1
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Tavernier EK, Perroud PF, Lockwood E, Nogué F, McDaniel SF. Establishing CRISPR-Cas9 in the sexually dimorphic moss, Ceratodon purpureus. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 39154335 DOI: 10.1111/tpj.16946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 07/07/2024] [Accepted: 07/13/2024] [Indexed: 08/20/2024]
Abstract
The development of CRISPR technologies provides a powerful tool for understanding the evolution and functionality of essential biological processes. Here we demonstrate successful CRISPR-Cas9 genome editing in the dioecious moss species, Ceratodon purpureus. Using an existing selection system from the distantly related hermaphroditic moss, Physcomitrium patens, we generated knock-outs of the APT reporter gene by employing CRISPR-targeted mutagenesis under expression of native U6 snRNA promoters. Next, we used the native homology-directed repair (HDR) pathway, combined with CRISPR-Cas9, to knock in two reporter genes under expression of an endogenous RPS5A promoter in a newly developed landing site in C. purpureus. Our results show that the molecular tools developed in P. patens can be extended to other mosses across this ecologically important and developmentally variable group. These findings pave the way for precise and powerful experiments aimed at identifying the genetic basis of key functional variation within the bryophytes and between the bryophytes and other land plants.
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Affiliation(s)
- Emilie-Katherine Tavernier
- Department of Biology, University of Florida, Gainesville, Florida, USA
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, 78000, France
| | - Pierre-François Perroud
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, 78000, France
| | - Emily Lockwood
- Department of Biology, University of Florida, Gainesville, Florida, USA
| | - Fabien Nogué
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, 78000, France
| | - Stuart F McDaniel
- Department of Biology, University of Florida, Gainesville, Florida, USA
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2
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Wang Y, Liu M, Lin X, Wang H, Dong N, Liu H, Shao H, Zhang W. Genome Editing of Mammalian Cells Through RNA Transcript-Mediated Homologous Recombination Repair. Hum Gene Ther 2024; 35:555-563. [PMID: 39046112 DOI: 10.1089/hum.2024.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2024] Open
Abstract
Double-stranded break (DSB) repair of eukaryotic DNA is mainly accomplished by nonhomologous end joining and homologous recombination (HR). Providing exogenous templates during HR repair can result in the editing of target genes, which is the central mechanism of the well-established clustered regularly interspaced short palindromic repeats (CRISPR) gene editing system. Currently, exogenous templates are mainly DNA molecules, which can provoke a cellular immune response within the cell. In order to verify the feasibility of RNA molecules as repair templates for HR in mammalian cell genome editing, we fused RNA template molecules to the 3'-end of single guide RNA (sgRNA), so that the sgRNA and the homologous template RNA form a single RNA molecule. The results show this construct can be used as a repair template to achieve target gene editing in mammalian cells. In addition, the factors influencing HR mediated by RNA template molecules were investigated, and it was found that increasing the length of homologous arms and inducing an R-loop near the DSBcan effectively promote HR repair. Furthermore, intracellular homologous chromosomes may compete with exogenous RNA templates. The findings in this article provide a reference for the utilization of RNA template molecules to mediate target gene editing in eukaryotic cells, as well as a basis for the study of the mechanism by which RNA molecules mediate the repair of DSBs.
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Affiliation(s)
- Yangmin Wang
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
- Biopharmaceutical Institute, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
| | - Meilin Liu
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
- Biopharmaceutical Institute, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
| | - Xinjian Lin
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
- Biopharmaceutical Institute, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
| | - Haozheng Wang
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
- Biopharmaceutical Institute, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
| | - Na Dong
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
- Biopharmaceutical Institute, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
| | - Hengshen Liu
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
- Biopharmaceutical Institute, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
| | - Hongwei Shao
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
- Biopharmaceutical Institute, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
| | - Wenfeng Zhang
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
- Biopharmaceutical Institute, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
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3
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Dai L, Yu P, Fan H, Xia W, Zhao Y, Zhang P, Zhang JZH, Zhang H, Chen Y. Identification and Validation of New DNA-PKcs Inhibitors through High-Throughput Virtual Screening and Experimental Verification. Int J Mol Sci 2024; 25:7982. [PMID: 39063224 PMCID: PMC11277333 DOI: 10.3390/ijms25147982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 07/12/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024] Open
Abstract
DNA-PKcs is a crucial protein target involved in DNA repair and response pathways, with its abnormal activity closely associated with the occurrence and progression of various cancers. In this study, we employed a deep learning-based screening and molecular dynamics (MD) simulation-based pipeline, identifying eight candidates for DNA-PKcs targets. Subsequent experiments revealed the effective inhibition of DNA-PKcs-mediated cell proliferation by three small molecules (5025-0002, M769-1095, and V008-1080). These molecules exhibited anticancer activity with IC50 (inhibitory concentration at 50%) values of 152.6 μM, 30.71 μM, and 74.84 μM, respectively. Notably, V008-1080 enhanced homology-directed repair (HDR) mediated by CRISPR/Cas9 while inhibiting non-homologous end joining (NHEJ) efficiency. Further investigations into the structure-activity relationships unveiled the binding sites and critical interactions between these small molecules and DNA-PKcs. This is the first application of DeepBindGCN_RG in a real drug screening task, and the successful discovery of a novel DNA-PKcs inhibitor demonstrates its efficiency as a core component in the screening pipeline. Moreover, this study provides important insights for exploring novel anticancer therapeutics and advancing the development of gene editing techniques by targeting DNA-PKcs.
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Affiliation(s)
- Liujiang Dai
- Department of Physiology, Guangxi University of Chinese Medicine, Nanning 530200, China
- Guangdong Immune Cell Therapy Engineering and Technology Research Center, Center for Protein and Cell-Based Drugs, Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Pengfei Yu
- Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, China
| | - Hongjie Fan
- Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, China
| | - Wei Xia
- Faculty of Synthetic Biology and Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yaopeng Zhao
- Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, China
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Pengfei Zhang
- Guangdong Key Laboratory of Nanomedicine, CAS-HK Joint Lab of Biomaterials, CAS Key Laboratory of Biomedical Imaging Science and System, Shenzhen Engineering Laboratory of Nanomedicine and Nanoformulations, CAS Key Lab for Health Informatics, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - John Z. H. Zhang
- Faculty of Synthetic Biology and Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Haiping Zhang
- Faculty of Synthetic Biology and Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yang Chen
- Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, China
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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4
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Rosch T, Tenhaef J, Stoltmann T, Redeker T, Kösters D, Hollmann N, Krumbach K, Wiechert W, Bott M, Matamouros S, Marienhagen J, Noack S. AutoBioTech─A Versatile Biofoundry for Automated Strain Engineering. ACS Synth Biol 2024; 13:2227-2237. [PMID: 38975718 PMCID: PMC11264319 DOI: 10.1021/acssynbio.4c00298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 07/02/2024] [Accepted: 07/02/2024] [Indexed: 07/09/2024]
Abstract
The inevitable transition from petrochemical production processes to renewable alternatives has sparked the emergence of biofoundries in recent years. Manual engineering of microbes will not be sufficient to meet the ever-increasing demand for novel producer strains. Here we describe the AutoBioTech platform, a fully automated laboratory system with 14 devices to perform operations for strain construction without human interaction. Using modular workflows, this platform enables automated transformations of Escherichia coli with plasmids assembled via modular cloning. A CRISPR/Cas9 toolbox compatible with existing modular cloning frameworks allows automated and flexible genome editing of E. coli. In addition, novel workflows have been established for the fully automated transformation of the Gram-positive model organism Corynebacterium glutamicum by conjugation and electroporation, with the latter proving to be the more robust technique. Overall, the AutoBioTech platform excels at versatility due to the modularity of workflows and seamless transitions between modules. This will accelerate strain engineering of Gram-negative and Gram-positive bacteria.
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Affiliation(s)
- Tobias
Michael Rosch
- Institute
of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Julia Tenhaef
- Institute
of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Tim Stoltmann
- Institute
of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Till Redeker
- Institute
of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Dominic Kösters
- Institute
of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, D-52425 Jülich, Germany
- Institute
of Biotechnology, RWTH Aachen University, Worringer Weg 3, D-52074 Aachen, Germany
| | - Niels Hollmann
- Institute
of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, D-52425 Jülich, Germany
- Institute
of Biotechnology, RWTH Aachen University, Worringer Weg 3, D-52074 Aachen, Germany
| | - Karin Krumbach
- Institute
of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Wolfgang Wiechert
- Institute
of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Michael Bott
- Institute
of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, D-52425 Jülich, Germany
- The
Bioeconomy Science Center (BioSC), Forschungszentrum
Jülich, D-52425 Jülich, Germany
| | - Susana Matamouros
- Institute
of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Jan Marienhagen
- Institute
of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, D-52425 Jülich, Germany
- Institute
of Biotechnology, RWTH Aachen University, Worringer Weg 3, D-52074 Aachen, Germany
| | - Stephan Noack
- Institute
of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, D-52425 Jülich, Germany
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5
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Chen Z, Hu J, Dai J, Zhou C, Hua Y, Hua X, Zhao Y. Precise CRISPR/Cpf1 genome editing system in the Deinococcus radiodurans with superior DNA repair mechanisms. Microbiol Res 2024; 284:127713. [PMID: 38608339 DOI: 10.1016/j.micres.2024.127713] [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: 12/04/2023] [Revised: 02/20/2024] [Accepted: 04/06/2024] [Indexed: 04/14/2024]
Abstract
Deinococcus radiodurans, with its high homologous recombination (HR) efficiency of double-stranded DNA breaks (DSBs), is a model organism for studying genome stability maintenance and an attractive microbe for industrial applications. Here, we developed an efficient CRISPR/Cpf1 genome editing system in D. radiodurans by evaluating and optimizing double-plasmid strategies and four Cas effector proteins from various organisms, which can precisely introduce different types of template-dependent mutagenesis without off-target toxicity. Furthermore, the role of DNA repair genes in determining editing efficiency in D. radiodurans was evaluated by introducing the CRISPR/Cpf1 system into 13 mutant strains lacking various DNA damage response and repair factors. In addition to the crucial role of RecA-dependent HR required for CRISPR/Cpf1 editing, D. radiodurans showed higher editing efficiency when lacking DdrB, the single-stranded DNA annealing (SSA) protein involved in the RecA-independent DSB repair pathway. This suggests a possible competition between HR and SSA pathways in the CRISPR editing of D. radiodurans. Moreover, off-target effects were observed during the genome editing of the pprI knockout strain, a master DNA damage response gene in Deinococcus species, which suggested that precise regulation of DNA damage response is critical for a high-fidelity genome editing system.
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Affiliation(s)
- Zijing Chen
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China; MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jing Hu
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China; MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jingli Dai
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China; MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, Zhejiang, China
| | - Congli Zhou
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China; MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yuejin Hua
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China; MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaoting Hua
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Ye Zhao
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China; MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, Zhejiang, China.
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6
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Pandey S, Gao XD, Krasnow NA, McElroy A, Tao YA, Duby JE, Steinbeck BJ, McCreary J, Pierce SE, Tolar J, Meissner TB, Chaikof EL, Osborn MJ, Liu DR. Efficient site-specific integration of large genes in mammalian cells via continuously evolved recombinases and prime editing. Nat Biomed Eng 2024:10.1038/s41551-024-01227-1. [PMID: 38858586 DOI: 10.1038/s41551-024-01227-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 05/09/2024] [Indexed: 06/12/2024]
Abstract
Methods for the targeted integration of genes in mammalian genomes suffer from low programmability, low efficiencies or low specificities. Here we show that phage-assisted continuous evolution enhances prime-editing-assisted site-specific integrase gene editing (PASSIGE), which couples the programmability of prime editing with the ability of recombinases to precisely integrate large DNA cargoes exceeding 10 kilobases. Evolved and engineered Bxb1 recombinase variants (evoBxb1 and eeBxb1) mediated up to 60% donor integration (3.2-fold that of wild-type Bxb1) in human cell lines with pre-installed recombinase landing sites. In single-transfection experiments at safe-harbour and therapeutically relevant sites, PASSIGE with eeBxb1 led to an average targeted-gene-integration efficiencies of 23% (4.2-fold that of wild-type Bxb1). Notably, integration efficiencies exceeded 30% at multiple sites in primary human fibroblasts. PASSIGE with evoBxb1 or eeBxb1 outperformed PASTE (for 'programmable addition via site-specific targeting elements', a method that uses prime editors fused to recombinases) on average by 9.1-fold and 16-fold, respectively. PASSIGE with continuously evolved recombinases is an unusually efficient method for the targeted integration of genes in mammalian cells.
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Affiliation(s)
- Smriti Pandey
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Xin D Gao
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Nicholas A Krasnow
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Amber McElroy
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Y Allen Tao
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Jordyn E Duby
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Benjamin J Steinbeck
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Julia McCreary
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Sarah E Pierce
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Jakub Tolar
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Torsten B Meissner
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Wyss Institute of Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Elliot L Chaikof
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Wyss Institute of Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Mark J Osborn
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
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7
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Sakai Y, Okabe Y, Itai G, Shiozawa S. An efficient evaluation system for factors affecting the genome editing efficiency in mouse. Exp Anim 2023; 72:526-534. [PMID: 37407493 PMCID: PMC10658088 DOI: 10.1538/expanim.23-0045] [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: 03/27/2023] [Accepted: 06/23/2023] [Indexed: 07/07/2023] Open
Abstract
Genome editing technology is widely used in the field of laboratory animal science for the production of genetic disease models and the analysis of gene function. One of the major technical problems in genome editing is the low efficiency of precise knock-in by homologous recombination compared to simple knockout via non-homologous end joining. Many studies have focused on this issue, and various solutions have been proposed; however, they have yet to be fully resolved. In this study, we established a system that can easily determine the genotype at the mouse (Mus musculus) Tyr gene locus for genome editing both in vitro and in vivo. In this genome editing system, by designing the Cas9 cleavage site and donor template, wild-type, knockout, and knock-in genotypes can be distinguished by restriction fragment length polymorphisms of PCR products. Moreover, the introduction of the H420R mutation in tyrosinase allows the determination of knock-in mice with specific coat color patterns. Using this system, we evaluated the effects of small-molecule compounds on the efficiency of genome editing in mouse embryos. Consequently, we successfully identified a small-molecule compound that improves knock-in efficiency in genome editing in mouse embryos. Thus, this genome editing system is suitable for screening compounds that can improve knock-in efficiency.
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Affiliation(s)
- Yusuke Sakai
- Institute for Disease Modeling, Kurume University School of Medicine, 67 Asahimachi, Kurume city, Fukuoka 830-0011, Japan
| | - Yuri Okabe
- Institute for Disease Modeling, Kurume University School of Medicine, 67 Asahimachi, Kurume city, Fukuoka 830-0011, Japan
| | - Gen Itai
- Center for Integrated Medical Research, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
- JAC Inc., 1-2-7 Higashiyama, Meguro-ku, Tokyo 153-0043, Japan
| | - Seiji Shiozawa
- Institute for Disease Modeling, Kurume University School of Medicine, 67 Asahimachi, Kurume city, Fukuoka 830-0011, Japan
- Center for Integrated Medical Research, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
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8
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Li Y, Huang B, Chen J, Huang L, Xu J, Wang Y, Cui G, Zhao H, Xin B, Song W, Zhu J, Lai J. Targeted large fragment deletion in plants using paired crRNAs with type I CRISPR system. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:2196-2208. [PMID: 37641539 PMCID: PMC10579709 DOI: 10.1111/pbi.14122] [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: 02/08/2023] [Revised: 05/19/2023] [Accepted: 06/25/2023] [Indexed: 08/31/2023]
Abstract
The CRISPR-Cas systems have been widely used as genome editing tools, with type II and V systems typically introducing small indels, and type I system mediating long-range deletions. However, the precision of type I systems for large fragment deletion is still remained to be optimized. Here, we developed a compact Cascade-Cas3 Dvu I-C system with Cas11c for plant genome editing. The Dvu I-C system was efficient to introduce controllable large fragment deletion up to at least 20 kb using paired crRNAs. The paired-crRNAs design also improved the controllability of deletions for the type I-E system. Dvu I-C system was sensitive to spacer length and mismatch, which was benefit for target specificity. In addition, we showed that the Dvu I-C system was efficient for generating stable transgenic lines in maize and rice with the editing efficiency up to 86.67%. Overall, Dvu I-C system we developed here is powerful for achieving controllable large fragment deletions.
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Affiliation(s)
- Yingnan Li
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Boyu Huang
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Jian Chen
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Liangliang Huang
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Jianghai Xu
- College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Yingying Wang
- College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Guanghui Cui
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Haiming Zhao
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Beibei Xin
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Weibin Song
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Jian‐Kang Zhu
- Institute of Advanced Biotechnology and School of Life SciencesSouthern University of Science and TechnologyShenzhenChina
- Center for Advanced Bioindustry TechnologiesChinese Academy of Agricultural SciencesBeijingChina
| | - Jinsheng Lai
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
- Frontiers Science Center for Molecular Design BreedingChina Agricultural UniversityBeijingChina
- Center for Crop Functional Genomics and Molecular BreedingChina Agricultural UniversityBeijingChina
- Sanya Institute of China Agricultural UniversitySanyaChina
- Hainan Yazhou Bay Seed LaboratorySanyaChina
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9
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Liu Z, Liu J, Yang Z, Zhu L, Zhu Z, Huang H, Jiang L. Endogenous CRISPR-Cas mediated in situ genome editing: State-of-the-art and the road ahead for engineering prokaryotes. Biotechnol Adv 2023; 68:108241. [PMID: 37633620 DOI: 10.1016/j.biotechadv.2023.108241] [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: 04/18/2023] [Revised: 08/23/2023] [Accepted: 08/23/2023] [Indexed: 08/28/2023]
Abstract
The CRISPR-Cas systems have shown tremendous promise as heterologous tools for genome editing in various prokaryotes. However, the perturbation of DNA homeostasis and the inherent toxicity of Cas9/12a proteins could easily lead to cell death, which led to the development of endogenous CRISPR-Cas systems. Programming the widespread endogenous CRISPR-Cas systems for in situ genome editing represents a promising tool in prokaryotes, especially in genetically intractable species. Here, this review briefly summarizes the advances of endogenous CRISPR-Cas-mediated genome editing, covering aspects of establishing and optimizing the genetic tools. In particular, this review presents the application of different types of endogenous CRISPR-Cas tools for strain engineering, including genome editing and genetic regulation. Notably, this review also provides a detailed discussion of the transposon-associated CRISPR-Cas systems, and the programmable RNA-guided transposition using endogenous CRISPR-Cas systems to enable editing of microbial communities for understanding and control. Therefore, they will be a powerful tool for targeted genetic manipulation. Overall, this review will not only facilitate the development of standard genetic manipulation tools for non-model prokaryotes but will also enable more non-model prokaryotes to be genetically tractable.
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Affiliation(s)
- Zhenlei Liu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Jiayu Liu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Zhihan Yang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Liying Zhu
- College of Chemical and Molecular Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Zhengming Zhu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China.
| | - He Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210046, China.
| | - Ling Jiang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China; State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China.
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10
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Elhawary NA, AlJahdali IA, Abumansour IS, Azher ZA, Falemban AH, Madani WM, Alosaimi W, Alghamdi G, Sindi IA. Phenotypic variability to medication management: an update on fragile X syndrome. Hum Genomics 2023; 17:60. [PMID: 37420260 DOI: 10.1186/s40246-023-00507-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 07/03/2023] [Indexed: 07/09/2023] Open
Abstract
This review discusses the discovery, epidemiology, pathophysiology, genetic etiology, molecular diagnosis, and medication-based management of fragile X syndrome (FXS). It also highlights the syndrome's variable expressivity and common comorbid and overlapping conditions. FXS is an X-linked dominant disorder associated with a wide spectrum of clinical features, including but not limited to intellectual disability, autism spectrum disorder, language deficits, macroorchidism, seizures, and anxiety. Its prevalence in the general population is approximately 1 in 5000-7000 men and 1 in 4000-6000 women worldwide. FXS is associated with the fragile X messenger ribonucleoprotein 1 (FMR1) gene located at locus Xq27.3 and encodes the fragile X messenger ribonucleoprotein (FMRP). Most individuals with FXS have an FMR1 allele with > 200 CGG repeats (full mutation) and hypermethylation of the CpG island proximal to the repeats, which silences the gene's promoter. Some individuals have mosaicism in the size of the CGG repeats or in hypermethylation of the CpG island, both produce some FMRP and give rise to milder cognitive and behavioral deficits than in non-mosaic individuals with FXS. As in several monogenic disorders, modifier genes influence the penetrance of FMR1 mutations and FXS's variable expressivity by regulating the pathophysiological mechanisms related to the syndrome's behavioral features. Although there is no cure for FXS, prenatal molecular diagnostic testing is recommended to facilitate early diagnosis. Pharmacologic agents can reduce some behavioral features of FXS, and researchers are investigating whether gene editing can be used to demethylate the FMR1 promoter region to improve patient outcomes. Moreover, clustered regularly interspaced palindromic repeats (CRISPR)/Cas9 and developed nuclease defective Cas9 (dCas9) strategies have promised options of genome editing in gain-of-function mutations to rewrite new genetic information into a specified DNA site, are also being studied.
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Affiliation(s)
- Nasser A Elhawary
- Department of Medical Genetics, College of Medicine, Umm Al-Qura University, Mecca, 21955, Saudi Arabia.
| | - Imad A AlJahdali
- Department of Community Medicine, College of Medicine, Umm Al-Qura University, Mecca, Saudi Arabia
| | - Iman S Abumansour
- Department of Medical Genetics, College of Medicine, Umm Al-Qura University, Mecca, 21955, Saudi Arabia
| | - Zohor A Azher
- Department of Medical Genetics, College of Medicine, Umm Al-Qura University, Mecca, 21955, Saudi Arabia
| | - Alaa H Falemban
- Department of Pharmacology and Toxicology, College of Medicine, Umm Al-Qura University, Mecca, 24382, Saudi Arabia
| | - Wefaq M Madani
- Department of Hematology and Immunology, Faculty of Medicine, Umm Al-Qura University, Mecca, Saudi Arabia
| | - Wafaa Alosaimi
- Department of Hematology, Maternity and Children Hospital, Mecca, Saudi Arabia
| | - Ghydda Alghamdi
- Department of Medical Genetics, College of Medicine, Umm Al-Qura University, Mecca, 21955, Saudi Arabia
| | - Ikhlas A Sindi
- Department of Biology, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
- Preparatory Year Program, Batterjee Medical College, Jeddah, 21442, Saudi Arabia
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11
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Chai R, Zhang Q, Wu J, Shi Z, Li Y, Gao Y, Qi Y, Qiu L. Single-Stranded DNA-Binding Proteins Mediate DSB Repair and Effectively Improve CRISPR/Cas9 Genome Editing in Escherichia coli and Pseudomonas. Microorganisms 2023; 11:microorganisms11040850. [PMID: 37110272 PMCID: PMC10143710 DOI: 10.3390/microorganisms11040850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 03/22/2023] [Accepted: 03/25/2023] [Indexed: 03/29/2023] Open
Abstract
Single-stranded DNA-binding proteins (SSBs) are essential for all living organisms. Whether SSBs can repair DNA double-strand breaks (DSBs) and improve the efficiency of CRISPR/Cas9-mediated genome editing has not been determined. Here, based on a pCas/pTargetF system, we constructed pCas-SSB and pCas-T4L by replacing the λ-Red recombinases with Escherichia coli SSB and phage T4 DNA ligase in pCas, respectively. Inactivation of the E. coli lacZ gene with homologous donor dsDNA increased the gene editing efficiency of pCas-SSB/pTargetF by 21.4% compared to pCas/pTargetF. Inactivation of the E. coli lacZ gene via NHEJ increased the gene editing efficiency of pCas-SSB/pTargetF by 33.2% compared to pCas-T4L/pTargetF. Furthermore, the gene-editing efficiency of pCas-SSB/pTargetF in E. coli (ΔrecA, ΔrecBCD, ΔSSB) with or without donor dsDNA did not differ. Additionally, pCas-SSB/pTargetF with donor dsDNA successfully deleted the wp116 gene in Pseudomonas sp. UW4. These results demonstrate that E. coli SSB repairs DSBs caused by CRISPR/Cas9 and effectively improves CRISPR/Cas9 genome editing in E. coli and Pseudomonas.
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12
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Patel VK, Das A, Kumari R, Kajla S. Recent progress and challenges in CRISPR-Cas9 engineered algae and cyanobacteria. ALGAL RES 2023. [DOI: 10.1016/j.algal.2023.103068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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13
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Ben Yacoub T, Wohlschlegel J, Sahel JA, Zeitz C, Audo I. [CRISPR/Cas9: From research to therapeutic application]. J Fr Ophtalmol 2023; 46:398-407. [PMID: 36759244 DOI: 10.1016/j.jfo.2022.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/12/2022] [Accepted: 10/21/2022] [Indexed: 02/10/2023]
Abstract
For several decades, genome engineering has raised interest among many researchers and physicians in the study of genetic disorders and their treatments. Compared to its predecessors, zinc-finger nucleases (ZFN) and transcription activator-like effectors (TALEN), clustered regularly interspaced short palindromic repeats (CRISPR/Cas9) is currently the most efficient molecular tool for genome editing. This system, originally identified as a bacterial adaptive immune system, is capable of cutting and modifying any gene of a large number of living organisms. Numerous trials using this technology are being developed to provide effective treatment for several diseases, such as cancer, cardiovascular and ophthalmic disorders. In research, this technology is increasingly used for genetic disease modelling, providing meaningful models of relevant studies as well as a better understanding of underlying pathological mechanisms. Many molecular tools are now available to put this technique into practice in laboratories, and despite the technical and ethical issues raised by manipulation of the genome, CRIPSR/Cas9 offers a new breath of hope for therapeutic research around the world.
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Affiliation(s)
- T Ben Yacoub
- Sorbonne université, Inserm, CNRS, institut de la Vision, 75012 Paris, France.
| | - J Wohlschlegel
- Sorbonne université, Inserm, CNRS, institut de la Vision, 75012 Paris, France
| | - J-A Sahel
- Sorbonne université, Inserm, CNRS, institut de la Vision, 75012 Paris, France; CHNO des Quinze-Vingts, Inserm-DGOS CIC 1423, 75012 Paris, France; Department of ophthalmology, fondation ophtalmologique Adolphe De Rothschild, 75019 Paris, France; Department of ophthalmology, the university of Pittsburgh School of Medicine, Pittsburgh PA 15213, United States; Académie des sciences, institut de France, 75006 Paris, France
| | - C Zeitz
- Sorbonne université, Inserm, CNRS, institut de la Vision, 75012 Paris, France
| | - I Audo
- Sorbonne université, Inserm, CNRS, institut de la Vision, 75012 Paris, France; CHNO des Quinze-Vingts, Inserm-DGOS CIC 1423, 75012 Paris, France; Institute of ophthalmology, university College of London, London EC1V 9EL, United Kingdom
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14
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Abstract
The advent of clustered regularly interspaced short palindromic repeat (CRISPR) genome editing, coupled with advances in computing and imaging capabilities, has initiated a new era in which genetic diseases and individual disease susceptibilities are both predictable and actionable. Likewise, genes responsible for plant traits can be identified and altered quickly, transforming the pace of agricultural research and plant breeding. In this Review, we discuss the current state of CRISPR-mediated genetic manipulation in human cells, animals, and plants along with relevant successes and challenges and present a roadmap for the future of this technology.
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Affiliation(s)
- Joy Y Wang
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Jennifer A Doudna
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.,California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA.,Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Gladstone Institutes, University of California, San Francisco, San Francisco, CA, USA.,Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
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15
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Panchal SS, Vasava DV. Synthetic biodegradable polymeric materials in non-viral gene delivery. INT J POLYM MATER PO 2023. [DOI: 10.1080/00914037.2023.2167081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Siddhi S. Panchal
- Department of Chemistry, School of Sciences, Gujarat University, Ahmedabad, India
| | - Dilip V. Vasava
- Department of Chemistry, School of Sciences, Gujarat University, Ahmedabad, India
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16
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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.
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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.
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17
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CRISPR/Cas9 in the era of nanomedicine and synthetic biology. Drug Discov Today 2023; 28:103375. [PMID: 36174966 DOI: 10.1016/j.drudis.2022.103375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 08/15/2022] [Accepted: 09/22/2022] [Indexed: 02/02/2023]
Abstract
The CRISPR/Cas system was first discovered as a defense mechanism in bacteria and is now used as a tool for precise gene-editing applications. Rapidly evolving, it is increasingly applied in therapeutics. However, concerns about safety, specificity, and delivery still limit its potential. In this context, we introduce the concept of nanogenetics and speculate how the rational engineering of the CRISPR/Cas machinery could advance the biomedical field. In nanogenetics, the advantages of traditional approaches of synthetic biology could be expanded by nanotechnology approaches, enabling the design of a new generation of intrinsically safe and specific genome-editing platforms.
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18
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Kazemizadeh H, Kashefizadeh A. CRISPR-Cas9-mediated gene therapy in lung cancer. Clin Transl Oncol 2022; 25:1156-1166. [PMID: 36495467 DOI: 10.1007/s12094-022-03039-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 11/25/2022] [Indexed: 12/14/2022]
Abstract
As the largest cause of cancer-related deaths worldwide, pulmonary cancer is the most common form of the disease. Several genetic, epigenetic, and environmental factors come into play during the multi-step mechanism of tumorigenesis. The heterogeneity that makes discovering successful therapeutics for pulmonary cancer problematic is significantly influenced by the epigenetic landscape, including DNA methylation, chromatin architecture, histone modifications, and noncoding RNA control. Clinical activity of epigenetic-targeted medicines has been reported in hematological tumors, and these compounds may also have therapeutic effects in solid tumors. Over the course of the past few years, some researchers have successfully modified the expression of genes in cells using the clustered regularly interspaced short palindromic repeats (CRISPR)-Cas (CRISPR-associated proteins) technique. The utilization of this technology allows for the induction of site-specific mutagenesis, epigenetic alterations, and the regulation of gene expression. This study will present an overview of the primary epigenetic alterations seen in pulmonary cancer, as well as a summary of therapeutic implications for targeting epigenetics in the management of pulmonary cancer, with a particular emphasis on the technique known as CRISPR/Cas9.
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Affiliation(s)
- Hossein Kazemizadeh
- Advanced Thoracic Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Alireza Kashefizadeh
- Department of Pulmonology, Shahid Labbafinejad Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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19
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Song Y, He S, Jopkiewicz A, Setroikromo R, van Merkerk R, Quax WJ. Development and application of CRISPR-based genetic tools in Bacillus species and Bacillus phages. J Appl Microbiol 2022; 133:2280-2298. [PMID: 35797344 PMCID: PMC9796756 DOI: 10.1111/jam.15704] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 07/02/2022] [Accepted: 07/06/2022] [Indexed: 01/07/2023]
Abstract
Recently, the clustered regularly interspaced short palindromic repeats (CRISPR) system has been developed into a precise and efficient genome editing tool. Since its discovery as an adaptive immune system in prokaryotes, it has been applied in many different research fields including biotechnology and medical sciences. The high demand for rapid, highly efficient and versatile genetic tools to thrive in bacteria-based cell factories accelerates this process. This review mainly focuses on significant advancements of the CRISPR system in Bacillus subtilis, including the achievements in gene editing, and on problems still remaining. Next, we comprehensively summarize this genetic tool's up-to-date development and utilization in other Bacillus species, including B. licheniformis, B. methanolicus, B. anthracis, B. cereus, B. smithii and B. thuringiensis. Furthermore, we describe the current application of CRISPR tools in phages to increase Bacillus hosts' resistance to virulent phages and phage genetic modification. Finally, we suggest potential strategies to further improve this advanced technique and provide insights into future directions of CRISPR technologies for rendering Bacillus species cell factories more effective and more powerful.
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Affiliation(s)
- Yafeng Song
- Department of Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy, University of GroningenGroningenThe Netherlands,Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern ChinaInstitute of Microbiology, Guangdong Acadamy of SciencesGuangzhouChina
| | - Siqi He
- Department of Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy, University of GroningenGroningenThe Netherlands
| | - Anita Jopkiewicz
- Department of Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy, University of GroningenGroningenThe Netherlands
| | - Rita Setroikromo
- Department of Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy, University of GroningenGroningenThe Netherlands
| | - Ronald van Merkerk
- Department of Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy, University of GroningenGroningenThe Netherlands
| | - Wim J. Quax
- Department of Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy, University of GroningenGroningenThe Netherlands
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20
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Kim HJ, Cho HB, Lee S, Lyu J, Kim HR, Lee S, Park JI, Park KH. Strategies for accelerating osteogenesis through nanoparticle-based DNA/mitochondrial damage repair. Am J Cancer Res 2022; 12:6409-6421. [PMID: 36168629 PMCID: PMC9475457 DOI: 10.7150/thno.77089] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 08/18/2022] [Indexed: 11/05/2022] Open
Abstract
The efficiency of gene therapy is often dictated by the gene delivery system. Cationic polymers are essential elements of gene delivery systems. The relatively cheap cationic polymer, polyethyleneimine, has high gene delivery efficiency and is often used for gene delivery. However, the efficiency of gene therapy with polyethyleneimine-pDNA polyplex (PEI) is low. Human mesenchymal stem cells transfected with polyethyleneimine and a plasmid carrying the important osteogenic differentiation gene runt-related transcription factor 2 (RUNX2) accumulated DNA double-strand breaks and mitochondrial damage proportional to the amount of polyethyleneimine, reducing viability. Genomic/cellular stabilizer mediating RUNX2 delivery (GuaRD), a new reagent incorporating RS-1 NPs developed in this study, promoted DNA repair and prevented the accumulation of cell damage, allowing the delivery of pRUNX2 into hMSCs. while maintaining genome and mitochondrial stability. DNA damage was significantly lower and the expression of DNA repair-related genes significantly higher with GuaRD than with PEI. In addition, GuaRD improved mitochondrial stability, decreased the level of reactive oxygen species, and increased mitochondrial membrane potential. Osteogenic extracellular matrix (ECM) expression and calcification were higher with GuaRD than with PEI, suggesting improved osteogenic differentiation. These results indicate that lowering the cytotoxicity of PEI and improving cell stability are key to overcoming the limitations of conventional gene therapy, and that GuaRD can help resolve these limitations.
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Affiliation(s)
- Hye Jin Kim
- Laboratory of Nano-regenerative Medicine, Department of Biomedical Science, College of Life Science, CHA University, CHA Biocomplex, Sampyeong-Dong, Bundang-gu, Seongnam-si, 13488, Republic of Korea
| | - Hui Bang Cho
- Laboratory of Nano-regenerative Medicine, Department of Biomedical Science, College of Life Science, CHA University, CHA Biocomplex, Sampyeong-Dong, Bundang-gu, Seongnam-si, 13488, Republic of Korea
| | - Sujin Lee
- Laboratory of Nano-regenerative Medicine, Department of Biomedical Science, College of Life Science, CHA University, CHA Biocomplex, Sampyeong-Dong, Bundang-gu, Seongnam-si, 13488, Republic of Korea
| | - Jiyon Lyu
- School of Medicine, CHA University, CHA Biocomplex, Sampyeong-Dong, Bundang-gu, Seongnam-si, 13488, Republic of Korea
| | - Hye-Ryoung Kim
- Laboratory of Nano-regenerative Medicine, Department of Biomedical Science, College of Life Science, CHA University, CHA Biocomplex, Sampyeong-Dong, Bundang-gu, Seongnam-si, 13488, Republic of Korea
| | - Sujeong Lee
- Laboratory of Nano-regenerative Medicine, Department of Biomedical Science, College of Life Science, CHA University, CHA Biocomplex, Sampyeong-Dong, Bundang-gu, Seongnam-si, 13488, Republic of Korea
| | - Ji-In Park
- Laboratory of Nano-regenerative Medicine, Department of Biomedical Science, College of Life Science, CHA University, CHA Biocomplex, Sampyeong-Dong, Bundang-gu, Seongnam-si, 13488, Republic of Korea
| | - Keun-Hong Park
- Laboratory of Nano-regenerative Medicine, Department of Biomedical Science, College of Life Science, CHA University, CHA Biocomplex, Sampyeong-Dong, Bundang-gu, Seongnam-si, 13488, Republic of Korea
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21
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Cui Y, Dong H, Tong B, Wang H, Chen X, Liu G, Zhang D. A versatile Cas12k-based genetic engineering toolkit (C12KGET) for metabolic engineering in genetic manipulation-deprived strains. Nucleic Acids Res 2022; 50:8961-8973. [PMID: 35920322 PMCID: PMC9410911 DOI: 10.1093/nar/gkac655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 07/07/2022] [Accepted: 07/22/2022] [Indexed: 12/01/2022] Open
Abstract
The genetic modification of microorganisms is conducive to the selection of high-yield producers of high-value-added chemicals, but a lack of genetic tools hinders the industrialization of most wild species. Therefore, it is crucial to develop host-independent gene editing tools that can be used for genetic manipulation-deprived strains. The Tn7-like transposon from Scytonema hofmanni has been shown to mediate homologous recombination-independent genomic integration after heterologous expression in Escherichia coli, but the integration efficiency of heterologous sequences larger than 5 kb remains suboptimal. Here, we constructed a versatile Cas12k-based genetic engineering toolkit (C12KGET) that can achieve genomic integration of fragments up to 10 kb in size with up to 100% efficiency in challenging strains. Using C12KGET, we achieved the first example of highly efficient genome editing in Sinorhizobium meliloti, which successfully solved the problem that industrial strains are difficult to genetically modify, and increased vitamin B12 production by 25%. In addition, Cas12k can be directly used for transcriptional regulation of genes with up to 92% efficiency due to its naturally inactivated nuclease domain. The C12KGET established in this study is a versatile and efficient marker-free tool for gene integration as well as transcriptional regulation that can be used for challenging strains with underdeveloped genetic toolkits.
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Affiliation(s)
- Yali Cui
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Huina Dong
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Baisong Tong
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Huiying Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Xipeng Chen
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Guangqing Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Dawei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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22
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Gao K, Zhang X, Zhang Z, Wu X, Guo Y, Fu P, Sun A, Peng J, Zheng J, Yu P, Wang T, Ye Q, Jiang J, Wang H, Lin CP, Gao G. Transcription-coupled donor DNA expression increases homologous recombination for efficient genome editing. Nucleic Acids Res 2022; 50:e109. [PMID: 35929067 DOI: 10.1093/nar/gkac676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/18/2022] [Accepted: 07/26/2022] [Indexed: 11/14/2022] Open
Abstract
Genomes can be edited by homologous recombination stimulated by CRISPR/Cas9 [clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated peptide 9]-induced DNA double-strand breaks. However, this approach is inefficient for inserting or deleting long fragments in mammalian cells. Here, we describe a simple genome-editing method, termed transcription-coupled Cas9-mediated editing (TEd), that can achieve higher efficiencies than canonical Cas9-mediated editing (CEd) in deleting genomic fragments, inserting/replacing large DNA fragments and introducing point mutations into mammalian cell lines. We also found that the transcription on DNA templates is crucial for the promotion of homology-directed repair, and that tethering transcripts from TEd donors to targeted sites further improves editing efficiency. The superior efficiency of TEd for the insertion and deletion of long DNA fragments expands the applications of CRISPR for editing mammalian genomes.
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Affiliation(s)
- Kaixuan Gao
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xuedi Zhang
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Zhenwu Zhang
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xiangyu Wu
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yan Guo
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Pengchong Fu
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Angyang Sun
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Ju Peng
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jie Zheng
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Pengfei Yu
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Tengfei Wang
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Qinying Ye
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jingwei Jiang
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Haopeng Wang
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Chao-Po Lin
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Guanjun Gao
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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23
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Guo Y, Oliveros CF, Ohshima T. CRMP2 and CRMP4 are required for the formation of commissural tracts in the developing zebrafish forebrain. Dev Neurobiol 2022; 82:533-544. [PMID: 35929227 DOI: 10.1002/dneu.22897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 05/27/2022] [Accepted: 07/26/2022] [Indexed: 11/06/2022]
Abstract
Axonal connections between the two sides of the brain are essential for processing sensorimotor functions, especially in animals with bilateral symmetry. The anterior commissure and post-optic commissure are two crucial axonal projections that develop early in the zebrafish central nervous system. In this study, we characterized the function of collapsin response mediator protein 2 (CRMP2) and CRMP4 in patterning the development of the anterior and post-optic commissures by analyzing morpholino-knockdown zebrafish morphants and CRISPR/Cas9-edited gene-knockout mutants. We observed a loss of commissural structures or a significant reduction in axon bundles connecting the two hemispheres, but the defects could be largely recovered by co-injecting CRMP2 or CRMP4 mRNA. Loss of both CRMP2 and CRMP4 function resulted in a synergistic increase in the number of commissural defects. To elucidate the mechanism by which CRMP2 and CRMP4 provide guidance cues for the development of the anterior and post-optic commissures, we included neuropilin 1a (Nrp1a) morphants and double morphants (CRMP2/Nrp1a and CRMP4/Nrp1a) for analysis. Our experimental results indicated that CRMP2 and CRMP4 might mediate their activities through the common semaphorin 3/Nrp1a signaling pathway. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Youjia Guo
- Department of Life Science and Medical Bio-Science, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Carolina Fiallos Oliveros
- Department of Life Science and Medical Bio-Science, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Toshio Ohshima
- Department of Life Science and Medical Bio-Science, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
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Shams F, Bayat H, Mohammadian O, Mahboudi S, Vahidnezhad H, Soosanabadi M, Rahimpour A. Advance trends in targeting homology-directed repair for accurate gene editing: An inclusive review of small molecules and modified CRISPR-Cas9 systems. BIOIMPACTS 2022; 12:371-391. [PMID: 35975201 PMCID: PMC9376165 DOI: 10.34172/bi.2022.23871] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 11/21/2021] [Accepted: 11/21/2021] [Indexed: 11/25/2022]
Abstract
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Introduction: Clustered regularly interspaced short palindromic repeat and its associated protein (CRISPR-Cas)-based technologies generate targeted modifications in host genome by inducing site-specific double-strand breaks (DSBs) that can serve as a substrate for homology-directed repair (HDR) in both in vitro and in vivo models. HDR pathway could enhance incorporation of exogenous DNA templates into the CRISPR-Cas9-mediated DSB site. Owing to low rate of HDR pathway, the efficiency of accurate genome editing is diminished. Enhancing the efficiency of HDR can provide fast, easy, and accurate technologies based on CRISPR-Cas9 technologies.
Methods: The current study presents an overview of attempts conducted on the precise genome editing strategies based on small molecules and modified CRISPR-Cas9 systems.
Results: In order to increase HDR rate in targeted cells, several logical strategies have been introduced such as generating CRISPR effector chimeric proteins, anti-CRISPR proteins, modified Cas9 with donor template, and using validated synthetic or natural small molecules for either inhibiting non-homologous end joining (NHEJ), stimulating HDR, or synchronizing cell cycle. Recently, high-throughput screening methods have been applied for identification of small molecules which along with the CRISPR system can regulate precise genome editing through HDR.
Conclusion: The stimulation of HDR components or inhibiting NHEJ can increase the accuracy of CRISPR-Cas-mediated engineering systems. Generating chimeric programmable endonucleases provide this opportunity to direct DNA template close proximity of CRISPR-Cas-mediated DSB. Small molecules and their derivatives can also proficiently block or activate certain DNA repair pathways and bring up novel perspectives for increasing HDR efficiency, especially in human cells. Further, high throughput screening of small molecule libraries could result in more discoveries of promising chemicals that improve HDR efficiency and CRISPR-Cas9 systems.
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Affiliation(s)
- Forough Shams
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hadi Bayat
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Omid Mohammadian
- Medical Nano-Technology and Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Somayeh Mahboudi
- Department of Food Science and Technology, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Hassan Vahidnezhad
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
- Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA, USA
| | - Mohsen Soosanabadi
- Department of Medical Genetics, Semnan University of Medical Sciences, Semnan, Iran
| | - Azam Rahimpour
- Medical Nano-Technology and Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Ma L, Xing J, Li Q, Zhang Z, Xu K. Development of a universal antibiotic resistance screening reporter for improving efficiency of cytosine and adenine base editing. J Biol Chem 2022; 298:102103. [PMID: 35671823 PMCID: PMC9287484 DOI: 10.1016/j.jbc.2022.102103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 11/24/2022] Open
Abstract
Base editing has emerged as a revolutionary technology for single nucleotide modifications. The cytosine and adenine base editors (CBEs and ABEs) have demonstrated great potential in clinical and fundamental research. However, screening and isolating target-edited cells remains challenging. In the current study, we developed a universal Adenine and Cytosine Base-Editing Antibiotic Resistance Screening Reporter (ACBE-ARSR) for improving the editing efficiency. To develop the reporter, the CBE-ARSR was first constructed and shown to be capable of enriching cells for those that had undergone CBE editing activity. Then, the ACBE-ARSR was constructed and was further validated in the editing assays by four different CBEs and two versions of ABE at several different genomic loci. Our results demonstrated that ACBE-ARSR, compared to the reporter of transfection (RoT) screening strategy, improved the editing efficiency of CBE and ABE by 4.6- and 1.9-fold on average, respectively. We found the highest CBE and ABE editing efficiencies as enriched by ACBE-ARSR reached 90% and 88.7%. Moreover, we also demonstrated ACBE-ARSR could be employed for enhancing simultaneous multiplexed genome editing. In conclusion, both CBE and ABE activity can be improved significantly using our novel ACBE-ARSR screening strategy, which we believe will facilitate the development of base editors and their application in biomedical and fundamental research studies.
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Affiliation(s)
- Lixia Ma
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China; Central Laboratory, Changzhi Medical College, Changzhi, Shanxi, China
| | - Jiani Xing
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Qian Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Zhiying Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.
| | - Kun Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.
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26
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Yang S, Joesaar A, Bögels BWA, Mann S, de Greef TFA. Protocellular CRISPR/Cas‐Based Diffusive Communication Using Transcriptional RNA Signaling. Angew Chem Int Ed Engl 2022; 61:e202202436. [PMID: 35385207 PMCID: PMC9320857 DOI: 10.1002/anie.202202436] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Indexed: 11/29/2022]
Abstract
Protocells containing enzyme‐driven biomolecular circuits that can process and exchange information offer a promising approach for mimicking cellular features and developing molecular information platforms. Here, we employ synthetic transcriptional circuits together with CRISPR/Cas‐based DNA processing inside semipermeable protein‐polymer microcompartments. We first establish a transcriptional protocell that can be activated by external DNA strands and produce functional RNA aptamers. Subsequently, we engineer a transcriptional module to generate RNA strands functioning as diffusive signals that can be sensed by neighboring protocells and trigger the activation of internalized DNA probes or localization of Cas nucleases. Our results highlight the opportunities to combine CRISPR/Cas machinery and DNA nanotechnology for protocellular communication and provide a step towards the development of protocells capable of distributed molecular information processing.
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Affiliation(s)
- Shuo Yang
- Institute for Complex Molecular Systems Eindhoven University of Technology P.O. Box 513 5600 MB Eindhoven The Netherlands
| | - Alex Joesaar
- Department of Bionanoscience Kavli Institute of Nanoscience Delft University of Technology 2629 HZ Delft The Netherlands
| | - Bas W. A. Bögels
- Institute for Complex Molecular Systems Eindhoven University of Technology P.O. Box 513 5600 MB Eindhoven The Netherlands
| | - Stephen Mann
- Centre for Protolife Research and Centre for Organized Matter Chemistry School of Chemistry and Max Planck-Bristol Centre for Minimal Biology School of Chemistry, University of Bristol Bristol BS8 1TS UK
- School of Materials Science and Engineering Institute of Molecular Medicine (IMM) Renji Hospital Shanghai Jiao Tong University School of Medicine Shanghai Jiao Tong University Shanghai 200240 P. R. China
| | - Tom F. A. de Greef
- Institute for Complex Molecular Systems Eindhoven University of Technology P.O. Box 513 5600 MB Eindhoven The Netherlands
- Computational Biology group Department of Biomedical Engineering Eindhoven University of Technology The Netherlands
- Institute for Molecules and Materials Faculty of Science Radboud University Radboud University Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
- Center for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht Princetonlaan 6 3584 CB Utrecht The Netherlands
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27
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Small-molecule enhancers of CRISPR-induced homology-directed repair in gene therapy: A medicinal chemist's perspective. Drug Discov Today 2022; 27:2510-2525. [PMID: 35738528 DOI: 10.1016/j.drudis.2022.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/19/2022] [Accepted: 06/16/2022] [Indexed: 11/20/2022]
Abstract
CRISPR technologies are increasingly being investigated and utilized for the treatment of human genetic diseases via genome editing. CRISPR-Cas9 first generates a targeted DNA double-stranded break, and a functional gene can then be introduced to replace the defective copy in a precise manner by templated repair via the homology-directed repair (HDR) pathway. However, this is challenging owing to the relatively low efficiency of the HDR pathway compared with a rival random repair pathway known as non-homologous end joining (NHEJ). Small molecules can be employed to increase the efficiency of HDR and decrease that of NHEJ to improve the efficiency of precise knock-in genome editing. This review discusses the potential usage of such small molecules in the context of gene therapy and their drug-likeness, from a medicinal chemist's perspective.
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28
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Li J, Feng X, Wei X. Modeling hypertrophic cardiomyopathy with human cardiomyocytes derived from induced pluripotent stem cells. Stem Cell Res Ther 2022; 13:232. [PMID: 35659761 PMCID: PMC9166443 DOI: 10.1186/s13287-022-02905-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 05/18/2022] [Indexed: 12/16/2022] Open
Abstract
One of the obstacles in studying the pathogenesis of hypertrophic cardiomyopathy (HCM) is the poor availability of myocardial tissue samples at the early stages of disease development. This has been addressed by the advent of induced pluripotent stem cells (iPSCs), which allow us to differentiate patient-derived iPSCs into cardiomyocytes (iPSC-CMs) in vitro. In this review, we summarize different approaches to establishing iPSC models and the application of genome editing techniques in iPSC. Because iPSC-CMs cultured at the present stage are immature in structure and function, researchers have attempted several methods to mature iPSC-CMs, such as prolonged culture duration, and mechanical and electrical stimulation. Currently, many researchers have established iPSC-CM models of HCM and employed diverse methods for performing measurements of cellular morphology, contractility, electrophysiological property, calcium handling, mitochondrial function, and metabolism. Here, we review published results in humans to date within the growing field of iPSC-CM models of HCM. Although there is no unified consensus, preliminary results suggest that this approach to modeling disease would provide important insights into our understanding of HCM pathogenesis and facilitate drug development and safety testing.
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Affiliation(s)
- Jiangtao Li
- Division of Cardiothoracic and Vascular Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Jiefang Avenue, Wuhan, 430030, Hubei, China
| | - Xin Feng
- Division of Cardiothoracic and Vascular Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Jiefang Avenue, Wuhan, 430030, Hubei, China
| | - Xiang Wei
- Division of Cardiothoracic and Vascular Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China; Key Laboratory of Organ Transplantation, Ministry of Education; NHC Key Laboratory of Organ Transplantation; Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, No. 1095 Jiefang Avenue, Wuhan, 430030, Hubei, China.
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29
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Abstract
The rapid development of CRISPR-Cas genome editing tools has greatly changed the way to conduct research and holds tremendous promise for clinical applications. During genome editing, CRISPR-Cas enzymes induce DNA breaks at the target sites and subsequently the DNA repair pathways are recruited to generate diverse editing outcomes. Besides off-target cleavage, unwanted editing outcomes including chromosomal structural variations and exogenous DNA integrations have recently raised concerns for clinical safety. To eliminate these unwanted editing byproducts, we need to explore the underlying mechanisms for the formation of diverse editing outcomes from the perspective of DNA repair. Here, we describe the involved DNA repair pathways in sealing Cas enzyme-induced DNA double-stranded breaks and discuss the origins and effects of unwanted editing byproducts on genome stability. Furthermore, we propose the potential risk of inhibiting DNA repair pathways to enhance gene editing. The recent combined studies of DNA repair and CRISPR-Cas editing provide a framework for further optimizing genome editing to enhance editing safety.
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30
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Anzalone AV, Gao XD, Podracky CJ, Nelson AT, Koblan LW, Raguram A, Levy JM, Mercer JAM, Liu DR. Programmable deletion, replacement, integration and inversion of large DNA sequences with twin prime editing. Nat Biotechnol 2022; 40:731-740. [PMID: 34887556 PMCID: PMC9117393 DOI: 10.1038/s41587-021-01133-w] [Citation(s) in RCA: 222] [Impact Index Per Article: 111.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 10/22/2021] [Indexed: 12/17/2022]
Abstract
The targeted deletion, replacement, integration or inversion of genomic sequences could be used to study or treat human genetic diseases, but existing methods typically require double-strand DNA breaks (DSBs) that lead to undesired consequences, including uncontrolled indel mixtures and chromosomal abnormalities. Here we describe twin prime editing (twinPE), a DSB-independent method that uses a prime editor protein and two prime editing guide RNAs (pegRNAs) for the programmable replacement or excision of DNA sequences at endogenous human genomic sites. The two pegRNAs template the synthesis of complementary DNA flaps on opposing strands of genomic DNA, which replace the endogenous DNA sequence between the prime-editor-induced nick sites. When combined with a site-specific serine recombinase, twinPE enabled targeted integration of gene-sized DNA plasmids (>5,000 bp) and targeted sequence inversions of 40 kb in human cells. TwinPE expands the capabilities of precision gene editing and might synergize with other tools for the correction or complementation of large or complex human pathogenic alleles.
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Affiliation(s)
- Andrew V Anzalone
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Xin D Gao
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Christopher J Podracky
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Andrew T Nelson
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Luke W Koblan
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Aditya Raguram
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Jonathan M Levy
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Jaron A M Mercer
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
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31
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Yang S, Joesaar A, Bögels BWA, Mann S, Greef T. Protocellular CRISPR/Cas‐based Diffusive Communication Using Transcriptional RNA Signaling. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202202436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Shuo Yang
- Eindhoven University of Technology: Technische Universiteit Eindhoven Biomedical Engineering NETHERLANDS
| | - Alex Joesaar
- Eindhoven University of Technology: Technische Universiteit Eindhoven Biomedical Engineering NETHERLANDS
| | - Bas W. A. Bögels
- Eindhoven University of Technology: Technische Universiteit Eindhoven Biomedical Engineering NETHERLANDS
| | - Stephen Mann
- Bristol University School of Chemistry UNITED KINGDOM
| | - Tom Greef
- Eindhoven University of Technology Den Dolech 2CE 1.44B 5612 AZ Eindhoven NETHERLANDS
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32
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Kelm JM, Samarbakhsh A, Pillai A, VanderVere-Carozza PS, Aruri H, Pandey DS, Pawelczak KS, Turchi JJ, Gavande NS. Recent Advances in the Development of Non-PIKKs Targeting Small Molecule Inhibitors of DNA Double-Strand Break Repair. Front Oncol 2022; 12:850883. [PMID: 35463312 PMCID: PMC9020266 DOI: 10.3389/fonc.2022.850883] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 02/22/2022] [Indexed: 01/09/2023] Open
Abstract
The vast majority of cancer patients receive DNA-damaging drugs or ionizing radiation (IR) during their course of treatment, yet the efficacy of these therapies is tempered by DNA repair and DNA damage response (DDR) pathways. Aberrations in DNA repair and the DDR are observed in many cancer subtypes and can promote de novo carcinogenesis, genomic instability, and ensuing resistance to current cancer therapy. Additionally, stalled or collapsed DNA replication forks present a unique challenge to the double-strand DNA break (DSB) repair system. Of the various inducible DNA lesions, DSBs are the most lethal and thus desirable in the setting of cancer treatment. In mammalian cells, DSBs are typically repaired by the error prone non-homologous end joining pathway (NHEJ) or the high-fidelity homology directed repair (HDR) pathway. Targeting DSB repair pathways using small molecular inhibitors offers a promising mechanism to synergize DNA-damaging drugs and IR while selective inhibition of the NHEJ pathway can induce synthetic lethality in HDR-deficient cancer subtypes. Selective inhibitors of the NHEJ pathway and alternative DSB-repair pathways may also see future use in precision genome editing to direct repair of resulting DSBs created by the HDR pathway. In this review, we highlight the recent advances in the development of inhibitors of the non-phosphatidylinositol 3-kinase-related kinases (non-PIKKs) members of the NHEJ, HDR and minor backup SSA and alt-NHEJ DSB-repair pathways. The inhibitors described within this review target the non-PIKKs mediators of DSB repair including Ku70/80, Artemis, DNA Ligase IV, XRCC4, MRN complex, RPA, RAD51, RAD52, ERCC1-XPF, helicases, and DNA polymerase θ. While the DDR PIKKs remain intensely pursued as therapeutic targets, small molecule inhibition of non-PIKKs represents an emerging opportunity in drug discovery that offers considerable potential to impact cancer treatment.
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Affiliation(s)
- Jeremy M. Kelm
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, United States
| | - Amirreza Samarbakhsh
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, United States
| | - Athira Pillai
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, United States
| | | | - Hariprasad Aruri
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, United States
| | - Deepti S. Pandey
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, United States
| | | | - John J. Turchi
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States,NERx Biosciences, Indianapolis, IN, United States,Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Navnath S. Gavande
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, United States,Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, United States,*Correspondence: Navnath S. Gavande, ; orcid.org/0000-0002-2413-0235
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33
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Modulating DNA Repair Pathways to Diversify Genomic Alterations in Saccharomyces cerevisiae. Microbiol Spectr 2022; 10:e0232621. [PMID: 35352941 PMCID: PMC9045378 DOI: 10.1128/spectrum.02326-21] [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] [Indexed: 11/29/2022] Open
Abstract
Nuclease based genome editing systems have emerged as powerful tools to drive genomic alterations and enhance genome evolution via precise engineering in the various human and microbial cells. However, error-prone DNA repair has not been well studied previously to generate diverse genomic alterations and novel phenotypes. Here, we systematically investigated the potential interplay between DNA double strand break (DSB) repair and genome editing tools, and found that modulating the DSB end resection proteins could significantly improve mutational efficiency and diversity without exogenous DNA template in yeast. Deleting SAE2, EXO1, or FUN30, or overexpressing MRE11-H125N (nuclease-dead allele of MRE11), for DSB end resection markedly increased the efficiency of CRISPR/SpCas9 (more than 22-fold) and CRISPR/AsCpf1 (more than 30-fold)-induced mutagenesis. Deleting SAE2 or overexpressing MRE11-H125N substantially diversified CRISPR/SpCas9 or AsCpf1-induced mutation 2–3-fold at URA3 locus, and 3–5-fold at ADE2 locus. Thus, the error-prone DNA repair protein was employed to develop a novel mutagenic genome editing (mGE) strategy, which can increase the mutation numbers and effectively improve the ethanol/glycerol ratio of Saccharomyces cerevisiae through modulating the expression of FPS1 and GPD1. This study highlighted the feasibility of potentially reshaping the capability of genome editing by regulating the different DSB repair proteins and can thus expand the application of genome editing in diversifying gene expression and enhancing genome evolution. IMPORTANCE Most of the published papers about nuclease-assisted genome editing focused on precision engineering in human cells. However, the topic of inducing mutagenesis via error-prone repair has often been ignored in yeast. In this study, we reported that perturbing DNA repair, especially modifications of the various DSB end resection-related proteins, could greatly improve the mutational efficiency and diversity, and thus functionally reshape the capability of the different genome editing tools without requiring an exogenous DNA template in yeast. Specifically, mutagenic genome editing (mGE) was developed based on CRISPR/AsCpf1 and MRE11-H125N overexpression, and used to generate promoters of different strengths more efficiently. Thus, this work provides a novel method to diversify gene expression and enhance genome evolution.
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34
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Lan T, Que H, Luo M, Zhao X, Wei X. Genome editing via non-viral delivery platforms: current progress in personalized cancer therapy. Mol Cancer 2022; 21:71. [PMID: 35277177 PMCID: PMC8915502 DOI: 10.1186/s12943-022-01550-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 02/24/2022] [Indexed: 02/08/2023] Open
Abstract
Cancer is a severe disease that substantially jeopardizes global health. Although considerable efforts have been made to discover effective anti-cancer therapeutics, the cancer incidence and mortality are still growing. The personalized anti-cancer therapies present themselves as a promising solution for the dilemma because they could precisely destroy or fix the cancer targets based on the comprehensive genomic analyses. In addition, genome editing is an ideal way to implement personalized anti-cancer therapy because it allows the direct modification of pro-tumor genes as well as the generation of personalized anti-tumor immune cells. Furthermore, non-viral delivery system could effectively transport genome editing tools (GETs) into the cell nucleus with an appreciable safety profile. In this manuscript, the important attributes and recent progress of GETs will be discussed. Besides, the laboratory and clinical investigations that seek for the possibility of combining non-viral delivery systems with GETs for the treatment of cancer will be assessed in the scope of personalized therapy.
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Affiliation(s)
- Tianxia Lan
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, Sichuan, 610041, Chengdu, China
| | - Haiying Que
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, Sichuan, 610041, Chengdu, China
| | - Min Luo
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, Sichuan, 610041, Chengdu, China
| | - Xia Zhao
- Department of Gynecology and Obstetrics, Development and Related Diseases of Women and Children Key Laboratory of Sichuan Province, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second Hospital, Sichuan University, Sichuan, 610041, Chengdu, China.
| | - Xiawei Wei
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, Sichuan, 610041, Chengdu, China.
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35
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Feng S, Wang Z, Li A, Xie X, Liu J, Li S, Li Y, Wang B, Hu L, Yang L, Guo T. Strategies for High-Efficiency Mutation Using the CRISPR/Cas System. Front Cell Dev Biol 2022; 9:803252. [PMID: 35198566 PMCID: PMC8860194 DOI: 10.3389/fcell.2021.803252] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/22/2021] [Indexed: 12/15/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-associated systems have revolutionized traditional gene-editing tools and are a significant tool for ameliorating gene defects. Characterized by high target specificity, extraordinary efficiency, and cost-effectiveness, CRISPR/Cas systems have displayed tremendous potential for genetic manipulation in almost any organism and cell type. Despite their numerous advantages, however, CRISPR/Cas systems have some inherent limitations, such as off-target effects, unsatisfactory efficiency of delivery, and unwanted adverse effects, thereby resulting in a desire to explore approaches to address these issues. Strategies for improving the efficiency of CRISPR/Cas-induced mutations, such as reducing off-target effects, improving the design and modification of sgRNA, optimizing the editing time and the temperature, choice of delivery system, and enrichment of sgRNA, are comprehensively described in this review. Additionally, several newly emerging approaches, including the use of Cas variants, anti-CRISPR proteins, and mutant enrichment, are discussed in detail. Furthermore, the authors provide a deep analysis of the current challenges in the utilization of CRISPR/Cas systems and the future applications of CRISPR/Cas systems in various scenarios. This review not only serves as a reference for improving the maturity of CRISPR/Cas systems but also supplies practical guidance for expanding the applicability of this technology.
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Affiliation(s)
- Shuying Feng
- Medical College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Zilong Wang
- Medical College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Aifang Li
- Medical College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Xin Xie
- Medical College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Junjie Liu
- Medical College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Shuxuan Li
- Medical College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Yalan Li
- Medical College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Baiyan Wang
- Medical College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Lina Hu
- Medical College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Lianhe Yang
- Medical College, Henan University of Chinese Medicine, Zhengzhou, China
| | - Tao Guo
- Department of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China
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36
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VanderVere-Carozza PS, Gavande NS, Jalal SI, Pollok KE, Ekinci E, Heyza J, Patrick SM, Masters A, Turchi JJ, Pawelczak KS. In Vivo Targeting Replication Protein A for Cancer Therapy. Front Oncol 2022; 12:826655. [PMID: 35251993 PMCID: PMC8895377 DOI: 10.3389/fonc.2022.826655] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/18/2022] [Indexed: 02/04/2023] Open
Abstract
Replication protein A (RPA) plays essential roles in DNA replication, repair, recombination, and the DNA damage response (DDR). Retrospective analysis of lung cancer patient data demonstrates high RPA expression as a negative prognostic biomarker for overall survival in smoking-related lung cancers. Similarly, relative expression of RPA is a predictive marker for response to chemotherapy. These observations are consistent with the increase in RPA expression serving as an adaptive mechanism that allows tolerance of the genotoxic stress resulting from carcinogen exposure. We have developed second-generation RPA inhibitors (RPAis) that block the RPA-DNA interaction and optimized formulation for in vivo analyses. Data demonstrate that unlike first-generation RPAis, second-generation molecules show increased cellular permeability and induce cell death via apoptosis. Second-generation RPAis elicit single-agent in vitro anticancer activity across a broad spectrum of cancers, and the cellular response suggests existence of a threshold before chemical RPA exhaustion induces cell death. Chemical RPA inhibition potentiates the anticancer activity of a series of DDR inhibitors and traditional DNA-damaging cancer therapeutics. Consistent with chemical RPA exhaustion, we demonstrate that the effects of RPAi on replication fork dynamics are similar to other known DDR inhibitors. An optimized formulation of RPAi NERx 329 was developed that resulted in single-agent anticancer activity in two non-small cell lung cancer models. These data demonstrate a unique mechanism of action of RPAis eliciting a state of chemical RPA exhaustion and suggest they will provide an effective therapeutic option for difficult-to-treat lung cancers.
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Affiliation(s)
| | - Navnath S. Gavande
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States,Department of Pharmaceutical Sciences, Wayne State University College of Pharmacy and Health Sciences, Detroit, MI, United States
| | - Shadia I. Jalal
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Karen E. Pollok
- Herman B. Wells Center for Pediatric Research, Departments of Pediatrics, Pharmacology and Toxicology, Medical and Molecular Genetics Indiana University Simon Comprehensive Cancer Center, Indianapolis, IN, United States
| | - Elmira Ekinci
- Department of Oncology, Wayne State University School of Medicine and Barbara Ann Karmanos Cancer Institute, Detroit, MI, United States
| | - Joshua Heyza
- Department of Oncology, Wayne State University School of Medicine and Barbara Ann Karmanos Cancer Institute, Detroit, MI, United States
| | - Steve M. Patrick
- Department of Oncology, Wayne State University School of Medicine and Barbara Ann Karmanos Cancer Institute, Detroit, MI, United States
| | - Andi Masters
- Indiana University Cancer Center, Indiana University School of Medicine, Indianapolis, IN, United States
| | - John J. Turchi
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States,NERx BioSciences, Indianapolis, IN, United States,*Correspondence: John J. Turchi, ; Katherine S. Pawelczak,
| | - Katherine S. Pawelczak
- NERx BioSciences, Indianapolis, IN, United States,*Correspondence: John J. Turchi, ; Katherine S. Pawelczak,
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37
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Fierro J, DiPasquale J, Perez J, Chin B, Chokpapone Y, Tran AM, Holden A, Factoriza C, Sivagnanakumar N, Aguilar R, Mazal S, Lopez M, Dou H. Dual-sgRNA CRISPR/Cas9 knockout of PD-L1 in human U87 glioblastoma tumor cells inhibits proliferation, invasion, and tumor-associated macrophage polarization. Sci Rep 2022; 12:2417. [PMID: 35165339 PMCID: PMC8844083 DOI: 10.1038/s41598-022-06430-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 01/25/2022] [Indexed: 12/12/2022] Open
Abstract
Programmed death ligand 1 (PD-L1) plays a key role in glioblastoma multiforme (GBM) immunosuppression, vitality, proliferation, and migration, and is therefore a promising target for treating GBM. CRISPR/Cas9-mediated genomic editing can delete both cell surface and intracellular PD-L1. This systemic deliverable genomic PD-L1 deletion system can be used as an effective anti-GBM therapy by inhibiting tumor growth and migration, and overcoming immunosuppression. To target PD-L1 for CRISPR/Cas9 gene editing, we first identified two single guide RNA (sgRNA) sequences located on PD-L1 exon 3. The first sgRNA recognizes the forward strand of human PD-L1 near the beginning of exon 3 that allows editing by Cas9 at approximately base pair 82 (g82). The second sgRNA recognizes the forward strand of exon 3 that directs cutting at base pair 165 (g165). A homology-directed repair template (HDR) combined with the dual-sgRNAs was used to improve PD-L1 knockout specificity and efficiency. sgRNAs g82 and g165 were cloned into the multiplex CRISPR/Cas9 assembly system and co-transfected with the HDR template in human U87 GBM cells (g82/165 + HDR). T7E1 analysis suggests that the dual-sgRNA CRISPR/Cas9 strategy with a repair template was capable of editing the genomic level of PD-L1. This was further confirmed by examining PD-L1 protein levels by western blot and immunofluorescence assays. Western blot analysis showed that the dual-sgRNAs with the repair template caused a 64% reduction of PD-L1 protein levels in U87 cells, while immunostaining showed a significant reduction of intracellular PD-L1. PD-L1 deletion inhibited proliferation, growth, invasion and migration of U87 cells, indicating intracellular PD-L1 is necessary for tumor progression. Importantly, U87 cells treated with g82/165 + HDR polarized tumor-associated macrophages (TAM) toward an M1 phenotype, as indicated by an increase in TNF-α and a decrease in IL-4 secretions. This was further confirmed with flow cytometry that showed an increase in the M1 markers Ly6C + and CD80 +, and a decrease in the M2 marker CD206 + both in vitro and in vivo. Utilizing dual-sgRNAs and an HDR template with the CRISPR/Cas9 gene-editing system is a promising avenue for the treatment of GBM.
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Affiliation(s)
- Javier Fierro
- Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Science Center, 5001 El Paso Drive, El Paso, TX, 79905-2827, USA
| | - Jake DiPasquale
- Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Science Center, 5001 El Paso Drive, El Paso, TX, 79905-2827, USA
| | - Joshua Perez
- Graduate School of Biomedical Sciences, Texas Tech University Health Science Center, El Paso, TX, USA
| | - Brandon Chin
- Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Science Center, 5001 El Paso Drive, El Paso, TX, 79905-2827, USA
| | - Yathip Chokpapone
- Graduate School of Biomedical Sciences, Texas Tech University Health Science Center, El Paso, TX, USA
| | - An M Tran
- Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Science Center, 5001 El Paso Drive, El Paso, TX, 79905-2827, USA
| | - Arabella Holden
- Graduate School of Biomedical Sciences, Texas Tech University Health Science Center, El Paso, TX, USA
| | - Chris Factoriza
- Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Science Center, 5001 El Paso Drive, El Paso, TX, 79905-2827, USA
| | - Nikhi Sivagnanakumar
- Graduate School of Biomedical Sciences, Texas Tech University Health Science Center, El Paso, TX, USA
| | - Rocio Aguilar
- Graduate School of Biomedical Sciences, Texas Tech University Health Science Center, El Paso, TX, USA
| | - Sarah Mazal
- Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Science Center, 5001 El Paso Drive, El Paso, TX, 79905-2827, USA
| | - Melissa Lopez
- Graduate School of Biomedical Sciences, Texas Tech University Health Science Center, El Paso, TX, USA
| | - Huanyu Dou
- Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Science Center, 5001 El Paso Drive, El Paso, TX, 79905-2827, USA.
- Graduate School of Biomedical Sciences, Texas Tech University Health Science Center, El Paso, TX, USA.
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dCas9-based gene editing for cleavage-free genomic knock-in of long sequences. Nat Cell Biol 2022; 24:268-278. [PMID: 35145221 PMCID: PMC8843813 DOI: 10.1038/s41556-021-00836-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 12/21/2021] [Indexed: 12/14/2022]
Abstract
Gene editing is a powerful tool for genome and cell engineering. Exemplified by CRISPR–Cas, gene editing could cause DNA damage and trigger DNA repair processes that are often error-prone. Such unwanted mutations and safety concerns can be exacerbated when altering long sequences. Here we couple microbial single-strand annealing proteins (SSAPs) with catalytically inactive dCas9 for gene editing. This cleavage-free gene editor, dCas9–SSAP, promotes the knock-in of long sequences in mammalian cells. The dCas9–SSAP editor has low on-target errors and minimal off-target effects, showing higher accuracy than canonical Cas9 methods. It is effective for inserting kilobase-scale sequences, with an efficiency of up to approximately 20% and robust performance across donor designs and cell types, including human stem cells. We show that dCas9–SSAP is less sensitive to inhibition of DNA repair enzymes than Cas9 references. We further performed truncation and aptamer engineering to minimize its size to fit into a single adeno-associated-virus vector for future application. Together, this tool opens opportunities towards safer long-sequence genome engineering. Wang, Qu et al. developed a genome-editing system, utilizing catalytically inactive Cas9 fused to microbial single-strand annealing proteins, for kilobase-scale insertion in human cells without introducing DNA nicks or breaks.
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39
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Lee MJ, Lee I, Wang K. Recent Advances in RNA Therapy and Its Carriers to Treat the Single-Gene Neurological Disorders. Biomedicines 2022; 10:biomedicines10010158. [PMID: 35052837 PMCID: PMC8773368 DOI: 10.3390/biomedicines10010158] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/07/2022] [Accepted: 01/11/2022] [Indexed: 02/07/2023] Open
Abstract
The development of new sequencing technologies in the post-genomic era has accelerated the identification of causative mutations of several single gene disorders. Advances in cell and animal models provide insights into the underlining pathogenesis, which facilitates the development and maturation of new treatment strategies. The progress in biochemistry and molecular biology has established a new class of therapeutics—the short RNAs and expressible long RNAs. The sequences of therapeutic RNAs can be optimized to enhance their stability and translatability with reduced immunogenicity. The chemically-modified RNAs can also increase their stability during intracellular trafficking. In addition, the development of safe and high efficiency carriers that preserves the integrity of therapeutic RNA molecules also accelerates the transition of RNA therapeutics into the clinic. For example, for diseases that are caused by genetic defects in a specific protein, an effective approach termed “protein replacement therapy” can provide treatment through the delivery of modified translatable mRNAs. Short interference RNAs can also be used to treat diseases caused by gain of function mutations or restore the splicing aberration defects. Here we review the applications of newly developed RNA-based therapeutics and its delivery and discuss the clinical evidence supporting the potential of RNA-based therapy in single-gene neurological disorders.
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Affiliation(s)
- Ming-Jen Lee
- Department of Neurology, National Taiwan University Hospital, Taipei 10012, Taiwan;
- Department of Medical Genetics, National Taiwan University Hospital, Taipei 10012, Taiwan
| | - Inyoul Lee
- Institute for Systems Biology, Seattle, WA 98109, USA;
| | - Kai Wang
- Institute for Systems Biology, Seattle, WA 98109, USA;
- Correspondence: ; Tel.: +1-206-732-1336
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40
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Wu G, Du X, Li Z, Du Y, Lv J, Li X, Xu Y, Liu S. The emerging role of long non-coding RNAs in schizophrenia. Front Psychiatry 2022; 13:995956. [PMID: 36226104 PMCID: PMC9548578 DOI: 10.3389/fpsyt.2022.995956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 09/06/2022] [Indexed: 11/13/2022] Open
Abstract
Schizophrenia (SZ) is a severe psychiatric disorder which is contributed by both genetic and environmental factors. However, at present, its specific pathogenesis is still not very clear, and there is a lack of objective and reliable biomarkers. Accumulating evidence indicates that long non-coding RNAs (lncRNAs) are involved in the pathophysiology of several psychiatric disorders, including SZ, and hold promise as potential biomarkers and therapeutic targets for psychiatric disorders. In this review, we summarize and discuss the role of lncRNAs in the pathogenesis of SZ and their potential value as biomarkers and therapeutic targets.
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Affiliation(s)
- Guangxian Wu
- Shanxi Key Laboratory of Artificial Intelligence Assisted Diagnosis and Treatment for Mental Disorder, First Hospital of Shanxi Medical University, Taiyuan, China.,Department of Physiology, School of Basic Medical Sciences, Shanxi Medical University, Taiyuan, China
| | - Xinzhe Du
- Shanxi Key Laboratory of Artificial Intelligence Assisted Diagnosis and Treatment for Mental Disorder, First Hospital of Shanxi Medical University, Taiyuan, China.,Department of Psychiatry, First Hospital/First Clinical Medical College of Shanxi Medical University, Taiyuan, China
| | - Zexuan Li
- Shanxi Key Laboratory of Artificial Intelligence Assisted Diagnosis and Treatment for Mental Disorder, First Hospital of Shanxi Medical University, Taiyuan, China.,Department of Psychiatry, First Hospital/First Clinical Medical College of Shanxi Medical University, Taiyuan, China
| | - Yanhong Du
- Shanxi Key Laboratory of Artificial Intelligence Assisted Diagnosis and Treatment for Mental Disorder, First Hospital of Shanxi Medical University, Taiyuan, China.,Department of Psychiatry, First Hospital/First Clinical Medical College of Shanxi Medical University, Taiyuan, China
| | - Jinzhi Lv
- Shanxi Key Laboratory of Artificial Intelligence Assisted Diagnosis and Treatment for Mental Disorder, First Hospital of Shanxi Medical University, Taiyuan, China.,Department of Physiology, School of Basic Medical Sciences, Shanxi Medical University, Taiyuan, China
| | - Xinrong Li
- Department of Psychiatry, First Hospital/First Clinical Medical College of Shanxi Medical University, Taiyuan, China
| | - Yong Xu
- Shanxi Key Laboratory of Artificial Intelligence Assisted Diagnosis and Treatment for Mental Disorder, First Hospital of Shanxi Medical University, Taiyuan, China.,Department of Mental Health, Shanxi Medical University, Taiyuan, China
| | - Sha Liu
- Shanxi Key Laboratory of Artificial Intelligence Assisted Diagnosis and Treatment for Mental Disorder, First Hospital of Shanxi Medical University, Taiyuan, China.,Department of Psychiatry, First Hospital/First Clinical Medical College of Shanxi Medical University, Taiyuan, China
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41
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Yan J, Kang DD, Turnbull G, Dong Y. Delivery of CRISPR-Cas9 system for screening and editing RNA binding proteins in cancer. Adv Drug Deliv Rev 2022; 180:114042. [PMID: 34767864 PMCID: PMC8724402 DOI: 10.1016/j.addr.2021.114042] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/25/2021] [Accepted: 11/04/2021] [Indexed: 02/07/2023]
Abstract
RNA-binding proteins (RBPs) play an important role in RNA metabolism, regulating the stability, localization, and functional dynamics of RNAs. Alternation in the RBP-RNA network has profound implications in cellular physiology, and is related to the development and spread of cancer in certain cases. To regulate the expression of specific genes and their biological activities, various strategies have been applied to target RBPs for cancer treatments, including small-molecule inhibitors, small-interfering RNA, peptides, and aptamers. Recently, the deployment of the CRISPR-Cas9 technology has provided a new platform for RBP screening and regulation. This review summarizes the delivery systems of the CRISPR-Cas9 system and their role in RBP-based cancer therapeutics, including identification of novel RBPs and regulation of cancer-associated RBPs. The efficient delivery of the CRISPR-Cas9 system is important to the profound understanding and clinical transition of RBPs as cancer therapeutic targets.
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Affiliation(s)
- Jingyue Yan
- Division of Pharmaceutics & Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Diana D. Kang
- Division of Pharmaceutics & Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Gillian Turnbull
- Division of Pharmaceutics & Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Yizhou Dong
- Division of Pharmaceutics & Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States,Department of Biomedical Engineering; The Center for Clinical and Translational Science; The Comprehensive Cancer Center; Dorothy M. Davis Heart & Lung Research Institute; Department of Radiation Oncology, The Ohio State University, Columbus, Ohio 43210, United States
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42
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Wang Y, Wang H, Jian Y, Luo Z, Shao H, Zhang W. Strategies for optimization of the CRISPR-based genome editing system for enhanced editing specificity. Hum Gene Ther 2021; 33:358-370. [PMID: 34963339 DOI: 10.1089/hum.2021.283] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR) system is inarguably the most valuable gene editing tool ever discovered. Currently, three classes of CRISPR-based genome editing systems have been developed for gene editing, including CRISPR/Cas nucleases, base editors (BEs) and prime editors (PEs). Ever-evolving CRISPR technology plays an important role in medicine; however, the biggest obstacle to its use in clinical practice is the induction of off-target effects (OTEs) during targeted editing. Therefore, continuous improvement and optimization of the CRISPR system for reduction of OTEs is a major focus in the field of CRISPR research. This review aims to provide a comprehensive guide for optimization of the CRISPR-based genome editing system.
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Affiliation(s)
- Yangmin Wang
- Guangdong Pharmaceutical University, 71237, Guangzhou, Guangdong, China;
| | - Haozheng Wang
- Guangdong Pharmaceutical University, 71237, Guangzhou, Guangdong, China;
| | - Yingzhen Jian
- Guangdong Pharmaceutical University, 71237, Guangzhou, Guangdong, China;
| | - Zhongtao Luo
- Guangdong Pharmaceutical University, 71237, Guangzhou, Guangdong, China;
| | - Hongwei Shao
- Guangdong Pharmaceutical University, 71237, Guangzhou, Guangdong, China;
| | - Wenfeng Zhang
- Guangdong Pharmaceutical University, 71237, School of Biosciences and Biopharmaceutics , 28 E. Rd outside the City of Guangzhou University, Guangzhou, China, 510006;
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43
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Zhang H, Qin C, An C, Zheng X, Wen S, Chen W, Liu X, Lv Z, Yang P, Xu W, Gao W, Wu Y. Application of the CRISPR/Cas9-based gene editing technique in basic research, diagnosis, and therapy of cancer. Mol Cancer 2021; 20:126. [PMID: 34598686 PMCID: PMC8484294 DOI: 10.1186/s12943-021-01431-6] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 09/19/2021] [Indexed: 02/06/2023] Open
Abstract
The 2020 Nobel Prize in Chemistry was awarded to Emmanuelle Charpentier and Jennifer Doudna for the development of the Clustered regularly interspaced short palindromic repeats/CRISPR-associated nuclease9 (CRISPR/Cas9) gene editing technology that provided new tools for precise gene editing. It is possible to target any genomic locus virtually using only a complex nuclease protein with short RNA as a site-specific endonuclease. Since cancer is caused by genomic changes in tumor cells, CRISPR/Cas9 can be used in the field of cancer research to edit genomes for exploration of the mechanisms of tumorigenesis and development. In recent years, the CRISPR/Cas9 system has been increasingly used in cancer research and treatment and remarkable results have been achieved. In this review, we introduced the mechanism and development of the CRISPR/Cas9-based gene editing system. Furthermore, we summarized current applications of this technique for basic research, diagnosis and therapy of cancer. Moreover, the potential applications of CRISPR/Cas9 in new emerging hotspots of oncology research were discussed, and the challenges and future directions were highlighted.
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Affiliation(s)
- Huimin Zhang
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, Department of Otolaryngology Head & Neck Surgery, First Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Chunhong Qin
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, Department of Otolaryngology Head & Neck Surgery, First Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi, China.,Department of Biochemistry & Molecular Biology, Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Changming An
- Department of Head and Neck Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Xiwang Zheng
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, Department of Otolaryngology Head & Neck Surgery, First Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi, China.,General Hospital, Clinical Medical Academy, Shenzhen University, Shenzhen, 518055, Guangdong, China
| | - Shuxin Wen
- Department of Otolaryngology Head & Neck Surgery, Shanxi Bethune Hospital, Taiyuan, 030032, Shanxi, China
| | - Wenjie Chen
- Department of Otolaryngology Head & Neck Surgery, Shanxi Bethune Hospital, Taiyuan, 030032, Shanxi, China
| | - Xianfang Liu
- Department of Otolaryngology-Head and Neck Surgery, Shandong Provincial ENT Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250022, Shandong, China
| | - Zhenghua Lv
- Department of Otolaryngology-Head and Neck Surgery, Shandong Provincial ENT Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250022, Shandong, China
| | - Pingchang Yang
- Research Center of Allergy and Immunology, Shenzhen University School of Medicine, Shenzhen, 518055, Guangdong, China.,Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Shenzhen, 518055, Guangdong, China
| | - Wei Xu
- Department of Otolaryngology-Head and Neck Surgery, Shandong Provincial ENT Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250022, Shandong, China.
| | - Wei Gao
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, Department of Otolaryngology Head & Neck Surgery, First Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi, China. .,General Hospital, Clinical Medical Academy, Shenzhen University, Shenzhen, 518055, Guangdong, China. .,Department of Cell biology and Genetics, Basic Medical School of Shanxi Medical University, Taiyuan, 030001, Shanxi, China.
| | - Yongyan Wu
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, Department of Otolaryngology Head & Neck Surgery, First Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi, China. .,Department of Biochemistry & Molecular Biology, Shanxi Medical University, Taiyuan, 030001, Shanxi, China. .,General Hospital, Clinical Medical Academy, Shenzhen University, Shenzhen, 518055, Guangdong, China.
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Abstract
The CRISPR-Cas system has revolutionized the biomedical research field with its simple and flexible genome editing method. In October 2020, Emmanuelle Charpentier and Jennifer A. Doudna were awarded the 2020 Nobel Prize in chemistry in recognition of their outstanding contributions to the discovery of CRISPR-Cas9 genetic scissors, which allow scientists to alter DNA sequences with high precision. Recently, the first phase I clinical trials in cancer patients affirmed the safety and feasibility of ex vivo CRISPR-edited T cells. However, specific and effective CRISPR delivery in vivo remains challenging due to the multiple extracellular and intracellular barriers. Here, we discuss the recent advances in novel lipid nanomaterials for CRISPR delivery and describe relevant examples of potential therapeutics in cancers, genetic disorders, and infectious diseases.
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Affiliation(s)
- Jingyue Yan
- Division of Pharmaceutics & Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, USA.
| | - Diana D Kang
- Division of Pharmaceutics & Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, USA.
| | - Yizhou Dong
- Division of Pharmaceutics & Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, USA.
- Department of Biomedical Engineering; The Center for Clinical and Translational Science; The Comprehensive Cancer Center; Dorothy M. Davis Heart & Lung Research Institute; Department of Radiation Oncology, The Ohio State University, Columbus, Ohio 43210, USA
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45
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Zhi L, Su X, Yin M, Zhang Z, Lu H, Niu Z, Guo C, Zhu W, Zhang X. Genetical engineering for NK and T cell immunotherapy with CRISPR/Cas9 technology: Implications and challenges. Cell Immunol 2021; 369:104436. [PMID: 34500148 DOI: 10.1016/j.cellimm.2021.104436] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 08/07/2021] [Accepted: 08/25/2021] [Indexed: 12/23/2022]
Abstract
Immunotherapy has become one of the most promising strategies in cancer therapies. Among the therapeutic alternatives, genetically engineered NK/T cell therapies have emerged as powerful and innovative therapeutic modalities for cancer patients with precise targeting and impressive efficacy. Nonetheless, this approach still faces multiple challenges, such as immunosuppressive tumor microenvironment, exhaustion of immune effector cells in tumors, off-target effects manufacturing complexity, and poor infiltration of effector cells, all of which need to be overcome for further utilization to cancers. Recently, CRISPR/Cas9 genome editing technology, with the goal of enhancing the efficacy and increasing the availability of engineered effector cell therapies, has shown considerable potential in the novel strategies and options to overcome these limitations. Here we review the current progress of the applications of CRISPR in cancer immunotherapy. Furthermore, we discuss issues related to the NK/T cell applications, gene delivery methods, efficiency, challenges, and implications of CRISPR/Cas9.
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Affiliation(s)
- Lingtong Zhi
- Synthetic Biology Engineering Lab of Henan Province, School of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, Henan Province, PR China
| | - Xin Su
- Synthetic Biology Engineering Lab of Henan Province, School of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, Henan Province, PR China
| | - Meichen Yin
- Synthetic Biology Engineering Lab of Henan Province, School of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, Henan Province, PR China
| | - Zikang Zhang
- Synthetic Biology Engineering Lab of Henan Province, School of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, Henan Province, PR China
| | - Hui Lu
- Synthetic Biology Engineering Lab of Henan Province, School of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, Henan Province, PR China
| | - Zhiyuan Niu
- Synthetic Biology Engineering Lab of Henan Province, School of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, Henan Province, PR China
| | - Changjiang Guo
- Synthetic Biology Engineering Lab of Henan Province, School of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, Henan Province, PR China
| | - Wuling Zhu
- Synthetic Biology Engineering Lab of Henan Province, School of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, Henan Province, PR China.
| | - Xuan Zhang
- Department of Physiology and Neurobiology, Xinxiang Medical University, Xinxiang, Henan, PR China.
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46
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Aquino-Jarquin G. Current advances in overcoming obstacles of CRISPR/Cas9 off-target genome editing. Mol Genet Metab 2021; 134:77-86. [PMID: 34391646 DOI: 10.1016/j.ymgme.2021.08.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 08/03/2021] [Accepted: 08/03/2021] [Indexed: 12/14/2022]
Abstract
CRISPR/Cas9-based technology has revolutionized biomedical research by providing a high-fidelity gene-editing method, foreshadowing a significant impact on the therapeutics of many human genetic disorders previously considered untreatable. However, off-target events represent a critical hurdle before genome editing can be fully established in clinical practice. This mini-review recapitulates some recent advances for detecting and overcoming off-target effects mediated by the CRISPR/Cas9 system that could increase the likelihood of clinical success of the CRISPR-based approaches.
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Affiliation(s)
- Guillermo Aquino-Jarquin
- Laboratorio de Investigación en Genómica, Genética y Bioinformática, Hospital Infantil de México, Federico Gómez, Ciudad de México, Mexico; Departamento de Ciencias Naturales, Unidad Cuajimalpa, Universidad Autónoma Metropolitana, Ciudad de México, Mexico.
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47
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Sizova I, Kelterborn S, Verbenko V, Kateriya S, Hegemann P. Chlamydomonas POLQ is necessary for CRISPR/Cas9-mediated gene targeting. G3 (BETHESDA, MD.) 2021; 11:jkab114. [PMID: 33836052 PMCID: PMC8495919 DOI: 10.1093/g3journal/jkab114] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 03/18/2021] [Indexed: 02/06/2023]
Abstract
The use of CRISPR/Cas endonucleases has revolutionized gene editing techniques for research on Chlamydomonas reinhardtii. To better utilize the CRISPR/Cas system, it is essential to develop a more comprehensive understanding of the DNA repair pathways involved in genome editing. In this study, we have analyzed contributions from canonical KU80/KU70-dependent nonhomologous end-joining (cNHEJ) and DNA polymerase theta (POLQ)-mediated end joining on SpCas9-mediated untemplated mutagenesis and homology-directed repair (HDR)/gene inactivation in Chlamydomonas. Using CRISPR/SpCas9 technology, we generated DNA repair-defective mutants ku80, ku70, polQ for gene targeting experiments. Our results show that untemplated repair of SpCas9-induced double strand breaks results in mutation spectra consistent with an involvement of both KU80/KU70 and POLQ. In addition, the inactivation of POLQ was found to negatively affect HDR of the inactivated paromomycin-resistant mut-aphVIII gene when donor single-stranded oligos were used. Nevertheless, mut-aphVIII was still repaired by homologous recombination in these mutants. POLQ inactivation suppressed random integration of transgenes co-transformed with the donor ssDNA. KU80 deficiency did not affect these events but instead was surprisingly found to stimulate HDR/gene inactivation. Our data suggest that in Chlamydomonas, POLQ is the main contributor to CRISPR/Cas-induced HDR and random integration of transgenes, whereas KU80/KU70 potentially plays a secondary role. We expect our results will lead to improvement of genome editing in C. reinhardtii and can be used for future development of algal biotechnology.
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Affiliation(s)
- Irina Sizova
- Experimental Biophysics, Institute of Biology, Humboldt University of Berlin, Berlin D-10099, Germany
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre “Kurchatov Institute”, Gatchina 188300, Russia
- Kurchatov Genome Center - PNPI, Gatchina 188300, Russia
| | - Simon Kelterborn
- Experimental Biophysics, Institute of Biology, Humboldt University of Berlin, Berlin D-10099, Germany
| | - Valeriy Verbenko
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre “Kurchatov Institute”, Gatchina 188300, Russia
- Kurchatov Genome Center - PNPI, Gatchina 188300, Russia
| | - Suneel Kateriya
- Laboratory of Optobiology School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Peter Hegemann
- Experimental Biophysics, Institute of Biology, Humboldt University of Berlin, Berlin D-10099, Germany
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48
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Wheatley MS, Yang Y. Versatile Applications of the CRISPR/Cas Toolkit in Plant Pathology and Disease Management. PHYTOPATHOLOGY 2021; 111:1080-1090. [PMID: 33356427 DOI: 10.1094/phyto-08-20-0322-ia] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
New tools and advanced technologies have played key roles in facilitating basic research in plant pathology and practical approaches for disease management and crop health. Recently, the CRISPR/Cas (clustered regularly interspersed short palindromic repeats/CRISPR-associated) system has emerged as a powerful and versatile tool for genome editing and other molecular applications. This review aims to introduce and highlight the CRISPR/Cas toolkit and its current and future impact on plant pathology and disease management. We will cover the rapidly expanding horizon of various CRISPR/Cas applications in the basic study of plant-pathogen interactions, genome engineering of plant disease resistance, and molecular diagnosis of diverse pathogens. Using the citrus greening disease as an example, various CRISPR/Cas-enabled strategies are presented to precisely edit the host genome for disease resistance, to rapidly detect the pathogen for disease management, and to potentially use gene drive for insect population control. At the cutting edge of nucleic acid manipulation and detection, the CRISPR/Cas toolkit will accelerate plant breeding and reshape crop production and disease management as we face the challenges of 21st century agriculture.
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Affiliation(s)
- Matthew S Wheatley
- Department of Plant Pathology and Environmental Microbiology, and the Huck Institute of the Life Sciences, the Pennsylvania State University, University Park, PA 16802
| | - Yinong Yang
- Department of Plant Pathology and Environmental Microbiology, and the Huck Institute of the Life Sciences, the Pennsylvania State University, University Park, PA 16802
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49
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Chen L, Gao H, Zhou B, Wang Y. Comprehensive optimization of a reporter assay toolbox for three distinct CRISPR-Cas systems. FEBS Open Bio 2021; 11:1965-1980. [PMID: 33999508 PMCID: PMC8255852 DOI: 10.1002/2211-5463.13198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/30/2021] [Accepted: 05/14/2021] [Indexed: 12/18/2022] Open
Abstract
The clustered, regularly interspaced, short palindromic repeats‐associated DNA nuclease (CRISPR‐Cas) protein system allows programmable gene editing through inducing double‐strand breaks. Reporter assays for DNA cleavage and DNA repair events play an important role in advancing the CRISPR technology and improving our understanding of the underlying molecular mechanisms. Here, we developed a series of reporter assays to probe mechanisms of action of various editing processes, including nonhomologous DNA end joining, homology‐directed repair and single‐strand annealing. With special target design, the reporter assays as an optimized toolbox can be used to take advantage of three distinct CRISPR‐Cas systems (Streptococcus pyogenes Cas9, Staphylococcus aureus Cas9 and Francisella novicida U112 Cpf1) and two different reporters (GFP and Gaussia luciferase). We further validated the Gaussia reporter assays using a series of small molecules, including NU7441, RI‐1 and Mirin, and showcased the use of a GFP reporter assay as an effective tool for enrichment of cells with edited genome.
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Affiliation(s)
- Li Chen
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Haoyuan Gao
- College of Life Sciences and Oceanography, Shenzhen University, China.,Department of Biology, Oberlin College, OH, USA
| | - Bing Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Yu Wang
- College of Life Sciences and Oceanography, Shenzhen University, China
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50
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Wang C, Cheng JKW, Zhang Q, Hughes NW, Xia Q, Winslow MM, Cong L. Microbial single-strand annealing proteins enable CRISPR gene-editing tools with improved knock-in efficiencies and reduced off-target effects. Nucleic Acids Res 2021; 49:e36. [PMID: 33619540 PMCID: PMC8034634 DOI: 10.1093/nar/gkaa1264] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 12/15/2020] [Accepted: 12/19/2020] [Indexed: 12/15/2022] Open
Abstract
Several existing technologies enable short genomic alterations including generating indels and short nucleotide variants, however, engineering more significant genomic changes is more challenging due to reduced efficiency and precision. Here, we developed RecT Editor via Designer-Cas9-Initiated Targeting (REDIT), which leverages phage single-stranded DNA-annealing proteins (SSAP) RecT for mammalian genome engineering. Relative to Cas9-mediated homology-directed repair (HDR), REDIT yielded up to a 5-fold increase of efficiency to insert kilobase-scale exogenous sequences at defined genomic regions. We validated our REDIT approach using different formats and lengths of knock-in templates. We further demonstrated that REDIT tools using Cas9 nickase have efficient gene-editing activities and reduced off-target errors, measured using a combination of targeted sequencing, genome-wide indel, and insertion mapping assays. Our experiments inhibiting repair enzyme activities suggested that REDIT has the potential to overcome limitations of endogenous DNA repair steps. Finally, our REDIT method is applicable across cell types including human stem cells, and is generalizable to different Cas9 enzymes.
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Affiliation(s)
- Chengkun Wang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Jason K W Cheng
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Qianhe Zhang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Nicholas W Hughes
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Qiong Xia
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Monte M Winslow
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Le Cong
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.,Wu Tsai Neuroscience Institute, Stanford University, Stanford, CA, USA
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