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: 05/17/2023] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 02/28/2024] Open
Abstract
Precise genome-editing platforms are versatile tools for generating specific, site-directed DNA insertions, deletions, and substitutions. The continuous enhancement of these tools has led to a revolution in the life sciences, which promises to deliver novel therapies for genetic disease. Precise genome-editing can be traced back to the 1950s with the discovery of DNA's double-helix and, after 70 years of development, has evolved from crude in vitro applications to a wide range of sophisticated capabilities, including in vivo applications. Nonetheless, precise genome-editing faces constraints such as modest efficiency, delivery challenges, and off-target effects. In this review, we explore precise genome-editing, with a focus on introduction of the landmark events in its history, various platforms, delivery systems, and applications. First, we discuss the landmark events in the history of precise genome-editing. Second, we describe the current state of precise genome-editing strategies and explain how these techniques offer unprecedented precision and versatility for modifying the human genome. Third, we introduce the current delivery systems used to deploy precise genome-editing components through DNA, RNA, and RNPs. Finally, we summarize the current applications of precise genome-editing in labeling endogenous genes, screening genetic variants, molecular recording, generating disease models, and gene therapy, including ex vivo therapy and in vivo therapy, and discuss potential future advances.
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Affiliation(s)
- Yanjiang Zheng
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yifei Li
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Kaiyu Zhou
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Tiange Li
- Department of Cardiovascular Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Nathan J VanDusen
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
| | - Yimin Hua
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
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2
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David M, Monteferrario D, Saviane G, Jeanneau C, Marchetti I, Dupont CF, Dumont C, Fontenot JD, Rosa MDL, Fenard D. Production of therapeutic levels of human FIX-R338L by engineered B cells using GMP-compatible medium. Mol Ther Methods Clin Dev 2023; 31:101111. [PMID: 37790246 PMCID: PMC10543988 DOI: 10.1016/j.omtm.2023.101111] [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: 03/10/2023] [Accepted: 09/13/2023] [Indexed: 10/05/2023]
Abstract
B cells can differentiate into plasmablast and plasma cells, capable of producing antibodies for decades. Gene editing using zinc-finger nucleases (ZFN) enables the engineering of B cells capable of secreting sustained and high levels of therapeutic proteins. In this study, we established an advanced in vitro good manufacturing practice-compatible culturing system characterized by robust and consistent expansion rate, high viability, and efficient B cell differentiation. Using this process, an optimized B cell editing protocol was developed by combining ZFN/adeno-associated virus 6 technology to achieve site-specific insertion of the human factor IX R338L Padua into the silent TRAC locus. In vitro analysis revealed high levels of secreted human immunoglobulins and human factor IX-Padua. Following intravenous infusion in a mouse model, human plasma cells were detected in spleen and bone marrow, indicating successful and potentially long-term engraftment in vivo. Moreover, high levels of human immunoglobin and therapeutic levels of human factor IX-Padua were detected in mouse plasma, correlating with 15% of normal human factor IX activity. These data suggest that the proposed process promotes the production of functional and differentiated engineered B cells. In conclusion, this study represents an important step toward the development of a manufacturing platform for potential B cell-derived therapeutic products.
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Affiliation(s)
- Marion David
- Sangamo Therapeutics France, Allée de la Nertière, F-06560 Valbonne Sophia-Antipolis, France
| | - Davide Monteferrario
- Sangamo Therapeutics France, Allée de la Nertière, F-06560 Valbonne Sophia-Antipolis, France
| | - Gaëlle Saviane
- Sangamo Therapeutics France, Allée de la Nertière, F-06560 Valbonne Sophia-Antipolis, France
| | - Caroline Jeanneau
- Sangamo Therapeutics France, Allée de la Nertière, F-06560 Valbonne Sophia-Antipolis, France
| | - Irène Marchetti
- Sangamo Therapeutics France, Allée de la Nertière, F-06560 Valbonne Sophia-Antipolis, France
| | - Coralie F. Dupont
- Sangamo Therapeutics France, Allée de la Nertière, F-06560 Valbonne Sophia-Antipolis, France
| | - Céline Dumont
- Sangamo Therapeutics France, Allée de la Nertière, F-06560 Valbonne Sophia-Antipolis, France
| | - Jason D. Fontenot
- Sangamo Therapeutics, 7000 Marina Boulevard, Brisbane, CA 94005, USA
| | - Maurus de la Rosa
- Sangamo Therapeutics France, Allée de la Nertière, F-06560 Valbonne Sophia-Antipolis, France
| | - David Fenard
- Sangamo Therapeutics France, Allée de la Nertière, F-06560 Valbonne Sophia-Antipolis, France
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3
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Hino T, Omura SN, Nakagawa R, Togashi T, Takeda SN, Hiramoto T, Tasaka S, Hirano H, Tokuyama T, Uosaki H, Ishiguro S, Kagieva M, Yamano H, Ozaki Y, Motooka D, Mori H, Kirita Y, Kise Y, Itoh Y, Matoba S, Aburatani H, Yachie N, Karvelis T, Siksnys V, Ohmori T, Hoshino A, Nureki O. An AsCas12f-based compact genome-editing tool derived by deep mutational scanning and structural analysis. Cell 2023; 186:4920-4935.e23. [PMID: 37776859 DOI: 10.1016/j.cell.2023.08.031] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/27/2023] [Accepted: 08/23/2023] [Indexed: 10/02/2023]
Abstract
SpCas9 and AsCas12a are widely utilized as genome-editing tools in human cells. However, their relatively large size poses a limitation for delivery by cargo-size-limited adeno-associated virus (AAV) vectors. The type V-F Cas12f from Acidibacillus sulfuroxidans is exceptionally compact (422 amino acids) and has been harnessed as a compact genome-editing tool. Here, we developed an approach, combining deep mutational scanning and structure-informed design, to successfully generate two AsCas12f activity-enhanced (enAsCas12f) variants. Remarkably, the enAsCas12f variants exhibited genome-editing activities in human cells comparable with those of SpCas9 and AsCas12a. The cryoelectron microscopy (cryo-EM) structures revealed that the mutations stabilize the dimer formation and reinforce interactions with nucleic acids to enhance their DNA cleavage activities. Moreover, enAsCas12f packaged with partner genes in an all-in-one AAV vector exhibited efficient knock-in/knock-out activities and transcriptional activation in mice. Taken together, enAsCas12f variants could offer a minimal genome-editing platform for in vivo gene therapy.
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Affiliation(s)
- Tomohiro Hino
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
| | - Satoshi N Omura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Ryoya Nakagawa
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Tomoki Togashi
- Department of Biochemistry, Jichi Medical University School of Medicine, Tochigi 329-0498, Japan; Department of Clinical Laboratory Science, Division of Health Sciences, Graduate School of Medical Science, Kanazawa University, Ishikawa 920-0942, Japan
| | - Satoru N Takeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Takafumi Hiramoto
- Department of Biochemistry, Jichi Medical University School of Medicine, Tochigi 329-0498, Japan
| | - Satoshi Tasaka
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
| | - Hisato Hirano
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Takeshi Tokuyama
- Division of Regenerative Medicine, Center for Molecular Medicine, Jichi Medical University, Tochigi 329-0498, Japan
| | - Hideki Uosaki
- Division of Regenerative Medicine, Center for Molecular Medicine, Jichi Medical University, Tochigi 329-0498, Japan
| | - Soh Ishiguro
- School of Biomedical Engineering, Faculty of Applied Science and Faculty of Medicine, The University of British Columbia, Vancouver, BC V6S 0L4, Canada
| | - Madina Kagieva
- School of Biomedical Engineering, Faculty of Applied Science and Faculty of Medicine, The University of British Columbia, Vancouver, BC V6S 0L4, Canada
| | - Hiroyuki Yamano
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Yuki Ozaki
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Daisuke Motooka
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan; Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka 565-0871, Japan
| | - Hideto Mori
- Institute for Advanced Biosciences, Keio University, Yamagata 997-0035, Japan; Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa 252-0882, Japan; Premium Research Institute for Human Metaverse Medicine (WPI-PRIMe), Osaka University, Suita, Osaka, 565-0871, Japan
| | - Yuhei Kirita
- Department of Nephrology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
| | - Yoshiaki Kise
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan; Curreio, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yuzuru Itoh
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Satoaki Matoba
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
| | - Hiroyuki Aburatani
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan
| | - Nozomu Yachie
- School of Biomedical Engineering, Faculty of Applied Science and Faculty of Medicine, The University of British Columbia, Vancouver, BC V6S 0L4, Canada; Premium Research Institute for Human Metaverse Medicine (WPI-PRIMe), Osaka University, Suita, Osaka, 565-0871, Japan; Synthetic Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan
| | - Tautvydas Karvelis
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Virginijus Siksnys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Tsukasa Ohmori
- Department of Biochemistry, Jichi Medical University School of Medicine, Tochigi 329-0498, Japan; Center for Gene Therapy Research, Jichi Medical University, Tochigi 329-0498, Japan.
| | - Atsushi Hoshino
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan.
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.
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Chen FW, Davies JP, Calvo R, Chaudhari J, Dolios G, Taylor MK, Patnaik S, Dehdashti J, Mull R, Dranchack P, Wang A, Xu X, Hughes E, Southall N, Ferrer M, Wang R, Marugan JJ, Ioannou YA. Activation of mitochondrial TRAP1 stimulates mitochondria-lysosome crosstalk and correction of lysosomal dysfunction. iScience 2022; 25:104941. [PMID: 36065186 PMCID: PMC9440283 DOI: 10.1016/j.isci.2022.104941] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 04/27/2022] [Accepted: 08/11/2022] [Indexed: 11/29/2022] Open
Affiliation(s)
- Fannie W. Chen
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Joanna P. Davies
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Raul Calvo
- Early Translation Branch, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Jagruti Chaudhari
- Cell Therapy and Cell Engineering Facility, Memorial Sloan Kettering Cancer Center, 1250 1st Avenue, New York, NY 10065, USA
| | - Georgia Dolios
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mercedes K. Taylor
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
| | - Samarjit Patnaik
- Early Translation Branch, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Jean Dehdashti
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Rebecca Mull
- Early Translation Branch, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Patricia Dranchack
- Early Translation Branch, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Amy Wang
- Early Translation Branch, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Xin Xu
- Early Translation Branch, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Emma Hughes
- Early Translation Branch, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Noel Southall
- Early Translation Branch, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Marc Ferrer
- Early Translation Branch, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Rong Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Juan J. Marugan
- Early Translation Branch, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
- Corresponding author
| | - Yiannis A. Ioannou
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Corresponding author
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5
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Zabaleta N, Torella L, Weber ND, Gonzalez‐Aseguinolaza G. mRNA and gene editing: Late breaking therapies in liver diseases. Hepatology 2022; 76:869-887. [PMID: 35243655 PMCID: PMC9546265 DOI: 10.1002/hep.32441] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 12/13/2022]
Abstract
The efficient delivery of RNA molecules to restore the expression of a missing or inadequately functioning protein in a target cell and the intentional specific modification of the host genome using engineered nucleases represent therapeutic concepts that are revolutionizing modern medicine. The initiation of several clinical trials using these approaches to treat metabolic liver disorders as well as the recently reported remarkable results obtained by patients with transthyretin amyloidosis highlight the advances in this field and show the potential of these therapies to treat these diseases safely and efficaciously. These advances have been possible due, firstly, to significant improvements made in RNA chemistry that increase its stability and prevent activation of the innate immune response and, secondly, to the development of very efficient liver-targeted RNA delivery systems. In parallel, the breakout of CRISPR/CRISPR-associated 9-based technology in the gene editing field has marked a turning point in in vivo modification of the cellular genome with therapeutic purposes, which can be based on gene supplementation, correction, or silencing. In the coming years we are likely to witness the therapeutic potential of these two strategies both separately and in combination. In this review we summarize the preclinical data obtained in animal models treated with mRNA as a therapeutic agent and discuss the different gene editing strategies applied to the treatment of liver diseases, highlighting both their therapeutic efficacy as well as safety concerns.
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Affiliation(s)
- Nerea Zabaleta
- Grousbeck Gene Therapy CenterSchepens Eye Research InstituteMass Eye and EarBostonMassachusettsUSA
| | - Laura Torella
- Gene Therapy and Regulation of Gene expression Program, Foundation for Applied Medical ResearchUniversity of NavarraIdisNAPamplonaSpain
| | | | - Gloria Gonzalez‐Aseguinolaza
- Gene Therapy and Regulation of Gene expression Program, Foundation for Applied Medical ResearchUniversity of NavarraIdisNAPamplonaSpain,Vivet TherapeuticsPamplonaSpain
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Nagree MS, Felizardo TC, Faber ML, Rybova J, Rupar CA, Foley SR, Fuller M, Fowler DH, Medin JA. Autologous, lentivirus-modified, T-rapa cell "micropharmacies" for lysosomal storage disorders. EMBO Mol Med 2022; 14:e14297. [PMID: 35298086 PMCID: PMC8988206 DOI: 10.15252/emmm.202114297] [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: 03/18/2021] [Revised: 02/07/2022] [Accepted: 02/09/2022] [Indexed: 11/11/2022] Open
Abstract
T cells are the current choice for many cell therapy applications. They are relatively easy to access, expand in culture, and genetically modify. Rapamycin‐conditioning ex vivo reprograms T cells, increasing their memory properties and capacity for survival, while reducing inflammatory potential and the amount of preparative conditioning required for engraftment. Rapamycin‐conditioned T cells have been tested in patients and deemed to be safe to administer in numerous settings, with reduced occurrence of infusion‐related adverse events. We demonstrate that ex vivo lentivirus‐modified, rapamycin‐conditioned CD4+ T cells can also act as next‐generation cellular delivery vehicles—that is, “micropharmacies”—to disseminate corrective enzymes for multiple lysosomal storage disorders. We evaluated the therapeutic potential of this treatment platform for Fabry, Gaucher, Farber, and Pompe diseases in vitro and in vivo. For example, such micropharmacies expressing α‐galactosidase A for treatment of Fabry disease were transplanted in mice where they provided functional enzyme in key affected tissues such as kidney and heart, facilitating clearance of pathogenic substrate after a single administration.
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Affiliation(s)
- Murtaza S Nagree
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.,Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
| | | | - Mary L Faber
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Jitka Rybova
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - C Anthony Rupar
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - S Ronan Foley
- Juravinski Hospital and Cancer Centre, McMaster University, Hamilton, ON, Canada
| | - Maria Fuller
- Genetics and Molecular Pathology, SA Pathology at Women's and Children's Hospital, North Adelaide, SA, Australia
| | | | - Jeffrey A Medin
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.,Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA.,Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
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Phenocopies of sarcomere gene mediated hypertrophic cardiomyopathy in children. PROGRESS IN PEDIATRIC CARDIOLOGY 2021. [DOI: 10.1016/j.ppedcard.2021.101419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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