1
|
Ramos-Valle A, Kirst H, Fanarraga ML. Biodegradable silica nanoparticles for efficient linear DNA gene delivery. Drug Deliv 2024; 31:2385376. [PMID: 39101224 DOI: 10.1080/10717544.2024.2385376] [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: 12/12/2023] [Revised: 07/04/2024] [Accepted: 07/23/2024] [Indexed: 08/06/2024] Open
Abstract
Targeting, safety, scalability, and storage stability of vectors are still challenges in the field of nucleic acid delivery for gene therapy. Silica-based nanoparticles have been widely studied as gene carriers, exhibiting key features such as biocompatibility, simplistic synthesis, and enabling easy surface modifications for targeting. However, the ability of the formulation to incorporate DNA is limited, which restricts the number of DNA molecules that can be incorporated into the particle, thereby reducing gene expression. Here we use polymerase chain reaction (PCR)-generated linear DNA molecules to augment the coding sequences of gene-carrying nanoparticles, thereby maximizing nucleic acid loading and minimizing the size of these nanocarriers. This approach results in a remarkable 16-fold increase in protein expression six days post-transfection in cells transfected with particles carrying the linear DNA compared with particles bearing circular plasmid DNA. The study also showed that the use of linear DNA entrapped in DNA@SiO2 resulted in a much more efficient level of gene expression compared to standard transfection reagents. The system developed in this study features simplicity, scalability, and increased transfection efficiency and gene expression over existing approaches, enabled by improved embedment capabilities for linear DNA, compared to conventional methods such as lipids or polymers, which generally show greater transfection efficiency with plasmid DNA. Therefore, this novel methodology can find applications not only in gene therapy but also in research settings for high-throughput gene expression screenings.
Collapse
Affiliation(s)
- Andrés Ramos-Valle
- The Nanomedicine Group, Institute Valdecilla-IDIVAL, Santander, Spain
- Molecular Biology Department, Universidad de Cantabria, Santander, Spain
| | - Henning Kirst
- The Nanomedicine Group, Institute Valdecilla-IDIVAL, Santander, Spain
- Molecular Biology Department, Universidad de Cantabria, Santander, Spain
| | - Mónica L Fanarraga
- The Nanomedicine Group, Institute Valdecilla-IDIVAL, Santander, Spain
- Molecular Biology Department, Universidad de Cantabria, Santander, Spain
| |
Collapse
|
2
|
Shang J, Song F, Zhang Z, Chen D, Yang S. Application of novel CRISPR tools in brain therapy. Life Sci 2024; 352:122855. [PMID: 38908787 DOI: 10.1016/j.lfs.2024.122855] [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: 03/28/2024] [Revised: 06/07/2024] [Accepted: 06/16/2024] [Indexed: 06/24/2024]
Abstract
In recent years, the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-based genome editing toolkit has been widely used to modify the genome sequence of organisms. As the CRISPR toolbox continues to grow and new CRISPR-associated (Cas) proteins are discovered, its applications have expanded beyond conventional genome editing. This now encompass epigenetic editing, gene expression control, and various other functions. Notably, these advancements are finding practical application in the treatment of brain diseases. Furthermore, the amalgamation of CRISPR and Chimeric Antigen Receptor T-cell (CAR-T) technologies has emerged as a potential approach for disease treatment. With this in mind, this review commences by offering a comprehensive overview of recent advancements in CRISPR gene editing tools. This encompasses an exploration of various Cas proteins, gene expression control, epigenetic editing, base editing and primer editing. Additionally, we present an in-depth examination of the manifold applications of these innovative CRISPR tools in the realms of brain therapeutics, such as neurodegenerative diseases, neurological syndromes and genetic disorders, epileptic disorders, and brain tumors, also explore the pathogenesis of these diseases. This includes their utilization in modeling, gene screening, therapeutic gene editing, as well as their emerging synergy with CAR-T technology. Finally, we discuss the remaining technical challenges that need to be addressed for effective utilization of CRISPR tools in disease treatment.
Collapse
Affiliation(s)
- Jiawen Shang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Fei Song
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Zhenzhong Zhang
- School of Pharmaceutical Sciences, Zhengzhou University, Henan Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou 450001, China.
| | - Di Chen
- School of Pharmaceutical Sciences, Zhengzhou University, Henan Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou 450001, China.
| | - Sen Yang
- School of Pharmaceutical Sciences, Zhengzhou University, Henan Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou 450001, China.
| |
Collapse
|
3
|
Jin YY, Zhang P, Liu LL, Zhao X, Hu XQ, Liu SZ, Li ZK, Liu Q, Wang JQ, Hao DL, Zhang ZQ, Chen HZ, Liu DP. Enhancing homology-directed repair efficiency with HDR-boosting modular ssDNA donor. Nat Commun 2024; 15:6843. [PMID: 39122671 PMCID: PMC11315919 DOI: 10.1038/s41467-024-50788-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 07/22/2024] [Indexed: 08/12/2024] Open
Abstract
Despite the potential of small molecules and recombinant proteins to enhance the efficiency of homology-directed repair (HDR), single-stranded DNA (ssDNA) donors, as currently designed and chemically modified, remain suboptimal for precise gene editing. Here, we screen the biased ssDNA binding sequences of DNA repair-related proteins and engineer RAD51-preferred sequences into HDR-boosting modules for ssDNA donors. Donors with these modules exhibit an augmented affinity for RAD51, thereby enhancing HDR efficiency across various genomic loci and cell types when cooperated with Cas9, nCas9, and Cas12a. By combining with an inhibitor of non-homologous end joining (NHEJ) or the HDRobust strategy, these modular ssDNA donors achieve up to 90.03% (median 74.81%) HDR efficiency. The HDR-boosting modules targeting an endogenous protein enable a chemical modification-free strategy to improve the efficacy of ssDNA donors for precise gene editing.
Collapse
Affiliation(s)
- Ying-Ying Jin
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Peng Zhang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Le-Le Liu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Xiang Zhao
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Xiao-Qing Hu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Si-Zhe Liu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Ze-Kun Li
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Qian Liu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Jian-Qiao Wang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - De-Long Hao
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Zhu-Qin Zhang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Hou-Zao Chen
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China.
- Medical Epigenetics Research Center, Chinese Academy of Medical Sciences, Beijing, 100005, China.
| | - De-Pei Liu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China.
- Medical Epigenetics Research Center, Chinese Academy of Medical Sciences, Beijing, 100005, China.
- Haihe Laboratory of Cell Ecosystem, Tianjin, 300301, China.
| |
Collapse
|
4
|
Li T, Li S, Kang Y, Zhou J, Yi M. Harnessing the evolving CRISPR/Cas9 for precision oncology. J Transl Med 2024; 22:749. [PMID: 39118151 PMCID: PMC11312220 DOI: 10.1186/s12967-024-05570-4] [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: 04/30/2024] [Accepted: 08/04/2024] [Indexed: 08/10/2024] Open
Abstract
The Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)/Cas9 system, a groundbreaking innovation in genetic engineering, has revolutionized our approach to surmounting complex diseases, culminating in CASGEVY™ approved for sickle cell anemia. Derived from a microbial immune defense mechanism, CRISPR/Cas9, characterized as precision, maneuverability and universality in gene editing, has been harnessed as a versatile tool for precisely manipulating DNA in mammals. In the process of applying it to practice, the consecutive exploitation of novel orthologs and variants never ceases. It's conducive to understanding the essentialities of diseases, particularly cancer, which is crucial for diagnosis, prevention, and treatment. CRISPR/Cas9 is used not only to investigate tumorous genes functioning but also to model disparate cancers, providing valuable insights into tumor biology, resistance, and immune evasion. Upon cancer therapy, CRISPR/Cas9 is instrumental in developing individual and precise cancer therapies that can selectively activate or deactivate genes within tumor cells, aiming to cripple tumor growth and invasion and sensitize cancer cells to treatments. Furthermore, it facilitates the development of innovative treatments, enhancing the targeting efficiency of reprogrammed immune cells, exemplified by advancements in CAR-T regimen. Beyond therapy, it is a potent tool for screening susceptible genes, offering the possibility of intervening before the tumor initiative or progresses. However, despite its vast potential, the application of CRISPR/Cas9 in cancer research and therapy is accompanied by significant efficacy, efficiency, technical, and safety considerations. Escalating technology innovations are warranted to address these issues. The CRISPR/Cas9 system is revolutionizing cancer research and treatment, opening up new avenues for advancements in our understanding and management of cancers. The integration of this evolving technology into clinical practice promises a new era of precision oncology, with targeted, personalized, and potentially curative therapies for cancer patients.
Collapse
Affiliation(s)
- Tianye Li
- Department of Gynecology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, People's Republic of China
- Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Hangzhou, 310000, People's Republic of China
| | - Shuiquan Li
- Department of Rehabilitation and Traditional Chinese Medicine, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, People's Republic of China
| | - Yue Kang
- Department of Obstetrics and Gynecology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
| | - Jianwei Zhou
- Department of Gynecology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, People's Republic of China.
- Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Hangzhou, 310000, People's Republic of China.
| | - Ming Yi
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310000, People's Republic of China.
| |
Collapse
|
5
|
Lang LI, Wang ZZ, Liu B, Chang-Qing SHEN, Jing-Yi TU, Shi-Cheng WANG, Rui-Ling LEI, Si-Qi PENG, Xiong XIAO, Yong-Ju ZHAO, Qiu XY. The effects and mechanisms of heat stress on mammalian oocyte and embryo development. J Therm Biol 2024; 124:103927. [PMID: 39153259 DOI: 10.1016/j.jtherbio.2024.103927] [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: 10/26/2023] [Revised: 07/15/2024] [Accepted: 07/20/2024] [Indexed: 08/19/2024]
Abstract
The sum of nonspecific physiological responses exhibited by mammals in response to the disruption of thermal balance caused by high-temperature environments is referred to as heat stress (HS). HS affects the normal development of mammalian oocyte and embryos and leads to significant economic losses. Therefore, it is of great importance to gain a deep understanding of the mechanisms underlying the effects of HS on oocyte and embryonic development and to explore strategies for mitigating or preventing its detrimental impacts in the livestock industry. This article provides an overview of the negative effects of HS on mammalian oocyte growth, granulosa cell maturation and function, and embryonic development. It summarizes the mechanisms by which HS affects embryonic development, including generation of reactive oxygen species (ROS), endocrine disruption, the heat shock system, mitochondrial autophagy, and molecular-level alterations. Furthermore, it discusses various measures to ameliorate the effects of HS, such as antioxidant use, enhancement of mitochondrial function, gene editing, cultivating varieties possessing heat-resistant genes, and optimizing the animals'rearing environment. This article serves as a valuable reference for better understanding the relationship between HS and mammalian embryonic development as well as for improving the development of mammalian embryos and economic benefits under HS conditions in livestock production.
Collapse
Affiliation(s)
- L I Lang
- College of Animal Science and Technology, Southwest University, Chongqing Key Laboratory of Herbivore Science, Chongqing, 400715, China
| | - Zhen-Zhen Wang
- College of Animal Science and Technology, Southwest University, Chongqing Key Laboratory of Herbivore Science, Chongqing, 400715, China
| | - Bin Liu
- College of Animal Science and Technology, Southwest University, Chongqing Key Laboratory of Herbivore Science, Chongqing, 400715, China
| | - S H E N Chang-Qing
- College of Animal Science and Technology, Southwest University, Chongqing Key Laboratory of Herbivore Science, Chongqing, 400715, China
| | - T U Jing-Yi
- College of Animal Science and Technology, Southwest University, Chongqing Key Laboratory of Herbivore Science, Chongqing, 400715, China
| | - W A N G Shi-Cheng
- College of Animal Science and Technology, Southwest University, Chongqing Key Laboratory of Herbivore Science, Chongqing, 400715, China
| | - L E I Rui-Ling
- College of Animal Science and Technology, Southwest University, Chongqing Key Laboratory of Herbivore Science, Chongqing, 400715, China
| | - P E N G Si-Qi
- College of Animal Science and Technology, Southwest University, Chongqing Key Laboratory of Herbivore Science, Chongqing, 400715, China
| | - X I A O Xiong
- College of Veterinary Medicine, Southwest University, Chongqing, 400715, China
| | - Z H A O Yong-Ju
- College of Animal Science and Technology, Southwest University, Chongqing Key Laboratory of Herbivore Science, Chongqing, 400715, China
| | - Xiao-Yan Qiu
- College of Animal Science and Technology, Southwest University, Chongqing Key Laboratory of Herbivore Science, Chongqing, 400715, China.
| |
Collapse
|
6
|
Leandro K, Rufino-Ramos D, Breyne K, Di Ianni E, Lopes SM, Jorge Nobre R, Kleinstiver BP, Perdigão PRL, Breakefield XO, Pereira de Almeida L. Exploring the potential of cell-derived vesicles for transient delivery of gene editing payloads. Adv Drug Deliv Rev 2024; 211:115346. [PMID: 38849005 DOI: 10.1016/j.addr.2024.115346] [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: 12/10/2023] [Revised: 05/28/2024] [Accepted: 05/30/2024] [Indexed: 06/09/2024]
Abstract
Gene editing technologies have the potential to correct genetic disorders by modifying, inserting, or deleting specific DNA sequences or genes, paving the way for a new class of genetic therapies. While gene editing tools continue to be improved to increase their precision and efficiency, the limited efficacy of in vivo delivery remains a major hurdle for clinical use. An ideal delivery vehicle should be able to target a sufficient number of diseased cells in a transient time window to maximize on-target editing and mitigate off-target events and immunogenicity. Here, we review major advances in novel delivery platforms based on cell-derived vesicles - extracellular vesicles and virus-like particles - for transient delivery of gene editing payloads. We discuss major findings regarding packaging, in vivo biodistribution, therapeutic efficacy, and safety concerns of cell-derived vesicles delivery of gene editing cargos and their potential for clinical translation.
Collapse
Affiliation(s)
- Kevin Leandro
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-504 Coimbra, Portugal; Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal; GeneT - Gene Therapy Center of Excellence Portugal, University of Coimbra, Coimbra, Portugal
| | - David Rufino-Ramos
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-504 Coimbra, Portugal; Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal; GeneT - Gene Therapy Center of Excellence Portugal, University of Coimbra, Coimbra, Portugal; Center for Genomic Medicine and Department of Pathology, Massachusetts General Hospital, Boston, MA 02115, USA; Department of Pathology, Harvard Medical School, Boston, MA 02114, USA
| | - Koen Breyne
- Molecular Neurogenetics Unit, Department of Neurology and Center for Molecular Imaging Research, Department of Radiology, Massachusetts General Hospital and Program in Neuroscience, Harvard Medical School, Boston, MA 02129, USA
| | - Emilio Di Ianni
- Molecular Neurogenetics Unit, Department of Neurology and Center for Molecular Imaging Research, Department of Radiology, Massachusetts General Hospital and Program in Neuroscience, Harvard Medical School, Boston, MA 02129, USA
| | - Sara M Lopes
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-504 Coimbra, Portugal; GeneT - Gene Therapy Center of Excellence Portugal, University of Coimbra, Coimbra, Portugal; IIIUC - Institute for Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal
| | - Rui Jorge Nobre
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-504 Coimbra, Portugal; GeneT - Gene Therapy Center of Excellence Portugal, University of Coimbra, Coimbra, Portugal; IIIUC - Institute for Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal; ViraVector - Viral Vector for Gene Transfer Core Facility, University of Coimbra, Coimbra 3004-504, Portugal
| | - Benjamin P Kleinstiver
- Center for Genomic Medicine and Department of Pathology, Massachusetts General Hospital, Boston, MA 02115, USA; Department of Pathology, Harvard Medical School, Boston, MA 02114, USA
| | - Pedro R L Perdigão
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-504 Coimbra, Portugal; GeneT - Gene Therapy Center of Excellence Portugal, University of Coimbra, Coimbra, Portugal; IIIUC - Institute for Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal
| | - Xandra O Breakefield
- Molecular Neurogenetics Unit, Department of Neurology and Center for Molecular Imaging Research, Department of Radiology, Massachusetts General Hospital and Program in Neuroscience, Harvard Medical School, Boston, MA 02129, USA
| | - Luís Pereira de Almeida
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-504 Coimbra, Portugal; Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal; GeneT - Gene Therapy Center of Excellence Portugal, University of Coimbra, Coimbra, Portugal; ViraVector - Viral Vector for Gene Transfer Core Facility, University of Coimbra, Coimbra 3004-504, Portugal.
| |
Collapse
|
7
|
Karasu ME, Jahnke L, Joseph BJ, Amerzhanova Y, Mironov A, Shu X, Schröder MS, Gvozdenovic A, Sala I, Zavolan M, Jonas S, Corn JE. CCAR1 promotes DNA repair via alternative splicing. Mol Cell 2024; 84:2634-2647.e9. [PMID: 38964321 DOI: 10.1016/j.molcel.2024.06.011] [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: 09/12/2023] [Revised: 04/29/2024] [Accepted: 06/12/2024] [Indexed: 07/06/2024]
Abstract
DNA repair is directly performed by hundreds of core factors and indirectly regulated by thousands of others. We massively expanded a CRISPR inhibition and Cas9-editing screening system to discover factors indirectly modulating homology-directed repair (HDR) in the context of ∼18,000 individual gene knockdowns. We focused on CCAR1, a poorly understood gene that we found the depletion of reduced both HDR and interstrand crosslink repair, phenocopying the loss of the Fanconi anemia pathway. CCAR1 loss abrogated FANCA protein without substantial reduction in the level of its mRNA or that of other FA genes. We instead found that CCAR1 prevents inclusion of a poison exon in FANCA. Transcriptomic analysis revealed that the CCAR1 splicing modulatory activity is not limited to FANCA, and it instead regulates widespread changes in alternative splicing that would damage coding sequences in mouse and human cells. CCAR1 therefore has an unanticipated function as a splicing fidelity factor.
Collapse
Affiliation(s)
- Mehmet E Karasu
- Institute of Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology Zurich (ETH Zurich), Zurich 8093, Switzerland
| | - Leonard Jahnke
- Institute of Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology Zurich (ETH Zurich), Zurich 8093, Switzerland
| | - Brian J Joseph
- Department of Pathology and Cell Biology, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
| | - Yerkezhan Amerzhanova
- Institute of Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology Zurich (ETH Zurich), Zurich 8093, Switzerland
| | - Aleksei Mironov
- Computational and Systems Biology, Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Xuan Shu
- Institute of Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology Zurich (ETH Zurich), Zurich 8093, Switzerland
| | - Markus S Schröder
- Institute of Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology Zurich (ETH Zurich), Zurich 8093, Switzerland
| | - Ana Gvozdenovic
- Institute of Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology Zurich (ETH Zurich), Zurich 8093, Switzerland
| | - Irene Sala
- Institute of Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology Zurich (ETH Zurich), Zurich 8093, Switzerland
| | - Mihaela Zavolan
- Computational and Systems Biology, Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Stefanie Jonas
- Institute of Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology Zurich (ETH Zurich), Zurich 8093, Switzerland
| | - Jacob E Corn
- Institute of Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology Zurich (ETH Zurich), Zurich 8093, Switzerland.
| |
Collapse
|
8
|
Ferreira da Silva J, Tou CJ, King EM, Eller ML, Rufino-Ramos D, Ma L, Cromwell CR, Metovic J, Benning FMC, Chao LH, Eichler FS, Kleinstiver BP. Click editing enables programmable genome writing using DNA polymerases and HUH endonucleases. Nat Biotechnol 2024:10.1038/s41587-024-02324-x. [PMID: 39039307 DOI: 10.1038/s41587-024-02324-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 06/24/2024] [Indexed: 07/24/2024]
Abstract
Genome editing technologies based on DNA-dependent polymerases (DDPs) could offer several benefits compared with other types of editors to install diverse edits. Here, we develop click editing, a genome writing platform that couples the advantageous properties of DDPs with RNA-programmable nickases to permit the installation of a range of edits, including substitutions, insertions and deletions. Click editors (CEs) leverage the 'click'-like bioconjugation ability of HUH endonucleases with single-stranded DNA substrates to covalently tether 'click DNA' (clkDNA) templates encoding user-specifiable edits at targeted genomic loci. Through iterative optimization of the modular components of CEs and their clkDNAs, we demonstrate the ability to install precise genome edits with minimal indels in diverse immortalized human cell types and primary fibroblasts with precise editing efficiencies of up to ~30%. Editing efficiency can be improved by rapidly screening clkDNA oligonucleotides with various modifications, including repair-evading substitutions. Click editing is a precise and versatile genome editing approach for diverse biological applications.
Collapse
Affiliation(s)
- Joana Ferreira da Silva
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Connor J Tou
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Biological Engineering Program, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Emily M King
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Biological and Biomedical Sciences Program, Harvard University, Boston, MA, USA
| | - Madeline L Eller
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - David Rufino-Ramos
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Linyuan Ma
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Christopher R Cromwell
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Jasna Metovic
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Friederike M C Benning
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Luke H Chao
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Florian S Eichler
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Benjamin P Kleinstiver
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.
- Department of Pathology, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
9
|
Song X, Liu J, Chen T, Zheng T, Wang X, Guo X. Gene therapy and gene editing strategies in inherited blood disorders. J Genet Genomics 2024:S1673-8527(24)00180-2. [PMID: 38986807 DOI: 10.1016/j.jgg.2024.07.004] [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: 04/30/2024] [Revised: 07/01/2024] [Accepted: 07/02/2024] [Indexed: 07/12/2024]
Abstract
Gene therapy has shown significant potential in treating various diseases, particularly inherited blood disorders such as hemophilia, sickle cell disease, and thalassemia. Advances in understanding the regulatory network of disease-associated genes have led to the identification of additional therapeutic targets for treatment, especially for β-hemoglobinopathies. Erythroid regulatory factor BCL11A offers the most promising therapeutic target for β-hemoglobinopathies and reduction of its expression using the commercialized gene therapy product Casgevy was approved for use in the UK and USA in 2023. Notably, the emergence of innovative gene editing technologies has further broadened the gene therapy landscape, presenting new possibilities for treatment. Intensive studies indicate that base editing and prime editing, built upon CRISPR technology, enable precise single-base modification in hematopoietic stem cells for addressing inherited blood disorders ex vivo and in vivo. In this review, we present an overview of the current landscape of gene therapies, focusing on clinical research and gene therapy products for inherited blood disorders, evaluation of potential gene targets, and the gene editing tools employed in current gene therapy practices, which provides an insight for the establishment of safer and more effective gene therapy methods for a wider range of diseases in the future.
Collapse
Affiliation(s)
- Xuemei Song
- Institute of Blood Diseases, Department of Hematology, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine of University of Electronic Science and Technology of China, Chengdu, Sichuan 610000, China
| | - JinLei Liu
- Institute of Blood Diseases, Department of Hematology, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine of University of Electronic Science and Technology of China, Chengdu, Sichuan 610000, China
| | - Tangcong Chen
- Institute of Blood Diseases, Department of Hematology, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine of University of Electronic Science and Technology of China, Chengdu, Sichuan 610000, China
| | - Tingfeng Zheng
- Institute of Blood Diseases, Department of Hematology, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine of University of Electronic Science and Technology of China, Chengdu, Sichuan 610000, China
| | - Xiaolong Wang
- Institute of Blood Diseases, Department of Hematology, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine of University of Electronic Science and Technology of China, Chengdu, Sichuan 610000, China
| | - Xiang Guo
- Institute of Blood Diseases, Department of Hematology, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine of University of Electronic Science and Technology of China, Chengdu, Sichuan 610000, China.
| |
Collapse
|
10
|
Zakas PM, Cunningham SC, Doherty A, van Dijk EB, Ibraheim R, Yu S, Mekonnen BD, Lang B, English EJ, Sun G, Duncan MC, Benczkowski MS, Altshuler RC, Singh MJ, Kibbler ES, Tonga GY, Wang ZJ, Wang ZJ, Li G, An D, Rottman JB, Bhavsar Y, Purcell C, Jain R, Alberry R, Roquet N, Fu Y, Citorik RJ, Rubens JR, Holmes MC, Cotta-Ramusino C, Querbes W, Alexander IE, Salomon WE. Sleeping Beauty mRNA-LNP enables stable rAAV transgene expression in mouse and NHP hepatocytes and improves vector potency. Mol Ther 2024:S1525-0016(24)00403-9. [PMID: 38981468 DOI: 10.1016/j.ymthe.2024.06.021] [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: 12/22/2023] [Revised: 05/05/2024] [Accepted: 06/14/2024] [Indexed: 07/11/2024] Open
Abstract
Recombinant adeno-associated virus (rAAV) vector gene delivery systems have demonstrated great promise in clinical trials but continue to face durability and dose-related challenges. Unlike rAAV gene therapy, integrating gene addition approaches can provide curative expression in mitotically active cells and pediatric populations. We explored a novel in vivo delivery approach based on an engineered transposase, Sleeping Beauty (SB100X), delivered as an mRNA within a lipid nanoparticle (LNP), in combination with an rAAV-delivered transposable transgene. This combinatorial approach achieved correction of ornithine transcarbamylase deficiency in the neonatal Spfash mouse model following a single delivery to dividing hepatocytes in the newborn liver. Correction remained stable into adulthood, while a conventional rAAV approach resulted in a return to the disease state. In non-human primates, integration by transposition, mediated by this technology, improved gene expression 10-fold over conventional rAAV-mediated gene transfer while requiring 5-fold less vector. Additionally, integration site analysis confirmed a random profile while specifically targeting TA dinucleotides across the genome. Together, these findings demonstrate that transposable elements can improve rAAV-delivered therapies by lowering the vector dose requirement and associated toxicity while expanding target cell types.
Collapse
Affiliation(s)
| | - Sharon C Cunningham
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, NSW 2145, Australia
| | - Ann Doherty
- Tessera Therapeutics, Inc., Somerville, MA 02143, USA
| | - Eva B van Dijk
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, NSW 2145, Australia
| | - Raed Ibraheim
- Tessera Therapeutics, Inc., Somerville, MA 02143, USA
| | - Stephanie Yu
- Tessera Therapeutics, Inc., Somerville, MA 02143, USA
| | | | - Brendan Lang
- Tessera Therapeutics, Inc., Somerville, MA 02143, USA
| | | | - Gang Sun
- Tessera Therapeutics, Inc., Somerville, MA 02143, USA
| | | | | | | | | | | | - Gulen Y Tonga
- Tessera Therapeutics, Inc., Somerville, MA 02143, USA
| | - Zi Jun Wang
- Tessera Therapeutics, Inc., Somerville, MA 02143, USA
| | - Z Jane Wang
- Tessera Therapeutics, Inc., Somerville, MA 02143, USA
| | - Guangde Li
- Tessera Therapeutics, Inc., Somerville, MA 02143, USA
| | - Ding An
- Tessera Therapeutics, Inc., Somerville, MA 02143, USA
| | | | | | | | - Rachit Jain
- Tessera Therapeutics, Inc., Somerville, MA 02143, USA
| | - Ryan Alberry
- Tessera Therapeutics, Inc., Somerville, MA 02143, USA
| | | | - Yanfang Fu
- Tessera Therapeutics, Inc., Somerville, MA 02143, USA
| | | | | | | | | | | | - Ian E Alexander
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, NSW 2145, Australia; Discipline of Child and Adolescent Health, University of Sydney, Westmead, NSW 2145, Australia.
| | | |
Collapse
|
11
|
Muurmann AT, Banovic M, Gilbert MTP, Sogari G, Limborg MT, Sicheritz-Pontén T, Bahrndorff S. Framework for valorizing waste- and by-products through insects and their microbiomes for food and feed. Food Res Int 2024; 187:114358. [PMID: 38763642 DOI: 10.1016/j.foodres.2024.114358] [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: 12/15/2023] [Revised: 04/10/2024] [Accepted: 04/17/2024] [Indexed: 05/21/2024]
Abstract
One third of the food produced for human consumption is currently lost or wasted. Insects have a high potential for converting organic waste- and by-products into food and feed for a growing human population due to symbiosis with microorganisms. These symbioses provide an untapped reservoir of functional microbiomes that can be used to improve industrial insect production but are poorly studied in most insect species. Here we review the most current understanding and challenges of valorizing organic waste- and by-products through insects and their microbiomes for food and feed, and emerging novel food technologies that can be used to investigate and manipulate host(insects)-microbiome interactions. We further construct a holistic framework, by integration of novel food technologies including holo-omics, genome editing, breeding, phage therapy, and administration of prebiotics and probiotics to investigate and manipulate host(insects)-microbiome interactions, and solutions for achieving stakeholder acceptance of novel food technologies for a sustainable food production.
Collapse
Affiliation(s)
- Asmus Toftkær Muurmann
- Aalborg University, Department of Chemistry and Bioscience, Fredrik Bajers Vej 7H, 9220 Aalborg Ø, Denmark.
| | - Marija Banovic
- Aarhus University, Aarhus BSS, Department of Management, MAPP Centre, Fuglsangs Allé 4, 8210 Aarhus V, Denmark.
| | - M Thomas P Gilbert
- University of Copenhagen, GLOBE Institute, Øster Farimagsgade 5, 1014 København K, Denmark; University Museum, NTNU, Erling Skakkes gate 47B, 7012 Trondheim, Norway.
| | - Giovanni Sogari
- University of Parma, Department of Food and Drug, Parco Area delle Scienze, 45, 43124 Parma, Italy.
| | | | - Thomas Sicheritz-Pontén
- University of Copenhagen, GLOBE Institute, Øster Farimagsgade 5, 1014 København K, Denmark; AIMST University, Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Jalan Bedong-Semeling, 08100 Bedong, Kedah, Malaysia.
| | - Simon Bahrndorff
- Aalborg University, Department of Chemistry and Bioscience, Fredrik Bajers Vej 7H, 9220 Aalborg Ø, Denmark.
| |
Collapse
|
12
|
Liu Y, Kong J, Liu G, Li Z, Xiao Y. Precise Gene Knock-In Tools with Minimized Risk of DSBs: A Trend for Gene Manipulation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2401797. [PMID: 38728624 PMCID: PMC11267366 DOI: 10.1002/advs.202401797] [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: 02/20/2024] [Revised: 04/29/2024] [Indexed: 05/12/2024]
Abstract
Gene knock-in refers to the insertion of exogenous functional genes into a target genome to achieve continuous expression. Currently, most knock-in tools are based on site-directed nucleases, which can induce double-strand breaks (DSBs) at the target, following which the designed donors carrying functional genes can be inserted via the endogenous gene repair pathway. The size of donor genes is limited by the characteristics of gene repair, and the DSBs induce risks like genotoxicity. New generation tools, such as prime editing, transposase, and integrase, can insert larger gene fragments while minimizing or eliminating the risk of DSBs, opening new avenues in the development of animal models and gene therapy. However, the elimination of off-target events and the production of delivery carriers with precise requirements remain challenging, restricting the application of the current knock-in treatments to mainly in vitro settings. Here, a comprehensive review of the knock-in tools that do not/minimally rely on DSBs and use other mechanisms is provided. Moreover, the challenges and recent advances of in vivo knock-in treatments in terms of the therapeutic process is discussed. Collectively, the new generation of DSBs-minimizing and large-fragment knock-in tools has revolutionized the field of gene editing, from basic research to clinical treatment.
Collapse
Affiliation(s)
- Yongfeng Liu
- Department of PharmacologySchool of PharmacyChina Pharmaceutical UniversityNanjing210009China
- State Key Laboratory of Natural MedicinesChina Pharmaceutical UniversityNanjing210009China
- Mudi Meng Honors CollegeChina Pharmaceutical UniversityNanjing210009China
| | - Jianping Kong
- Department of PharmacologySchool of PharmacyChina Pharmaceutical UniversityNanjing210009China
- State Key Laboratory of Natural MedicinesChina Pharmaceutical UniversityNanjing210009China
| | - Gongyu Liu
- Department of PharmacologySchool of PharmacyChina Pharmaceutical UniversityNanjing210009China
- State Key Laboratory of Natural MedicinesChina Pharmaceutical UniversityNanjing210009China
| | - Zhaoxing Li
- Department of PharmacologySchool of PharmacyChina Pharmaceutical UniversityNanjing210009China
- State Key Laboratory of Natural MedicinesChina Pharmaceutical UniversityNanjing210009China
- Chongqing Innovation Institute of China Pharmaceutical UniversityChongqing401135China
| | - Yibei Xiao
- Department of PharmacologySchool of PharmacyChina Pharmaceutical UniversityNanjing210009China
- State Key Laboratory of Natural MedicinesChina Pharmaceutical UniversityNanjing210009China
- Chongqing Innovation Institute of China Pharmaceutical UniversityChongqing401135China
| |
Collapse
|
13
|
Kansal R. The CRISPR-Cas System and Clinical Applications of CRISPR-Based Gene Editing in Hematology with a Focus on Inherited Germline Predisposition to Hematologic Malignancies. Genes (Basel) 2024; 15:863. [PMID: 39062641 PMCID: PMC11276294 DOI: 10.3390/genes15070863] [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: 06/06/2024] [Revised: 06/27/2024] [Accepted: 06/27/2024] [Indexed: 07/28/2024] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-based gene editing has begun to transform the treatment landscape of genetic diseases. The history of the discovery of CRISPR/CRISPR-associated (Cas) proteins/single-guide RNA (sgRNA)-based gene editing since the first report of repetitive sequences of unknown significance in 1987 is fascinating, highly instructive, and inspiring for future advances in medicine. The recent approval of CRISPR-Cas9-based gene therapy to treat patients with severe sickle cell anemia and transfusion-dependent β-thalassemia has renewed hope for treating other hematologic diseases, including patients with a germline predisposition to hematologic malignancies, who would benefit greatly from the development of CRISPR-inspired gene therapies. The purpose of this paper is three-fold: first, a chronological description of the history of CRISPR-Cas9-sgRNA-based gene editing; second, a brief description of the current state of clinical research in hematologic diseases, including selected applications in treating hematologic diseases with CRISPR-based gene therapy, preceded by a brief description of the current tools being used in clinical genome editing; and third, a presentation of the current progress in gene therapies in inherited hematologic diseases and bone marrow failure syndromes, to hopefully stimulate efforts towards developing these therapies for patients with inherited bone marrow failure syndromes and other inherited conditions with a germline predisposition to hematologic malignancies.
Collapse
Affiliation(s)
- Rina Kansal
- Molecular Oncology and Genetics, Diagnostic Laboratories, Versiti Blood Center of Wisconsin, Milwaukee, WI 53233, USA;
- Department of Pathology and Anatomical Sciences, The University at Buffalo, Buffalo, NY 14260, USA
| |
Collapse
|
14
|
Chen D, Zhao C, Zhang J, Knol CWJ, Osipyan A, Majerníková N, Chen T, Xiao Z, Adriana J, Griffith AJ, Gamez AS, van der Wouden PE, Coppes RP, Dolga AM, Haisma HJ, Dekker FJ. Small Molecule MIF Modulation Enhances Ferroptosis by Impairing DNA Repair Mechanisms. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2403963. [PMID: 38924362 DOI: 10.1002/advs.202403963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 06/07/2024] [Indexed: 06/28/2024]
Abstract
Ferroptosis is a form of regulated cell death that can be modulated by small molecules and has the potential for the development of therapeutics for oncology. Although excessive lipid peroxidation is the defining hallmark of ferroptosis, DNA damage may also play a significant role. In this study, a potential mechanistic role for MIF in homologous recombination (HR) DNA repair is identified. The inhibition or genetic depletion of MIF or other HR proteins, such as breast cancer type 1 susceptibility protein (BRCA1), is demonstrated to significantly enhance the sensitivity of cells to ferroptosis. The interference with HR results in the translocation of the tumor suppressor protein p53 to the mitochondria, which in turn stimulates the production of reactive oxygen species. Taken together, the findings demonstrate that MIF-directed small molecules enhance ferroptosis via a putative MIF-BRCA1-RAD51 axis in HR, which causes resistance to ferroptosis. This suggests a potential novel druggable route to enhance ferroptosis by targeted anticancer therapeutics in the future.
Collapse
Affiliation(s)
- Deng Chen
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Chunlong Zhao
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Jianqiu Zhang
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Catharina W J Knol
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Angelina Osipyan
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Nad'a Majerníková
- Research School of Behavioural and Cognitive Neuroscience, University of Groningen, Groningen, 9713 AV, The Netherlands
- Department of Pathology and Medical Biology, University Medical Centre Groningen, University of Groningen, Groningen, 9713 GZ, The Netherlands
- Department of Molecular Pharmacology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, 9713 AV, The Netherlands
| | - Tingting Chen
- Department of Molecular Pharmacology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, 9713 AV, The Netherlands
| | - Zhangping Xiao
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Jeaunice Adriana
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Andrew J Griffith
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Abel Soto Gamez
- Department of Biomedical Sciences of Cell & Systems, Section Molecular Cell Biology, University Medical Center Groningen, University of Groningen, Groningen, 9712 CP, The Netherlands
- Department of Radiation Oncology, University Medical Center Groningen, Hanzeplein 1, Groningen, 9713 GZ, Netherlands
| | - Petra E van der Wouden
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Robert P Coppes
- Department of Biomedical Sciences of Cell & Systems, Section Molecular Cell Biology, University Medical Center Groningen, University of Groningen, Groningen, 9712 CP, The Netherlands
- Department of Radiation Oncology, University Medical Center Groningen, Hanzeplein 1, Groningen, 9713 GZ, Netherlands
| | - Amalia M Dolga
- Research School of Behavioural and Cognitive Neuroscience, University of Groningen, Groningen, 9713 AV, The Netherlands
- Department of Molecular Pharmacology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, 9713 AV, The Netherlands
| | - Hidde J Haisma
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Frank J Dekker
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| |
Collapse
|
15
|
Villiger L, Joung J, Koblan L, Weissman J, Abudayyeh OO, Gootenberg JS. CRISPR technologies for genome, epigenome and transcriptome editing. Nat Rev Mol Cell Biol 2024; 25:464-487. [PMID: 38308006 DOI: 10.1038/s41580-023-00697-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/18/2023] [Indexed: 02/04/2024]
Abstract
Our ability to edit genomes lags behind our capacity to sequence them, but the growing understanding of CRISPR biology and its application to genome, epigenome and transcriptome engineering is narrowing this gap. In this Review, we discuss recent developments of various CRISPR-based systems that can transiently or permanently modify the genome and the transcriptome. The discovery of further CRISPR enzymes and systems through functional metagenomics has meaningfully broadened the applicability of CRISPR-based editing. Engineered Cas variants offer diverse capabilities such as base editing, prime editing, gene insertion and gene regulation, thereby providing a panoply of tools for the scientific community. We highlight the strengths and weaknesses of current CRISPR tools, considering their efficiency, precision, specificity, reliance on cellular DNA repair mechanisms and their applications in both fundamental biology and therapeutics. Finally, we discuss ongoing clinical trials that illustrate the potential impact of CRISPR systems on human health.
Collapse
Affiliation(s)
- Lukas Villiger
- McGovern Institute for Brain Research, Massachusetts Institute of Technology Cambridge, Cambridge, MA, USA
| | - Julia Joung
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Luke Koblan
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jonathan Weissman
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Omar O Abudayyeh
- McGovern Institute for Brain Research, Massachusetts Institute of Technology Cambridge, Cambridge, MA, USA.
| | - Jonathan S Gootenberg
- McGovern Institute for Brain Research, Massachusetts Institute of Technology Cambridge, Cambridge, MA, USA.
| |
Collapse
|
16
|
Shi H, Li L, Mu S, Gou S, Liu X, Chen F, Chen M, Jin Q, Lai L, Wang K. Exonuclease editor promotes precision of gene editing in mammalian cells. BMC Biol 2024; 22:119. [PMID: 38769511 PMCID: PMC11107001 DOI: 10.1186/s12915-024-01918-w] [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: 04/28/2023] [Accepted: 05/13/2024] [Indexed: 05/22/2024] Open
Abstract
BACKGROUND Many efforts have been made to improve the precision of Cas9-mediated gene editing through increasing knock-in efficiency and decreasing byproducts, which proved to be challenging. RESULTS Here, we have developed a human exonuclease 1-based genome-editing tool, referred to as exonuclease editor. When compared to Cas9, the exonuclease editor gave rise to increased HDR efficiency, reduced NHEJ repair frequency, and significantly elevated HDR/indel ratio. Robust gene editing precision of exonuclease editor was even superior to the fusion of Cas9 with E1B or DN1S, two previously reported precision-enhancing domains. Notably, exonuclease editor inhibited NHEJ at double strand breaks locally rather than globally, reducing indel frequency without compromising genome integrity. The replacement of Cas9 with single-strand DNA break-creating Cas9 nickase further increased the HDR/indel ratio by 453-fold than the original Cas9. In addition, exonuclease editor resulted in high microhomology-mediated end joining efficiency, allowing accurate and flexible deletion of targeted sequences with extended lengths with the aid of paired sgRNAs. Exonuclease editor was further used for correction of DMD patient-derived induced pluripotent stem cells, where 30.0% of colonies were repaired by HDR versus 11.1% in the control. CONCLUSIONS Therefore, the exonuclease editor system provides a versatile and safe genome editing tool with high precision and holds promise for therapeutic gene correction.
Collapse
Affiliation(s)
- Hui Shi
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya, 572000, China
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, 510530, China
| | - Lei Li
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuangshuang Mu
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shixue Gou
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya, 572000, China
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, 510530, China
| | - Xiaoyi Liu
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fangbing Chen
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya, 572000, China
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, 510530, China
- Guangdong Provincial Key Laboratory of Large Animal models for Biomedicine, Wuyi University, Jiangmen, 529020, China
| | - Menglong Chen
- Department of Neurology and Stroke Centre, The First Affiliated Hospital, Jinan University, Guangzhou, 510630, China
- Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Qin Jin
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya, 572000, China.
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, 510530, China.
| | - Liangxue Lai
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya, 572000, China.
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, 510530, China.
- Guangdong Provincial Key Laboratory of Large Animal models for Biomedicine, Wuyi University, Jiangmen, 529020, China.
| | - Kepin Wang
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya, 572000, China.
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, 510530, China.
- Guangdong Provincial Key Laboratory of Large Animal models for Biomedicine, Wuyi University, Jiangmen, 529020, China.
| |
Collapse
|
17
|
Huang Z, Gu R, Huang S, Chen Q, Yan J, Cui X, Jiang H, Yao D, Shen C, Su J, Liu T, Wu J, Luo Z, Hu Y, Yuan A. Chiral coordination polymer nanowires boost radiation-induced in situ tumor vaccination. Nat Commun 2024; 15:3902. [PMID: 38724527 PMCID: PMC11082158 DOI: 10.1038/s41467-024-48423-w] [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: 06/25/2023] [Accepted: 04/25/2024] [Indexed: 05/12/2024] Open
Abstract
Radiation-induced in situ tumor vaccination alone is very weak and insufficient to elicit robust antitumor immune responses. In this work, we address this issue by developing chiral vidarabine monophosphate-gadolinium nanowires (aAGd-NWs) through coordination-driven self-assembly. We elucidate the mechanism of aAGd-NW assembly and characterize their distinct features, which include a negative surface charge, ultrafine topography, and right-handed chirality. Additionally, aAGd-NWs not only enhance X-ray deposition but also inhibit DNA repair, thereby enhancing radiation-induced in situ vaccination. Consequently, the in situ vaccination induced by aAGd-NWs sensitizes radiation enhances CD8+ T-cell-dependent antitumor immunity and synergistically potentiates the efficacy immune checkpoint blockade therapies against both primary and metastatic tumors. The well-established aAGd-NWs exhibit exceptional therapeutic capacity and biocompatibility, offering a promising avenue for the development of radioimmunotherapy approaches.
Collapse
Affiliation(s)
- Zhusheng Huang
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School and School of Life Science, Nanjing University, Nanjing, 210093, China
- State Key Laboratory for Organic Electronics and Information Displays (SKLOEID), School of Chemistry and Life Sciences, Nanjing University of Posts and Telecommunications, Nanjing, 210023, China
- Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau, SAR 999078, China
| | - Rong Gu
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School and School of Life Science, Nanjing University, Nanjing, 210093, China
| | - Shiqian Huang
- State Key Laboratory for Organic Electronics and Information Displays (SKLOEID), School of Chemistry and Life Sciences, Nanjing University of Posts and Telecommunications, Nanjing, 210023, China
| | - Qian Chen
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School and School of Life Science, Nanjing University, Nanjing, 210093, China
| | - Jing Yan
- The Comprehensive Cancer Centre of Drum Tower Hospital, Medical School of Nanjing University, Nanjing, 210023, China
| | - Xiaoya Cui
- Beijing Frontier Research Center for Biological Structures, School of Life Sciences, Tsinghua University, Beijing, 100083, China
| | - Haojie Jiang
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School and School of Life Science, Nanjing University, Nanjing, 210093, China
| | - Dan Yao
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School and School of Life Science, Nanjing University, Nanjing, 210093, China
| | - Chuang Shen
- State Key Laboratory for Organic Electronics and Information Displays (SKLOEID), School of Chemistry and Life Sciences, Nanjing University of Posts and Telecommunications, Nanjing, 210023, China
| | - Jiayue Su
- Beijing Frontier Research Center for Biological Structures, School of Life Sciences, Tsinghua University, Beijing, 100083, China
| | - Tao Liu
- Beijing Frontier Research Center for Biological Structures, School of Life Sciences, Tsinghua University, Beijing, 100083, China
| | - Jinhui Wu
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School and School of Life Science, Nanjing University, Nanjing, 210093, China
| | - Zhimin Luo
- State Key Laboratory for Organic Electronics and Information Displays (SKLOEID), School of Chemistry and Life Sciences, Nanjing University of Posts and Telecommunications, Nanjing, 210023, China.
| | - Yiqiao Hu
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School and School of Life Science, Nanjing University, Nanjing, 210093, China.
| | - Ahu Yuan
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School and School of Life Science, Nanjing University, Nanjing, 210093, China.
| |
Collapse
|
18
|
Jia S, Liang R, Chen J, Liao S, Lin J, Li W. Emerging technology has a brilliant future: the CRISPR-Cas system for senescence, inflammation, and cartilage repair in osteoarthritis. Cell Mol Biol Lett 2024; 29:64. [PMID: 38698311 PMCID: PMC11067114 DOI: 10.1186/s11658-024-00581-x] [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: 12/29/2023] [Accepted: 04/19/2024] [Indexed: 05/05/2024] Open
Abstract
Osteoarthritis (OA), known as one of the most common types of aseptic inflammation of the musculoskeletal system, is characterized by chronic pain and whole-joint lesions. With cellular and molecular changes including senescence, inflammatory alterations, and subsequent cartilage defects, OA eventually leads to a series of adverse outcomes such as pain and disability. CRISPR-Cas-related technology has been proposed and explored as a gene therapy, offering potential gene-editing tools that are in the spotlight. Considering the genetic and multigene regulatory mechanisms of OA, we systematically review current studies on CRISPR-Cas technology for improving OA in terms of senescence, inflammation, and cartilage damage and summarize various strategies for delivering CRISPR products, hoping to provide a new perspective for the treatment of OA by taking advantage of CRISPR technology.
Collapse
Affiliation(s)
- Shicheng Jia
- Department of Sports Medicine and Rehabilitation, Peking University Shenzhen Hospital, Shenzhen, 518036, China
- Shantou University Medical College, Shantou, 515041, China
| | - Rongji Liang
- Shantou University Medical College, Shantou, 515041, China
| | - Jiayou Chen
- Department of Sports Medicine and Rehabilitation, Peking University Shenzhen Hospital, Shenzhen, 518036, China
- Shantou University Medical College, Shantou, 515041, China
| | - Shuai Liao
- Department of Bone and Joint, Peking University Shenzhen Hospital, Shenzhen, 518036, China
- Shenzhen University School of Medicine, Shenzhen, 518060, China
| | - Jianjing Lin
- Department of Sports Medicine and Rehabilitation, Peking University Shenzhen Hospital, Shenzhen, 518036, China.
| | - Wei Li
- Department of Sports Medicine and Rehabilitation, Peking University Shenzhen Hospital, Shenzhen, 518036, China.
| |
Collapse
|
19
|
Zhang ML, Li HB, Jin Y. Application and perspective of CRISPR/Cas9 genome editing technology in human diseases modeling and gene therapy. Front Genet 2024; 15:1364742. [PMID: 38666293 PMCID: PMC11043577 DOI: 10.3389/fgene.2024.1364742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 03/11/2024] [Indexed: 04/28/2024] Open
Abstract
The Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) mediated Cas9 nuclease system has been extensively used for genome editing and gene modification in eukaryotic cells. CRISPR/Cas9 technology holds great potential for various applications, including the correction of genetic defects or mutations within the human genome. The application of CRISPR/Cas9 genome editing system in human disease research is anticipated to solve a multitude of intricate molecular biology challenges encountered in life science research. Here, we review the fundamental principles underlying CRISPR/Cas9 technology and its recent application in neurodegenerative diseases, cardiovascular diseases, autoimmune related diseases, and cancer, focusing on the disease modeling and gene therapy potential of CRISPR/Cas9 in these diseases. Finally, we provide an overview of the limitations and future prospects associated with employing CRISPR/Cas9 technology for diseases study and treatment.
Collapse
Affiliation(s)
- Man-Ling Zhang
- Department of Rheumatology and Immunology, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
- Inner Mongolia Key Laboratory for Pathogenesis and Diagnosis of Rheumatic and Autoimmune Diseases, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Hong-Bin Li
- Department of Rheumatology and Immunology, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
- Inner Mongolia Key Laboratory for Pathogenesis and Diagnosis of Rheumatic and Autoimmune Diseases, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Yong Jin
- Department of Rheumatology and Immunology, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
- Inner Mongolia Key Laboratory for Pathogenesis and Diagnosis of Rheumatic and Autoimmune Diseases, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| |
Collapse
|
20
|
Galanti L, Peritore M, Gnügge R, Cannavo E, Heipke J, Palumbieri MD, Steigenberger B, Symington LS, Cejka P, Pfander B. Dbf4-dependent kinase promotes cell cycle controlled resection of DNA double-strand breaks and repair by homologous recombination. Nat Commun 2024; 15:2890. [PMID: 38570537 PMCID: PMC10991553 DOI: 10.1038/s41467-024-46951-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 03/13/2024] [Indexed: 04/05/2024] Open
Abstract
DNA double-strand breaks (DSBs) can be repaired by several pathways. In eukaryotes, DSB repair pathway choice occurs at the level of DNA end resection and is controlled by the cell cycle. Upon cell cycle-dependent activation, cyclin-dependent kinases (CDKs) phosphorylate resection proteins and thereby stimulate end resection and repair by homologous recombination (HR). However, inability of CDK phospho-mimetic mutants to bypass this cell cycle regulation, suggests that additional cell cycle regulators may be important. Here, we identify Dbf4-dependent kinase (DDK) as a second major cell cycle regulator of DNA end resection. Using inducible genetic and chemical inhibition of DDK in budding yeast and human cells, we show that end resection and HR require activation by DDK. Mechanistically, DDK phosphorylates at least two resection nucleases in budding yeast: the Mre11 activator Sae2, which promotes resection initiation, as well as the Dna2 nuclease, which promotes resection elongation. Notably, synthetic activation of DDK allows limited resection and HR in G1 cells, suggesting that DDK is a key component of DSB repair pathway selection.
Collapse
Affiliation(s)
- Lorenzo Galanti
- Cell Biology, Dortmund Life Science Center (DOLCE), TU Dortmund University, Faculty of Chemistry and Chemical Biology, Dortmund, Germany
- Research Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
- Genome Maintenance Mechanisms in Health and Disease, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
- Institute for Genome Stability in Aging and Disease, University of Cologne, Medical Faculty, CECAD Research Center, Cologne, Germany
| | - Martina Peritore
- Research Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
- Genome Maintenance Mechanisms in Health and Disease, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
- Institute for Genome Stability in Aging and Disease, University of Cologne, Medical Faculty, CECAD Research Center, Cologne, Germany
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Robert Gnügge
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Elda Cannavo
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera Italiana (USI), Bellinzona, Switzerland
| | - Johannes Heipke
- Cell Biology, Dortmund Life Science Center (DOLCE), TU Dortmund University, Faculty of Chemistry and Chemical Biology, Dortmund, Germany
- Research Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
- Institute for Genome Stability in Aging and Disease, University of Cologne, Medical Faculty, CECAD Research Center, Cologne, Germany
| | - Maria Dilia Palumbieri
- Genome Maintenance Mechanisms in Health and Disease, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
- Institute for Genome Stability in Aging and Disease, University of Cologne, Medical Faculty, CECAD Research Center, Cologne, Germany
- Research Group of Proteomics and ADP-Ribosylation Signaling, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Barbara Steigenberger
- Mass Spectrometry Core Facility, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Lorraine S Symington
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Petr Cejka
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera Italiana (USI), Bellinzona, Switzerland
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), Zürich, Switzerland
| | - Boris Pfander
- Cell Biology, Dortmund Life Science Center (DOLCE), TU Dortmund University, Faculty of Chemistry and Chemical Biology, Dortmund, Germany.
- Research Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany.
- Genome Maintenance Mechanisms in Health and Disease, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany.
- Institute for Genome Stability in Aging and Disease, University of Cologne, Medical Faculty, CECAD Research Center, Cologne, Germany.
| |
Collapse
|
21
|
Kim HS, Kweon J, Kim Y. Recent advances in CRISPR-based functional genomics for the study of disease-associated genetic variants. Exp Mol Med 2024; 56:861-869. [PMID: 38556550 PMCID: PMC11058232 DOI: 10.1038/s12276-024-01212-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 01/15/2024] [Accepted: 01/30/2024] [Indexed: 04/02/2024] Open
Abstract
Advances in sequencing technology have greatly increased our ability to gather genomic data, yet understanding the impact of genetic mutations, particularly variants of uncertain significance (VUSs), remains a challenge in precision medicine. The CRISPR‒Cas system has emerged as a pivotal tool for genome engineering, enabling the precise incorporation of specific genetic variations, including VUSs, into DNA to facilitate their functional characterization. Additionally, the integration of CRISPR‒Cas technology with sequencing tools allows the high-throughput evaluation of mutations, transforming uncertain genetic data into actionable insights. This allows researchers to comprehensively study the functional consequences of point mutations, paving the way for enhanced understanding and increasing application to precision medicine. This review summarizes the current genome editing tools utilizing CRISPR‒Cas systems and their combination with sequencing tools for functional genomics, with a focus on point mutations.
Collapse
Affiliation(s)
- Heon Seok Kim
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul, Republic of Korea
- Hanyang Institute of Bioscience and Biotechnology, Hanyang University, Seoul, Republic of Korea
- Hanyang Institute of Advanced BioConvergence, Hanyang University, Seongdong-gu, Seoul, Republic of Korea
| | - Jiyeon Kweon
- Department of Cell and Genetic Engineering, Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Yongsub Kim
- Department of Cell and Genetic Engineering, Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea.
- Stem Cell Immunomodulation Research Center, University of Ulsan College of Medicine, Seoul, Republic of Korea.
| |
Collapse
|
22
|
Haber Z, Sharma D, Selvaraj KSV, Sade N. Is CRISPR/Cas9-based multi-trait enhancement of wheat forthcoming? PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 341:112021. [PMID: 38311249 DOI: 10.1016/j.plantsci.2024.112021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/25/2024] [Accepted: 01/31/2024] [Indexed: 02/09/2024]
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) technologies have been implemented in recent years in the genome editing of eukaryotes, including plants. The original system of knocking out a single gene by causing a double-strand break (DSB), followed by non-homologous end joining (NHEJ) or Homology-directed repair (HDR) has undergone many adaptations. These adaptations include employing CRISPR/Cas9 to upregulate gene expression or to cause specific small changes to the DNA sequence of the gene-of-interest. In plants, multiplexing, i.e., inducing multiple changes by CRISPR/Cas9, is extremely relevant due to the redundancy of many plant genes, and the time- and labor-consuming generation of stable transgenic plant lines via crossing. Here we discuss relevant examples of various traits, such as yield, biofortification, gluten content, abiotic stress tolerance, and biotic stress resistance, which have been successfully manipulated using CRISPR/Cas9 in plants. While existing studies have primarily focused on proving the impact of CRISPR/Cas9 on a single trait, there is a growing interest among researchers in creating a multi-stress tolerant wheat cultivar 'super wheat', to commercially and sustainably enhance wheat yields under climate change. Due to the complexity of the technical difficulties in generating multi-target CRISPR/Cas9 lines and of the interactions between stress responses, we propose enhancing already commercial local landraces with higher yield traits along with stress tolerances specific to the respective localities, instead of generating a general 'super wheat'. We hope this will serve as the sustainable solution to commercially enhancing crop yields under both stable and challenging environmental conditions.
Collapse
Affiliation(s)
- Zechariah Haber
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 69978, Israel
| | - Davinder Sharma
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 69978, Israel
| | - K S Vijai Selvaraj
- Vegetable Research Station, Tamil Nadu Agricultural University, Palur 607102, Tamil Nadu, India
| | - Nir Sade
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 69978, Israel.
| |
Collapse
|
23
|
Hermantara R, Richmond L, Taqi AF, Chilaka S, Jeantet V, Guerrini I, West K, West A. Improving CRISPR-Cas9 directed faithful transgene integration outcomes by reducing unwanted random DNA integration. J Biomed Sci 2024; 31:32. [PMID: 38532479 DOI: 10.1186/s12929-024-01020-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 03/09/2024] [Indexed: 03/28/2024] Open
Abstract
BACKGROUND The field of genome editing has been revolutionized by the development of an easily programmable editing tool, the CRISPR-Cas9. Despite its promise, off-target activity of Cas9 posed a great disadvantage for genome editing purposes by causing DNA double strand breaks at off-target locations and causing unwanted editing outcomes. Furthermore, for gene integration applications, which introduce transgene sequences, integration of transgenes to off-target sites could be harmful, hard to detect, and reduce faithful genome editing efficiency. METHOD Here we report the development of a multicolour fluorescence assay for studying CRISPR-Cas9-directed gene integration at an endogenous locus in human cell lines. We examine genetic integration of reporter genes in transiently transfected cells as well as puromycin-selected stable cell lines to determine the fidelity of multiple CRISPR-Cas9 strategies. RESULT We found that there is a high occurrence of unwanted DNA integration which tarnished faithful knock-in efficiency. Integration outcomes are influenced by the type of DNA DSBs, donor design, the use of enhanced specificity Cas9 variants, with S-phase regulated Cas9 activity. Moreover, restricting Cas9 expression with a self-cleaving system greatly improves knock-in outcomes by substantially reducing the percentage of cells with unwanted DNA integration. CONCLUSION Our results highlight the need for a more stringent assessment of CRISPR-Cas9-mediated knock-in outcomes, and the importance of careful strategy design to maximise efficient and faithful transgene integration.
Collapse
Affiliation(s)
- Rio Hermantara
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.
- Department of Biomedicine, School of Life Sciences, Indonesia International Institute for Life Sciences, Jakarta, Indonesia.
| | - Laura Richmond
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Aqeel Faisal Taqi
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Sabari Chilaka
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Valentine Jeantet
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Ileana Guerrini
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Katherine West
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Adam West
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| |
Collapse
|
24
|
Perez-Bermejo JA, Efagene O, Matern WM, Holden JK, Kabir S, Chew GM, Andreoletti G, Catton E, Ennis CL, Garcia A, Gerstenberg TL, Hill KA, Jain A, Krassovsky K, Lalisan CD, Lord D, Quejarro BJ, Sales-Lee J, Shah M, Silva BJ, Skowronski J, Strukov YG, Thomas J, Veraz M, Vijay T, Wallace KA, Yuan Y, Grogan JL, Wienert B, Lahiri P, Treusch S, Dever DP, Soros VB, Partridge JR, Seim KL. Functional screening in human HSPCs identifies optimized protein-based enhancers of Homology Directed Repair. Nat Commun 2024; 15:2625. [PMID: 38521763 PMCID: PMC10960832 DOI: 10.1038/s41467-024-46816-5] [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: 08/07/2023] [Accepted: 03/06/2024] [Indexed: 03/25/2024] Open
Abstract
Homology Directed Repair (HDR) enables precise genome editing, but the implementation of HDR-based therapies is hindered by limited efficiency in comparison to methods that exploit alternative DNA repair routes, such as Non-Homologous End Joining (NHEJ). In this study, we develop a functional, pooled screening platform to identify protein-based reagents that improve HDR in human hematopoietic stem and progenitor cells (HSPCs). We leverage this screening platform to explore sequence diversity at the binding interface of the NHEJ inhibitor i53 and its target, 53BP1, identifying optimized variants that enable new intermolecular bonds and robustly increase HDR. We show that these variants specifically reduce insertion-deletion outcomes without increasing off-target editing, synergize with a DNAPK inhibitor molecule, and can be applied at manufacturing scale to increase the fraction of cells bearing repaired alleles. This screening platform can enable the discovery of future gene editing reagents that improve HDR outcomes.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Meet Shah
- Graphite Bio, South San Francisco, CA, USA
| | | | | | | | | | | | | | | | - Yue Yuan
- Graphite Bio, South San Francisco, CA, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Jiang H, Tang M, Xu Z, Wang Y, Li M, Zheng S, Zhu J, Lin Z, Zhang M. CRISPR/Cas9 system and its applications in nervous system diseases. Genes Dis 2024; 11:675-686. [PMID: 37692518 PMCID: PMC10491921 DOI: 10.1016/j.gendis.2023.03.017] [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: 11/28/2022] [Accepted: 03/05/2023] [Indexed: 09/12/2023] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system is an acquired immune system of many bacteria and archaea, comprising CRISPR loci, Cas genes, and its associated proteins. This system can recognize exogenous DNA and utilize the Cas9 protein's nuclease activity to break DNA double-strand and to achieve base insertion or deletion by subsequent DNA repair. In recent years, multiple laboratory and clinical studies have revealed the therapeutic role of the CRISPR/Cas9 system in neurological diseases. This article reviews the CRISPR/Cas9-mediated gene editing technology and its potential for clinical application against neurological diseases.
Collapse
Affiliation(s)
- Haibin Jiang
- The Second School of Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Mengyan Tang
- The First School of Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Zidi Xu
- The Second School of Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Yanan Wang
- The Second School of Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Mopu Li
- The Second School of Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Shuyin Zheng
- The Second School of Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Jianghu Zhu
- Department of Pediatrics, The Second School of Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
- Key Laboratory of Perinatal Medicine of Wenzhou, Wenzhou, Zhejiang 325027, China
- Key Laboratory of Structural Malformations in Children of Zhejiang Province, Wenzhou, Zhejiang 325000, China
- Zhejiang Provincial Clinical Research Center for Pediatric Disease, Wenzhou, Zhejiang 325027, China
| | - Zhenlang Lin
- Department of Pediatrics, The Second School of Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
- Key Laboratory of Perinatal Medicine of Wenzhou, Wenzhou, Zhejiang 325027, China
- Key Laboratory of Structural Malformations in Children of Zhejiang Province, Wenzhou, Zhejiang 325000, China
- Zhejiang Provincial Clinical Research Center for Pediatric Disease, Wenzhou, Zhejiang 325027, China
| | - Min Zhang
- Department of Pediatrics, The Second School of Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
- Key Laboratory of Perinatal Medicine of Wenzhou, Wenzhou, Zhejiang 325027, China
- Key Laboratory of Structural Malformations in Children of Zhejiang Province, Wenzhou, Zhejiang 325000, China
- Zhejiang Provincial Clinical Research Center for Pediatric Disease, Wenzhou, Zhejiang 325027, China
| |
Collapse
|
26
|
Salomonsson SE, Clelland CD. Building CRISPR Gene Therapies for the Central Nervous System: A Review. JAMA Neurol 2024; 81:283-290. [PMID: 38285472 PMCID: PMC11164426 DOI: 10.1001/jamaneurol.2023.4983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
Importance Gene editing using clustered regularly interspaced short palindromic repeats (CRISPR) holds the promise to arrest or cure monogenic disease if it can be determined which genetic change to create without inducing unintended cellular dysfunction and how to deliver this technology to the target organ reliably and safely. Clinical trials for blood and liver disorders, for which delivery of CRISPR is not limiting, show promise, yet no trials have begun for central nervous system (CNS) indications. Observations The CNS is arguably the most challenging target given its innate exclusion of large molecules and its defenses against bacterial invasion (from which CRISPR originates). Herein, the types of CRISPR editing (DNA cutting, base editing, and templated repair) and how these are applied to different genetic variants are summarized. The challenges of delivering genome editors to the CNS, including the viral and nonviral delivery vehicles that may ultimately circumvent these challenges, are discussed. Also, ways to minimize the potential in vivo genotoxic effects of genome editors through delivery vehicle design and preclinical off-target testing are considered. The ethical considerations of germline editing, a potential off-target outcome of any gene editing therapy, are explored. The unique regulatory challenges of a human-specific therapy that cannot be derisked solely in animal models are also discussed. Conclusions and Relevance An understanding of both the potential benefits and challenges of CRISPR gene therapy better informs the scientific, clinical, regulatory, and timeline considerations of developing CRISPR gene therapy for neurologic diseases.
Collapse
Affiliation(s)
- Sally E Salomonsson
- Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco
- Department of Neurology, Memory and Aging Center, University of California, San Francisco
| | - Claire D Clelland
- Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco
- Department of Neurology, Memory and Aging Center, University of California, San Francisco
| |
Collapse
|
27
|
Pacesa M, Pelea O, Jinek M. Past, present, and future of CRISPR genome editing technologies. Cell 2024; 187:1076-1100. [PMID: 38428389 DOI: 10.1016/j.cell.2024.01.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/23/2024] [Accepted: 01/26/2024] [Indexed: 03/03/2024]
Abstract
Genome editing has been a transformative force in the life sciences and human medicine, offering unprecedented opportunities to dissect complex biological processes and treat the underlying causes of many genetic diseases. CRISPR-based technologies, with their remarkable efficiency and easy programmability, stand at the forefront of this revolution. In this Review, we discuss the current state of CRISPR gene editing technologies in both research and therapy, highlighting limitations that constrain them and the technological innovations that have been developed in recent years to address them. Additionally, we examine and summarize the current landscape of gene editing applications in the context of human health and therapeutics. Finally, we outline potential future developments that could shape gene editing technologies and their applications in the coming years.
Collapse
Affiliation(s)
- Martin Pacesa
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Station 19, CH-1015 Lausanne, Switzerland
| | - Oana Pelea
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
| |
Collapse
|
28
|
Zheng Y, Li Y, Zhou K, Li T, VanDusen NJ, Hua Y. Precise genome-editing in human diseases: mechanisms, strategies and applications. Signal Transduct Target Ther 2024; 9:47. [PMID: 38409199 PMCID: PMC10897424 DOI: 10.1038/s41392-024-01750-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 02/28/2024] Open
Abstract
Precise genome-editing platforms are versatile tools for generating specific, site-directed DNA insertions, deletions, and substitutions. The continuous enhancement of these tools has led to a revolution in the life sciences, which promises to deliver novel therapies for genetic disease. Precise genome-editing can be traced back to the 1950s with the discovery of DNA's double-helix and, after 70 years of development, has evolved from crude in vitro applications to a wide range of sophisticated capabilities, including in vivo applications. Nonetheless, precise genome-editing faces constraints such as modest efficiency, delivery challenges, and off-target effects. In this review, we explore precise genome-editing, with a focus on introduction of the landmark events in its history, various platforms, delivery systems, and applications. First, we discuss the landmark events in the history of precise genome-editing. Second, we describe the current state of precise genome-editing strategies and explain how these techniques offer unprecedented precision and versatility for modifying the human genome. Third, we introduce the current delivery systems used to deploy precise genome-editing components through DNA, RNA, and RNPs. Finally, we summarize the current applications of precise genome-editing in labeling endogenous genes, screening genetic variants, molecular recording, generating disease models, and gene therapy, including ex vivo therapy and in vivo therapy, and discuss potential future advances.
Collapse
Affiliation(s)
- Yanjiang Zheng
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yifei Li
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Kaiyu Zhou
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Tiange Li
- Department of Cardiovascular Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Nathan J VanDusen
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
| | - Yimin Hua
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
| |
Collapse
|
29
|
Li S, Wang Y, van der Stoel M, Zhou X, Madhusudan S, Kanerva K, Nguyen VD, Eskici N, Olkkonen VM, Zhou Y, Raivio T, Ikonen E. HiHo-AID2: boosting homozygous knock-in efficiency enables robust generation of human auxin-inducible degron cells. Genome Biol 2024; 25:58. [PMID: 38409044 PMCID: PMC10895734 DOI: 10.1186/s13059-024-03187-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 02/14/2024] [Indexed: 02/28/2024] Open
Abstract
Recent developments in auxin-inducible degron (AID) technology have increased its popularity for chemogenetic control of proteolysis. However, generation of human AID cell lines is challenging, especially in human embryonic stem cells (hESCs). Here, we develop HiHo-AID2, a streamlined procedure for rapid, one-step generation of human cancer and hESC lines with high homozygous degron-tagging efficiency based on an optimized AID2 system and homology-directed repair enhancers. We demonstrate its application for rapid and inducible functional inactivation of twelve endogenous target proteins in five cell lines, including targets with diverse expression levels and functions in hESCs and cells differentiated from hESCs.
Collapse
Affiliation(s)
- Shiqian Li
- Department of Anatomy and Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland.
- Minerva Foundation Institute for Medical Research, 00290, Helsinki, Finland.
| | - Yafei Wang
- Stem Cells and Metabolism Research Program, Research Programs Unit, and Department of Physiology, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
| | - Miesje van der Stoel
- Department of Anatomy and Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, 00290, Helsinki, Finland
| | - Xin Zhou
- Department of Anatomy and Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, 00290, Helsinki, Finland
| | - Shrinidhi Madhusudan
- Stem Cells and Metabolism Research Program, Research Programs Unit, and Department of Physiology, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
| | - Kristiina Kanerva
- Department of Anatomy and Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, 00290, Helsinki, Finland
| | - Van Dien Nguyen
- Systems Immunity Research Institute, Cardiff University, Cardiff, CF14 4XN, UK
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Nazli Eskici
- Stem Cells and Metabolism Research Program, Research Programs Unit, and Department of Physiology, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
| | - Vesa M Olkkonen
- Department of Anatomy and Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, 00290, Helsinki, Finland
| | - You Zhou
- Systems Immunity Research Institute, Cardiff University, Cardiff, CF14 4XN, UK
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Taneli Raivio
- Stem Cells and Metabolism Research Program, Research Programs Unit, and Department of Physiology, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
- New Children's Hospital, Pediatric Research Center, Helsinki University Hospital, 00290, Helsinki, Finland
| | - Elina Ikonen
- Department of Anatomy and Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland.
- Minerva Foundation Institute for Medical Research, 00290, Helsinki, Finland.
| |
Collapse
|
30
|
Shalwitz R, Day T, Ruehlmann AK, Julio L, Gordon S, Vandeuren A, Nelson M, Lyman M, Kelly K, Altvater A, Ondeck C, O'Brien S, Hamilton T, Hanson RL, Wayman K, Miller A, Shalwitz I, Batchelor E, McNutt P. Treatment of Sulfur Mustard Corneal Injury by Augmenting the DNA Damage Response (DDR): A Novel Approach. J Pharmacol Exp Ther 2024; 388:526-535. [PMID: 37977813 PMCID: PMC10801765 DOI: 10.1124/jpet.123.001686] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 11/19/2023] Open
Abstract
Sulfur mustard (SM) is a highly reactive organic chemical has been used as a chemical warfare agent and terrorist threat since World War I. The cornea is highly sensitive to SM toxicity and exposure to low vapor doses can cause incapacitating acute injuries. Exposure to higher doses can elicit persistent secondary keratopathies that cause reduced quality of life and impaired or lost vision. Despite a century of research, there are no specific treatments for acute or persistent ocular SM injuries. SM cytotoxicity emerges, in part, through DNA alkylation and double-strand breaks (DSBs). Because DSBs can naturally be repaired by DNA damage response pathways with low efficiency, we hypothesized that enhancing the homologous recombination pathway could pose a novel approach to mitigate SM injury. Here, we demonstrate that a dilithium salt of adenosine diphosphoribose (INV-102) increases protein levels of p53 and Sirtuin 6, upregulates transcription of BRCA1/2, enhances γH2AX focus formation, and promotes assembly of repair complexes at DSBs. Based on in vitro evidence showing INV-102 enhancement of DNA damage response through both p53-dependent and p53-independent pathways, we next tested INV-102 in a rabbit preclinical model of corneal injury. In vivo studies demonstrate a marked reduction in the incidence and severity of secondary keratopathies in INV-102-treated eyes compared with vehicle-treated eyes when treatment was started 24 hours after SM vapor exposure. These results suggest DNA repair mechanisms are a viable therapeutic target for SM injury and suggest topical treatment with INV-102 is a promising approach for SM as well as other conditions associated with DSBs. SIGNIFICANCE STATEMENT: Sulfur mustard gas corneal injury currently has no therapeutic treatment. This study aims to show the therapeutic potential of activating the body's natural DNA damage response to activate tissue repair.
Collapse
Affiliation(s)
- Robert Shalwitz
- Invirsa, Inc., Columbus, Ohio (R.S., A.K.R., A.M., I.S.); Department of Biology, Northeastern University, Boston, Massachusetts (T.D., L.J., S.G., A.V.); Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, Minnesota (R.L.H., K.W., E.B.); United States Army Medical Research Institute for Chemical Defense, Gunpowder, Maryland (M.N., M.L., K.K., A.A., C.O., S.O., T.H., P.M.); and Wake Forest Institute for Regenerative Medicine, School of Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina (S.O., C.O., P.M.)
| | - Tovah Day
- Invirsa, Inc., Columbus, Ohio (R.S., A.K.R., A.M., I.S.); Department of Biology, Northeastern University, Boston, Massachusetts (T.D., L.J., S.G., A.V.); Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, Minnesota (R.L.H., K.W., E.B.); United States Army Medical Research Institute for Chemical Defense, Gunpowder, Maryland (M.N., M.L., K.K., A.A., C.O., S.O., T.H., P.M.); and Wake Forest Institute for Regenerative Medicine, School of Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina (S.O., C.O., P.M.)
| | - Anna Kotsakis Ruehlmann
- Invirsa, Inc., Columbus, Ohio (R.S., A.K.R., A.M., I.S.); Department of Biology, Northeastern University, Boston, Massachusetts (T.D., L.J., S.G., A.V.); Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, Minnesota (R.L.H., K.W., E.B.); United States Army Medical Research Institute for Chemical Defense, Gunpowder, Maryland (M.N., M.L., K.K., A.A., C.O., S.O., T.H., P.M.); and Wake Forest Institute for Regenerative Medicine, School of Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina (S.O., C.O., P.M.)
| | - Lindsay Julio
- Invirsa, Inc., Columbus, Ohio (R.S., A.K.R., A.M., I.S.); Department of Biology, Northeastern University, Boston, Massachusetts (T.D., L.J., S.G., A.V.); Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, Minnesota (R.L.H., K.W., E.B.); United States Army Medical Research Institute for Chemical Defense, Gunpowder, Maryland (M.N., M.L., K.K., A.A., C.O., S.O., T.H., P.M.); and Wake Forest Institute for Regenerative Medicine, School of Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina (S.O., C.O., P.M.)
| | - Shellaina Gordon
- Invirsa, Inc., Columbus, Ohio (R.S., A.K.R., A.M., I.S.); Department of Biology, Northeastern University, Boston, Massachusetts (T.D., L.J., S.G., A.V.); Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, Minnesota (R.L.H., K.W., E.B.); United States Army Medical Research Institute for Chemical Defense, Gunpowder, Maryland (M.N., M.L., K.K., A.A., C.O., S.O., T.H., P.M.); and Wake Forest Institute for Regenerative Medicine, School of Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina (S.O., C.O., P.M.)
| | - Adrianna Vandeuren
- Invirsa, Inc., Columbus, Ohio (R.S., A.K.R., A.M., I.S.); Department of Biology, Northeastern University, Boston, Massachusetts (T.D., L.J., S.G., A.V.); Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, Minnesota (R.L.H., K.W., E.B.); United States Army Medical Research Institute for Chemical Defense, Gunpowder, Maryland (M.N., M.L., K.K., A.A., C.O., S.O., T.H., P.M.); and Wake Forest Institute for Regenerative Medicine, School of Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina (S.O., C.O., P.M.)
| | - Marian Nelson
- Invirsa, Inc., Columbus, Ohio (R.S., A.K.R., A.M., I.S.); Department of Biology, Northeastern University, Boston, Massachusetts (T.D., L.J., S.G., A.V.); Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, Minnesota (R.L.H., K.W., E.B.); United States Army Medical Research Institute for Chemical Defense, Gunpowder, Maryland (M.N., M.L., K.K., A.A., C.O., S.O., T.H., P.M.); and Wake Forest Institute for Regenerative Medicine, School of Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina (S.O., C.O., P.M.)
| | - Megan Lyman
- Invirsa, Inc., Columbus, Ohio (R.S., A.K.R., A.M., I.S.); Department of Biology, Northeastern University, Boston, Massachusetts (T.D., L.J., S.G., A.V.); Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, Minnesota (R.L.H., K.W., E.B.); United States Army Medical Research Institute for Chemical Defense, Gunpowder, Maryland (M.N., M.L., K.K., A.A., C.O., S.O., T.H., P.M.); and Wake Forest Institute for Regenerative Medicine, School of Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina (S.O., C.O., P.M.)
| | - Kyle Kelly
- Invirsa, Inc., Columbus, Ohio (R.S., A.K.R., A.M., I.S.); Department of Biology, Northeastern University, Boston, Massachusetts (T.D., L.J., S.G., A.V.); Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, Minnesota (R.L.H., K.W., E.B.); United States Army Medical Research Institute for Chemical Defense, Gunpowder, Maryland (M.N., M.L., K.K., A.A., C.O., S.O., T.H., P.M.); and Wake Forest Institute for Regenerative Medicine, School of Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina (S.O., C.O., P.M.)
| | - Amber Altvater
- Invirsa, Inc., Columbus, Ohio (R.S., A.K.R., A.M., I.S.); Department of Biology, Northeastern University, Boston, Massachusetts (T.D., L.J., S.G., A.V.); Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, Minnesota (R.L.H., K.W., E.B.); United States Army Medical Research Institute for Chemical Defense, Gunpowder, Maryland (M.N., M.L., K.K., A.A., C.O., S.O., T.H., P.M.); and Wake Forest Institute for Regenerative Medicine, School of Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina (S.O., C.O., P.M.)
| | - Celinia Ondeck
- Invirsa, Inc., Columbus, Ohio (R.S., A.K.R., A.M., I.S.); Department of Biology, Northeastern University, Boston, Massachusetts (T.D., L.J., S.G., A.V.); Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, Minnesota (R.L.H., K.W., E.B.); United States Army Medical Research Institute for Chemical Defense, Gunpowder, Maryland (M.N., M.L., K.K., A.A., C.O., S.O., T.H., P.M.); and Wake Forest Institute for Regenerative Medicine, School of Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina (S.O., C.O., P.M.)
| | - Sean O'Brien
- Invirsa, Inc., Columbus, Ohio (R.S., A.K.R., A.M., I.S.); Department of Biology, Northeastern University, Boston, Massachusetts (T.D., L.J., S.G., A.V.); Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, Minnesota (R.L.H., K.W., E.B.); United States Army Medical Research Institute for Chemical Defense, Gunpowder, Maryland (M.N., M.L., K.K., A.A., C.O., S.O., T.H., P.M.); and Wake Forest Institute for Regenerative Medicine, School of Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina (S.O., C.O., P.M.)
| | - Tracey Hamilton
- Invirsa, Inc., Columbus, Ohio (R.S., A.K.R., A.M., I.S.); Department of Biology, Northeastern University, Boston, Massachusetts (T.D., L.J., S.G., A.V.); Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, Minnesota (R.L.H., K.W., E.B.); United States Army Medical Research Institute for Chemical Defense, Gunpowder, Maryland (M.N., M.L., K.K., A.A., C.O., S.O., T.H., P.M.); and Wake Forest Institute for Regenerative Medicine, School of Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina (S.O., C.O., P.M.)
| | - Ryan L Hanson
- Invirsa, Inc., Columbus, Ohio (R.S., A.K.R., A.M., I.S.); Department of Biology, Northeastern University, Boston, Massachusetts (T.D., L.J., S.G., A.V.); Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, Minnesota (R.L.H., K.W., E.B.); United States Army Medical Research Institute for Chemical Defense, Gunpowder, Maryland (M.N., M.L., K.K., A.A., C.O., S.O., T.H., P.M.); and Wake Forest Institute for Regenerative Medicine, School of Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina (S.O., C.O., P.M.)
| | - Kayla Wayman
- Invirsa, Inc., Columbus, Ohio (R.S., A.K.R., A.M., I.S.); Department of Biology, Northeastern University, Boston, Massachusetts (T.D., L.J., S.G., A.V.); Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, Minnesota (R.L.H., K.W., E.B.); United States Army Medical Research Institute for Chemical Defense, Gunpowder, Maryland (M.N., M.L., K.K., A.A., C.O., S.O., T.H., P.M.); and Wake Forest Institute for Regenerative Medicine, School of Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina (S.O., C.O., P.M.)
| | - Alexandrea Miller
- Invirsa, Inc., Columbus, Ohio (R.S., A.K.R., A.M., I.S.); Department of Biology, Northeastern University, Boston, Massachusetts (T.D., L.J., S.G., A.V.); Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, Minnesota (R.L.H., K.W., E.B.); United States Army Medical Research Institute for Chemical Defense, Gunpowder, Maryland (M.N., M.L., K.K., A.A., C.O., S.O., T.H., P.M.); and Wake Forest Institute for Regenerative Medicine, School of Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina (S.O., C.O., P.M.)
| | - Isaiah Shalwitz
- Invirsa, Inc., Columbus, Ohio (R.S., A.K.R., A.M., I.S.); Department of Biology, Northeastern University, Boston, Massachusetts (T.D., L.J., S.G., A.V.); Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, Minnesota (R.L.H., K.W., E.B.); United States Army Medical Research Institute for Chemical Defense, Gunpowder, Maryland (M.N., M.L., K.K., A.A., C.O., S.O., T.H., P.M.); and Wake Forest Institute for Regenerative Medicine, School of Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina (S.O., C.O., P.M.)
| | - Eric Batchelor
- Invirsa, Inc., Columbus, Ohio (R.S., A.K.R., A.M., I.S.); Department of Biology, Northeastern University, Boston, Massachusetts (T.D., L.J., S.G., A.V.); Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, Minnesota (R.L.H., K.W., E.B.); United States Army Medical Research Institute for Chemical Defense, Gunpowder, Maryland (M.N., M.L., K.K., A.A., C.O., S.O., T.H., P.M.); and Wake Forest Institute for Regenerative Medicine, School of Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina (S.O., C.O., P.M.)
| | - Patrick McNutt
- Invirsa, Inc., Columbus, Ohio (R.S., A.K.R., A.M., I.S.); Department of Biology, Northeastern University, Boston, Massachusetts (T.D., L.J., S.G., A.V.); Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, Minnesota (R.L.H., K.W., E.B.); United States Army Medical Research Institute for Chemical Defense, Gunpowder, Maryland (M.N., M.L., K.K., A.A., C.O., S.O., T.H., P.M.); and Wake Forest Institute for Regenerative Medicine, School of Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina (S.O., C.O., P.M.)
| |
Collapse
|
31
|
Baik R, Cromer MK, Glenn SE, Vakulskas CA, Chmielewski KO, Dudek AM, Feist WN, Klermund J, Shipp S, Cathomen T, Dever DP, Porteus MH. Transient inhibition of 53BP1 increases the frequency of targeted integration in human hematopoietic stem and progenitor cells. Nat Commun 2024; 15:111. [PMID: 38169468 PMCID: PMC10762240 DOI: 10.1038/s41467-023-43413-w] [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: 02/23/2023] [Accepted: 11/08/2023] [Indexed: 01/05/2024] Open
Abstract
Genome editing by homology directed repair (HDR) is leveraged to precisely modify the genome of therapeutically relevant hematopoietic stem and progenitor cells (HSPCs). Here, we present a new approach to increasing the frequency of HDR in human HSPCs by the delivery of an inhibitor of 53BP1 (named "i53") as a recombinant peptide. We show that the use of i53 peptide effectively increases the frequency of HDR-mediated genome editing at a variety of therapeutically relevant loci in HSPCs as well as other primary human cell types. We show that incorporating the use of i53 recombinant protein allows high frequencies of HDR while lowering the amounts of AAV6 needed by 8-fold. HDR edited HSPCs were capable of long-term and bi-lineage hematopoietic reconstitution in NSG mice, suggesting that i53 recombinant protein might be safely integrated into the standard CRISPR/AAV6-mediated genome editing protocol to gain greater numbers of edited cells for transplantation of clinically meaningful cell populations.
Collapse
Affiliation(s)
- Ron Baik
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - M Kyle Cromer
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Steve E Glenn
- Integrated DNA Technologies, Inc., Coralville, IA, USA
| | | | - Kay O Chmielewski
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, 79106, Freiburg, Germany
- Center for Chronic Immunodeficiency, University of Freiburg, 79106, Freiburg, Germany
- Ph.D. Program, Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
| | - Amanda M Dudek
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - William N Feist
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Julia Klermund
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, 79106, Freiburg, Germany
- Center for Chronic Immunodeficiency, University of Freiburg, 79106, Freiburg, Germany
| | - Suzette Shipp
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, 79106, Freiburg, Germany
- Center for Chronic Immunodeficiency, University of Freiburg, 79106, Freiburg, Germany
| | - Daniel P Dever
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Matthew H Porteus
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA.
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
| |
Collapse
|
32
|
Kuhns S, Juhl AD, Anvarian Z, Wüstner D, Pedersen LB, Andersen JS. Endogenous Tagging of Ciliary Genes in Human RPE1 Cells for Live-Cell Imaging. Methods Mol Biol 2024; 2725:147-166. [PMID: 37856023 DOI: 10.1007/978-1-0716-3507-0_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Abstract
CRISPR-mediated endogenous tagging of genes provides unique possibilities to explore the function and dynamic subcellular localization of proteins in living cells. Here, we describe experimental strategies for endogenous PCR-tagging of ciliary genes in human RPE1 cells and how image acquisition and analysis of the expressed fluorescently tagged proteins can be utilized to study the dynamic ciliary processes of intraflagellar transport and vesicular trafficking.
Collapse
Affiliation(s)
- Stefanie Kuhns
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Alice Dupont Juhl
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Zeinab Anvarian
- Department of Biology, University of Copenhagen, Copenhagen Ø, Denmark
| | - Daniel Wüstner
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Lotte B Pedersen
- Department of Biology, University of Copenhagen, Copenhagen Ø, Denmark
| | - Jens S Andersen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark.
| |
Collapse
|
33
|
Lampe GD, King RT, Halpin-Healy TS, Klompe SE, Hogan MI, Vo PLH, Tang S, Chavez A, Sternberg SH. Targeted DNA integration in human cells without double-strand breaks using CRISPR-associated transposases. Nat Biotechnol 2024; 42:87-98. [PMID: 36991112 PMCID: PMC10620015 DOI: 10.1038/s41587-023-01748-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 03/13/2023] [Indexed: 03/31/2023]
Abstract
Conventional genome engineering with CRISPR-Cas9 creates double-strand breaks (DSBs) that lead to undesirable byproducts and reduce product purity. Here we report an approach for programmable integration of large DNA sequences in human cells that avoids the generation of DSBs by using Type I-F CRISPR-associated transposases (CASTs). We optimized DNA targeting by the QCascade complex through protein design and developed potent transcriptional activators by exploiting the multi-valent recruitment of the AAA+ ATPase TnsC to genomic sites targeted by QCascade. After initial detection of plasmid-based integration, we screened 15 additional CAST systems from a wide range of bacterial hosts, identified a homolog from Pseudoalteromonas that exhibits improved activity and further increased integration efficiencies. Finally, we discovered that bacterial ClpX enhances genomic integration by multiple orders of magnitude, likely by promoting active disassembly of the post-integration CAST complex, akin to its known role in Mu transposition. Our work highlights the ability to reconstitute complex, multi-component machineries in human cells and establishes a strong foundation to exploit CRISPR-associated transposases for eukaryotic genome engineering.
Collapse
Affiliation(s)
- George D Lampe
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Rebeca T King
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Tyler S Halpin-Healy
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA
| | - Sanne E Klompe
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Department of Genomes and Genetics, Institut Pasteur, Paris, France
| | - Marcus I Hogan
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Phuc Leo H Vo
- Department of Molecular Pharmacology and Therapeutics, Columbia University, New York, NY, USA
- Vertex Pharmaceuticals, Inc., Boston, MA, USA
| | - Stephen Tang
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Alejandro Chavez
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Samuel H Sternberg
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
| |
Collapse
|
34
|
Park CS, Habib O, Lee Y, Hur JK. Applications of CRISPR technologies to the development of gene and cell therapy. BMB Rep 2024; 57:2-11. [PMID: 38178651 PMCID: PMC10828430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/14/2023] [Accepted: 12/26/2023] [Indexed: 01/06/2024] Open
Abstract
Advancements in gene and cell therapy have resulted in novel therapeutics for diseases previously considered incurable or challenging to treat. Among the various contributing technologies, genome editing stands out as one of the most crucial for the progress in gene and cell therapy. The discovery of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and the subsequent evolution of genetic engineering technology have markedly expanded the field of target-specific gene editing. Originally studied in the immune systems of bacteria and archaea, the CRISPR system has demonstrated wide applicability to effective genome editing of various biological systems including human cells. The development of CRISPR-based base editing has enabled directional cytosine-tothymine and adenine-to-guanine substitutions of select DNA bases at the target locus. Subsequent advances in prime editing further elevated the flexibility of the edit multiple consecutive bases to desired sequences. The recent CRISPR technologies also have been actively utilized for the development of in vivo and ex vivo gene and cell therapies. We anticipate that the medical applications of CRISPR will rapidly progress to provide unprecedented possibilities to develop novel therapeutics towards various diseases. [BMB Reports 2024; 57(1): 2-11].
Collapse
Affiliation(s)
- Chul-Sung Park
- Department of Biomedical Science, Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 04763, Korea
| | - Omer Habib
- Division of R&D, RedGene Inc., Seoul 08790, Korea
| | - Younsu Lee
- Division of R&D, RedGene Inc., Seoul 08790, Korea
| | - Junho K. Hur
- Department of Biomedical Science, Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 04763, Korea
- Department of Genetics, College of Medicine, Hanyang University, Seoul 04763, Korea
- Hanyang Institute of Bioscience and Biotechnology, Hanyang University, Seoul 04763, Korea
| |
Collapse
|
35
|
Tenjo-Castaño F, Montoya G, Carabias A. Transposons and CRISPR: Rewiring Gene Editing. Biochemistry 2023; 62:3521-3532. [PMID: 36130724 PMCID: PMC10734217 DOI: 10.1021/acs.biochem.2c00379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/11/2022] [Indexed: 11/30/2022]
Abstract
CRISPR-Cas is driving a gene editing revolution because of its simple reprogramming. However, off-target effects and dependence on the double-strand break repair pathways impose important limitations. Because homology-directed repair acts primarily in actively dividing cells, many of the current gene correction/replacement approaches are restricted to a minority of cell types. Furthermore, current approaches display low efficiency upon insertion of large DNA cargos (e.g., sequences containing multiple gene circuits with tunable functionalities). Recent research has revealed new links between CRISPR-Cas systems and transposons providing new scaffolds that might overcome some of these limitations. Here, we comment on two new transposon-associated RNA-guided mechanisms considering their potential as new gene editing solutions. Initially, we focus on a group of small RNA-guided endonucleases of the IS200/IS605 family of transposons, which likely evolved into class 2 CRISPR effector nucleases (Cas9s and Cas12s). We explore the diversity of these nucleases (named OMEGA, obligate mobile element-guided activity) and analyze their similarities with class 2 gene editors. OMEGA nucleases can perform gene editing in human cells and constitute promising candidates for the design of new compact RNA-guided platforms. Then, we address the co-option of the RNA-guided activity of different CRISPR effector nucleases by a specialized group of Tn7-like transposons to target transposon integration. We describe the various mechanisms used by these RNA-guided transposons for target site selection and integration. Finally, we assess the potential of these new systems to circumvent some of the current gene editing challenges.
Collapse
Affiliation(s)
- Francisco Tenjo-Castaño
- Structural Molecular Biology Group,
Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3-B, Copenhagen 2200, Denmark
| | - Guillermo Montoya
- Structural Molecular Biology Group,
Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3-B, Copenhagen 2200, Denmark
| | - Arturo Carabias
- Structural Molecular Biology Group,
Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3-B, Copenhagen 2200, Denmark
| |
Collapse
|
36
|
Tou CJ, Kleinstiver BP. Recent Advances in Double-Strand Break-Free Kilobase-Scale Genome Editing Technologies. Biochemistry 2023; 62:3493-3499. [PMID: 36049184 PMCID: PMC10239562 DOI: 10.1021/acs.biochem.2c00311] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Genome editing approaches have transformed the ability to make user-defined changes to genomes in both ex vivo and in vivo contexts. Despite the abundant development of technologies that permit the installation of nucleotide-level changes, until recently, larger-scale sequence edits via technologies independent of DNA double-strand breaks (DSBs) had remained less explored. Here, we review recent advances toward DSB-free technologies that enable kilobase-scale modifications including insertions, deletions, inversions, replacements, and others. These technologies provide new capabilities for users, while offering hope for the simplification of putative therapeutic strategies by moving away from small mutation-specific edits and toward more generalizable kilobase-scale approaches.
Collapse
Affiliation(s)
- Connor J. Tou
- Biological Engineering Program, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Benjamin P. Kleinstiver
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Pathology, Harvard Medical School, Boston, MA, 02115, USA
| |
Collapse
|
37
|
Mehryar MM, Shi X, Li J, Wu Q. DNA polymerases in precise and predictable CRISPR/Cas9-mediated chromosomal rearrangements. BMC Biol 2023; 21:288. [PMID: 38066536 PMCID: PMC10709867 DOI: 10.1186/s12915-023-01784-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Recent studies have shown that, owning to its cohesive cleavage, Cas9-mediated CRISPR gene editing outcomes at junctions of chromosomal rearrangements or DNA-fragment editing are precise and predictable; however, the underlying mechanisms are poorly understood due to lack of suitable assay system and analysis tool. RESULTS Here we developed a customized computer program to take account of staggered or cohesive Cas9 cleavage and to rapidly process large volumes of junctional sequencing reads from chromosomal rearrangements or DNA-fragment editing, including DNA-fragment inversions, duplications, and deletions. We also established a sensitive assay system using HPRT1 and DCK as reporters for cell growth during DNA-fragment editing by Cas9 with dual sgRNAs and found prominent large resections or long deletions at junctions of chromosomal rearrangements. In addition, we found that knockdown of PolQ (encoding Polθ polymerase), which has a prominent role in theta-mediated end joining (TMEJ) or microhomology-mediated end joining (MMEJ), results in increased large resections but decreased small deletions. We also found that the mechanisms for generating small deletions of 1bp and >1bp during DNA-fragment editing are different with regard to their opposite dependencies on Polθ and Polλ (encoded by the PolL gene). Specifically, Polθ suppresses 1bp deletions but promotes >1bp deletions, whereas Polλ promotes 1bp deletions but suppresses >1bp deletions. Finally, we found that Polλ is the main DNA polymerase responsible for fill-in of the 5' overhangs of staggered Cas9 cleavage ends. CONCLUSIONS These findings contribute to our understanding of the molecular mechanisms of CRISPR/Cas9-mediated DNA-fragment editing and have important implications for controllable, precise, and predictable gene editing.
Collapse
Affiliation(s)
- Mohammadreza M Mehryar
- Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Systems Medicine for Cancer, School of Life Sciences and Biotechnology, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
- WLA Laboratories, Shanghai, 201203, China
| | - Xin Shi
- Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Systems Medicine for Cancer, School of Life Sciences and Biotechnology, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
- WLA Laboratories, Shanghai, 201203, China
| | - Jingwei Li
- Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Systems Medicine for Cancer, School of Life Sciences and Biotechnology, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
- WLA Laboratories, Shanghai, 201203, China
| | - Qiang Wu
- Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Systems Medicine for Cancer, School of Life Sciences and Biotechnology, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China.
- WLA Laboratories, Shanghai, 201203, China.
| |
Collapse
|
38
|
Niwa R, Sakai K, Lung MSY, Matsumoto T, Mikawa R, Maehana S, Suzuki M, Yamamoto Y, Maurissen TL, Hirabayashi A, Noda T, Kubo M, Gotoh S, Woltjen K. ACE2 knockout hinders SARS-CoV-2 propagation in iPS cell-derived airway and alveolar epithelial cells. Front Cell Dev Biol 2023; 11:1290876. [PMID: 38149046 PMCID: PMC10750251 DOI: 10.3389/fcell.2023.1290876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 10/26/2023] [Indexed: 12/28/2023] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, continues to spread around the world with serious cases and deaths. It has also been suggested that different genetic variants in the human genome affect both the susceptibility to infection and severity of disease in COVID-19 patients. Angiotensin-converting enzyme 2 (ACE2) has been identified as a cell surface receptor for SARS-CoV and SARS-CoV-2 entry into cells. The construction of an experimental model system using human iPS cells would enable further studies of the association between viral characteristics and genetic variants. Airway and alveolar epithelial cells are cell types of the lung that express high levels of ACE2 and are suitable for in vitro infection experiments. Here, we show that human iPS cell-derived airway and alveolar epithelial cells are highly susceptible to viral infection of SARS-CoV-2. Using gene knockout with CRISPR-Cas9 in human iPS cells we demonstrate that ACE2 plays an essential role in the airway and alveolar epithelial cell entry of SARS-CoV-2 in vitro. Replication of SARS-CoV-2 was strongly suppressed in ACE2 knockout (KO) lung cells. Our model system based on human iPS cell-derived lung cells may be applied to understand the molecular biology regulating viral respiratory infection leading to potential therapeutic developments for COVID-19 and the prevention of future pandemics.
Collapse
Affiliation(s)
- Ryo Niwa
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
- Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kouji Sakai
- Department of Veterinary Science, National Institute of Infectious Diseases, Tokyo, Japan
- Management Department of Biosafety, Laboratory Animal, and Pathogen Bank, National Institute of Infectious Diseases, Tokyo, Japan
| | - Mandy Siu Yu Lung
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Tomoko Matsumoto
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Ryuta Mikawa
- Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Clinical Application, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Shotaro Maehana
- Department of Microbiology, Kitasato University School of Allied Health Sciences, Kanagawa, Japan
- Regenerative Medicine and Cell Design Research Facility, Kitasato University School of Allied Health Sciences, Kanagawa, Japan
| | - Masato Suzuki
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yuki Yamamoto
- Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Thomas L. Maurissen
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Ai Hirabayashi
- Laboratory of Ultrastructural Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Takeshi Noda
- Laboratory of Ultrastructural Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Laboratory of Ultrastructural Virology, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Makoto Kubo
- Department of Microbiology, Kitasato University School of Allied Health Sciences, Kanagawa, Japan
- Regenerative Medicine and Cell Design Research Facility, Kitasato University School of Allied Health Sciences, Kanagawa, Japan
| | - Shimpei Gotoh
- Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Clinical Application, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Knut Woltjen
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| |
Collapse
|
39
|
Bai W, Huang M, Li C, Li J. The biological principles and advanced applications of DSB repair in CRISPR-mediated yeast genome editing. Synth Syst Biotechnol 2023; 8:584-596. [PMID: 37711546 PMCID: PMC10497738 DOI: 10.1016/j.synbio.2023.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 08/24/2023] [Accepted: 08/29/2023] [Indexed: 09/16/2023] Open
Abstract
To improve the performance of yeast cell factories for industrial production, extensive CRISPR-mediated genome editing systems have been applied by artificially creating double-strand breaks (DSBs) to introduce mutations with the assistance of intracellular DSB repair. Diverse strategies of DSB repair are required to meet various demands, including precise editing or random editing with customized gRNAs or a gRNA library. Although most yeasts remodeling techniques have shown rewarding performance in laboratory verification, industrial yeast strain manipulation relies only on very limited strategies. Here, we comprehensively reviewed the molecular mechanisms underlying recent industrial applications to provide new insights into DSB cleavage and repair pathways in both Saccharomyces cerevisiae and other unconventional yeast species. The discussion of DSB repair covers the most frequently used homologous recombination (HR) and nonhomologous end joining (NHEJ) strategies to the less well-studied illegitimate recombination (IR) pathways, such as single-strand annealing (SSA) and microhomology-mediated end joining (MMEJ). Various CRISPR-based genome editing tools and corresponding gene editing efficiencies are described. Finally, we summarize recently developed CRISPR-based strategies that use optimized DSB repair for genome-scale editing, providing a direction for further development of yeast genome editing.
Collapse
Affiliation(s)
- Wenxin Bai
- Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, 100081, Beijing, PR China
- The BIT-QUB International Joint Laboratory in Synthetic Biology, Beijing, 100081, PR China
| | - Meilan Huang
- School of Chemistry and Chemical Engineering, David Keir Building, Queen's University Belfast, Stranmillis Road, Northern Ireland, BT9 5AG, Belfast, United Kingdom
- The BIT-QUB International Joint Laboratory in Synthetic Biology, Beijing, 100081, PR China
| | - Chun Li
- Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, 100081, Beijing, PR China
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, PR China
| | - Jun Li
- Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, 100081, Beijing, PR China
- The BIT-QUB International Joint Laboratory in Synthetic Biology, Beijing, 100081, PR China
| |
Collapse
|
40
|
Chen Y, Paramo MI, Zhang Y, Yao L, Shah SR, Jin Y, Zhang J, Pan X, Yu H. Finding Needles in the Haystack: Strategies for Uncovering Noncoding Regulatory Variants. Annu Rev Genet 2023; 57:201-222. [PMID: 37562413 DOI: 10.1146/annurev-genet-030723-120717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
Despite accumulating evidence implicating noncoding variants in human diseases, unraveling their functionality remains a significant challenge. Systematic annotations of the regulatory landscape and the growth of sequence variant data sets have fueled the development of tools and methods to identify causal noncoding variants and evaluate their regulatory effects. Here, we review the latest advances in the field and discuss potential future research avenues to gain a more in-depth understanding of noncoding regulatory variants.
Collapse
Affiliation(s)
- You Chen
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, USA;
| | - Mauricio I Paramo
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, USA;
| | - Yingying Zhang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, USA;
| | - Li Yao
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, USA;
- Department of Computational Biology, Cornell University, Ithaca, New York, USA
| | - Sagar R Shah
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, USA;
| | - Yiyang Jin
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, USA;
| | - Junke Zhang
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, USA;
- Department of Computational Biology, Cornell University, Ithaca, New York, USA
| | - Xiuqi Pan
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, USA;
| | - Haiyuan Yu
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, USA;
- Department of Computational Biology, Cornell University, Ithaca, New York, USA
| |
Collapse
|
41
|
Guo Q, Yan Y, Zhang Z, Xu B, Bangash HL, Sui X, Yang Y, Zhou Z, Zhao S, Peng N. Developing the Limosilactobacillus reuteri Chassis through an Endogenous Programmable Endonuclease-Based Genome Editing Tool. ACS Synth Biol 2023; 12:3487-3496. [PMID: 37934952 DOI: 10.1021/acssynbio.3c00450] [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: 11/09/2023]
Abstract
Using genetically tractable probiotics to engineer live biotherapeutic products (LBPs) for disease treatment is urgently needed. Limosilactobacillus reuteri is an important vertebrate gut symbiont, which has great potential for developing LBPs. However, in L. reuteri, synthetic biology work is largely limited by the long editing cycle. In this study, we identified a subtype II-A CRISPR-Cas9 system in L. reuteri 03 and found the endogenous Cas9 (LrCas9) recognizing a broad protospacer-adjacent motif (PAM) sequence (3'-NDR; N = A, G, T, C; D = A, G, T; R = A, G). We reprogrammed the LrCas9 for efficient gene deletion (95.46%), point mutation (86.36%), large fragment deletion (40 kb), and gene integration (1743 bp, 73.9%), which uncovered the function of the repeated conserved domains in mucus-binding protein. Moreover, we analyzed the distribution of endogenous endonucleases in 304 strains of L. reuteri and found the existence of programmable endonucleases in 98.36% of L. reuteri strains suggesting the potential to reprogram endogenous endonucleases for genetic manipulation in the majority of L. reuteri strains. In conclusion, this study highlights the development of a new probiotic chassis based on endogenous endonucleases in L. reuteri 03, which paves the way for the development of genome editing tools for functional genetic studies in other L. reuteri. We believe that the development of an endogenous endonuclease-based genetic tool will greatly facilitate the construction of LBPs.
Collapse
Affiliation(s)
- Qiujin Guo
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 Hubei, P.R. China
| | - Yiting Yan
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 Hubei, P.R. China
| | - Zhenting Zhang
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 Hubei, P.R. China
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang, 550025 Guizhou, P.R. China
| | - Boya Xu
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 Hubei, P.R. China
| | - Hina Lqbal Bangash
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 Hubei, P.R. China
| | - Xin Sui
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 Hubei, P.R. China
| | - Yalin Yang
- Sino-Norway Joint Lab on Fish Gut Microbiota, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R. China
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R. China
| | - Zhigang Zhou
- Sino-Norway Joint Lab on Fish Gut Microbiota, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R. China
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R. China
| | - Shumiao Zhao
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 Hubei, P.R. China
| | - Nan Peng
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 Hubei, P.R. China
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R. China
| |
Collapse
|
42
|
Clark B, Kuwalekar M, Fischer B, Woltering J, Biran J, Juntti S, Kratochwil CF, Santos ME, Almeida MV. Genome editing in East African cichlids and tilapias: state-of-the-art and future directions. Open Biol 2023; 13:230257. [PMID: 38018094 PMCID: PMC10685126 DOI: 10.1098/rsob.230257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 10/27/2023] [Indexed: 11/30/2023] Open
Abstract
African cichlid fishes of the Cichlidae family are a group of teleosts important for aquaculture and research. A thriving research community is particularly interested in the cichlid radiations of the East African Great Lakes. One key goal is to pinpoint genetic variation underlying phenotypic diversification, but the lack of genetic tools has precluded thorough dissection of the genetic basis of relevant traits in cichlids. Genome editing technologies are well established in teleost models like zebrafish and medaka. However, this is not the case for emerging model organisms, such as East African cichlids, where these technologies remain inaccessible to most laboratories, due in part to limited exchange of knowledge and expertise. The Cichlid Science 2022 meeting (Cambridge, UK) hosted for the first time a Genome Editing Workshop, where the community discussed recent advances in genome editing, with an emphasis on CRISPR/Cas9 technologies. Based on the workshop findings and discussions, in this review we define the state-of-the-art of cichlid genome editing, share resources and protocols, and propose new possible avenues to further expand the cichlid genome editing toolkit.
Collapse
Affiliation(s)
- Bethan Clark
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Muktai Kuwalekar
- Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Uusimaa 00014, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Uusimaa 00014, Finland
| | - Bettina Fischer
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Joost Woltering
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Baden-Württemberg 78457, Germany
| | - Jakob Biran
- Department of Poultry and Aquaculture, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel
| | - Scott Juntti
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Claudius F. Kratochwil
- Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Uusimaa 00014, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Uusimaa 00014, Finland
| | | | - Miguel Vasconcelos Almeida
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Cambridge, UK
| |
Collapse
|
43
|
Tsuchida CA, Brandes N, Bueno R, Trinidad M, Mazumder T, Yu B, Hwang B, Chang C, Liu J, Sun Y, Hopkins CR, Parker KR, Qi Y, Hofman L, Satpathy AT, Stadtmauer EA, Cate JHD, Eyquem J, Fraietta JA, June CH, Chang HY, Ye CJ, Doudna JA. Mitigation of chromosome loss in clinical CRISPR-Cas9-engineered T cells. Cell 2023; 186:4567-4582.e20. [PMID: 37794590 PMCID: PMC10664023 DOI: 10.1016/j.cell.2023.08.041] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 05/11/2023] [Accepted: 08/31/2023] [Indexed: 10/06/2023]
Abstract
CRISPR-Cas9 genome editing has enabled advanced T cell therapies, but occasional loss of the targeted chromosome remains a safety concern. To investigate whether Cas9-induced chromosome loss is a universal phenomenon and evaluate its clinical significance, we conducted a systematic analysis in primary human T cells. Arrayed and pooled CRISPR screens revealed that chromosome loss was generalizable across the genome and resulted in partial and entire loss of the targeted chromosome, including in preclinical chimeric antigen receptor T cells. T cells with chromosome loss persisted for weeks in culture, implying the potential to interfere with clinical use. A modified cell manufacturing process, employed in our first-in-human clinical trial of Cas9-engineered T cells (NCT03399448), reduced chromosome loss while largely preserving genome editing efficacy. Expression of p53 correlated with protection from chromosome loss observed in this protocol, suggesting both a mechanism and strategy for T cell engineering that mitigates this genotoxicity in the clinic.
Collapse
Affiliation(s)
- Connor A Tsuchida
- University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Nadav Brandes
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Raymund Bueno
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Marena Trinidad
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Thomas Mazumder
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Bingfei Yu
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA; Parker Institute for Cancer Immunotherapy, Stanford University School of Medicine, Stanford, CA, USA
| | - Byungjin Hwang
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Christopher Chang
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA; Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Parker Institute for Cancer Immunotherapy, University of California, San Francisco, San Francisco, CA, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Jamin Liu
- University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Yang Sun
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Caitlin R Hopkins
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kevin R Parker
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Yanyan Qi
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Laura Hofman
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA; Graduate School of Life Sciences, Utrecht University, Utrecht, the Netherlands
| | - Ansuman T Satpathy
- Parker Institute for Cancer Immunotherapy, Stanford University School of Medicine, Stanford, CA, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Edward A Stadtmauer
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jamie H D Cate
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Justin Eyquem
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Parker Institute for Cancer Immunotherapy, University of California, San Francisco, San Francisco, CA, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Joseph A Fraietta
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Carl H June
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA; Parker Institute for Cancer Immunotherapy, Stanford University School of Medicine, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Chun Jimmie Ye
- University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, USA; Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Parker Institute for Cancer Immunotherapy, University of California, San Francisco, San Francisco, CA, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA; Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, CA, USA; Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA.
| | - Jennifer A Doudna
- University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA; Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Department of Chemistry, University of California Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA, USA.
| |
Collapse
|
44
|
Fernandes DA. Liposomes for Cancer Theranostics. Pharmaceutics 2023; 15:2448. [PMID: 37896208 PMCID: PMC10610083 DOI: 10.3390/pharmaceutics15102448] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/16/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
Cancer is one of the most well-studied diseases and there have been significant advancements over the last few decades in understanding its molecular and cellular mechanisms. Although the current treatments (e.g., chemotherapy, radiotherapy, gene therapy and immunotherapy) have provided complete cancer remission for many patients, cancer still remains one of the most common causes of death in the world. The main reasons for the poor response rates for different cancers include the lack of drug specificity, drug resistance and toxic side effects (i.e., in healthy tissues). For addressing the limitations of conventional cancer treatments, nanotechnology has shown to be an important field for constructing different nanoparticles for destroying cancer cells. Due to their size (i.e., less than 1 μm), nanoparticles can deliver significant amounts of cancer drugs to tumors and are able to carry moieties (e.g., folate, peptides) for targeting specific types of cancer cells (i.e., through receptor-mediated endocytosis). Liposomes, composed of phospholipids and an interior aqueous core, can be used as specialized delivery vehicles as they can load different types of cancer therapy agents (e.g., drugs, photosensitizers, genetic material). In addition, the ability to load imaging agents (e.g., fluorophores, radioisotopes, MRI contrast media) enable these nanoparticles to be used for monitoring the progress of treatment. This review examines a wide variety of different liposomes for cancer theranostics, with the different available treatments (e.g., photothermal, photodynamic) and imaging modalities discussed for different cancers.
Collapse
|
45
|
Wu Y, Feng S, Sun Z, Hu Y, Jia X, Zeng B. An outlook to sophisticated technologies and novel developments for metabolic regulation in the Saccharomyces cerevisiae expression system. Front Bioeng Biotechnol 2023; 11:1249841. [PMID: 37869712 PMCID: PMC10586203 DOI: 10.3389/fbioe.2023.1249841] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 09/04/2023] [Indexed: 10/24/2023] Open
Abstract
Saccharomyces cerevisiae is one of the most extensively used biosynthetic systems for the production of diverse bioproducts, especially biotherapeutics and recombinant proteins. Because the expression and insertion of foreign genes are always impaired by the endogenous factors of Saccharomyces cerevisiae and nonproductive procedures, various technologies have been developed to enhance the strength and efficiency of transcription and facilitate gene editing procedures. Thus, the limitations that block heterologous protein secretion have been overcome. Highly efficient promoters responsible for the initiation of transcription and the accurate regulation of expression have been developed that can be precisely regulated with synthetic promoters and double promoter expression systems. Appropriate codon optimization and harmonization for adaption to the genomic codon abundance of S. cerevisiae are expected to further improve the transcription and translation efficiency. Efficient and accurate translocation can be achieved by fusing a specifically designed signal peptide to an upstream foreign gene to facilitate the secretion of newly synthesized proteins. In addition to the widely applied promoter engineering technology and the clear mechanism of the endoplasmic reticulum secretory pathway, the innovative genome editing technique CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated system) and its derivative tools allow for more precise and efficient gene disruption, site-directed mutation, and foreign gene insertion. This review focuses on sophisticated engineering techniques and emerging genetic technologies developed for the accurate metabolic regulation of the S. cerevisiae expression system.
Collapse
Affiliation(s)
| | | | | | | | | | - Bin Zeng
- College of Pharmacy, Shenzhen Technology University, Shenzhen, Guangdong, China
| |
Collapse
|
46
|
Seo BJ, Na SB, Choi J, Ahn B, Habib O, Park C, Hong K, Do JT. Metabolic and cell cycle shift induced by the deletion of Dnm1l attenuates the dissolution of pluripotency in mouse embryonic stem cells. Cell Mol Life Sci 2023; 80:302. [PMID: 37747543 PMCID: PMC11073397 DOI: 10.1007/s00018-023-04962-x] [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: 04/20/2023] [Revised: 09/12/2023] [Accepted: 09/12/2023] [Indexed: 09/26/2023]
Abstract
Mitochondria are versatile organelles that continuously change their morphology via fission and fusion. However, the detailed functions of mitochondrial dynamics-related genes in pluripotent stem cells remain largely unclear. Here, we aimed to determine the effects on energy metabolism and differentiation ability of mouse embryonic stem cells (ESCs) following deletion of the mitochondrial fission-related gene Dnml1. Resultant Dnm1l-/- ESCs maintained major pluripotency characteristics. However, Dnm1l-/- ESCs showed several phenotypic changes, including the inhibition of differentiation ability (dissolution of pluripotency). Notably, Dnm1l-/- ESCs maintained the expression of the pluripotency marker Oct4 and undifferentiated colony types upon differentiation induction. RNA sequencing analysis revealed that the most frequently differentially expressed genes were enriched in the glutathione metabolic pathway. Our data suggested that differentiation inhibition of Dnm1l-/- ESCs was primarily due to metabolic shift from glycolysis to OXPHOS, G2/M phase retardation, and high level of Nanog and 2-cell-specific gene expression.
Collapse
Affiliation(s)
- Bong Jong Seo
- Department of Stem Cell and Regenerative Biotechnology, Konkuk Institute of Technology, Konkuk University, Seoul, 05029, Republic of Korea
| | - Seung Bin Na
- Department of Stem Cell and Regenerative Biotechnology, Konkuk Institute of Technology, Konkuk University, Seoul, 05029, Republic of Korea
| | - Joonhyuk Choi
- Department of Stem Cell and Regenerative Biotechnology, Konkuk Institute of Technology, Konkuk University, Seoul, 05029, Republic of Korea
| | - Byeongyong Ahn
- Department of Stem Cell and Regenerative Biotechnology, Konkuk Institute of Technology, Konkuk University, Seoul, 05029, Republic of Korea
| | - Omer Habib
- Department of Chemistry, Hanyang University, Seoul, 04763, Republic of Korea
| | - Chankyu Park
- Department of Stem Cell and Regenerative Biotechnology, Konkuk Institute of Technology, Konkuk University, Seoul, 05029, Republic of Korea
| | - Kwonho Hong
- Department of Stem Cell and Regenerative Biotechnology, Konkuk Institute of Technology, Konkuk University, Seoul, 05029, Republic of Korea
| | - Jeong Tae Do
- Department of Stem Cell and Regenerative Biotechnology, Konkuk Institute of Technology, Konkuk University, Seoul, 05029, Republic of Korea.
| |
Collapse
|
47
|
Takahashi G, Miyaoka Y. Large-scale single-cell cloning of genome-edited cultured human cells by On-chip SPiS. STAR Protoc 2023; 4:102364. [PMID: 37329509 PMCID: PMC10285693 DOI: 10.1016/j.xpro.2023.102364] [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: 03/30/2023] [Revised: 05/01/2023] [Accepted: 05/17/2023] [Indexed: 06/19/2023] Open
Abstract
Single-cell cloning is the simplest strategy to isolate genome-edited cell clones, although its scalability has been an issue. Here, we present a protocol to establish genome-edited human cultured cell clones using the On-chip SPiS, a single-cell auto-dispensing device with image recognition technology. Human cultured cells are transfected with plasmids of the CRISPR-Cas9 components, and Cas9-expressing cells are sorted and individually plated into multi-well plates by the On-chip SPiS. For complete details on the use and execution of this protocol, please refer to Takahashi et al. (2022).1.
Collapse
Affiliation(s)
- Gou Takahashi
- Regenerative Medicine Project, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan.
| | - Yuichiro Miyaoka
- Regenerative Medicine Project, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan; Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo 113-8510, Japan; Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo 112-8610, Japan.
| |
Collapse
|
48
|
da Silva JF, Tou CJ, King EM, Eller ML, Ma L, Rufino-Ramos D, Kleinstiver BP. Click editing enables programmable genome writing using DNA polymerases and HUH endonucleases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.12.557440. [PMID: 37745481 PMCID: PMC10515857 DOI: 10.1101/2023.09.12.557440] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Genome editing technologies that install diverse edits can widely enable genetic studies and new therapeutics. Here we develop click editing, a genome writing platform that couples the advantageous properties of DNA-dependent DNA polymerases with RNA-programmable nickases (e.g. CRISPR-Cas) to permit the installation of a range of edits including substitutions, insertions, and deletions. Click editors (CEs) leverage the "click"-like bioconjugation ability of HUH endonucleases (HUHes) with single stranded DNA substrates to covalently tether "click DNA" (clkDNA) templates encoding user-specifiable edits at targeted genomic loci. Through iterative optimization of the modular components of CEs (DNA polymerase and HUHe orthologs, architectural modifications, etc.) and their clkDNAs (template configurations, repair evading substitutions, etc.), we demonstrate the ability to install precise genome edits with minimal indels and no unwanted byproduct insertions. Since clkDNAs can be ordered as simple DNA oligonucleotides for cents per base, it is possible to screen many different clkDNA parameters rapidly and inexpensively to maximize edit efficiency. Together, click editing is a precise and highly versatile platform for modifying genomes with a simple workflow and broad utility across diverse biological applications.
Collapse
Affiliation(s)
- Joana Ferreira da Silva
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Pathology, Harvard Medical School, Boston, MA, 02115, USA
| | - Connor J. Tou
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Biological Engineering Program, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Emily M. King
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Biological and Biomedical Sciences Program, Harvard University, Boston, MA, 02115, USA
| | - Madeline L. Eller
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Linyuan Ma
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Pathology, Harvard Medical School, Boston, MA, 02115, USA
| | - David Rufino-Ramos
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Pathology, Harvard Medical School, Boston, MA, 02115, USA
| | - Benjamin P. Kleinstiver
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Pathology, Harvard Medical School, Boston, MA, 02115, USA
| |
Collapse
|
49
|
Hamaker NK, Lee KH. High-efficiency and multilocus targeted integration in CHO cells using CRISPR-mediated donor nicking and DNA repair inhibitors. Biotechnol Bioeng 2023; 120:2419-2440. [PMID: 37039773 PMCID: PMC10524319 DOI: 10.1002/bit.28393] [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: 11/23/2022] [Revised: 03/20/2023] [Accepted: 03/24/2023] [Indexed: 04/12/2023]
Abstract
Efforts to leverage clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) for targeted genomic modifications in mammalian cells are limited by low efficiencies and heterogeneous outcomes. To aid method optimization, we developed an all-in-one reporter system, including a novel superfolder orange fluorescent protein (sfOrange), to simultaneously quantify gene disruption, site-specific integration (SSI), and random integration (RI). SSI strategies that utilize different donor plasmid formats and Cas9 nuclease variants were evaluated for targeting accuracy and efficiency in Chinese hamster ovary cells. Double-cut and double-nick donor formats significantly improved targeting accuracy by 2.3-8.3-fold and 19-22-fold, respectively, compared to standard circular donors. Notably, Cas9-mediated donor linearization was associated with increased RI events, whereas donor nicking minimized RI without sacrificing SSI efficiency and avoided low-fidelity outcomes. A screen of 10 molecules that modulate the major mammalian DNA repair pathways identified two inhibitors that further enhance targeting accuracy and efficiency to achieve SSI in 25% of transfected cells without selection. The optimized methods integrated transgene expression cassettes with 96% efficiency at a single locus and with 53%-55% efficiency at two loci simultaneously in selected clones. The CRISPR-based tools and methods developed here could inform the use of CRISPR/Cas9 in mammalian cell lines, accelerate mammalian cell line engineering, and support advanced recombinant protein production applications.
Collapse
Affiliation(s)
- Nathaniel K. Hamaker
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, 19716, USA
| | - Kelvin H. Lee
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, 19716, USA
- The National Institute for Innovation in Manufacturing Biopharmaceuticals (NIIMBL), University of Delaware, Newark, DE, 19713, USA
| |
Collapse
|
50
|
Zhao Z, Shang P, Mohanraju P, Geijsen N. Prime editing: advances and therapeutic applications. Trends Biotechnol 2023; 41:1000-1012. [PMID: 37002157 DOI: 10.1016/j.tibtech.2023.03.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 02/24/2023] [Accepted: 03/03/2023] [Indexed: 04/01/2023]
Abstract
Clustered regularly interspaced short palindromic repeats-associated protein 9 (CRISPR-Cas)-mediated genome editing has revolutionized biomedical research and will likely change the therapeutic and diagnostic landscape. However, CRISPR-Cas9, which edits DNA by activating DNA double-strand break (DSB) repair pathways, is not always sufficient for gene therapy applications where precise mutation repair is required. Prime editing, the latest revolution in genome-editing technologies, can achieve any possible base substitution, insertion, or deletion without the requirement for DSBs. However, prime editing is still in its infancy, and further development is needed to improve editing efficiency and delivery strategies for therapeutic applications. We summarize latest developments in the optimization of prime editor (PE) variants with improved editing efficiency and precision. Moreover, we highlight some potential therapeutic applications.
Collapse
Affiliation(s)
- Zhihan Zhao
- Leiden University Medical Center, Einthovenweg 20, 2300 RC Leiden, The Netherlands; The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden node, The Netherlands
| | - Peng Shang
- Leiden University Medical Center, Einthovenweg 20, 2300 RC Leiden, The Netherlands; The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden node, The Netherlands
| | - Prarthana Mohanraju
- Leiden University Medical Center, Einthovenweg 20, 2300 RC Leiden, The Netherlands; The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden node, The Netherlands.
| | - Niels Geijsen
- Leiden University Medical Center, Einthovenweg 20, 2300 RC Leiden, The Netherlands; The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden node, The Netherlands.
| |
Collapse
|