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Jiao L, Zhou Q, Sun D. CRISPR-Based Regulation for High-Throughput Screening. ACS Synth Biol 2025. [PMID: 40401794 DOI: 10.1021/acssynbio.5c00076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2025]
Abstract
CRISPR technology has revolutionized genome editing by enabling precise, permanent modifications to genetic material. To circumvent the irreversible alterations associated with traditional CRISPR methods and facilitate research on both essential and nonessential genes, CRISPR interference or inhibition (CRISPRi) and CRISPR activation (CRISPRa) were developed. The gene-silencing approach leverages an inactivated Cas effector protein paired with guide RNA to obstruct transcription initiation or elongation, while the gene-activation approach exploits the programmability of CRISPR to activate gene expression. Recent advances in CRISPRi technology, in combination with other technologies (e.g., biosensing, sequencing), have significantly expanded its applications, allowing for genome-wide high-throughput screening (HTS) to identify genetic determinants of phenotypes. These screening strategies have been applied in biomedicine, industry, and basic research. This review explores the CRISPR regulation mechanisms, offers an overview of the workflow for genome-wide CRISPR-based regulation for screens, and highlights its superior suitability for HTS across biomedical and industrial applications. Finally, we discuss the limitations of current CRISPRi/a HTS screening methods and envision future directions in CRISPR-mediated HTS research, considering its potential for broader application across diverse fields.
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Affiliation(s)
- Lingling Jiao
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
| | - Qi Zhou
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
| | - Dongchang Sun
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
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2
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Xing L, Xu J, Gong M, Liu Y, Li X, Meng L, Du R, Zhou Y, Ouyang Z, Liu X, Tao S, Cao Y, Liu C, Gao F, Han R, Shen H, Dong Y, Xu Y, Li T, Chen H, Zhao Y, Fan B, Sui L, Feng S, Liu J, Liu D, Wu X. Targeted disruption of PRC1.1 complex enhances bone remodeling. Nat Commun 2025; 16:4294. [PMID: 40341537 PMCID: PMC12062457 DOI: 10.1038/s41467-025-59638-w] [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: 11/14/2024] [Accepted: 04/29/2025] [Indexed: 05/10/2025] Open
Abstract
Polycomb repressive complexes (PRCs) are pivotal epigenetic regulators that preserve cell identity by restricting transcription responses to sub-threshold extracellular signals. Their roles in osteoblast function and bone formation remain unclear. Here in aging osteoblasts, we found marked activation of PRC1.1 complex, with KDM2B acting as a chromatin-binding factor and BCOR and PCGF1 enabling histone H2A monoubiquitylation (H2AK119ub1). Osteoblast-specific Kdm2b inactivation significantly enhances bone remodeling under steady-state conditions and in scenarios of bone loss. This enhancement is attributed to H2AK119ub1 downregulation and subsequent Wnt signaling derepression. Furthermore, we developed a small molecule termed iBP, that specifically inhibits the interaction between BCOR and PCGF1, thereby suppressing PRC1.1 activity. Notably, iBP administration promotes bone formation in mouse models of bone loss. Therefore, our findings identify PRC1.1 as a critical epigenetic brake on bone formation and demonstrate that therapeutic targeting of this complex enhances Wnt pathway activation, offering a promising strategy against skeletal deterioration.
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Affiliation(s)
- Liangyu Xing
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Endodontics, Tianjin Medical University School and Hospital of Stomatology & Tianjin Key Laboratory of Oral Soft and Hard Tissues Restoration and Regeneration, Tianjin Medical University, Tianjin, China
- Department of Cell Biology, Tianjin Medical University, Tianjin, China
| | - Jinxin Xu
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Institute of Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Meihan Gong
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Endodontics, Tianjin Medical University School and Hospital of Stomatology & Tianjin Key Laboratory of Oral Soft and Hard Tissues Restoration and Regeneration, Tianjin Medical University, Tianjin, China
- Department of Cell Biology, Tianjin Medical University, Tianjin, China
| | - Yunzhi Liu
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Endodontics, Tianjin Medical University School and Hospital of Stomatology & Tianjin Key Laboratory of Oral Soft and Hard Tissues Restoration and Regeneration, Tianjin Medical University, Tianjin, China
- Department of Cell Biology, Tianjin Medical University, Tianjin, China
| | - Xuanyuan Li
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Endodontics, Tianjin Medical University School and Hospital of Stomatology & Tianjin Key Laboratory of Oral Soft and Hard Tissues Restoration and Regeneration, Tianjin Medical University, Tianjin, China
- Department of Cell Biology, Tianjin Medical University, Tianjin, China
| | - Lingyu Meng
- Institute of Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Ruyue Du
- Institute of Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Ying Zhou
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Endodontics, Tianjin Medical University School and Hospital of Stomatology & Tianjin Key Laboratory of Oral Soft and Hard Tissues Restoration and Regeneration, Tianjin Medical University, Tianjin, China
| | - Zhaoguang Ouyang
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Endodontics, Tianjin Medical University School and Hospital of Stomatology & Tianjin Key Laboratory of Oral Soft and Hard Tissues Restoration and Regeneration, Tianjin Medical University, Tianjin, China
| | - Xu Liu
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Endodontics, Tianjin Medical University School and Hospital of Stomatology & Tianjin Key Laboratory of Oral Soft and Hard Tissues Restoration and Regeneration, Tianjin Medical University, Tianjin, China
| | - Shaofei Tao
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Endodontics, Tianjin Medical University School and Hospital of Stomatology & Tianjin Key Laboratory of Oral Soft and Hard Tissues Restoration and Regeneration, Tianjin Medical University, Tianjin, China
| | - Yuxin Cao
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Endodontics, Tianjin Medical University School and Hospital of Stomatology & Tianjin Key Laboratory of Oral Soft and Hard Tissues Restoration and Regeneration, Tianjin Medical University, Tianjin, China
| | - Chunyi Liu
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Endodontics, Tianjin Medical University School and Hospital of Stomatology & Tianjin Key Laboratory of Oral Soft and Hard Tissues Restoration and Regeneration, Tianjin Medical University, Tianjin, China
| | - Feng Gao
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Endodontics, Tianjin Medical University School and Hospital of Stomatology & Tianjin Key Laboratory of Oral Soft and Hard Tissues Restoration and Regeneration, Tianjin Medical University, Tianjin, China
| | - Ruohui Han
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Endodontics, Tianjin Medical University School and Hospital of Stomatology & Tianjin Key Laboratory of Oral Soft and Hard Tissues Restoration and Regeneration, Tianjin Medical University, Tianjin, China
| | - Hui Shen
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yan Dong
- Institute of Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yong Xu
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Institute of Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Tao Li
- Department of Medicinal Chemistry, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - He Chen
- Department of Medicinal Chemistry, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Yingying Zhao
- Department of Cell Biology, Tianjin Medical University, Tianjin, China
- Department of Medicinal Chemistry, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Baoyou Fan
- International Science and Technology Cooperation Base of Spinal Cord Injury, Department of Orthopedic Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Lei Sui
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Endodontics, Tianjin Medical University School and Hospital of Stomatology & Tianjin Key Laboratory of Oral Soft and Hard Tissues Restoration and Regeneration, Tianjin Medical University, Tianjin, China
| | - Shiqing Feng
- International Science and Technology Cooperation Base of Spinal Cord Injury, Department of Orthopedic Surgery, Tianjin Medical University General Hospital, Tianjin, China.
- The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.
| | - Jinsong Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
| | - Dayong Liu
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Endodontics, Tianjin Medical University School and Hospital of Stomatology & Tianjin Key Laboratory of Oral Soft and Hard Tissues Restoration and Regeneration, Tianjin Medical University, Tianjin, China.
- Shanghai Engineering Research Center of Tooth Restoration and Regeneration & Tongji Research Institute of Stomatology & Department of Endodontics, Shanghai Tongji Stomatological Hospital and Dental School, Tongji University, Shanghai, China.
| | - Xudong Wu
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Endodontics, Tianjin Medical University School and Hospital of Stomatology & Tianjin Key Laboratory of Oral Soft and Hard Tissues Restoration and Regeneration, Tianjin Medical University, Tianjin, China.
- Department of Cell Biology, Tianjin Medical University, Tianjin, China.
- International Science and Technology Cooperation Base of Spinal Cord Injury, Department of Orthopedic Surgery, Tianjin Medical University General Hospital, Tianjin, China.
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3
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Kirk RW, Sun L, Xiao R, Clark EA, Nelson S. Multiplexed CRISPRi Reveals a Transcriptional Switch Between KLF Activators and Repressors in the Maturing Neocortex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.07.636951. [PMID: 39975013 PMCID: PMC11839100 DOI: 10.1101/2025.02.07.636951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/21/2025]
Abstract
A critical phase of mammalian brain development takes place after birth. Neurons of the mouse neocortex undergo dramatic changes in their morphology, physiology, and synaptic connections during the first postnatal month, while properties of immature neurons, such as the capacity for robust axon outgrowth, are lost. The genetic and epigenetic programs controlling prenatal development are well studied, but our understanding of the transcriptional mechanisms that regulate postnatal neuronal maturation is comparatively lacking. By integrating chromatin accessibility and gene expression data from two subtypes of neocortical pyramidal neurons in the neonatal and maturing brain, we predicted a role for the Krüppel-Like Factor (KLF) family of Transcription Factors in the developmental regulation of neonatally expressed genes. Using a multiplexed CRISPR Interference (CRISPRi) knockdown strategy, we found that a shift in expression from KLF activators (Klf6, Klf7) to repressors (Klf9, Klf13) during early postnatal development functions as a transcriptional 'switch' to first activate, then repress a set of shared targets with cytoskeletal functions including Tubb2b and Dpysl3. We demonstrate that this switch is buffered by redundancy between KLF paralogs, which our multiplexed CRISPRi strategy is equipped to overcome and study. Our results indicate that competition between activators and repressors within the KLF family regulates a conserved component of the postnatal maturation program that may underlie the loss of intrinsic axon growth in maturing neurons. This could facilitate the transition from axon growth to synaptic refinement required to stabilize mature circuits.
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Affiliation(s)
- Ryan W Kirk
- Department of Biology, Brandeis University, Waltham, MA 02453, USA
| | - Liwei Sun
- Department of Biology, Brandeis University, Waltham, MA 02453, USA
| | - Ruixuan Xiao
- Department of Biology, Brandeis University, Waltham, MA 02453, USA
| | - Erin A Clark
- Department of Biology, Brandeis University, Waltham, MA 02453, USA
| | - Sacha Nelson
- Department of Biology, Brandeis University, Waltham, MA 02453, USA
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4
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Jin W, Deng Y, La Marca JE, Lelliott EJ, Diepstraten ST, König C, Tai L, Snetkova V, Dorighi KM, Hoberecht L, Hedditch MG, Whelan L, Healey G, Fayle D, Lau K, Potts MA, Chen MZ, Johnston APR, Liao Y, Shi W, Kueh AJ, Haley B, Fortin JP, Herold MJ. Advancing the genetic engineering toolbox by combining AsCas12a knock-in mice with ultra-compact screening. Nat Commun 2025; 16:974. [PMID: 39885149 PMCID: PMC11782673 DOI: 10.1038/s41467-025-56282-2] [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: 12/12/2024] [Accepted: 01/09/2025] [Indexed: 02/01/2025] Open
Abstract
Cas12a is a next-generation gene editing tool that enables multiplexed gene targeting. Here, we present a mouse model that constitutively expresses enhanced Acidaminococcus sp. Cas12a (enAsCas12a) linked to an mCherry fluorescent reporter. We demonstrate efficient single and multiplexed gene editing in vitro, using primary and transformed cells from enAsCas12a mice. We further demonstrate successful in vivo gene editing, using normal and cancer-prone enAsCas12a stem cells to reconstitute the haematopoietic system of wild-type mice. We also present compact, genome-wide Cas12a knockout libraries, with four crRNAs per gene encoded across one (Scherzo) or two (Menuetto) vectors, and demonstrate the utility of these libraries across methodologies: in vitro enrichment and drop-out screening in lymphoma cells and immortalised fibroblasts, respectively, and in vivo screens to identify lymphoma-driving events. Finally, we demonstrate CRISPR multiplexing via simultaneous gene knockout (via Cas12a) and activation (via dCas9-SAM) using primary T cells and fibroblasts. Our enAsCas12a mouse and accompanying crRNA libraries enhance genome engineering capabilities and complement current CRISPR technologies.
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Affiliation(s)
- Wei Jin
- Olivia Newton-John Cancer Research Institute, Heidelberg, Melbourne, Australia
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Melbourne, Australia
| | - Yexuan Deng
- Olivia Newton-John Cancer Research Institute, Heidelberg, Melbourne, Australia
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Melbourne, Australia
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - John E La Marca
- Olivia Newton-John Cancer Research Institute, Heidelberg, Melbourne, Australia
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Melbourne, Australia
| | - Emily J Lelliott
- Olivia Newton-John Cancer Research Institute, Heidelberg, Melbourne, Australia
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Melbourne, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, Melbourne, Australia
| | - Sarah T Diepstraten
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Melbourne, Australia
| | - Christina König
- Olivia Newton-John Cancer Research Institute, Heidelberg, Melbourne, Australia
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, Melbourne, Australia
| | - Lin Tai
- Olivia Newton-John Cancer Research Institute, Heidelberg, Melbourne, Australia
| | - Valentina Snetkova
- Department of Molecular Biology, Genentech, Inc., South San Francisco, California, USA
| | - Kristel M Dorighi
- Department of Molecular Biology, Genentech, Inc., South San Francisco, California, USA
| | - Luke Hoberecht
- Computational Sciences, Genentech, Inc., South San Francisco, California, USA
| | - Millicent G Hedditch
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Australia
| | - Lauren Whelan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Australia
| | - Geraldine Healey
- Olivia Newton-John Cancer Research Institute, Heidelberg, Melbourne, Australia
| | - Dan Fayle
- Olivia Newton-John Cancer Research Institute, Heidelberg, Melbourne, Australia
| | - Kieran Lau
- Olivia Newton-John Cancer Research Institute, Heidelberg, Melbourne, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, Melbourne, Australia
| | - Margaret A Potts
- Olivia Newton-John Cancer Research Institute, Heidelberg, Melbourne, Australia
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Melbourne, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, Melbourne, Australia
| | - Moore Z Chen
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Melbourne, Australia
| | - Angus P R Johnston
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Melbourne, Australia
| | - Yang Liao
- Olivia Newton-John Cancer Research Institute, Heidelberg, Melbourne, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, Melbourne, Australia
| | - Wei Shi
- Olivia Newton-John Cancer Research Institute, Heidelberg, Melbourne, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, Melbourne, Australia
| | - Andrew J Kueh
- Olivia Newton-John Cancer Research Institute, Heidelberg, Melbourne, Australia
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Melbourne, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, Melbourne, Australia
| | - Benjamin Haley
- Department of Molecular Biology, Genentech, Inc., South San Francisco, California, USA
- Université de Montréal, Centre de recherche de l'Hôpital Maisonneuve-Rosemont, Rosemont, Canada
| | | | - Marco J Herold
- Olivia Newton-John Cancer Research Institute, Heidelberg, Melbourne, Australia.
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Australia.
- Department of Medical Biology, University of Melbourne, Parkville, Melbourne, Australia.
- School of Cancer Medicine, La Trobe University, Bundoora, Melbourne, Australia.
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5
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Liu H, Ren Q, Gong M, Zuo F, Li Q, Huo D, Yuan Y, Zhang Y, Kong Y, Liu X, Lu C, Wu X. Enforced activation of the CREB/KDM2B axis prevents alcohol-induced embryonic developmental delay. Cell Rep 2024; 43:115075. [PMID: 39661511 DOI: 10.1016/j.celrep.2024.115075] [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: 05/17/2024] [Revised: 10/07/2024] [Accepted: 11/25/2024] [Indexed: 12/13/2024] Open
Abstract
Unintentional, early pregnancy alcohol consumption affects embryonic development. During the peri-implantation stage, coinciding with the transition from naive to primed pluripotency, the long isoform of KDM2B (KDM2BLF) underlies the de novo establishment of polycomb repressive complex (PRC) functions at promoters after fertilization. However, it remains unclear whether and how ethanol exposure affects this spatiotemporal chromatin setting. Here, we show that exposing peri-implantation mouse embryos to ethanol leads to impaired post-implantation development, mirrored by the delayed exit of naive pluripotency in acetaldehyde-treated embryonic stem cells. Remarkably, these abnormalities are linked to inadequate KDM2BLF expression and compromised deposition of PRC marks, which arise from cAMP response element-binding protein (CREB) inactivation. Accordingly, pharmacological activation of CREB effectively restores pluripotency transition partly dependent on KDM2BLF in vitro and ameliorates post-implantation embryonic defects in vivo. Therefore, our study highlights the pivotal role of the CREB/KDM2B axis in chromatin configuration and developmental programming, proposing potential preventive strategies against ethanol exposure-induced detrimental effects.
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Affiliation(s)
- Hang Liu
- State Key Laboratory of Experimental Hematology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Cell Biology, Tianjin Medical University, Qixiangtai Road 22, Tianjin 300070, China
| | - Qiyu Ren
- Department of Genetics, National Research Institute for Family Planning, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100081, China
| | - Meihan Gong
- State Key Laboratory of Experimental Hematology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Cell Biology, Tianjin Medical University, Qixiangtai Road 22, Tianjin 300070, China
| | - Feifei Zuo
- State Key Laboratory of Experimental Hematology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Cell Biology, Tianjin Medical University, Qixiangtai Road 22, Tianjin 300070, China
| | - Qian Li
- State Key Laboratory of Experimental Hematology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Cell Biology, Tianjin Medical University, Qixiangtai Road 22, Tianjin 300070, China
| | - Dawei Huo
- State Key Laboratory of Experimental Hematology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Cell Biology, Tianjin Medical University, Qixiangtai Road 22, Tianjin 300070, China; Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine, Liangzhu Laboratory, Institute of Hematology, Zhejiang University, Hangzhou 311113, China
| | - Ye Yuan
- State Key Laboratory of Experimental Hematology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Cell Biology, Tianjin Medical University, Qixiangtai Road 22, Tianjin 300070, China
| | - Yutong Zhang
- Department of Genetics, National Research Institute for Family Planning, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100081, China
| | - Yu Kong
- State Key Laboratory of Experimental Hematology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Cell Biology, Tianjin Medical University, Qixiangtai Road 22, Tianjin 300070, China
| | - Xiaozhi Liu
- Tianjin Key Laboratory of Epigenetics for Organ Development of Premature Infants, Tianjin 300450, China
| | - Cailing Lu
- Department of Genetics, National Research Institute for Family Planning, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100081, China.
| | - Xudong Wu
- State Key Laboratory of Experimental Hematology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Department of Cell Biology, Tianjin Medical University, Qixiangtai Road 22, Tianjin 300070, China; Tianjin Key Laboratory of Epigenetics for Organ Development of Premature Infants, Tianjin 300450, China.
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6
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Wu Y, Huang Z, Liu Y, He P, Wang Y, Yan L, Wang X, Gao S, Zhou X, Yoon CW, Sun K, Situ Y, Ho P, Zeng Y, Yuan Z, Zhu L, Zhou Q, Zhao Y, Liu T, Kwong GA, Chien S, Liu L, Wang Y. Ultrasound Control of Genomic Regulatory Toolboxes for Cancer Immunotherapy. Nat Commun 2024; 15:10444. [PMID: 39617755 PMCID: PMC11609292 DOI: 10.1038/s41467-024-54477-7] [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: 01/23/2024] [Accepted: 11/11/2024] [Indexed: 01/25/2025] Open
Abstract
There remains a critical need for the precise control of CRISPR (clustered regularly interspaced short palindromic repeats)-based technologies. Here, we engineer a set of inducible CRISPR-based tools controllable by focused ultrasound (FUS), which can penetrate deep and induce localized hyperthermia for transgene activation. We demonstrate the capabilities of FUS-inducible CRISPR, CRISPR activation (CRISPRa), and CRISPR epigenetic editor (CRISPRee) in modulating the genome and epigenome. We show that FUS-CRISPR-mediated telomere disruption primes solid tumours for chimeric antigen receptor (CAR)-T cell therapy. We further deliver FUS-CRISPR in vivo using adeno-associated viruses (AAVs), followed by FUS-induced telomere disruption and the expression of a clinically validated antigen in a subpopulation of tumour cells, functioning as "training centers" to activate synthetic Notch (synNotch) CAR-T cells to produce CARs against a universal tumour antigen to exterminate neighboring tumour cells. The FUS-CRISPR(a/ee) toolbox hence allows the noninvasive and spatiotemporal control of genomic/epigenomic reprogramming for cancer treatment.
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Affiliation(s)
- Yiqian Wu
- Shu Chien - Gene Lay Department of Bioengineering, Institute of Engineering in Medicine, University of California San Diego, La Jolla, CA, USA.
- National Biomedical Imaging Center, College of Future Technology, Peking University, Beijing, China.
| | - Ziliang Huang
- Shu Chien - Gene Lay Department of Bioengineering, Institute of Engineering in Medicine, University of California San Diego, La Jolla, CA, USA
- Alfred E. Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, USA
| | - Yahan Liu
- State Key Laboratory of Vascular Homeostasis and Remodeling, Institute of Cardiovascular Sciences, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Peixiang He
- Shu Chien - Gene Lay Department of Bioengineering, Institute of Engineering in Medicine, University of California San Diego, La Jolla, CA, USA
| | - Yuxuan Wang
- Alfred E. Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, USA
| | - Liyanran Yan
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Xinhui Wang
- National Biomedical Imaging Center, College of Future Technology, Peking University, Beijing, China
| | - Shanzi Gao
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Xintao Zhou
- National Biomedical Imaging Center, College of Future Technology, Peking University, Beijing, China
| | - Chi Woo Yoon
- Shu Chien - Gene Lay Department of Bioengineering, Institute of Engineering in Medicine, University of California San Diego, La Jolla, CA, USA
- Alfred E. Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, USA
| | - Kun Sun
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, China
| | - Yinglin Situ
- Shu Chien - Gene Lay Department of Bioengineering, Institute of Engineering in Medicine, University of California San Diego, La Jolla, CA, USA
| | - Phuong Ho
- Shu Chien - Gene Lay Department of Bioengineering, Institute of Engineering in Medicine, University of California San Diego, La Jolla, CA, USA
| | - Yushun Zeng
- Alfred E. Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, USA
| | - Zhou Yuan
- Shu Chien - Gene Lay Department of Bioengineering, Institute of Engineering in Medicine, University of California San Diego, La Jolla, CA, USA
- Alfred E. Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, USA
| | - Linshan Zhu
- Shu Chien - Gene Lay Department of Bioengineering, Institute of Engineering in Medicine, University of California San Diego, La Jolla, CA, USA
- Alfred E. Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, USA
| | - Qifa Zhou
- Alfred E. Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, USA
| | - Yunde Zhao
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Thomas Liu
- Center for Functional MRI, University of California San Diego, La Jolla, CA, USA
| | - Gabriel A Kwong
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology & Emory University, Atlanta, GA, USA
| | - Shu Chien
- Shu Chien - Gene Lay Department of Bioengineering, Institute of Engineering in Medicine, University of California San Diego, La Jolla, CA, USA
| | - Longwei Liu
- Shu Chien - Gene Lay Department of Bioengineering, Institute of Engineering in Medicine, University of California San Diego, La Jolla, CA, USA.
- Alfred E. Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, USA.
| | - Yingxiao Wang
- Shu Chien - Gene Lay Department of Bioengineering, Institute of Engineering in Medicine, University of California San Diego, La Jolla, CA, USA.
- Alfred E. Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, USA.
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7
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Edenhofer FC, Térmeg A, Ohnuki M, Jocher J, Kliesmete Z, Briem E, Hellmann I, Enard W. Generation and characterization of inducible KRAB-dCas9 iPSCs from primates for cross-species CRISPRi. iScience 2024; 27:110090. [PMID: 38947524 PMCID: PMC11214527 DOI: 10.1016/j.isci.2024.110090] [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: 09/15/2023] [Revised: 03/28/2024] [Accepted: 05/21/2024] [Indexed: 07/02/2024] Open
Abstract
Comparisons of molecular phenotypes across primates provide unique information to understand human biology and evolution, and single-cell RNA-seq CRISPR interference (CRISPRi) screens are a powerful approach to analyze them. Here, we generate and validate three human, three gorilla, and two cynomolgus iPS cell lines that carry a dox-inducible KRAB-dCas9 construct at the AAVS1 locus. We show that despite variable expression levels of KRAB-dCas9 among lines, comparable downregulation of target genes and comparable phenotypic effects are observed in a single-cell RNA-seq CRISPRi screen. Hence, we provide valuable resources for performing and further extending CRISPRi in human and non-human primates.
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Affiliation(s)
- Fiona C. Edenhofer
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Planegg, Germany
| | - Anita Térmeg
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Planegg, Germany
| | - Mari Ohnuki
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Planegg, Germany
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto 606-8501, Japan
- Hakubi Center, Kyoto University, Kyoto 606-8501, Japan
| | - Jessica Jocher
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Planegg, Germany
| | - Zane Kliesmete
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Planegg, Germany
| | - Eva Briem
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Planegg, Germany
| | - Ines Hellmann
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Planegg, Germany
| | - Wolfgang Enard
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Planegg, Germany
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8
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Murphy KC, Ruscetti M. Advances in Making Cancer Mouse Models More Accessible and Informative through Non-Germline Genetic Engineering. Cold Spring Harb Perspect Med 2024; 14:a041348. [PMID: 37277206 PMCID: PMC10982712 DOI: 10.1101/cshperspect.a041348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Genetically engineered mouse models (GEMMs) allow for modeling of spontaneous tumorigenesis within its native microenvironment in mice and have provided invaluable insights into mechanisms of tumorigenesis and therapeutic strategies to treat human disease. However, as their generation requires germline manipulation and extensive animal breeding that is time-, labor-, and cost-intensive, traditional GEMMs are not accessible to most researchers, and fail to model the full breadth of cancer-associated genetic alterations and therapeutic targets. Recent advances in genome-editing technologies and their implementation in somatic tissues of mice have ushered in a new class of mouse models: non-germline GEMMs (nGEMMs). nGEMM approaches can be leveraged to generate somatic tumors de novo harboring virtually any individual or group of genetic alterations found in human cancer in a mouse through simple procedures that do not require breeding, greatly increasing the accessibility and speed and scale on which GEMMs can be produced. Here we describe the technologies and delivery systems used to create nGEMMs and highlight new biological insights derived from these models that have rapidly informed functional cancer genomics, precision medicine, and immune oncology.
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Affiliation(s)
- Katherine C Murphy
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, USA
| | - Marcus Ruscetti
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, USA;
- Immunology and Microbiology Program, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, USA
- Cancer Center, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, USA
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9
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Chen Y, Luo X, Kang R, Cui K, Ou J, Zhang X, Liang P. Current therapies for osteoarthritis and prospects of CRISPR-based genome, epigenome, and RNA editing in osteoarthritis treatment. J Genet Genomics 2024; 51:159-183. [PMID: 37516348 DOI: 10.1016/j.jgg.2023.07.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 07/13/2023] [Accepted: 07/15/2023] [Indexed: 07/31/2023]
Abstract
Osteoarthritis (OA) is one of the most common degenerative joint diseases worldwide, causing pain, disability, and decreased quality of life. The balance between regeneration and inflammation-induced degradation results in multiple etiologies and complex pathogenesis of OA. Currently, there is a lack of effective therapeutic strategies for OA treatment. With the development of CRISPR-based genome, epigenome, and RNA editing tools, OA treatment has been improved by targeting genetic risk factors, activating chondrogenic elements, and modulating inflammatory regulators. Supported by cell therapy and in vivo delivery vectors, genome, epigenome, and RNA editing tools may provide a promising approach for personalized OA therapy. This review summarizes CRISPR-based genome, epigenome, and RNA editing tools that can be applied to the treatment of OA and provides insights into the development of CRISPR-based therapeutics for OA treatment. Moreover, in-depth evaluations of the efficacy and safety of these tools in human OA treatment are needed.
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Affiliation(s)
- Yuxi Chen
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Xiao Luo
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Rui Kang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Kaixin Cui
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Jianping Ou
- Center for Reproductive Medicine, The Third Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Xiya Zhang
- Center for Reproductive Medicine, The Third Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong 510630, China.
| | - Puping Liang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China.
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10
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Chen C, Wang Z, Qin Y. CRISPR/Cas9 system: recent applications in immuno-oncology and cancer immunotherapy. Exp Hematol Oncol 2023; 12:95. [PMID: 37964355 PMCID: PMC10647168 DOI: 10.1186/s40164-023-00457-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 11/08/2023] [Indexed: 11/16/2023] Open
Abstract
Clustered regulatory interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) is essentially an adaptive immunity weapon in prokaryotes against foreign DNA. This system inspires the development of genome-editing technology in eukaryotes. In biomedicine research, CRISPR has offered a powerful platform to establish tumor-bearing models and screen potential targets in the immuno-oncology field, broadening our insights into cancer genomics. In translational medicine, the versatile CRISPR/Cas9 system exhibits immense potential to break the current limitations of cancer immunotherapy, thereby expanding the feasibility of adoptive cell therapy (ACT) in treating solid tumors. Herein, we first explain the principles of CRISPR/Cas9 genome editing technology and introduce CRISPR as a tool in tumor modeling. We next focus on the CRISPR screening for target discovery that reveals tumorigenesis, immune evasion, and drug resistance mechanisms. Moreover, we discuss the recent breakthroughs of genetically modified ACT using CRISPR/Cas9. Finally, we present potential challenges and perspectives in basic research and clinical translation of CRISPR/Cas9. This review provides a comprehensive overview of CRISPR/Cas9 applications that advance our insights into tumor-immune interaction and lay the foundation to optimize cancer immunotherapy.
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Affiliation(s)
- Chen Chen
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zehua Wang
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yanru Qin
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
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11
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Armendariz DA, Sundarrajan A, Hon GC. Breaking enhancers to gain insights into developmental defects. eLife 2023; 12:e88187. [PMID: 37497775 PMCID: PMC10374278 DOI: 10.7554/elife.88187] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 07/19/2023] [Indexed: 07/28/2023] Open
Abstract
Despite ground-breaking genetic studies that have identified thousands of risk variants for developmental diseases, how these variants lead to molecular and cellular phenotypes remains a gap in knowledge. Many of these variants are non-coding and occur at enhancers, which orchestrate key regulatory programs during development. The prevailing paradigm is that non-coding variants alter the activity of enhancers, impacting gene expression programs, and ultimately contributing to disease risk. A key obstacle to progress is the systematic functional characterization of non-coding variants at scale, especially since enhancer activity is highly specific to cell type and developmental stage. Here, we review the foundational studies of enhancers in developmental disease and current genomic approaches to functionally characterize developmental enhancers and their variants at scale. In the coming decade, we anticipate systematic enhancer perturbation studies to link non-coding variants to molecular mechanisms, changes in cell state, and disease phenotypes.
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Affiliation(s)
- Daniel A Armendariz
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, United States
| | - Anjana Sundarrajan
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, United States
| | - Gary C Hon
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, United States
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, United States
- Lyda Hill Department of Bioinformatics, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, United States
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12
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Li Y, Wu P, Zhu M, Liang M, Zhang L, Zong Y, Wan M. High-Performance Delivery of a CRISPR Interference System via Lipid-Polymer Hybrid Nanoparticles Combined with Ultrasound-Mediated Microbubble Destruction for Tumor-Specific Gene Repression. Adv Healthc Mater 2023; 12:e2203082. [PMID: 36591868 DOI: 10.1002/adhm.202203082] [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] [Indexed: 01/03/2023]
Abstract
The dCas9-based CRISPR interference (CRISPRi) system efficiently silences genes without causing detectable off-target activity, thus showing great potential for the treatment of cancer at the transcriptional level. However, due to the large size of the commonly used CRISPRi system, effective delivery of the system has been a challenge that hinders its application in the clinic. Herein, a combination of pH-responsive lipid-polymer hybrid nanoparticles (PLPNs) and ultrasound-mediated microbubble destruction (UMMD) is used for the delivery of the CRISPRi system. The core-shell structure of PLPNs can effectively be loaded with the CRISPRi plasmid, and increases the time spent in the circulating in vivo, and "actively target" cancer cells. Moreover, the combination of PLPNs with UMMD achieves a higher cellular uptake of the CRISPRi plasmid in vitro and retention in vivo. Furthermore, when PLPNs loaded with a CRISPRi plasmid that targets microRNA-10b (miR-10b) are used in combination with UMMD, it results in the effective repression of miR-10b in breast cancer, simultaneous disturbance of multiple cell migration and invasion-related signaling pathways, and a significant inhibition of lung metastasis. Thus, the established system presents a versatile, highly efficient, and safe strategy for delivery of the CRISPRi system both in vitro and in vivo.
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Affiliation(s)
- Yan Li
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Department of Biomedical Engineering, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P. R. China
| | - Pengying Wu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Department of Biomedical Engineering, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P. R. China
| | - Mingting Zhu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Department of Biomedical Engineering, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P. R. China
| | - Meiling Liang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Department of Biomedical Engineering, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P. R. China
| | - Lei Zhang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Department of Biomedical Engineering, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P. R. China
| | - Yujin Zong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Department of Biomedical Engineering, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P. R. China
| | - Mingxi Wan
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Department of Biomedical Engineering, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P. R. China
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13
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Shi H, Doench JG, Chi H. CRISPR screens for functional interrogation of immunity. Nat Rev Immunol 2022:10.1038/s41577-022-00802-4. [DOI: 10.1038/s41577-022-00802-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2022] [Indexed: 12/13/2022]
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14
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Kanafi MM, Tavallaei M. Overview of advances in CRISPR/deadCas9 technology and its applications in human diseases. Gene 2022; 830:146518. [PMID: 35447246 DOI: 10.1016/j.gene.2022.146518] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 04/05/2022] [Accepted: 04/14/2022] [Indexed: 12/20/2022]
Abstract
Prokaryotes possess an adaptive immune system using various CRISPR associated (Cas) genes to make an archive of records from invading phages and eliminate them upon re-exposure when specialized Cas proteins cut foreign DNA into small pieces. On the basis of the different types of Cas proteins, CRISPR systems seen in some prokaryotic genomes, are different to each other. It has been proved that CRISPR has a great potential for genome engineering. Studies have also demonstrated that in comparison to the preceding genome engineering tools CRISPR/Cas systems can be harnessed as a flexible tool with easy multiplexing and scaling ability. Recent studies suggest that CRISPR/Cas systems can also be used for non-genome engineering roles. Isolation and identification of new Cas proteins or modification of existing ones are effectively increasing the number of CRISPR applications and helps its development. D10A and H840A mutations at RuvC and HNH endonuclease domains of wild type Streptococcus pyogenes Cas9 (SpCas9) respectively creates a nuclease, dead Cas9 (dCas9) molecule, that does not cut target DNA but still retains its capability for binding to target DNA based on the gRNA targeting sequence. In this article we review the potentials of this enzyme, dCas9, toward development of the applications of CRISPR/dCas9 technology in fields such as; visualization of genomic loci, disease diagnosis and transcriptional repression and activation.
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Affiliation(s)
| | - Mahmood Tavallaei
- Human Genetic Research Centre, Baqiyatallah University of Medical Science, Tehran, Iran
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15
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CpG island reconfiguration for the establishment and synchronization of polycomb functions upon exit from naive pluripotency. Mol Cell 2022; 82:1169-1185.e7. [PMID: 35202573 DOI: 10.1016/j.molcel.2022.01.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 12/03/2021] [Accepted: 01/27/2022] [Indexed: 12/12/2022]
Abstract
Polycomb group (PcG) proteins are essential for post-implantation development by depositing repressive histone modifications at promoters, mainly CpG islands (CGIs), of developmental regulator genes. However, promoter PcG marks are erased after fertilization and de novo established in peri-implantation embryos, coinciding with the transition from naive to primed pluripotency. Nevertheless, the molecular basis for this establishment remains unknown. In this study, we show that the expression of the long KDM2B isoform (KDM2BLF), which contains the demethylase domain, is specifically induced at peri-implantation and that its H3K36me2 demethylase activity is required for PcG enrichment at CGIs. Moreover, KDM2BLF interacts with BRG1/BRM-associated factor (BAF) and stabilizes BAF occupancy at CGIs for subsequent gain of accessibility, which precedes PcG enrichment. Consistently, KDM2BLF inactivation results in significantly delayed post-implantation development. In summary, our data unveil dynamic chromatin configuration of CGIs during exit from naive pluripotency and provide a conceptual framework for the spatiotemporal establishment of PcG functions.
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16
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Dong F, Qin X, Wang B, Li Q, Hu J, Cheng X, Guo D, Cheng F, Fang C, Tan Y, Yan H, He Y, Sun X, Yuan Y, Liu H, Li T, Zhao Y, Kang C, Wu X. ALKBH5 Facilitates Hypoxia-Induced Paraspeckle Assembly and IL8 Secretion to Generate an Immunosuppressive Tumor Microenvironment. Cancer Res 2021; 81:5876-5888. [PMID: 34670781 DOI: 10.1158/0008-5472.can-21-1456] [Citation(s) in RCA: 142] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 08/26/2021] [Accepted: 10/14/2021] [Indexed: 11/16/2022]
Abstract
The dynamic changes of RNA N6-methyl-adenosine (m6A) during cancer progression contribute to quick adaption to microenvironmental changes. Here, we profiled the cancer cell m6A dynamics in the hypoxic tumor niche and its pathological consequences in glioblastoma multiforme (GBM). The m6A demethylase ALKBH5 was induced in GBM models under hypoxic conditions and was associated with a hypoxic gene signature in GBM patient samples. Depletion or inactivation of ALKBH5 in GBM cells significantly suppressed hypoxia-induced tumor-associated macrophage (TAM) recruitment and immunosuppression in allograft tumors. Expression and secretion of CXCL8/IL8 were significantly suppressed in ALKBH5-deficient tumors. However, ALKBH5 did not regulate CXCL8 m6A directly. Instead, hypoxia-induced ALKBH5 erased m6A deposition from the lncRNA NEAT1, stabilizing the transcript and facilitating NEAT1-mediated paraspeckle assembly, which led to relocation of the transcriptional repressor SFPQ from the CXCL8 promoter to paraspeckles and, ultimately, upregulation of CXCL8/IL8 expression. Accordingly, ectopic expression of CXCL8 in ALKBH5-deficient GBM cells partially restored TAM recruitment and tumor progression. Together, this study links hypoxia-induced epitranscriptomic changes to the emergence of an immunosuppressive microenvironment facilitating tumor evasion. SIGNIFICANCE: Hypoxia induces tumor immune microenvironment remodeling through an ALKBH5-mediated epigenetic and epitranscriptomic mechanism, providing potential immunotherapeutic strategies for treating glioblastoma.
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Affiliation(s)
- Feng Dong
- Department of Neurosurgery, Tianjin Medical University General Hospital and Laboratory of Neuro-Oncology, Tianjin Neurological Institute, Tianjin, China
- Department of Cell Biology, State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University, Tianjin, China
| | - Xiaoyang Qin
- Department of Cell Biology, State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University, Tianjin, China
| | - Baofeng Wang
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qian Li
- Department of Cell Biology, State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University, Tianjin, China
| | - Jinyang Hu
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Neurosurgery, The People's Hospital of China Three Gorges University, Yichang, China
| | - Xuan Cheng
- The First Department of Breast Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Huanhuxi Road, Hexi District, Tianjin, China
| | - Dongsheng Guo
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fangling Cheng
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chuan Fang
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Yanli Tan
- Department of Pathology, Affiliated Hospital of Hebei University, Baoding, China
| | - Han Yan
- Department of Cell Biology, State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University, Tianjin, China
| | - You He
- Department of Cell Biology, State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University, Tianjin, China
| | - Xiaoyu Sun
- Department of Cell Biology, State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University, Tianjin, China
| | - Ye Yuan
- Department of Cell Biology, State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University, Tianjin, China
| | - Hang Liu
- Department of Cell Biology, State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University, Tianjin, China
| | - Ting Li
- Department of Cell Biology, State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University, Tianjin, China
| | - Yingying Zhao
- Department of Cell Biology, State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University, Tianjin, China
| | - Chunsheng Kang
- Department of Neurosurgery, Tianjin Medical University General Hospital and Laboratory of Neuro-Oncology, Tianjin Neurological Institute, Tianjin, China
| | - Xudong Wu
- Department of Neurosurgery, Tianjin Medical University General Hospital and Laboratory of Neuro-Oncology, Tianjin Neurological Institute, Tianjin, China.
- Department of Cell Biology, State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University, Tianjin, China
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Sino-US Center for Lymphoma and Leukemia Research, Tianjin, China
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17
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Dai Z, Li R, Hou Y, Li Q, Zhao K, Li T, Li MJ, Wu X. Inducible CRISPRa screen identifies putative enhancers. J Genet Genomics 2021; 48:917-927. [PMID: 34531148 DOI: 10.1016/j.jgg.2021.06.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/21/2021] [Accepted: 06/07/2021] [Indexed: 12/28/2022]
Abstract
Enhancers are critical cis-regulatory elements that regulate spatiotemporal gene expression and control cell fates. However, the identification of enhancers in native cellular contexts still remains a challenge. Here, we develop an inducible CRISPR activation (CRISPRa) system by transgenic expression of doxycycline (Dox)-inducible dCas9-VPR in mouse embryonic stem cells (iVPR ESC). With this line, a simple introduction of specific guide RNAs targeting promoters or enhancers allows us to realize the effect of CRISPRa in an inducible, reversible, and Dox concentration-dependent manner. Taking advantage of this system, we induce tiled CRISPRa across genomic regions (105 kilobases) surrounding T (Brachyury), one of the key mesodermal development regulator genes. Moreover, we identify several CRISPRa-responsive elements with chromatin features of putative enhancers, including a region the homologous sequence in which humans harbors a body height risk variant. Genetic deletion of this region in ESC does affect subsequent T gene activation and osteogenic differentiation. Therefore, our inducible CRISPRa ESC line provides a convenient platform for high-throughput screens of putative enhancers.
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Affiliation(s)
- Zhongye Dai
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases, Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Rui Li
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases, Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Yuying Hou
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases, Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Qian Li
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases, Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Ke Zhao
- Department of Pharmacology, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Tianjin 300070, China
| | - Ting Li
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases, Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Mulin Jun Li
- Department of Pharmacology, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Tianjin 300070, China
| | - Xudong Wu
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Cellular Homeostasis and Human Diseases, Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China; Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin 300052, China; Tianjin Key Laboratory of Epigenetics for Organ Development of Premature Infants, Tianjin 300450, China.
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Li Y, Zhou LQ. dCas9 techniques for transcriptional repression in mammalian cells: Progress, applications and challenges. Bioessays 2021; 43:e2100086. [PMID: 34327721 DOI: 10.1002/bies.202100086] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 07/07/2021] [Accepted: 07/08/2021] [Indexed: 01/10/2023]
Abstract
Innovative loss-of-function techniques developed in recent years have made it much easier to target specific genomic loci at transcriptional levels. CRISPR interference (CRISPRi) has been proven to be the most effective and specific tool to knock down any gene of interest in mammalian cells. The catalytically deactivated Cas9 (dCas9) can be fused with transcription repressors to downregulate gene expression specified by sgRNA complementary to target genomic sequence. Although CRISPRi has huge potential for gene knockdown, there is still a lack of systematic guidelines for efficient and widespread use. Here we describe the working mechanism and development of CRISPRi, designing principles of sgRNA, delivery methods and applications in mammalian cells in detail. Finally, we propose possible solutions and future directions with regard to current challenges.
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Affiliation(s)
- Yuanyuan Li
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Li-Quan Zhou
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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