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Li YR, Lyu Z, Tian Y, Fang Y, Zhu Y, Chen Y, Yang L. Advancements in CRISPR screens for the development of cancer immunotherapy strategies. Mol Ther Oncolytics 2023; 31:100733. [PMID: 37876793 PMCID: PMC10591018 DOI: 10.1016/j.omto.2023.100733] [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] [Indexed: 10/26/2023] Open
Abstract
CRISPR screen technology enables systematic and scalable interrogation of gene function by using the CRISPR-Cas9 system to perturb gene expression. In the field of cancer immunotherapy, this technology has empowered the discovery of genes, biomarkers, and pathways that regulate tumor development and progression, immune reactivity, and the effectiveness of immunotherapeutic interventions. By conducting large-scale genetic screens, researchers have successfully identified novel targets to impede tumor growth, enhance anti-tumor immune responses, and surmount immunosuppression within the tumor microenvironment (TME). Here, we present an overview of CRISPR screens conducted in tumor cells for the purpose of identifying novel therapeutic targets. We also explore the application of CRISPR screens in immune cells to propel the advancement of cell-based therapies, encompassing T cells, natural killer cells, dendritic cells, and macrophages. Furthermore, we outline the crucial components necessary for the successful implementation of immune-specific CRISPR screens and explore potential directions for future research.
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Affiliation(s)
- Yan-Ruide Li
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Zibai Lyu
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yanxin Tian
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Ying Fang
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yichen Zhu
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yuning Chen
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Lili Yang
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
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3
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Li Y, Xu J, Guo X, Li Z, Cao L, Liu S, Guo Y, Wang G, Luo Y, Zhang Z, Wei X, Zhao Y, Liu T, Wang X, Xia H, Kuang M, Guo Q, Li J, Chen L, Wang Y, Li Q, Wang F, Liu Q, You F. The collateral activity of RfxCas13d can induce lethality in a RfxCas13d knock-in mouse model. Genome Biol 2023; 24:20. [PMID: 36726140 PMCID: PMC9893547 DOI: 10.1186/s13059-023-02860-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 01/18/2023] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND The CRISPR-Cas13 system is an RNA-guided RNA-targeting system and has been widely used in transcriptome engineering with potentially important clinical applications. However, it is still controversial whether Cas13 exhibits collateral activity in mammalian cells. RESULTS Here, we find that knocking down gene expression using RfxCas13d in the adult brain neurons caused death of mice, which may result from the collateral activity of RfxCas13d rather than the loss of target gene function or off-target effects. Mechanistically, we show that RfxCas13d exhibits collateral activity in mammalian cells, which is positively correlated with the abundance of target RNA. The collateral activity of RfxCas13d could cleave 28s rRNA into two fragments, leading to translation attenuation and activation of the ZAKα-JNK/p38-immediate early gene pathway. CONCLUSIONS These findings provide new mechanistic insights into the collateral activity of RfxCas13d in mammalian cells and warn that the biosafety of the CRISPR-Cas13 system needs further evaluation before application to clinical treatments.
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Affiliation(s)
- Yunfei Li
- grid.11135.370000 0001 2256 9319Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, 100191 China
| | - Junjie Xu
- grid.12527.330000 0001 0662 3178National Institute of Biological Sciences, Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 102206 China ,grid.20513.350000 0004 1789 9964College of Life Sciences, Beijing Normal University, Beijing, 100875 China
| | - Xuefei Guo
- grid.11135.370000 0001 2256 9319Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, 100191 China
| | - Zhiwei Li
- grid.256885.40000 0004 1791 4722School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002 Hebei China
| | - Lili Cao
- grid.9227.e0000000119573309Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101 China
| | - Shengde Liu
- grid.412474.00000 0001 0027 0586Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital and Institute, Beijing, 100142 China
| | - Ying Guo
- grid.12527.330000 0001 0662 3178National Institute of Biological Sciences, Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 102206 China
| | - Guodong Wang
- grid.12527.330000 0001 0662 3178National Institute of Biological Sciences, Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 102206 China
| | - Yujie Luo
- grid.11135.370000 0001 2256 9319Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, 100191 China
| | - Zeming Zhang
- grid.11135.370000 0001 2256 9319Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, 100191 China
| | - Xuemei Wei
- grid.11135.370000 0001 2256 9319Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, 100191 China
| | - Yingchi Zhao
- grid.11135.370000 0001 2256 9319Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, 100191 China
| | - Tongtong Liu
- grid.11135.370000 0001 2256 9319Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, 100191 China
| | - Xiao Wang
- grid.11135.370000 0001 2256 9319Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, 100191 China
| | - Huawei Xia
- grid.11135.370000 0001 2256 9319Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, 100191 China
| | - Ming Kuang
- grid.11135.370000 0001 2256 9319Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, 100191 China
| | - Qirui Guo
- grid.11135.370000 0001 2256 9319Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, 100191 China
| | - Junhong Li
- grid.11135.370000 0001 2256 9319Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, 100191 China
| | - Luoying Chen
- grid.11135.370000 0001 2256 9319Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, 100191 China
| | - Yibing Wang
- grid.12527.330000 0001 0662 3178National Institute of Biological Sciences, Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 102206 China
| | - Qi Li
- grid.12527.330000 0001 0662 3178National Institute of Biological Sciences, Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 102206 China
| | - Fengchao Wang
- grid.12527.330000 0001 0662 3178National Institute of Biological Sciences, Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 102206 China
| | - Qinghua Liu
- grid.12527.330000 0001 0662 3178National Institute of Biological Sciences, Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 102206 China
| | - Fuping You
- grid.11135.370000 0001 2256 9319Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, 100191 China
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4
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Shin S, Jang S, Lim D. Small Molecules for Enhancing the Precision and Safety of Genome Editing. Molecules 2022; 27:6266. [PMID: 36234804 PMCID: PMC9573751 DOI: 10.3390/molecules27196266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/17/2022] [Accepted: 09/20/2022] [Indexed: 11/24/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-based genome-editing technologies have revolutionized biology, biotechnology, and medicine, and have spurred the development of new therapeutic modalities. However, there remain several barriers to the safe use of CRISPR technologies, such as unintended off-target DNA cleavages. Small molecules are important resources to solve these problems, given their facile delivery and fast action to enable temporal control of the CRISPR systems. Here, we provide a comprehensive overview of small molecules that can precisely modulate CRISPR-associated (Cas) nucleases and guide RNAs (gRNAs). We also discuss the small-molecule control of emerging genome editors (e.g., base editors) and anti-CRISPR proteins. These molecules could be used for the precise investigation of biological systems and the development of safer therapeutic modalities.
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Affiliation(s)
- Siyoon Shin
- School of Biopharmaceutical and Medical Sciences, Sungshin University, Seoul 01133, Korea
- Department of Next-Generation Applied Science, Sungshin University, Seoul 01133, Korea
| | - Seeun Jang
- School of Biopharmaceutical and Medical Sciences, Sungshin University, Seoul 01133, Korea
- Department of Next-Generation Applied Science, Sungshin University, Seoul 01133, Korea
| | - Donghyun Lim
- School of Biopharmaceutical and Medical Sciences, Sungshin University, Seoul 01133, Korea
- Department of Next-Generation Applied Science, Sungshin University, Seoul 01133, Korea
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5
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Lyadova I, Vasiliev A. Macrophages derived from pluripotent stem cells: prospective applications and research gaps. Cell Biosci 2022; 12:96. [PMID: 35725499 PMCID: PMC9207879 DOI: 10.1186/s13578-022-00824-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 05/29/2022] [Indexed: 11/10/2022] Open
Abstract
Induced pluripotent stem cells (iPSCs) represent a valuable cell source able to give rise to different cell types of the body. Among the various pathways of iPSC differentiation, the differentiation into macrophages is a recently developed and rapidly growing technique. Macrophages play a key role in the control of host homeostasis. Their dysfunction underlies many diseases, including hereditary, infectious, oncological, metabolic and other disorders. Targeting macrophage activity and developing macrophage-based cell therapy represent promising tools for the treatment of many pathological conditions. Macrophages generated from human iPSCs (iMphs) provide great opportunities in these areas. The generation of iMphs is based on a step-wise differentiation of iPSCs into mesoderm, hematopoietic progenitors, myeloid monocyte-like cells and macrophages. The technique allows to obtain standardizable populations of human macrophages from any individual, scale up macrophage production and introduce genetic modifications, which gives significant advantages over the standard source of human macrophages, monocyte-derived macrophages. The spectrum of iMph applications is rapidly growing. iMphs have been successfully used to model hereditary diseases and macrophage-pathogen interactions, as well as to test drugs. iMph use for cell therapy is another promising and rapidly developing area of research. The principles and the details of iMph generation have recently been reviewed. This review systemizes current and prospective iMph applications and discusses the problem of iMph safety and other issues that need to be explored before iMphs become clinically applicable.
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Affiliation(s)
- Irina Lyadova
- Koltzov Institute of Developmental Biology of RAS, Moscow, Russian Federation.
| | - Andrei Vasiliev
- Koltzov Institute of Developmental Biology of RAS, Moscow, Russian Federation
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Mamun MMA, Bukhari I. Fast-Track and Integration-Free Method of Genome Editing by CRISPR/Cas9 in Murine Pluripotent Stem Cells. Front Cell Dev Biol 2022; 10:819906. [PMID: 35372368 PMCID: PMC8972586 DOI: 10.3389/fcell.2022.819906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/04/2022] [Indexed: 11/13/2022] Open
Abstract
The CRISPR/Cas9 system has unprecedentedly revolutionized genome-editing technology, which is being successfully applied virtually in all branches of biological sciences. Although much success has been attained in gene manipulation, still the majority of methods are laborious and non-integration-free, and require prolonged time for the expansion of mutant cell pools/clones, while fewer cells exhibit functional knockout efficiency. To overcome these obstacles, here, we describe an efficient, inexpensive, integration-free, and rapid one-step protocol for CRISPR/Cas9-assisted gene knockout in murine pluripotent stem cells (PSCs). Our protocol has streamlined both the liposome-based transfection system and screening strategy to work more efficiently with small numbers of PSCs (∼2.0 × 104 cells) and to minimize laborious steps of lentiviral packaging, transduction, and single-clone passaging. In our method, around 90% (CI = 95%, 79.5230%-100%) of PSC colonies harbored functional knockout in the context of protein expression. Therefore, the current protocol is technically feasible, time-saving, and highly efficient for genome editing in pluripotent stem cells.
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Affiliation(s)
- Md Mahfuz Al Mamun
- Translational Research Institute, Henan Provincial People’s Hospital, Henan Key Laboratory of Stem Cell Differentiation and Modification, School of Clinical Medicine, Henan University, Zhengzhou, China
| | - Ihtisham Bukhari
- Translational Research Institute, Henan Provincial People’s Hospital, Henan Key Laboratory of Stem Cell Differentiation and Modification, School of Clinical Medicine, Henan University, Zhengzhou, China,Henan Key Laboratory of Helicobacter pylori, Microbiota and Gastrointestinal Cancer, Marshall Medical Research Center, Department of Gastroenterology, Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China,*Correspondence: Ihtisham Bukhari,
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