1
|
Lim SR, Kim HJ, Lee SJ. Efficient CRISPR-Cas12f1-Mediated Multiplex Bacterial Genome Editing via Low-Temperature Recovery. J Microbiol Biotechnol 2024; 34:1522-1529. [PMID: 38881238 PMCID: PMC11294644 DOI: 10.4014/jmb.2403.03033] [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: 03/18/2024] [Revised: 05/27/2024] [Accepted: 05/29/2024] [Indexed: 06/18/2024]
Abstract
CRISPR-Cas system is being used as a powerful genome editing tool with developments focused on enhancing its efficiency and accuracy. Recently, the miniature CRISPR-Cas12f1 system, which is small enough to be easily loaded onto various vectors for cellular delivery, has gained attention. In this study, we explored the influence of temperature conditions on multiplex genome editing using CRISPR-Cas12f1 in an Escherichia coli model. It was revealed that when two distinct targets in the genome are edited simultaneously, the editing efficiency can be enhanced by allowing cells to recover at a reduced temperature during the editing process. Additionally, employing 3'-end truncated sgRNAs facilitated the simultaneous single-nucleotide level editing of three targets. Our results underscore the potential of optimizing recovery temperature and sgRNA design protocols in developing more effective and precise strategies for multiplex genome editing across various organisms.
Collapse
Affiliation(s)
- Se Ra Lim
- Department of Systems Biotechnology and Institute of Microbiomics, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Hyun Ju Kim
- Department of Systems Biotechnology and Institute of Microbiomics, Chung-Ang University, Anseong 17546, Republic of Korea
- Nakdonggang National Institute of Biological Resources, Sangju 37242, Republic of Korea
| | - Sang Jun Lee
- Department of Systems Biotechnology and Institute of Microbiomics, Chung-Ang University, Anseong 17546, Republic of Korea
| |
Collapse
|
2
|
Husser MC, Pham NP, Law C, Araujo FRB, Martin VJJ, Piekny A. Endogenous tagging using split mNeonGreen in human iPSCs for live imaging studies. eLife 2024; 12:RP92819. [PMID: 38652106 PMCID: PMC11037917 DOI: 10.7554/elife.92819] [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: 04/25/2024] Open
Abstract
Endogenous tags have become invaluable tools to visualize and study native proteins in live cells. However, generating human cell lines carrying endogenous tags is difficult due to the low efficiency of homology-directed repair. Recently, an engineered split mNeonGreen protein was used to generate a large-scale endogenous tag library in HEK293 cells. Using split mNeonGreen for large-scale endogenous tagging in human iPSCs would open the door to studying protein function in healthy cells and across differentiated cell types. We engineered an iPS cell line to express the large fragment of the split mNeonGreen protein (mNG21-10) and showed that it enables fast and efficient endogenous tagging of proteins with the short fragment (mNG211). We also demonstrate that neural network-based image restoration enables live imaging studies of highly dynamic cellular processes such as cytokinesis in iPSCs. This work represents the first step towards a genome-wide endogenous tag library in human stem cells.
Collapse
Affiliation(s)
| | - Nhat P Pham
- Biology Department, Concordia University, Montreal, Canada
| | - Chris Law
- Biology Department, Concordia University, Montreal, Canada
- Center for Microscopy and Cellular Imaging, Concordia University, Montreal, Canada
| | - Flavia R B Araujo
- Center for Applied Synthetic Biology, Concordia University, Montreal, Canada
| | - Vincent J J Martin
- Biology Department, Concordia University, Montreal, Canada
- Center for Applied Synthetic Biology, Concordia University, Montreal, Canada
| | - Alisa Piekny
- Biology Department, Concordia University, Montreal, Canada
- Center for Microscopy and Cellular Imaging, Concordia University, Montreal, Canada
- Center for Applied Synthetic Biology, Concordia University, Montreal, Canada
| |
Collapse
|
3
|
Bouchareb A, Biggs D, Alghadban S, Preece C, Davies B. Increasing Knockin Efficiency in Mouse Zygotes by Transient Hypothermia. CRISPR J 2024; 7:111-119. [PMID: 38635329 PMCID: PMC7615915 DOI: 10.1089/crispr.2023.0077] [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: 04/20/2024] Open
Abstract
Integration of a point mutation to correct or edit a gene requires the repair of the CRISPR-Cas9-induced double-strand break by homology-directed repair (HDR). This repair pathway is more active in late S and G2 phases of the cell cycle, whereas the competing pathway of nonhomologous end-joining (NHEJ) operates throughout the cell cycle. Accordingly, modulation of the cell cycle by chemical perturbation or simply by the timing of gene editing to shift the editing toward the S/G2 phase has been shown to increase HDR rates. Using a traffic light reporter in mouse embryonic stem cells and a fluorescence conversion reporter in human-induced pluripotent stem cells, we confirm that a transient cold shock leads to an increase in the rate of HDR, with a corresponding decrease in the rate of NHEJ repair. We then investigated whether a similar cold shock could lead to an increase in the rate of HDR in the mouse embryo. By analyzing the efficiency of gene editing using single nucleotide polymorphism changes and loxP insertion at three different genetic loci, we found that a transient reduction in temperature after zygote electroporation of CRISPR-Cas9 ribonucleoprotein with a single-stranded oligodeoxynucleotide repair template did indeed increase knockin efficiency, without affecting embryonic development. The efficiency of gene editing with and without the cold shock was first assessed by genotyping blastocysts. As a proof of concept, we then confirmed that the modified embryo culture conditions were compatible with live births by targeting the coat color gene tyrosinase and observing the repair of the albino mutation. Taken together, our data suggest that a transient cold shock could offer a simple and robust way to improve knockin outcomes in both stem cells and zygotes.
Collapse
Affiliation(s)
| | - Daniel Biggs
- Wellcome Centre for Human Genetics, Oxford, United Kingdom
| | - Samy Alghadban
- Wellcome Centre for Human Genetics, Oxford, United Kingdom
| | | | - Benjamin Davies
- Wellcome Centre for Human Genetics, Oxford, United Kingdom
- The Francis Crick Institute, London, United Kingdom
| |
Collapse
|
4
|
Nakanishi-Koakutsu M, Miki K, Naka Y, Sasaki M, Wakimizu T, Napier SC, Okubo C, Narita M, Nishikawa M, Hata R, Chonabayashi K, Hotta A, Imahashi K, Nishimoto T, Yoshida Y. CD151 expression marks atrial- and ventricular- differentiation from human induced pluripotent stem cells. Commun Biol 2024; 7:231. [PMID: 38418926 PMCID: PMC10901864 DOI: 10.1038/s42003-024-05809-2] [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: 09/03/2022] [Accepted: 01/11/2024] [Indexed: 03/02/2024] Open
Abstract
Current differentiation protocols for human induced pluripotent stem cells (hiPSCs) produce heterogeneous cardiomyocytes (CMs). Although chamber-specific CM selection using cell surface antigens enhances biomedical applications, a cell surface marker that accurately distinguishes between hiPSC-derived atrial CMs (ACMs) and ventricular CMs (VCMs) has not yet been identified. We have developed an approach for obtaining functional hiPSC-ACMs and -VCMs based on CD151 expression. For ACM differentiation, we found that ACMs are enriched in the CD151low population and that CD151 expression is correlated with the expression of Notch4 and its ligands. Furthermore, Notch signaling inhibition followed by selecting the CD151low population during atrial differentiation leads to the highly efficient generation of ACMs as evidenced by gene expression and electrophysiology. In contrast, for VCM differentiation, VCMs exhibiting a ventricular-related gene signature and uniform action potentials are enriched in the CD151high population. Our findings enable the production of high-quality ACMs and VCMs appropriate for hiPSC-derived chamber-specific disease models and other applications.
Collapse
Affiliation(s)
- Misato Nakanishi-Koakutsu
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan
- Takeda-CiRA Joint program (T-CiRA), Fujisawa, 251-8555, Japan
- Division of Cardiology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Surgery, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Kenji Miki
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan.
- Center for Organ Engineering, Department of Surgery, Massachusetts General Hospital, Boston, MA, 02114, USA.
- Department of Surgery, Harvard Medical School, Boston, MA, 02114, USA.
- Premium Research Institute for Human Metaverse Medicine, Osaka University, Suita, 565-0871, Japan.
| | - Yuki Naka
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan
- Takeda-CiRA Joint program (T-CiRA), Fujisawa, 251-8555, Japan
| | - Masako Sasaki
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan
- Takeda-CiRA Joint program (T-CiRA), Fujisawa, 251-8555, Japan
| | - Takayuki Wakimizu
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan
- Takeda-CiRA Joint program (T-CiRA), Fujisawa, 251-8555, Japan
| | - Stephanie C Napier
- Takeda-CiRA Joint program (T-CiRA), Fujisawa, 251-8555, Japan
- Global Advanced Platform, Takeda Pharmaceutical Company Limited, Fujisawa, 251-8555, Japan
| | - Chikako Okubo
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan
| | - Megumi Narita
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan
| | - Misato Nishikawa
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan
| | - Reo Hata
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan
| | - Kazuhisa Chonabayashi
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan
| | - Akitsu Hotta
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan
- Takeda-CiRA Joint program (T-CiRA), Fujisawa, 251-8555, Japan
| | - Kenichi Imahashi
- Takeda-CiRA Joint program (T-CiRA), Fujisawa, 251-8555, Japan
- Global Advanced Platform, Takeda Pharmaceutical Company Limited, Fujisawa, 251-8555, Japan
| | - Tomoyuki Nishimoto
- Takeda-CiRA Joint program (T-CiRA), Fujisawa, 251-8555, Japan
- Orizuru Therapeutics Incorporated, Fujisawa, 251-8555, Japan
| | - Yoshinori Yoshida
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan.
- Takeda-CiRA Joint program (T-CiRA), Fujisawa, 251-8555, Japan.
| |
Collapse
|
5
|
Maurissen TL, Spielmann AJ, Schellenberg G, Bickle M, Vieira JR, Lai SY, Pavlou G, Fauser S, Westenskow PD, Kamm RD, Ragelle H. Modeling early pathophysiological phenotypes of diabetic retinopathy in a human inner blood-retinal barrier-on-a-chip. Nat Commun 2024; 15:1372. [PMID: 38355716 PMCID: PMC10866954 DOI: 10.1038/s41467-024-45456-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: 03/17/2023] [Accepted: 01/24/2024] [Indexed: 02/16/2024] Open
Abstract
Diabetic retinopathy (DR) is a microvascular disorder characterized by inner blood-retinal barrier (iBRB) breakdown and irreversible vision loss. While the symptoms of DR are known, disease mechanisms including basement membrane thickening, pericyte dropout and capillary damage remain poorly understood and interventions to repair diseased iBRB microvascular networks have not been developed. In addition, current approaches using animal models and in vitro systems lack translatability and predictivity to finding new target pathways. Here, we develop a diabetic iBRB-on-a-chip that produces pathophysiological phenotypes and disease pathways in vitro that are representative of clinical diagnoses. We show that diabetic stimulation of the iBRB-on-a-chip mirrors DR features, including pericyte loss, vascular regression, ghost vessels, and production of pro-inflammatory factors. We also report transcriptomic data from diabetic iBRB microvascular networks that may reveal drug targets, and examine pericyte-endothelial cell stabilizing strategies. In summary, our model recapitulates key features of disease, and may inform future therapies for DR.
Collapse
Affiliation(s)
- Thomas L Maurissen
- Roche Pharma Research and Early Development, Cardiovascular, Metabolism, Immunology, Infectious Diseases and Ophthalmology, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Alena J Spielmann
- Roche Pharma Research and Early Development, Cardiovascular, Metabolism, Immunology, Infectious Diseases and Ophthalmology, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Gabriella Schellenberg
- Roche Pharma Research and Early Development, Cardiovascular, Metabolism, Immunology, Infectious Diseases and Ophthalmology, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Marc Bickle
- Roche Pharma Research and Early Development, Institute of Human Biology, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Jose Ricardo Vieira
- Roche Pharma Research and Early Development, Cardiovascular, Metabolism, Immunology, Infectious Diseases and Ophthalmology, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Si Ying Lai
- Roche Pharma Research and Early Development, Cardiovascular, Metabolism, Immunology, Infectious Diseases and Ophthalmology, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Georgios Pavlou
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sascha Fauser
- Roche Pharma Research and Early Development, Cardiovascular, Metabolism, Immunology, Infectious Diseases and Ophthalmology, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Peter D Westenskow
- Roche Pharma Research and Early Development, Cardiovascular, Metabolism, Immunology, Infectious Diseases and Ophthalmology, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Roger D Kamm
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Héloïse Ragelle
- Roche Pharma Research and Early Development, Cardiovascular, Metabolism, Immunology, Infectious Diseases and Ophthalmology, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland.
| |
Collapse
|
6
|
Maurissen TL, Kawatou M, López-Dávila V, Minatoya K, Yamashita JK, Woltjen K. Modeling mutation-specific arrhythmogenic phenotypes in isogenic human iPSC-derived cardiac tissues. Sci Rep 2024; 14:2586. [PMID: 38297132 PMCID: PMC10831092 DOI: 10.1038/s41598-024-52871-1] [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: 10/27/2023] [Accepted: 01/24/2024] [Indexed: 02/02/2024] Open
Abstract
Disease modeling using human induced pluripotent stem cells (hiPSCs) from patients with genetic disease is a powerful approach for dissecting pathophysiology and drug discovery. Nevertheless, isogenic controls are required to precisely compare phenotypic outcomes from presumed causative mutations rather than differences in genetic backgrounds. Moreover, 2D cellular models often fail to exhibit authentic disease phenotypes resulting in poor validation in vitro. Here we show that a combination of precision gene editing and bioengineered 3D tissue models can establish advanced isogenic hiPSC-derived cardiac disease models, overcoming these drawbacks. To model inherited cardiac arrhythmias we selected representative N588D and N588K missense mutations affecting the same codon in the hERG potassium channel gene KCNH2, which are reported to cause long (LQTS) and short (SQTS) QT syndromes, respectively. We generated compound heterozygous variants in normal hiPSCs, and differentiated cardiomyocytes (CMs) and mesenchymal cells (MCs) to form 3D cardiac tissue sheets (CTSs). In hiPSC-derived CM monolayers and 3D CTSs, electrophysiological analysis with multielectrode arrays showed prolonged and shortened repolarization, respectively, compared to the isogenic controls. When pharmacologically inhibiting the hERG channels, mutant 3D CTSs were differentially susceptible to arrhythmic events than the isogenic controls. Thus, this strategy offers advanced disease models that can reproduce clinically relevant phenotypes and provide solid validation of gene mutations in vitro.
Collapse
Affiliation(s)
- Thomas L Maurissen
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, 606-8507, Japan
- Roche Pharma Research and Early Development, Cardiovascular, Metabolism, Immunology, Infectious Diseases and Ophthalmology, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Masahide Kawatou
- Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, 606-8507, Japan
- Department of Cardiovascular Surgery, Kyoto University Graduate School of Medicine, Kyoto, 606-8507, Japan
| | - Víctor López-Dávila
- Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, 606-8507, Japan
- Gourmey, Paris, France
| | - Kenji Minatoya
- Department of Cardiovascular Surgery, Kyoto University Graduate School of Medicine, Kyoto, 606-8507, Japan
| | - Jun K Yamashita
- Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, 606-8507, Japan.
- Department of Cellular and Tissue Communications, Graduate School of Medicine, University of Tokyo, Tokyo, Japan.
| | - Knut Woltjen
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, 606-8507, Japan.
| |
Collapse
|
7
|
Becker HJ, Yamazaki S. Understanding genetic heterogeneity in gene-edited hematopoietic stem cell products. Exp Hematol 2024; 129:104133. [PMID: 38036097 DOI: 10.1016/j.exphem.2023.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 11/10/2023] [Indexed: 12/02/2023]
Abstract
CRISPR/Cas gene editing has transformed genetic research and is poised to drive the next generation of gene therapies targeting hematopoietic stem cells (HSCs). However, the installation of the "desired" edit is most often only achieved in a minor subset of alleles. The array of cellular pathways triggered by gene editing tools produces a broad spectrum of "undesired" editing outcomes, including short insertions and deletions (indels) and chromosome rearrangements, leading to considerable genetic heterogeneity in gene-edited HSC populations. This heterogeneity may undermine the effect of the genetic intervention since only a subset of cells will carry the intended modification. Also, undesired mutations represent a potential safety concern as gene editing advances toward broader clinical use. Here, we will review the different sources of "undesired" edits and will discuss strategies for their mitigation and control.
Collapse
Affiliation(s)
- Hans Jiro Becker
- Laboratory for Stem Cell Therapy, Faculty of Medicine, Tsukuba University, Tsukuba, Japan; Division of Cell Regulation, Center of Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
| | - Satoshi Yamazaki
- Laboratory for Stem Cell Therapy, Faculty of Medicine, Tsukuba University, Tsukuba, Japan; Division of Cell Regulation, Center of Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
| |
Collapse
|
8
|
Nakade K, Tsukamoto S, Nakashima K, An Y, Sato I, Li J, Shimoda Y, Hemmi Y, Miwa Y, Hayashi Y. Efficient selection of knocked-in pluripotent stem cells using a dual cassette cellular elimination system. CELL REPORTS METHODS 2023; 3:100662. [PMID: 38086384 PMCID: PMC10753384 DOI: 10.1016/j.crmeth.2023.100662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 10/02/2023] [Accepted: 11/15/2023] [Indexed: 12/21/2023]
Abstract
Although recent advances in genome editing technology with homology-directed repair have enabled the insertion of various reporter genes into the genome of mammalian cells, the efficiency is still low due to the random insertion of donor vectors into the host genome. To efficiently select knocked-in cells without random insertion, we developed the "double-tk donor vector system," in which the expression units of the thymidine kinase of herpes simplex virus (HSV-tk) are placed on both outer sides of homology arms. This system is superior in enriching knocked-in human induced pluripotent stem cells (hiPSCs) than conventional donor vector systems with a single or no HSV-tk cassette. Using this system, we efficiently generated fluorescent reporter knockin hiPSCs targeting POU5F1 (OCT3/4), EEF1A1, H2BC21 (H2B clustered histone 21), ISL1, and MYH7 genes. These results indicate that the double-tk donor vector system enables efficient selection of knocked-in hiPSCs carrying reporter proteins.
Collapse
Affiliation(s)
- Koji Nakade
- Gene Engineering Division, BioResource Research Center, RIKEN, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan.
| | - Satomi Tsukamoto
- iPS Cell Advanced Characterization and Development Team, BioResource Research Center, RIKEN, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Kenichi Nakashima
- Gene Engineering Division, BioResource Research Center, RIKEN, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Yuri An
- iPS Cell Advanced Characterization and Development Team, BioResource Research Center, RIKEN, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Iori Sato
- iPS Cell Advanced Characterization and Development Team, BioResource Research Center, RIKEN, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Jingyue Li
- iPS Cell Advanced Characterization and Development Team, BioResource Research Center, RIKEN, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Yuzuno Shimoda
- iPS Cell Advanced Characterization and Development Team, BioResource Research Center, RIKEN, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan; School of Integrative and Global Majors, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Yasuko Hemmi
- iPS Cell Advanced Characterization and Development Team, BioResource Research Center, RIKEN, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Yoshihiro Miwa
- Gene Engineering Division, BioResource Research Center, RIKEN, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Yohei Hayashi
- iPS Cell Advanced Characterization and Development Team, BioResource Research Center, RIKEN, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan; School of Integrative and Global Majors, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan.
| |
Collapse
|
9
|
Niwa R, Sakai K, Lung MSY, Matsumoto T, Mikawa R, Maehana S, Suzuki M, Yamamoto Y, Maurissen TL, Hirabayashi A, Noda T, Kubo M, Gotoh S, Woltjen K. ACE2 knockout hinders SARS-CoV-2 propagation in iPS cell-derived airway and alveolar epithelial cells. Front Cell Dev Biol 2023; 11:1290876. [PMID: 38149046 PMCID: PMC10750251 DOI: 10.3389/fcell.2023.1290876] [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: 09/08/2023] [Accepted: 10/26/2023] [Indexed: 12/28/2023] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, continues to spread around the world with serious cases and deaths. It has also been suggested that different genetic variants in the human genome affect both the susceptibility to infection and severity of disease in COVID-19 patients. Angiotensin-converting enzyme 2 (ACE2) has been identified as a cell surface receptor for SARS-CoV and SARS-CoV-2 entry into cells. The construction of an experimental model system using human iPS cells would enable further studies of the association between viral characteristics and genetic variants. Airway and alveolar epithelial cells are cell types of the lung that express high levels of ACE2 and are suitable for in vitro infection experiments. Here, we show that human iPS cell-derived airway and alveolar epithelial cells are highly susceptible to viral infection of SARS-CoV-2. Using gene knockout with CRISPR-Cas9 in human iPS cells we demonstrate that ACE2 plays an essential role in the airway and alveolar epithelial cell entry of SARS-CoV-2 in vitro. Replication of SARS-CoV-2 was strongly suppressed in ACE2 knockout (KO) lung cells. Our model system based on human iPS cell-derived lung cells may be applied to understand the molecular biology regulating viral respiratory infection leading to potential therapeutic developments for COVID-19 and the prevention of future pandemics.
Collapse
Affiliation(s)
- Ryo Niwa
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
- Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kouji Sakai
- Department of Veterinary Science, National Institute of Infectious Diseases, Tokyo, Japan
- Management Department of Biosafety, Laboratory Animal, and Pathogen Bank, National Institute of Infectious Diseases, Tokyo, Japan
| | - Mandy Siu Yu Lung
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Tomoko Matsumoto
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Ryuta Mikawa
- Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Clinical Application, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Shotaro Maehana
- Department of Microbiology, Kitasato University School of Allied Health Sciences, Kanagawa, Japan
- Regenerative Medicine and Cell Design Research Facility, Kitasato University School of Allied Health Sciences, Kanagawa, Japan
| | - Masato Suzuki
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yuki Yamamoto
- Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Thomas L. Maurissen
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Ai Hirabayashi
- Laboratory of Ultrastructural Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Takeshi Noda
- Laboratory of Ultrastructural Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Laboratory of Ultrastructural Virology, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Makoto Kubo
- Department of Microbiology, Kitasato University School of Allied Health Sciences, Kanagawa, Japan
- Regenerative Medicine and Cell Design Research Facility, Kitasato University School of Allied Health Sciences, Kanagawa, Japan
| | - Shimpei Gotoh
- Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Clinical Application, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Knut Woltjen
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| |
Collapse
|
10
|
Ponnienselvan K, Liu P, Nyalile T, Oikemus S, Maitland S, Lawson N, Luban J, Wolfe S. Reducing the inherent auto-inhibitory interaction within the pegRNA enhances prime editing efficiency. Nucleic Acids Res 2023; 51:6966-6980. [PMID: 37246708 PMCID: PMC10359601 DOI: 10.1093/nar/gkad456] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 05/06/2023] [Accepted: 05/12/2023] [Indexed: 05/30/2023] Open
Abstract
Prime editing systems have enabled the incorporation of precise edits within a genome without introducing double strand breaks. Previous studies defined an optimal primer binding site (PBS) length for the pegRNA of ∼13 nucleotides depending on the sequence composition. However, optimal PBS length characterization has been based on prime editing outcomes using plasmid or lentiviral expression systems. In this study, we demonstrate that for prime editor (PE) ribonucleoprotein complexes, the auto-inhibitory interaction between the PBS and the spacer sequence affects pegRNA binding efficiency and target recognition. Destabilizing this auto-inhibitory interaction by reducing the complementarity between the PBS-spacer region enhances prime editing efficiency in multiple prime editing formats. In the case of end-protected pegRNAs, a shorter PBS length with a PBS-target strand melting temperature near 37°C is optimal in mammalian cells. Additionally, a transient cold shock treatment of the cells post PE-pegRNA delivery further increases prime editing outcomes for pegRNAs with optimized PBS lengths. Finally, we show that prime editor ribonucleoprotein complexes programmed with pegRNAs designed using these refined parameters efficiently correct disease-related genetic mutations in patient-derived fibroblasts and efficiently install precise edits in primary human T cells and zebrafish.
Collapse
Affiliation(s)
- Karthikeyan Ponnienselvan
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Pengpeng Liu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Thomas Nyalile
- Department of Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Sarah Oikemus
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Stacy A Maitland
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Nathan D Lawson
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Department of Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jeremy Luban
- Department of Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Scot A Wolfe
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA, USA
| |
Collapse
|
11
|
Kawamata M, Suzuki HI, Kimura R, Suzuki A. Optimization of Cas9 activity through the addition of cytosine extensions to single-guide RNAs. Nat Biomed Eng 2023; 7:672-691. [PMID: 37037965 DOI: 10.1038/s41551-023-01011-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 02/17/2023] [Indexed: 04/12/2023]
Abstract
The precise regulation of the activity of Cas9 is crucial for safe and efficient editing. Here we show that the genome-editing activity of Cas9 can be constrained by the addition of cytosine stretches to the 5'-end of conventional single-guide RNAs (sgRNAs). Such a 'safeguard sgRNA' strategy, which is compatible with Cas12a and with systems for gene activation and interference via CRISPR (clustered regularly interspaced short palindromic repeats), leads to the length-dependent inhibition of the formation of functional Cas9 complexes. Short cytosine extensions reduced p53 activation and cytotoxicity in human pluripotent stem cells, and enhanced homology-directed repair while maintaining bi-allelic editing. Longer extensions further decreased on-target activity yet improved the specificity and precision of mono-allelic editing. By monitoring indels through a fluorescence-based allele-specific system and computational simulations, we identified optimal windows of Cas9 activity for a number of genome-editing applications, including bi-allelic and mono-allelic editing, and the generation and correction of disease-associated single-nucleotide substitutions via homology-directed repair. The safeguard-sgRNA strategy may improve the safety and applicability of genome editing.
Collapse
Affiliation(s)
- Masaki Kawamata
- Division of Organogenesis and Regeneration, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.
| | - Hiroshi I Suzuki
- Division of Molecular Oncology, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan.
- Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, Japan.
- Center for One Medicine Innovative Translational Research, Gifu University Institute for Advanced Study, Gifu, Japan.
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Ryota Kimura
- Division of Organogenesis and Regeneration, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Atsushi Suzuki
- Division of Organogenesis and Regeneration, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.
| |
Collapse
|
12
|
Gao J, Makiyama T, Yamamoto Y, Kobayashi T, Aoki H, Maurissen TL, Wuriyanghai Y, Kashiwa A, Imamura T, Aizawa T, Huang H, Kohjitani H, Nishikawa M, Chonabayashi K, Fukuyama M, Manabe H, Nakau K, Wada T, Kato K, Toyoda F, Yoshida Y, Makita N, Woltjen K, Ohno S, Kurebayashi N, Murayama T, Sakurai T, Horie M, Kimura T. Novel Calmodulin Variant p.E46K Associated With Severe Catecholaminergic Polymorphic Ventricular Tachycardia Produces Robust Arrhythmogenicity in Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes. Circ Arrhythm Electrophysiol 2023; 16:e011387. [PMID: 36866681 DOI: 10.1161/circep.122.011387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
BACKGROUND CaM (calmodulin) is a ubiquitously expressed, multifunctional Ca2+ sensor protein that regulates numerous proteins. Recently, CaM missense variants have been identified in patients with malignant inherited arrhythmias, such as long QT syndrome and catecholaminergic polymorphic ventricular tachycardia (CPVT). However, the exact mechanism of CaM-related CPVT in human cardiomyocytes remains unclear. In this study, we sought to investigate the arrhythmogenic mechanism of CPVT caused by a novel variant using human induced pluripotent stem cell (iPSC) models and biochemical assays. METHODS We generated iPSCs from a patient with CPVT bearing CALM2 p.E46K. As comparisons, we used 2 control lines including an isogenic line, and another iPSC line from a patient with long QT syndrome bearing CALM2 p.N98S (also reported in CPVT). Electrophysiological properties were investigated using iPSC-cardiomyocytes. We further examined the RyR2 (ryanodine receptor 2) and Ca2+ affinities of CaM using recombinant proteins. RESULTS We identified a novel de novo heterozygous variant, CALM2 p.E46K, in 2 unrelated patients with CPVT accompanied by neurodevelopmental disorders. The E46K-cardiomyocytes exhibited more frequent abnormal electrical excitations and Ca2+ waves than the other lines in association with increased Ca2+ leakage from the sarcoplasmic reticulum via RyR2. Furthermore, the [3H]ryanodine binding assay revealed that E46K-CaM facilitated RyR2 function especially by activating at low [Ca2+] levels. The real-time CaM-RyR2 binding analysis demonstrated that E46K-CaM had a 10-fold increased RyR2 binding affinity compared with wild-type CaM which may account for the dominant effect of the mutant CaM. Additionally, the E46K-CaM did not affect CaM-Ca2+ binding or L-type calcium channel function. Finally, antiarrhythmic agents, nadolol and flecainide, suppressed abnormal Ca2+ waves in E46K-cardiomyocytes. CONCLUSIONS We, for the first time, established a CaM-related CPVT iPSC-CM model which recapitulated severe arrhythmogenic features resulting from E46K-CaM dominantly binding and facilitating RyR2. In addition, the findings in iPSC-based drug testing will contribute to precision medicine.
Collapse
Affiliation(s)
- Jingshan Gao
- Department of Cardiovascular Medicine (J.G., T. Makiyama, Y. Yamamoto, Y.W., A.K., T.I., T.A., H.H., H.K., T. Kimura), Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Takeru Makiyama
- Department of Cardiovascular Medicine (J.G., T. Makiyama, Y. Yamamoto, Y.W., A.K., T.I., T.A., H.H., H.K., T. Kimura), Kyoto University Graduate School of Medicine, Kyoto, Japan
- Department of Community Medicine Supporting System (T. Makiyama), Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Yuta Yamamoto
- Department of Cardiovascular Medicine (J.G., T. Makiyama, Y. Yamamoto, Y.W., A.K., T.I., T.A., H.H., H.K., T. Kimura), Kyoto University Graduate School of Medicine, Kyoto, Japan
- Department of Bioscience & Genetics (Y. Yamamoto, S.O.), National Cerebral & Cardiovascular Center, Suita, Japan
- Now with Division of Cardiovascular Medicine, Department of Medicine, Stanford University, Stanford, CA (Y. Yamamoto)
| | - Takuya Kobayashi
- Department of Pharmacology, Juntendo University School of Medicine, Tokyo, Japan (T. Kobayashi, N.K., T. Murayama, T.S.)
| | - Hisaaki Aoki
- Department of Pediatric Cardiology, Osaka Women's & Children's Hospital, Osaka, Japan (H.A.)
| | - Thomas L Maurissen
- Department of Life Science Frontiers (T.L.M., K.W.), Center for iPS Cell Research & Application (CiRA), Kyoto University, Kyoto, Japan
- Now with Roche Pharma Research & Early Development, Immunology, Infectious Diseases & Ophthalmology, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland (T.L.M.)
| | - Yimin Wuriyanghai
- Department of Cardiovascular Medicine (J.G., T. Makiyama, Y. Yamamoto, Y.W., A.K., T.I., T.A., H.H., H.K., T. Kimura), Kyoto University Graduate School of Medicine, Kyoto, Japan
- Now with Department of Internal medicine, Peking University Third Hospital, Beijing, China (Y.W.)
| | - Asami Kashiwa
- Department of Cardiovascular Medicine (J.G., T. Makiyama, Y. Yamamoto, Y.W., A.K., T.I., T.A., H.H., H.K., T. Kimura), Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Tomohiko Imamura
- Department of Cardiovascular Medicine (J.G., T. Makiyama, Y. Yamamoto, Y.W., A.K., T.I., T.A., H.H., H.K., T. Kimura), Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Takanori Aizawa
- Department of Cardiovascular Medicine (J.G., T. Makiyama, Y. Yamamoto, Y.W., A.K., T.I., T.A., H.H., H.K., T. Kimura), Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Hai Huang
- Department of Cardiovascular Medicine (J.G., T. Makiyama, Y. Yamamoto, Y.W., A.K., T.I., T.A., H.H., H.K., T. Kimura), Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Hirohiko Kohjitani
- Department of Cardiovascular Medicine (J.G., T. Makiyama, Y. Yamamoto, Y.W., A.K., T.I., T.A., H.H., H.K., T. Kimura), Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Misato Nishikawa
- Department of Cell Growth & Differentiation (M.N., K.C., Y. Yoshida), Center for iPS Cell Research & Application (CiRA), Kyoto University, Kyoto, Japan
| | - Kazuhisa Chonabayashi
- Department of Hematology & Oncology (K.C.), Kyoto University Graduate School of Medicine, Kyoto, Japan
- Department of Cell Growth & Differentiation (M.N., K.C., Y. Yoshida), Center for iPS Cell Research & Application (CiRA), Kyoto University, Kyoto, Japan
| | - Megumi Fukuyama
- Department of Cardiovascular Medicine (M.F., K.K., M.H.), Shiga University of Medical Science, Otsu, Japan
| | - Hiromi Manabe
- Department of Pediatrics, Asahikawa Kosei General Hospital (H.M.), Asahikawa Medical University, Asahikawa, Japan
| | - Kouichi Nakau
- Asahikawa, Japan and Department of Pediatrics (K.N.), Asahikawa Medical University, Asahikawa, Japan
| | - Tsutomu Wada
- Department of Pediatrics, Sapporo Medical University Hospital, Sapporo, Japan (T.W.)
| | - Koichi Kato
- Department of Cardiovascular Medicine (M.F., K.K., M.H.), Shiga University of Medical Science, Otsu, Japan
| | - Futoshi Toyoda
- Department of Physiology (F.T.), Shiga University of Medical Science, Otsu, Japan
| | - Yoshinori Yoshida
- Department of Cell Growth & Differentiation (M.N., K.C., Y. Yoshida), Center for iPS Cell Research & Application (CiRA), Kyoto University, Kyoto, Japan
| | - Naomasa Makita
- Omics Research Center (N.M.), National Cerebral & Cardiovascular Center, Suita, Japan
- Now with Department of Cardiology, Sapporo Teishinkai Hospital, Sapporo, Japan (N.M.)
| | - Knut Woltjen
- Department of Life Science Frontiers (T.L.M., K.W.), Center for iPS Cell Research & Application (CiRA), Kyoto University, Kyoto, Japan
| | - Seiko Ohno
- Department of Bioscience & Genetics (Y. Yamamoto, S.O.), National Cerebral & Cardiovascular Center, Suita, Japan
| | - Nagomi Kurebayashi
- Department of Pharmacology, Juntendo University School of Medicine, Tokyo, Japan (T. Kobayashi, N.K., T. Murayama, T.S.)
| | - Takashi Murayama
- Department of Pharmacology, Juntendo University School of Medicine, Tokyo, Japan (T. Kobayashi, N.K., T. Murayama, T.S.)
| | - Takashi Sakurai
- Department of Pharmacology, Juntendo University School of Medicine, Tokyo, Japan (T. Kobayashi, N.K., T. Murayama, T.S.)
| | - Minoru Horie
- Department of Cardiovascular Medicine (M.F., K.K., M.H.), Shiga University of Medical Science, Otsu, Japan
| | - Takeshi Kimura
- Department of Cardiovascular Medicine (J.G., T. Makiyama, Y. Yamamoto, Y.W., A.K., T.I., T.A., H.H., H.K., T. Kimura), Kyoto University Graduate School of Medicine, Kyoto, Japan
- Now with Department of Cardiology, Hirakata Kohsai Hospital, Osaka, Japan (T. Kimura)
| |
Collapse
|
13
|
Singh S, Chaudhary R, Deshmukh R, Tiwari S. Opportunities and challenges with CRISPR-Cas mediated homologous recombination based precise editing in plants and animals. PLANT MOLECULAR BIOLOGY 2023; 111:1-20. [PMID: 36315306 DOI: 10.1007/s11103-022-01321-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
We summarise recent advancements to achieve higher homologous recombination based gene targeting efficiency in different animals and plants. The genome editing has revolutionized the agriculture and human therapeutic sectors by its ability to create precise, stable and predictable mutations in the genome. It depends upon targeted double-strand breaks induction by the engineered endonucleases, which then gets repaired by highly conserved endogenous DNA repair mechanisms. The repairing could be done either through non-homologous end joining (NHEJ) or homology-directed repair (HDR) pathways. The HDR-based editing can be applied for precise gene targeting such as insertion of a new gene, gene replacement and altering of the regulatory sequence of a gene to control the existing protein expression. However, HDR-mediated editing is considered challenging because of lower efficiency in higher eukaryotes, thus, preventing its widespread application. This article reviews the recent progress of HDR-mediated editing and discusses novel strategies such as cell cycle synchronization, modulation of DNA damage repair factors, engineering of Cas protein favoring HDR and CRISPR-Cas reagents delivery methods to improve efficiency for generating knock-in events in both plants and animals. Further, multiplexing of described methods may be promising towards achieving higher donor template-assisted homologous recombination efficiency at the target locus.
Collapse
Affiliation(s)
- Surender Singh
- Plant Tissue Culture and Genetic Engineering Lab, National Agri-Food Biotechnology Institute (NABI), Department of Biotechnology, Ministry of Science and Technology (Government of India), Sector 81, Knowledge City, S.A.S. Nagar, Mohali, Punjab, 140306, India
- Regional Centre for Biotechnology, Faridabad, 121001, India
| | - Roni Chaudhary
- Plant Tissue Culture and Genetic Engineering Lab, National Agri-Food Biotechnology Institute (NABI), Department of Biotechnology, Ministry of Science and Technology (Government of India), Sector 81, Knowledge City, S.A.S. Nagar, Mohali, Punjab, 140306, India
- Regional Centre for Biotechnology, Faridabad, 121001, India
| | | | - Siddharth Tiwari
- Plant Tissue Culture and Genetic Engineering Lab, National Agri-Food Biotechnology Institute (NABI), Department of Biotechnology, Ministry of Science and Technology (Government of India), Sector 81, Knowledge City, S.A.S. Nagar, Mohali, Punjab, 140306, India.
| |
Collapse
|
14
|
Kanezaki R, Toki T, Terui K, Sato T, Kobayashi A, Kudo K, Kamio T, Sasaki S, Kawaguchi K, Watanabe K, Ito E. Mechanism of KIT gene regulation by GATA1 lacking the N-terminal domain in Down syndrome-related myeloid disorders. Sci Rep 2022; 12:20587. [PMID: 36447001 PMCID: PMC9708825 DOI: 10.1038/s41598-022-25046-z] [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: 05/16/2022] [Accepted: 11/23/2022] [Indexed: 12/03/2022] Open
Abstract
Children with Down syndrome (DS) are at high risk of transient abnormal myelopoiesis (TAM) and myeloid leukemia of DS (ML-DS). GATA1 mutations are detected in almost all TAM and ML-DS samples, with exclusive expression of short GATA1 protein (GATA1s) lacking the N-terminal domain (NTD). However, it remains to be clarified how GATA1s is involved with both disorders. Here, we established the K562 GATA1s (K562-G1s) clones expressing only GATA1s by CRISPR/Cas9 genome editing. The K562-G1s clones expressed KIT at significantly higher levels compared to the wild type of K562 (K562-WT). Chromatin immunoprecipitation studies identified the GATA1-bound regulatory sites upstream of KIT in K562-WT, K562-G1s clones and two ML-DS cell lines; KPAM1 and CMK11-5. Sonication-based chromosome conformation capture (3C) assay demonstrated that in K562-WT, the - 87 kb enhancer region of KIT was proximal to the - 115 kb, - 109 kb and + 1 kb region, while in a K562-G1s clone, CMK11-5 and primary TAM cells, the - 87 kb region was more proximal to the KIT transcriptional start site. These results suggest that the NTD of GATA1 is essential for proper genomic conformation and regulation of KIT gene expression, and that perturbation of this function might be involved in the pathogenesis of TAM and ML-DS.
Collapse
Affiliation(s)
- Rika Kanezaki
- grid.257016.70000 0001 0673 6172Department of Pediatrics, Hirosaki University Graduate School of Medicine, 5 Zaifucho, Hirosaki, Aomori 036-8562 Japan
| | - Tsutomu Toki
- grid.257016.70000 0001 0673 6172Department of Pediatrics, Hirosaki University Graduate School of Medicine, 5 Zaifucho, Hirosaki, Aomori 036-8562 Japan
| | - Kiminori Terui
- grid.257016.70000 0001 0673 6172Department of Pediatrics, Hirosaki University Graduate School of Medicine, 5 Zaifucho, Hirosaki, Aomori 036-8562 Japan
| | - Tomohiko Sato
- grid.257016.70000 0001 0673 6172Department of Pediatrics, Hirosaki University Graduate School of Medicine, 5 Zaifucho, Hirosaki, Aomori 036-8562 Japan
| | - Akie Kobayashi
- grid.257016.70000 0001 0673 6172Department of Pediatrics, Hirosaki University Graduate School of Medicine, 5 Zaifucho, Hirosaki, Aomori 036-8562 Japan
| | - Ko Kudo
- grid.257016.70000 0001 0673 6172Department of Pediatrics, Hirosaki University Graduate School of Medicine, 5 Zaifucho, Hirosaki, Aomori 036-8562 Japan
| | - Takuya Kamio
- grid.257016.70000 0001 0673 6172Department of Pediatrics, Hirosaki University Graduate School of Medicine, 5 Zaifucho, Hirosaki, Aomori 036-8562 Japan
| | - Shinya Sasaki
- grid.257016.70000 0001 0673 6172Department of Pediatrics, Hirosaki University Graduate School of Medicine, 5 Zaifucho, Hirosaki, Aomori 036-8562 Japan
| | - Koji Kawaguchi
- grid.415798.60000 0004 0378 1551Department of Hematology and Oncology, Shizuoka Children’s Hospital, Shizuoka, Japan
| | - Kenichiro Watanabe
- grid.415798.60000 0004 0378 1551Department of Hematology and Oncology, Shizuoka Children’s Hospital, Shizuoka, Japan
| | - Etsuro Ito
- grid.257016.70000 0001 0673 6172Department of Pediatrics, Hirosaki University Graduate School of Medicine, 5 Zaifucho, Hirosaki, Aomori 036-8562 Japan ,grid.257016.70000 0001 0673 6172Department of Community Medicine, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| |
Collapse
|
15
|
Marker-free co-selection for successive rounds of prime editing in human cells. Nat Commun 2022; 13:5909. [PMID: 36207338 PMCID: PMC9546848 DOI: 10.1038/s41467-022-33669-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 09/27/2022] [Indexed: 11/18/2022] Open
Abstract
Prime editing enables the introduction of precise point mutations, small insertions, or short deletions without requiring donor DNA templates. However, efficiency remains a key challenge in a broad range of human cell types. In this work, we design a robust co-selection strategy through coediting of the ubiquitous and essential sodium/potassium pump (Na+/K+ ATPase). We readily engineer highly modified pools of cells and clones with homozygous modifications for functional studies with minimal pegRNA optimization. This process reveals that nicking the non-edited strand stimulates multiallelic editing but often generates tandem duplications and large deletions at the target site, an outcome dictated by the relative orientation of the protospacer adjacent motifs. Our approach streamlines the production of cell lines with multiple genetic modifications to create cellular models for biological research and lays the foundation for the development of cell-type specific co-selection strategies. Prime editing enables the introduction of precise point mutations, small insertions, or short deletions without requiring donor DNA templates. Here the authors develop a co-selection strategy to facilitate prime editing in human cells and provide design principles to prevent the formation of undesired editing byproducts at the target site.
Collapse
|
16
|
Usher I, Ligammari L, Ahrabi S, Hepburn E, Connolly C, Bond GL, Flanagan AM, Cottone L. Optimizing CRISPR/Cas9 Editing of Repetitive Single Nucleotide Variants. Front Genome Ed 2022; 4:932434. [PMID: 35865001 PMCID: PMC9294353 DOI: 10.3389/fgeed.2022.932434] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 05/31/2022] [Indexed: 11/13/2022] Open
Abstract
CRISPR/Cas9, base editors and prime editors comprise the contemporary genome editing toolbox. Many studies have optimized the use of CRISPR/Cas9, as the original CRISPR genome editing system, in substituting single nucleotides by homology directed repair (HDR), although this remains challenging. Studies describing modifications that improve editing efficiency fall short of isolating clonal cell lines or have not been validated for challenging loci or cell models. We present data from 95 transfections using a colony forming and an immortalized cell line comparing the effect on editing efficiency of donor template modifications, concentration of components, HDR enhancing agents and cold shock. We found that in silico predictions of guide RNA efficiency correlated poorly withactivity in cells. Using NGS and ddPCR we detected editing efficiencies of 5–12% in the transfected populations which fell to 1% on clonal cell line isolation. Our data demonstrate the variability of CRISPR efficiency by cell model, target locus and other factors. Successful genome editing requires a comparison of systems and modifications to develop the optimal protocol for the cell model and locus. We describe the steps in this process in a flowchart for those embarking on genome editing using any system and incorporate validated HDR-boosting modifications for those using CRISPR/Cas9.
Collapse
Affiliation(s)
- Inga Usher
- Department of Pathology (Research), UCL Cancer Institute, University College London, London, United Kingdom
| | - Lorena Ligammari
- Department of Pathology (Research), UCL Cancer Institute, University College London, London, United Kingdom
| | - Sara Ahrabi
- Department of Haematology, UCL Cancer Institute, University College London, London, United Kingdom
| | - Emily Hepburn
- UCL Medical School, University College London, London, United Kingdom
| | - Calum Connolly
- UCL Medical School, University College London, London, United Kingdom
| | - Gareth L. Bond
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Adrienne M. Flanagan
- Department of Pathology (Research), UCL Cancer Institute, University College London, London, United Kingdom
- Department of Histopathology, Royal National Orthopaedic Hospital, London, United Kingdom
| | - Lucia Cottone
- Department of Pathology (Research), UCL Cancer Institute, University College London, London, United Kingdom
- *Correspondence: Lucia Cottone,
| |
Collapse
|
17
|
Improving Homology-Directed Repair in Genome Editing Experiments by Influencing the Cell Cycle. Int J Mol Sci 2022; 23:ijms23115992. [PMID: 35682671 PMCID: PMC9181127 DOI: 10.3390/ijms23115992] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 05/20/2022] [Accepted: 05/26/2022] [Indexed: 11/28/2022] Open
Abstract
Genome editing is currently widely used in biomedical research; however, the use of this method in the clinic is still limited because of its low efficiency and possible side effects. Moreover, the correction of mutations that cause diseases in humans seems to be extremely important and promising. Numerous attempts to improve the efficiency of homology-directed repair-mediated correction of mutations in mammalian cells have focused on influencing the cell cycle. Homology-directed repair is known to occur only in the late S and G2 phases of the cell cycle, so researchers are looking for safe ways to enrich the cell culture with cells in these phases of the cell cycle. This review surveys the main approaches to influencing the cell cycle in genome editing experiments (predominantly using Cas9), for example, the use of cell cycle synchronizers, mitogens, substances that affect cyclin-dependent kinases, hypothermia, inhibition of p53, etc. Despite the fact that all these approaches have a reversible effect on the cell cycle, it is necessary to use them with caution, since cells during the arrest of the cell cycle can accumulate mutations, which can potentially lead to their malignant transformation.
Collapse
|
18
|
Park JC, Kim J, Jang HK, Lee SY, Kim KT, Kwon EJ, Park S, Lee HS, Choi H, Park SY, Choi HJ, Park SJ, Moon SH, Bae S, Cha HJ. Multiple isogenic GNE-myopathy modeling with mutation specific phenotypes from human pluripotent stem cells by base editors. Biomaterials 2022; 282:121419. [DOI: 10.1016/j.biomaterials.2022.121419] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 01/28/2022] [Accepted: 02/15/2022] [Indexed: 12/19/2022]
|
19
|
Wang S, Li Y, Zhong L, Wu K, Zhang R, Kang T, Wu S, Wu Y. Efficient gene editing through an intronic selection marker in cells. Cell Mol Life Sci 2022; 79:111. [PMID: 35098362 PMCID: PMC8801403 DOI: 10.1007/s00018-022-04152-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 01/10/2022] [Accepted: 01/14/2022] [Indexed: 02/05/2023]
Abstract
BACKGROUND Gene editing technology has provided researchers with the ability to modify genome sequences in almost all eukaryotes. Gene-edited cell lines are being used with increasing frequency in both bench research and targeted therapy. However, despite the great importance and universality of gene editing, the efficiency of homology-directed DNA repair (HDR) is too low, and base editors (BEs) cannot accomplish desired indel editing tasks. RESULTS AND DISCUSSION Our group has improved HDR gene editing technology to indicate DNA variation with an independent selection marker using an HDR strategy, which we named Gene Editing through an Intronic Selection marker (GEIS). GEIS uses a simple process to avoid nonhomologous end joining (NHEJ)-mediated false-positive effects and achieves a DsRed positive rate as high as 87.5% after two rounds of fluorescence-activated cell sorter (FACS) selection without disturbing endogenous gene splicing and expression. We re-examined the correlation of the conversion tract and efficiency, and our data suggest that GEIS has the potential to edit approximately 97% of gene editing targets in human and mouse cells. The results of further comprehensive analysis suggest that the strategy may be useful for introducing multiple DNA variations in cells.
Collapse
Affiliation(s)
- Shang Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
- Institute of Urology, The Third Affiliated Hospital of Shenzhen University, Shenzhen, 518000, China
| | - Yuqing Li
- Institute of Urology, The Third Affiliated Hospital of Shenzhen University, Shenzhen, 518000, China
- Teaching Center of Shenzhen Luohu Hospital, Shantou University Medical College, Shantou, 515000, China
| | - Li Zhong
- Center of Digestive Diseases, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, 518107, China
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, 518107, China
| | - Kai Wu
- Institute of Urology, The Third Affiliated Hospital of Shenzhen University, Shenzhen, 518000, China
| | - Ruhua Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - Tiebang Kang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - Song Wu
- Institute of Urology, The Third Affiliated Hospital of Shenzhen University, Shenzhen, 518000, China.
- Teaching Center of Shenzhen Luohu Hospital, Shantou University Medical College, Shantou, 515000, China.
- Department of Urology, South China Hospital of Shenzhen University, Shenzhen, 518000, China.
| | - Yuanzhong Wu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China.
| |
Collapse
|
20
|
Maurissen TL, Pavlou G, Bichsel C, Villaseñor R, Kamm RD, Ragelle H. Microphysiological Neurovascular Barriers to Model the Inner Retinal Microvasculature. J Pers Med 2022; 12:jpm12020148. [PMID: 35207637 PMCID: PMC8876566 DOI: 10.3390/jpm12020148] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/14/2022] [Accepted: 01/18/2022] [Indexed: 02/07/2023] Open
Abstract
Blood-neural barriers regulate nutrient supply to neuronal tissues and prevent neurotoxicity. In particular, the inner blood-retinal barrier (iBRB) and blood–brain barrier (BBB) share common origins in development, and similar morphology and function in adult tissue, while barrier breakdown and leakage of neurotoxic molecules can be accompanied by neurodegeneration. Therefore, pre-clinical research requires human in vitro models that elucidate pathophysiological mechanisms and support drug discovery, to add to animal in vivo modeling that poorly predict patient responses. Advanced cellular models such as microphysiological systems (MPS) recapitulate tissue organization and function in many organ-specific contexts, providing physiological relevance, potential for customization to different population groups, and scalability for drug screening purposes. While human-based MPS have been developed for tissues such as lung, gut, brain and tumors, few comprehensive models exist for ocular tissues and iBRB modeling. Recent BBB in vitro models using human cells of the neurovascular unit (NVU) showed physiological morphology and permeability values, and reproduced brain neurological disorder phenotypes that could be applicable to modeling the iBRB. Here, we describe similarities between iBRB and BBB properties, compare existing neurovascular barrier models, propose leverage of MPS-based strategies to develop new iBRB models, and explore potentials to personalize cellular inputs and improve pre-clinical testing.
Collapse
Affiliation(s)
- Thomas L. Maurissen
- Roche Pharma Research and Early Development, Immunology, Infectious Diseases and Ophthalmology, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland;
| | - Georgios Pavlou
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., MIT Building, Room NE47-321, Cambridge, MA 02139, USA;
| | - Colette Bichsel
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland;
- Roche Pharma Research and Early Development, Institute for Translational Bioengineering, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Roberto Villaseñor
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland;
| | - Roger D. Kamm
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., MIT Building, Room NE47-321, Cambridge, MA 02139, USA;
- Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., MIT Building, Room NE47-321, Cambridge, MA 02139, USA
- Correspondence: (R.D.K.); (H.R.)
| | - Héloïse Ragelle
- Roche Pharma Research and Early Development, Immunology, Infectious Diseases and Ophthalmology, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland;
- Correspondence: (R.D.K.); (H.R.)
| |
Collapse
|
21
|
Nambiar TS, Baudrier L, Billon P, Ciccia A. CRISPR-based genome editing through the lens of DNA repair. Mol Cell 2022; 82:348-388. [PMID: 35063100 PMCID: PMC8887926 DOI: 10.1016/j.molcel.2021.12.026] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/18/2021] [Accepted: 12/20/2021] [Indexed: 01/22/2023]
Abstract
Genome editing technologies operate by inducing site-specific DNA perturbations that are resolved by cellular DNA repair pathways. Products of genome editors include DNA breaks generated by CRISPR-associated nucleases, base modifications induced by base editors, DNA flaps created by prime editors, and integration intermediates formed by site-specific recombinases and transposases associated with CRISPR systems. Here, we discuss the cellular processes that repair CRISPR-generated DNA lesions and describe strategies to obtain desirable genomic changes through modulation of DNA repair pathways. Advances in our understanding of the DNA repair circuitry, in conjunction with the rapid development of innovative genome editing technologies, promise to greatly enhance our ability to improve food production, combat environmental pollution, develop cell-based therapies, and cure genetic and infectious diseases.
Collapse
Affiliation(s)
- Tarun S. Nambiar
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032
| | - Lou Baudrier
- Department of Biochemistry and Molecular Biology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive N. W., Calgary, Alberta T2N 4N1, Canada
| | - Pierre Billon
- Department of Biochemistry and Molecular Biology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive N. W., Calgary, Alberta T2N 4N1, Canada,Corresponding authors: ,
| | - Alberto Ciccia
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032,Lead Contact,Corresponding authors: ,
| |
Collapse
|
22
|
Meneghini V, Peviani M, Luciani M, Zambonini G, Gritti A. Delivery Platforms for CRISPR/Cas9 Genome Editing of Glial Cells in the Central Nervous System. Front Genome Ed 2021; 3:644319. [PMID: 34713256 PMCID: PMC8525379 DOI: 10.3389/fgeed.2021.644319] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 01/21/2021] [Indexed: 12/14/2022] Open
Abstract
Glial cells (astrocytes, oligodendrocytes, and microglia) are emerging as key players in several physiological and pathological processes of the central nervous system (CNS). Astrocytes and oligodendrocytes are not only supportive cells that release trophic factors or regulate energy metabolism, but they also actively modulate critical neuronal processes and functions in the tripartite synapse. Microglia are defined as CNS-resident cells that provide immune surveillance; however, they also actively contribute to shaping the neuronal microenvironment by scavenging cell debris or regulating synaptogenesis and pruning. Given the many interconnected processes coordinated by glial cells, it is not surprising that both acute and chronic CNS insults not only cause neuronal damage but also trigger complex multifaceted responses, including neuroinflammation, which can critically contribute to the disease progression and worsening of symptoms in several neurodegenerative diseases. Overall, this makes glial cells excellent candidates for targeted therapies to treat CNS disorders. In recent years, the application of gene editing technologies has redefined therapeutic strategies to treat genetic and age-related neurological diseases. In this review, we discuss the advantages and limitations of clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9-based gene editing in the treatment of neurodegenerative disorders, focusing on the development of viral- and nanoparticle-based delivery methods for in vivo glial cell targeting.
Collapse
Affiliation(s)
- Vasco Meneghini
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Marco Peviani
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Marco Luciani
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Giada Zambonini
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Angela Gritti
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| |
Collapse
|
23
|
Matsumoto D, Nomura W. Molecular Switch Engineering for Precise Genome Editing. Bioconjug Chem 2021; 32:639-648. [PMID: 33825445 DOI: 10.1021/acs.bioconjchem.1c00088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Genome editing technology commenced in 1996 with the discovery of the first zinc-finger nuclease. Application of Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) associated protein 9 (Cas9) technology to genome editing of mammalian cells allowed researchers to use genome editing more easily and cost-effectively. However, one of the technological problems that remains to be solved is "off-target effects", which are unexpected mutations in nontarget DNA. One significant improvement in genome editing technology has been achieved with molecular/protein engineering. The key to this engineering is a "switch" to control function. In this review, we discuss recent efforts to design novel "switching" systems for precise editing using genome editing tools.
Collapse
Affiliation(s)
- Daisuke Matsumoto
- Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi Minami-ku, Hiroshima, 734-8553, Japan
| | - Wataru Nomura
- Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi Minami-ku, Hiroshima, 734-8553, Japan
| |
Collapse
|
24
|
Zhang M, Yang C, Tasan I, Zhao H. Expanding the Potential of Mammalian Genome Engineering via Targeted DNA Integration. ACS Synth Biol 2021; 10:429-446. [PMID: 33596056 DOI: 10.1021/acssynbio.0c00576] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Inserting custom designed DNA sequences into the mammalian genome plays an essential role in synthetic biology. In particular, the ability to introduce foreign DNA in a site-specific manner offers numerous advantages over random DNA integration. In this review, we focus on two mechanistically distinct systems that have been widely adopted for targeted DNA insertion in mammalian cells, the CRISPR/Cas9 system and site-specific recombinases. The CRISPR/Cas9 system has revolutionized the genome engineering field thanks to its high programmability and ease of use. However, due to its dependence on linearized DNA donor and endogenous cellular pathways to repair the induced double-strand break, CRISPR/Cas9-mediated DNA insertion still faces limitations such as small insert size, and undesired editing outcomes via error-prone repair pathways. In contrast, site-specific recombinases, in particular the Serine integrases, demonstrate large-cargo capability and no dependence on cellular repair pathways for DNA integration. Here we first describe recent advances in improving the overall efficacy of CRISPR/Cas9-based methods for DNA insertion. Moreover, we highlight the advantages of site-specific recombinases over CRISPR/Cas9 in the context of targeted DNA integration, with a special focus on the recent development of programmable recombinases. We conclude by discussing the importance of protein engineering to further expand the current toolkit for targeted DNA insertion in mammalian cells.
Collapse
Affiliation(s)
- Meng Zhang
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Che Yang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ipek Tasan
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| |
Collapse
|