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Zhang R, Chai N, Liu T, Zheng Z, Lin Q, Xie X, Wen J, Yang Z, Liu YG, Zhu Q. The type V effectors for CRISPR/Cas-mediated genome engineering in plants. Biotechnol Adv 2024; 74:108382. [PMID: 38801866 DOI: 10.1016/j.biotechadv.2024.108382] [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: 01/15/2024] [Revised: 05/07/2024] [Accepted: 05/24/2024] [Indexed: 05/29/2024]
Abstract
A plethora of CRISPR effectors, such as Cas3, Cas9, and Cas12a, are commonly employed as gene editing tools. Among these, Cas12 effectors developed based on Class II type V proteins exhibit distinct characteristics compared to Class II type VI and type II effectors, such as their ability to generate non-allelic DNA double-strand breaks, their compact structures, and the presence of a single RuvC-like nuclease domain. Capitalizing on these advantages, Cas12 family proteins have been increasingly explored and utilized in recent years. However, the characteristics and applications of different subfamilies within the type V protein family have not been systematically summarized. In this review, we focus on the characteristics of type V effector (CRISPR/Cas12) proteins and the current methods used to discover new effector proteins. We also summarize recent modifications based on engineering of type V effectors. In addition, we introduce the applications of type V effectors for gene editing in animals and plants, including the development of base editors, tools for regulating gene expression, methods for gene targeting, and biosensors. We emphasize the prospects for development and application of CRISPR/Cas12 effectors with the goal of better utilizing toolkits based on this protein family for crop improvement and enhanced agricultural production.
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Affiliation(s)
- Ruixiang Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Nan Chai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Taoli Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Zhiye Zheng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Qiupeng Lin
- College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Xianrong Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Jun Wen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Zi Yang
- College of Natural & Agricultural Sciences, University of California, Riverside, 900 University Ave, Riverside, CA 92507, USA
| | - Yao-Guang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; College of Agriculture, South China Agricultural University, Guangzhou 510642, China.
| | - Qinlong Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; College of Agriculture, South China Agricultural University, Guangzhou 510642, China.
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2
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Roth GV, Gengaro IR, Qi LS. Precision epigenetic editing: Technological advances, enduring challenges, and therapeutic applications. Cell Chem Biol 2024:S2451-9456(24)00309-X. [PMID: 39137782 DOI: 10.1016/j.chembiol.2024.07.007] [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: 03/04/2024] [Revised: 05/31/2024] [Accepted: 07/15/2024] [Indexed: 08/15/2024]
Abstract
The epigenome is a complex framework through which gene expression is precisely and flexibly modulated to incorporate heritable memory and responses to environmental stimuli. It governs diverse cellular processes, including cell fate, disease, and aging. The need to understand this system and precisely control gene expression outputs for therapeutic purposes has precipitated the development of a diverse set of epigenetic editing tools. Here, we review the existing toolbox for targeted epigenetic editing, technical considerations of the current technologies, and opportunities for future development. We describe applications of therapeutic epigenetic editing and their potential for treating disease, with a discussion of ongoing delivery challenges that impede certain clinical interventions, particularly in the brain. With simultaneous advancements in available engineering tools and appropriate delivery technologies, we predict that epigenetic editing will increasingly cement itself as a powerful approach for safely treating a wide range of disorders in all tissues of the body.
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Affiliation(s)
- Goldie V Roth
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
| | - Isabella R Gengaro
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA; Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Lei S Qi
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA; Department of Bioengineering, Stanford University, Stanford, CA, USA; Chan Zuckerberg Biohub - San Francisco, San Francisco, CA, USA.
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3
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Melore SM, Hamilton MC, Reddy TE. HyperCas12a enables highly-multiplexed epigenome editing screens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.08.602263. [PMID: 39026853 PMCID: PMC11257430 DOI: 10.1101/2024.07.08.602263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Interactions between multiple genes or cis-regulatory elements (CREs) underlie a wide range of biological processes in both health and disease. High-throughput screens using dCas9 fused to epigenome editing domains have allowed researchers to assess the impact of activation or repression of both coding and non-coding genomic regions on a phenotype of interest, but assessment of genetic interactions between those elements has been limited to pairs. Here, we combine a hyper-efficient version of Lachnospiraceae bacterium dCas12a (dHyperLbCas12a) with RNA Polymerase II expression of long CRISPR RNA (crRNA) arrays to enable efficient highly-multiplexed epigenome editing. We demonstrate that this system is compatible with several activation and repression domains, including the P300 histone acetyltransferase domain and SIN3A interacting domain (SID). We also show that the dCas12a platform can perform simultaneous activation and repression using a single crRNA array via co-expression of multiple dCas12a orthologues. Lastly, demonstrate that the dCas12a system is highly effective for high-throughput screens. We use dHyperLbCas12a-KRAB and a ~19,000-member barcoded library of crRNA arrays containing six crRNAs each to dissect the independent and combinatorial contributions of CREs to the dose-dependent control of gene expression at a glucocorticoid-responsive locus. The tools and methods introduced here create new possibilities for highly multiplexed control of gene expression in a wide variety of biological systems.
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Affiliation(s)
- Schuyler M. Melore
- University Program in Genetics & Genomics, Duke University, Durham, NC, USA
- Department of Biostatistics & Bioinformatics, Duke University School of Medicine, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
- Center for Combinatorial Gene Regulation, Duke University, Durham, NC, USA
| | - Marisa C. Hamilton
- University Program in Genetics & Genomics, Duke University, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
- Center for Combinatorial Gene Regulation, Duke University, Durham, NC, USA
| | - Timothy E. Reddy
- University Program in Genetics & Genomics, Duke University, Durham, NC, USA
- Department of Biostatistics & Bioinformatics, Duke University School of Medicine, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
- Center for Combinatorial Gene Regulation, Duke University, Durham, NC, USA
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4
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Zhou C, Wagner S, Liang FS. Induced proximity labeling and editing for epigenetic research. Cell Chem Biol 2024; 31:1118-1131. [PMID: 38866004 PMCID: PMC11193966 DOI: 10.1016/j.chembiol.2024.05.005] [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: 04/05/2024] [Revised: 05/12/2024] [Accepted: 05/21/2024] [Indexed: 06/14/2024]
Abstract
Epigenetic regulation plays a pivotal role in various biological and disease processes. Two key lines of investigation have been pursued that aim to unravel endogenous epigenetic events at particular genes (probing) and artificially manipulate the epigenetic landscape (editing). The concept of induced proximity has inspired the development of powerful tools for epigenetic research. Induced proximity strategies involve bringing molecular effectors into spatial proximity with specific genomic regions to achieve the probing or manipulation of local epigenetic environments with increased proximity. In this review, we detail the development of induced proximity methods and applications in shedding light on the intricacies of epigenetic regulation.
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Affiliation(s)
- Chenwei Zhou
- Department of Chemistry, Case Western Reserve University, 2080 Adelbert Road, Cleveland, OH 44106, USA
| | - Sarah Wagner
- Department of Chemistry, Case Western Reserve University, 2080 Adelbert Road, Cleveland, OH 44106, USA
| | - Fu-Sen Liang
- Department of Chemistry, Case Western Reserve University, 2080 Adelbert Road, Cleveland, OH 44106, USA.
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5
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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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6
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Fadul SM, Arshad A, Mehmood R. CRISPR-based epigenome editing: mechanisms and applications. Epigenomics 2023; 15:1137-1155. [PMID: 37990877 DOI: 10.2217/epi-2023-0281] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023] Open
Abstract
Epigenomic anomalies contribute significantly to the development of numerous human disorders. The development of epigenetic research tools is essential for understanding how epigenetic marks contribute to gene expression. A gene-editing technique known as CRISPR (clustered regularly interspaced short palindromic repeats) typically targets a particular DNA sequence using a guide RNA (gRNA). CRISPR/Cas9 technology has been remodeled for epigenome editing by generating a 'dead' Cas9 protein (dCas9) that lacks nuclease activity and juxtaposing it with an epigenetic effector domain. Based on fusion partners of dCas9, a specific epigenetic state can be achieved. CRISPR-based epigenome editing has widespread application in drug screening, cancer treatment and regenerative medicine. This paper discusses the tools developed for CRISPR-based epigenome editing and their applications.
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Affiliation(s)
- Shaima M Fadul
- Department of Life Sciences, College of Science & General Studies, Alfaisal University, Riyadh, 11533, Kingdom of Saudi Arabia
| | - Aleeza Arshad
- Medical Teaching Insitute, Ayub Teaching Hospital, Abbottabad, 22020, Pakistan
| | - Rashid Mehmood
- Department of Life Sciences, College of Science & General Studies, Alfaisal University, Riyadh, 11533, Kingdom of Saudi Arabia
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7
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Zhang X, Wang X, Lv J, Huang H, Wang J, Zhuo M, Tan Z, Huang G, Liu J, Liu Y, Li M, Lin Q, Li L, Ma S, Huang T, Lin Y, Zhao X, Rong Z. Engineered circular guide RNAs boost CRISPR/Cas12a- and CRISPR/Cas13d-based DNA and RNA editing. Genome Biol 2023; 24:145. [PMID: 37353840 PMCID: PMC10288759 DOI: 10.1186/s13059-023-02992-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: 05/04/2022] [Accepted: 06/15/2023] [Indexed: 06/25/2023] Open
Abstract
BACKGROUND The CRISPR/Cas12a and CRISPR/Cas13d systems are widely used for fundamental research and hold great potential for future clinical applications. However, the short half-life of guide RNAs (gRNAs), particularly free gRNAs without Cas nuclease binding, limits their editing efficiency and durability. RESULTS Here, we engineer circular free gRNAs (cgRNAs) to increase their stability, and thus availability for Cas12a and Cas13d processing and loading, to boost editing. cgRNAs increases the efficiency of Cas12a-based transcription activators and genomic DNA cleavage by approximately 2.1- to 40.2-fold for single gene editing and 1.7- to 2.1-fold for multiplexed gene editing than their linear counterparts, without compromising specificity, across multiple sites and cell lines. Similarly, the RNA interference efficiency of Cas13d is increased by around 1.8-fold. In in vivo mouse liver, cgRNAs are more potent in activating gene expression and cleaving genomic DNA. CONCLUSIONS CgRNAs enable more efficient programmable DNA and RNA editing for Cas12a and Cas13d with broad applicability for fundamental research and gene therapy.
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Affiliation(s)
- Xin Zhang
- Dongguan Institute of Clinical Cancer Research, Affiliated Dongguan Hospital, Southern Medical University, Dongguan, 523058, China
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, 510515, China
| | - Xinlong Wang
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, 510515, China
| | - Jie Lv
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, 510515, China
| | - Hongxin Huang
- Dermatology Hospital, Southern Medical University, Guangzhou, 510091, China
| | - Jiahong Wang
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, 510515, China
| | - Ma Zhuo
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, 510515, China
| | - Zhihong Tan
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, 510515, China
| | - Guanjie Huang
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, 510515, China
| | - Jiawei Liu
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, 510515, China
| | - Yuchen Liu
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, 510515, China
| | - Mengrao Li
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, 510515, China
| | - Qixiao Lin
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, 510515, China
| | - Lian Li
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, 510515, China
| | - Shufeng Ma
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, 510515, China
- Department of Nephrology, Shenzhen Hospital, Southern Medical University, Shenzhen, 518110, China
| | - Tao Huang
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, 510515, China
| | - Ying Lin
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, 510515, China
| | - Xiaoyang Zhao
- Department of Development, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, 510515, China
| | - Zhili Rong
- Dongguan Institute of Clinical Cancer Research, Affiliated Dongguan Hospital, Southern Medical University, Dongguan, 523058, China
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, 510515, China
- Dermatology Hospital, Southern Medical University, Guangzhou, 510091, China
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Ma S, Liao K, Li M, Wang X, Lv J, Zhang X, Huang H, Li L, Huang T, Guo X, Lin Y, Rong Z. Phase-separated DropCRISPRa platform for efficient gene activation in mammalian cells and mice. Nucleic Acids Res 2023; 51:5271-5284. [PMID: 37094074 PMCID: PMC10250237 DOI: 10.1093/nar/gkad301] [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: 04/05/2023] [Accepted: 04/21/2023] [Indexed: 04/26/2023] Open
Abstract
Liquid-liquid phase separation (LLPS) plays a critical role in regulating gene transcription via the formation of transcriptional condensates. However, LLPS has not been reported to be engineered as a tool to activate endogenous gene expression in mammalian cells or in vivo. Here, we developed a droplet-forming CRISPR (clustered regularly interspaced short palindromic repeats) gene activation system (DropCRISPRa) to activate transcription with high efficiency via combining the CRISPR-SunTag system with FETIDR-AD fusion proteins, which contain an N-terminal intrinsically disordered region (IDR) of a FET protein (FUS or TAF15) and a transcription activation domain (AD, VP64/P65/VPR). In this system, the FETIDR-AD fusion protein formed phase separation condensates at the target sites, which could recruit endogenous BRD4 and RNA polymerase II with an S2 phosphorylated C-terminal domain (CTD) to enhance transcription elongation. IDR-FUS9Y>S and IDR-FUSG156E, two mutants with deficient and aberrant phase separation respectively, confirmed that appropriate phase separation was required for efficient gene activation. Further, the DropCRISPRa system was compatible with a broad set of CRISPR-associated (Cas) proteins and ADs, including dLbCas12a, dAsCas12a, dSpCas9 and the miniature dUnCas12f1, and VP64, P65 and VPR. Finally, the DropCRISPRa system could activate target genes in mice. Therefore, this study provides a robust tool to activate gene expression for foundational research and potential therapeutics.
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Affiliation(s)
- Shufeng Ma
- Department of Nephrology, Shenzhen Hospital, Southern Medical University, Shenzhen 518110, China
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou 510515, China
| | - Kaitong Liao
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou 510515, China
| | - Mengrao Li
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou 510515, China
| | - Xinlong Wang
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou 510515, China
| | - Jie Lv
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou 510515, China
| | - Xin Zhang
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou 510515, China
- Affiliated Dongguan Hospital, Southern Medical University, (Dongguan People's Hospital), Dongguan 523058, China
| | - Hongxin Huang
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
| | - Lian Li
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou 510515, China
| | - Tao Huang
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou 510515, China
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
| | - Xiaohua Guo
- Department of Nephrology, Shenzhen Hospital, Southern Medical University, Shenzhen 518110, China
| | - Ying Lin
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou 510515, China
- Experimental Education/Administration Center, School of Basic Medical Science, Southern Medical University, Guangzhou 510515, China
| | - Zhili Rong
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou 510515, China
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
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9
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Meng X, Wu TG, Lou QY, Niu KY, Jiang L, Xiao QZ, Xu T, Zhang L. Optimization of CRISPR-Cas system for clinical cancer therapy. Bioeng Transl Med 2023; 8:e10474. [PMID: 36925702 PMCID: PMC10013785 DOI: 10.1002/btm2.10474] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/24/2022] [Accepted: 12/07/2022] [Indexed: 12/25/2022] Open
Abstract
Cancer is a genetic disease caused by alterations in genome and epigenome and is one of the leading causes for death worldwide. The exploration of disease development and therapeutic strategies at the genetic level have become the key to the treatment of cancer and other genetic diseases. The functional analysis of genes and mutations has been slow and laborious. Therefore, there is an urgent need for alternative approaches to improve the current status of cancer research. Gene editing technologies provide technical support for efficient gene disruption and modification in vivo and in vitro, in particular the use of clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems. Currently, the applications of CRISPR-Cas systems in cancer rely on different Cas effector proteins and the design of guide RNAs. Furthermore, effective vector delivery must be met for the CRISPR-Cas systems to enter human clinical trials. In this review article, we describe the mechanism of the CRISPR-Cas systems and highlight the applications of class II Cas effector proteins. We also propose a synthetic biology approach to modify the CRISPR-Cas systems, and summarize various delivery approaches facilitating the clinical application of the CRISPR-Cas systems. By modifying the CRISPR-Cas system and optimizing its in vivo delivery, promising and effective treatments for cancers using the CRISPR-Cas system are emerging.
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Affiliation(s)
- Xiang Meng
- College & Hospital of Stomatology Anhui Medical University, Key Laboratory of Oral Diseases Research of Anhui Province Hefei People's Republic of China
| | - Tian-Gang Wu
- College & Hospital of Stomatology Anhui Medical University, Key Laboratory of Oral Diseases Research of Anhui Province Hefei People's Republic of China
| | - Qiu-Yue Lou
- Anhui Provincial Center for Disease Control and Prevention Hefei People's Republic of China
| | - Kai-Yuan Niu
- Clinical Pharmacology, William Harvey Research Institute (WHRI), Barts and The London School of Medicine and Dentistry Queen Mary University of London (QMUL) Heart Centre (G23) London UK.,Department of Otolaryngology The Third Affiliated Hospital of Anhui Medical University Hefei China
| | - Lei Jiang
- College & Hospital of Stomatology Anhui Medical University, Key Laboratory of Oral Diseases Research of Anhui Province Hefei People's Republic of China
| | - Qing-Zhong Xiao
- Clinical Pharmacology, William Harvey Research Institute (WHRI), Barts and The London School of Medicine and Dentistry Queen Mary University of London (QMUL) Heart Centre (G23) London UK
| | - Tao Xu
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products Anhui Medical University Hefei China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province Hefei China
| | - Lei Zhang
- College & Hospital of Stomatology Anhui Medical University, Key Laboratory of Oral Diseases Research of Anhui Province Hefei People's Republic of China.,Department of Periodontology Anhui Stomatology Hospital Affiliated to Anhui Medical University Hefei China
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10
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Toward the Development of Epigenome Editing-Based Therapeutics: Potentials and Challenges. Int J Mol Sci 2023; 24:ijms24054778. [PMID: 36902207 PMCID: PMC10003136 DOI: 10.3390/ijms24054778] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/27/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
The advancement in epigenetics research over the past several decades has led to the potential application of epigenome-editing technologies for the treatment of various diseases. In particular, epigenome editing is potentially useful in the treatment of genetic and other related diseases, including rare imprinted diseases, as it can regulate the expression of the epigenome of the target region, and thereby the causative gene, with minimal or no modification of the genomic DNA. Various efforts are underway to successfully apply epigenome editing in vivo, such as improving target specificity, enzymatic activity, and drug delivery for the development of reliable therapeutics. In this review, we introduce the latest findings, summarize the current limitations and future challenges in the practical application of epigenome editing for disease therapy, and introduce important factors to consider, such as chromatin plasticity, for a more effective epigenome editing-based therapy.
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11
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Karagyaur M, Primak A, Efimenko A, Skryabina M, Tkachuk V. The Power of Gene Technologies: 1001 Ways to Create a Cell Model. Cells 2022; 11:cells11203235. [PMID: 36291103 PMCID: PMC9599997 DOI: 10.3390/cells11203235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/01/2022] [Accepted: 10/12/2022] [Indexed: 12/04/2022] Open
Abstract
Modern society faces many biomedical challenges that require urgent solutions. Two of the most important include the elucidation of mechanisms of socially significant diseases and the development of prospective drug treatments for these diseases. Experimental cell models are a convenient tool for addressing many of these problems. The power of cell models is further enhanced when combined with gene technologies, which allows the examination of even more subtle changes within the structure of the genome and permits testing of proteins in a native environment. The list and possibilities of these recently emerging technologies are truly colossal, which requires a rethink of a number of approaches for obtaining experimental cell models. In this review, we analyze the possibilities and limitations of promising gene technologies for obtaining cell models, and also give recommendations on the development and creation of relevant models. In our opinion, this review will be useful for novice cell biologists, as it provides some reference points in the rapidly growing universe of gene and cell technologies.
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Affiliation(s)
- Maxim Karagyaur
- Institute for Regenerative Medicine, Medical Research and Education Center, Lomonosov Moscow State University, 27/10, Lomonosovsky Ave., 119192 Moscow, Russia
- Faculty of Medicine, Lomonosov Moscow State University, 27/1, Lomonosovsky Ave., 119192 Moscow, Russia
- Correspondence:
| | - Alexandra Primak
- Faculty of Medicine, Lomonosov Moscow State University, 27/1, Lomonosovsky Ave., 119192 Moscow, Russia
| | - Anastasia Efimenko
- Institute for Regenerative Medicine, Medical Research and Education Center, Lomonosov Moscow State University, 27/10, Lomonosovsky Ave., 119192 Moscow, Russia
- Faculty of Medicine, Lomonosov Moscow State University, 27/1, Lomonosovsky Ave., 119192 Moscow, Russia
| | - Mariya Skryabina
- Faculty of Medicine, Lomonosov Moscow State University, 27/1, Lomonosovsky Ave., 119192 Moscow, Russia
| | - Vsevolod Tkachuk
- Institute for Regenerative Medicine, Medical Research and Education Center, Lomonosov Moscow State University, 27/10, Lomonosovsky Ave., 119192 Moscow, Russia
- Faculty of Medicine, Lomonosov Moscow State University, 27/1, Lomonosovsky Ave., 119192 Moscow, Russia
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12
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Zhai H, Cui L, Xiong Z, Qi Q, Hou J. CRISPR-mediated protein-tagging signal amplification systems for efficient transcriptional activation and repression in Saccharomyces cerevisiae. Nucleic Acids Res 2022; 50:5988-6000. [PMID: 35641106 PMCID: PMC9178002 DOI: 10.1093/nar/gkac463] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 04/24/2022] [Accepted: 05/17/2022] [Indexed: 11/14/2022] Open
Abstract
Saccharomyces cerevisiae is an important model eukaryotic microorganism and widely applied in fundamental research and the production of various chemicals. Its ability to efficiently and precisely control the expression of multiple genes is valuable for metabolic engineering. The clustered regularly interspaced short palindromic repeats (CRISPR)-mediated regulation enables complex gene expression programming; however, the regulation efficiency is often limited by the efficiency of pertinent regulators. Here, we developed CRISPR-mediated protein-tagging signal amplification system for simultaneous multiplexed gene activation and repression in S. cerevisiae. By introducing protein scaffolds (SPY and SunTag systems) to recruit multiple copies of regulators to different nuclease-deficient CRISPR proteins and design optimization, our system amplified gene regulation efficiency significantly. The gene activation and repression efficiencies reached as high as 34.9-fold and 95%, respectively, being 3.8- and 8.6-fold higher than those observed on the direct fusion of regulators with nuclease-deficient CRISPR proteins, respectively. We then applied the orthogonal bifunctional CRISPR-mediated transcriptional regulation system to regulate the expression of genes associated with 3-hydroxypropanoic acid production to deduce that CRISPR-associated regulator recruiting systems represent a robust method for simultaneously regulating multiple genes and rewiring metabolic pathways.
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Affiliation(s)
- Haotian Zhai
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, P.R. China
| | - Li Cui
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, P.R. China
| | - Zhen Xiong
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, P.R. China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, P.R. China
| | - Jin Hou
- To whom correspondence should be addressed. Tel: +86 532 5863 2401;
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13
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Huang H, Huang G, Tan Z, Hu Y, Shan L, Zhou J, Zhang X, Ma S, Lv W, Huang T, Liu Y, Wang D, Zhao X, Lin Y, Rong Z. Engineered Cas12a-Plus nuclease enables gene editing with enhanced activity and specificity. BMC Biol 2022; 20:91. [PMID: 35468792 PMCID: PMC9040236 DOI: 10.1186/s12915-022-01296-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 04/12/2022] [Indexed: 11/23/2022] Open
Abstract
Background The CRISPR-Cas12a (formerly Cpf1) system is a versatile gene-editing tool with properties distinct from the broadly used Cas9 system. Features such as recognition of T-rich protospacer-adjacent motif (PAM) and generation of sticky breaks, as well as amenability for multiplex editing in a single crRNA and lower off-target nuclease activity, broaden the targeting scope of available tools and enable more accurate genome editing. However, the widespread use of the nuclease for gene editing, especially in clinical applications, is hindered by insufficient activity and specificity despite previous efforts to improve the system. Currently reported Cas12a variants achieve high activity with a compromise of specificity. Here, we used structure-guided protein engineering to improve both editing efficiency and targeting accuracy of Acidaminococcus sp. Cas12a (AsCas12a) and Lachnospiraceae bacterium Cas12a (LbCas12a). Results We created new AsCas12a variant termed “AsCas12a-Plus” with increased activity (1.5~2.0-fold improvement) and specificity (reducing off-targets from 29 to 23 and specificity index increased from 92% to 94% with 33 sgRNAs), and this property was retained in multiplex editing and transcriptional activation. When used to disrupt the oncogenic BRAFV600E mutant, AsCas12a-Plus showed less off-target activity while maintaining comparable editing efficiency and BRAFV600E cancer cell killing. By introducing the corresponding substitutions into LbCas12a, we also generated LbCas12a-Plus (activity improved ~1.1-fold and off-targets decreased from 20 to 12 while specificity index increased from 78% to 89% with 15 sgRNAs), suggesting this strategy may be generally applicable across Cas12a orthologs. We compared Cas12a-Plus, other variants described in this study, and the reported enCas12a-HF, enCas12a, and Cas12a-ultra, and found that Cas12a-Plus outperformed other variants with a good balance for enhanced activity and improved specificity. Conclusions Our discoveries provide alternative AsCas12a and LbCas12a variants with high specificity and activity, which expand the gene-editing toolbox and can be more suitable for clinical applications. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01296-1.
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Affiliation(s)
- Hongxin Huang
- Dermatology Hospital, Southern Medical University, Guangzhou, 510091, China
| | - Guanjie Huang
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, 510515, China
| | - Zhihong Tan
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, 510515, China
| | - Yongfei Hu
- Dermatology Hospital, Southern Medical University, Guangzhou, 510091, China.,Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Lin Shan
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, 510515, China
| | - Jiajian Zhou
- Dermatology Hospital, Southern Medical University, Guangzhou, 510091, China
| | - Xin Zhang
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, 510515, China
| | - Shufeng Ma
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, 510515, China
| | - Weiqi Lv
- Dermatology Hospital, Southern Medical University, Guangzhou, 510091, China
| | - Tao Huang
- Dermatology Hospital, Southern Medical University, Guangzhou, 510091, China.,Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, 510515, China
| | - Yuchen Liu
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, 510515, China
| | - Dong Wang
- Dermatology Hospital, Southern Medical University, Guangzhou, 510091, China.,Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Xiaoyang Zhao
- Department of Development, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Ying Lin
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, 510515, China. .,Experimental Education/Administration Center, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China.
| | - Zhili Rong
- Dermatology Hospital, Southern Medical University, Guangzhou, 510091, China. .,Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou, 510515, China. .,Experimental Education/Administration Center, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China.
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14
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Elucidating miRNA Function in Cancer Biology via the Molecular Genetics’ Toolbox. Biomedicines 2022; 10:biomedicines10040915. [PMID: 35453665 PMCID: PMC9029477 DOI: 10.3390/biomedicines10040915] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/23/2021] [Accepted: 11/30/2021] [Indexed: 11/16/2022] Open
Abstract
Micro-RNA (miRNAs) are short non-coding RNAs of about 18–20 nucleotides in length and are implicated in many cellular processes including proliferation, development, differentiation, apoptosis and cell signaling. Furthermore, it is well known that miRNA expression is frequently dysregulated in many cancers. Therefore, this review will highlight the various mechanisms by which microRNAs are dysregulated in cancer. Further highlights include the abundance of molecular genetics tools that are currently available to study miRNA function as well as their advantages and disadvantages with a special focus on various CRISPR/Cas systems This review provides general workflows and some practical considerations when studying miRNA function thus enabling researchers to make informed decisions in regards to the appropriate molecular genetics tool to be utilized for their experiments.
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15
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Chakravarti R, Lenka SK, Gautam A, Singh R, Ravichandiran V, Roy S, Ghosh D. A Review on CRISPR-Mediated Epigenome Editing: A Future Directive for Therapeutic Management of Cancer. Curr Drug Targets 2022; 23:836-853. [DOI: 10.2174/1389450123666220117105531] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/15/2021] [Accepted: 12/14/2021] [Indexed: 11/22/2022]
Abstract
Abstract:
Recent studies have shed light on the role of epigenetic marks in certain diseases like cancer, type II diabetes mellitus (T2DM), obesity, and cardiovascular dysfunction, to name a few. Epigenetic marks like DNA methylation and histone acetylation are randomly altered in the disease state. It has been seen that methylation of DNA and histones can result in down-regulation of gene expression, whereas histone acetylation, ubiquitination, and phosphorylation are linked to enhanced expression of genes. How can we precisely target such epigenetic aberrations to prevent the advent of diseases? The answer lies in the amalgamation of the efficient genome editing technique, CRISPR, with certain effector molecules that can alter the status of epigenetic marks as well as employ certain transcriptional activators or repressors. In this review, we have discussed the rationale of epigenetic editing as a therapeutic strategy and how CRISPR-Cas9 technology coupled with epigenetic effector tags can efficiently edit epigenetic targets. In the later part, we have discussed how certain epigenetic effectors are tagged with dCas9 to elicit epigenetic changes in cancer. Increased interest in exploring the epigenetic background of cancer and non-communicable diseases like type II diabetes mellitus and obesity accompanied with technological breakthroughs has made it possible to perform large-scale epigenome studies.
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Affiliation(s)
- Rudra Chakravarti
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, India
| | - Swadhin Kumar Lenka
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, India
| | - Anupam Gautam
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076, Tübingen, Germany
| | - Rajveer Singh
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, India
| | - Velayutham Ravichandiran
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, India
| | - Syamal Roy
- CSIR-Indian Institute of Chemical Biology, Jadavpur, Kolkata, India
| | - Dipanjan Ghosh
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, India
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16
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Wang X, Dong K, Kong D, Zhou Y, Yin J, Cai F, Wang M, Ye H. A far-red light-inducible CRISPR-Cas12a platform for remote-controlled genome editing and gene activation. SCIENCE ADVANCES 2021; 7:eabh2358. [PMID: 34890237 PMCID: PMC8664267 DOI: 10.1126/sciadv.abh2358] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The CRISPR-Cas12a has been harnessed as a powerful tool for manipulating targeted gene expression. The possibility to manipulate the activity of CRISPR-Cas12a with a more precise spatiotemporal resolution and deep tissue permeability will enable targeted genome engineering and deepen our understanding of the gene functions underlying complex cellular behaviors. However, currently available inducible CRISPR-Cas12a systems are limited by diffusion, cytotoxicity, and poor tissue permeability. Here, we developed a far-red light (FRL)–inducible CRISPR-Cas12a (FICA) system that can robustly induce gene editing in mammalian cells, and an FRL-inducible CRISPR-dCas12a (FIdCA) system based on the protein-tagging system SUperNova (SunTag) that can be used for gene activation under light-emitting diode–based FRL. Moreover, we show that the FIdCA system can be deployed to activate target genes in mouse livers. These results demonstrate that these systems developed here provide robust and efficient platforms for programmable genome manipulation in a noninvasive and spatiotemporal fashion.
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Affiliation(s)
- Xinyi Wang
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Kaili Dong
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Deqiang Kong
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Yang Zhou
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Jianli Yin
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Fengfeng Cai
- Department of Breast Surgery, Yangpu Hospital, School of Medicine, Tongji University, 450 Tengyue Road, Shanghai 200090, China
| | - Meiyan Wang
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
- Corresponding author. (M.W.); (H.Y.)
| | - Haifeng Ye
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
- Corresponding author. (M.W.); (H.Y.)
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17
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Yang Y, Ye X, Dai R, Li Z, Zhang Y, Xue W, Zhu Y, Feng D, Qin L, Wang X, Lei B, Liao S, Hao B. Phase separation of Epstein-Barr virus EBNA2 protein reorganizes chromatin topology for epigenetic regulation. Commun Biol 2021; 4:967. [PMID: 34400762 PMCID: PMC8368186 DOI: 10.1038/s42003-021-02501-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 07/28/2021] [Indexed: 12/13/2022] Open
Abstract
Epstein-Barr virus nuclear antigen 2 (EBNA2) is a transactivator of viral and cellular gene expression, which plays a critical role in the Epstein-Barr virus-associated diseases. It was reported that EBNA2 regulates gene expression by reorganizing chromatin and manipulating epigenetics. Recent studies showed that liquid-liquid phase separation plays an essential role in epigenetic and transcriptional regulation. Here we show that EBNA2 reorganized chromatin topology to form accessible chromatin domains (ACDs) of the host genome by phase separation. The N-terminal region of EBNA2, which is necessary for phase separation, is sufficient to induce ACDs. The C-terminal domain of EBNA2 promotes the acetylation of accessible chromatin regions by recruiting histone acetylase p300 to ACDs. According to these observations, we proposed a model of EBNA2 reorganizing chromatin topology for its acetylation through phase separation to explain the mechanism of EBNA2 hijacking the host genome by controlling its epigenetics. Yang et al find that phase separation of the Epstein-Barr virus nuclear antigen 2 (EBNA2) is involved in the formation of accessible chromatin domains of the host genome. They also find that EBNA2 recruits histone acetyltransferase to promote histone acetylation on accessible chromatin regions and regulate gene expression and that these two functions are performed by the N- and Cterminus respectively.
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Affiliation(s)
- Yiting Yang
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Xidong Ye
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Ranran Dai
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Zhaoqiang Li
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Yan Zhang
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Wei Xue
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Yongchang Zhu
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Delong Feng
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Litao Qin
- Henan Medical Genetics Institute, Henan Provincial Key Laboratory of Genetic Diseases and Functional Genomics, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital, Zhengzhou, China
| | - Xin Wang
- Henan Medical Genetics Institute, Henan Provincial Key Laboratory of Genetic Diseases and Functional Genomics, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital, Zhengzhou, China
| | - Bo Lei
- Henan Eye Institute, Henan Eye Hospital, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, China.
| | - Shixiu Liao
- Henan Medical Genetics Institute, Henan Provincial Key Laboratory of Genetic Diseases and Functional Genomics, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital, Zhengzhou, China. .,National Health Commission Key Laboratory of Birth Defects Prevention, Henan Key Laboratory of Population Defects Prevention, Zhengzhou, China.
| | - Bingtao Hao
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China. .,Henan Medical Genetics Institute, Henan Provincial Key Laboratory of Genetic Diseases and Functional Genomics, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital, Zhengzhou, China. .,National Health Commission Key Laboratory of Birth Defects Prevention, Henan Key Laboratory of Population Defects Prevention, Zhengzhou, China.
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18
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Janowski M, Milewska M, Zare P, Pękowska A. Chromatin Alterations in Neurological Disorders and Strategies of (Epi)Genome Rescue. Pharmaceuticals (Basel) 2021; 14:765. [PMID: 34451862 PMCID: PMC8399958 DOI: 10.3390/ph14080765] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 07/23/2021] [Accepted: 07/24/2021] [Indexed: 12/26/2022] Open
Abstract
Neurological disorders (NDs) comprise a heterogeneous group of conditions that affect the function of the nervous system. Often incurable, NDs have profound and detrimental consequences on the affected individuals' lives. NDs have complex etiologies but commonly feature altered gene expression and dysfunctions of the essential chromatin-modifying factors. Hence, compounds that target DNA and histone modification pathways, the so-called epidrugs, constitute promising tools to treat NDs. Yet, targeting the entire epigenome might reveal insufficient to modify a chosen gene expression or even unnecessary and detrimental to the patients' health. New technologies hold a promise to expand the clinical toolkit in the fight against NDs. (Epi)genome engineering using designer nucleases, including CRISPR-Cas9 and TALENs, can potentially help restore the correct gene expression patterns by targeting a defined gene or pathway, both genetically and epigenetically, with minimal off-target activity. Here, we review the implication of epigenetic machinery in NDs. We outline syndromes caused by mutations in chromatin-modifying enzymes and discuss the functional consequences of mutations in regulatory DNA in NDs. We review the approaches that allow modifying the (epi)genome, including tools based on TALENs and CRISPR-Cas9 technologies, and we highlight how these new strategies could potentially change clinical practices in the treatment of NDs.
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Affiliation(s)
| | | | | | - Aleksandra Pękowska
- Dioscuri Centre for Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Pasteur Street, 02-093 Warsaw, Poland; (M.J.); (M.M.); (P.Z.)
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19
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Hendriks D, Clevers H, Artegiani B. CRISPR-Cas Tools and Their Application in Genetic Engineering of Human Stem Cells and Organoids. Cell Stem Cell 2021; 27:705-731. [PMID: 33157047 DOI: 10.1016/j.stem.2020.10.014] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
CRISPR-Cas technology has revolutionized biological research and holds great therapeutic potential. Here, we review CRISPR-Cas systems and their latest developments with an emphasis on application to human cells. We also discuss how different CRISPR-based strategies can be used to accomplish a particular genome engineering goal. We then review how different CRISPR tools have been used in genome engineering of human stem cells in vitro, covering both the pluripotent (iPSC/ESC) and somatic adult stem cell fields and, in particular, 3D organoid cultures. Finally, we discuss the progress and challenges associated with CRISPR-based genome editing of human stem cells for therapeutic use.
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Affiliation(s)
- Delilah Hendriks
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, and University Medical Center, Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, and University Medical Center, Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands; The Princess Maxima Center for Pediatric Oncology, Utrecht, the Netherlands.
| | - Benedetta Artegiani
- The Princess Maxima Center for Pediatric Oncology, Utrecht, the Netherlands.
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20
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Perspectives for epigenetic editing in crops. Transgenic Res 2021; 30:381-400. [PMID: 33891288 DOI: 10.1007/s11248-021-00252-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 03/29/2021] [Indexed: 01/10/2023]
Abstract
Site-specific nucleases (SSNs) have drawn much attention in plant biotechnology due to their ability to drive precision mutagenesis, gene targeting or allele replacement. However, when devoid of its nuclease activity, the underlying DNA-binding activity of SSNs can be used to bring other protein functional domains close to specific genomic sites, thus expanding further the range of applications of the technology. In particular, the addition of functional domains encoding epigenetic effectors and chromatin modifiers to the CRISPR/Cas ribonucleoprotein complex opens the possibility to introduce targeted epigenomic modifications in plants in an easily programmable manner. Here we examine some of the most important agronomic traits known to be controlled epigenetically and review the best studied epigenetic catalytic effectors in plants, such as DNA methylases/demethylases or histone acetylases/deacetylases and their associated marks. We also review the most efficient strategies developed to date to functionalize Cas proteins with both catalytic and non-catalytic epigenetic effectors, and the ability of these domains to influence the expression of endogenous genes in a regulatable manner. Based on these new technical developments, we discuss the possibilities offered by epigenetic editing tools in plant biotechnology and their implications in crop breeding.
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21
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Zhang X, Lv S, Luo Z, Hu Y, Peng X, Lv J, Zhao S, Feng J, Huang G, Wan QL, Liu J, Huang H, Luan B, Wang D, Zhao X, Lin Y, Zhou Q, Zhang ZN, Rong Z. MiniCAFE, a CRISPR/Cas9-based compact and potent transcriptional activator, elicits gene expression in vivo. Nucleic Acids Res 2021; 49:4171-4185. [PMID: 33751124 PMCID: PMC8053112 DOI: 10.1093/nar/gkab174] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 02/28/2021] [Accepted: 03/04/2021] [Indexed: 12/23/2022] Open
Abstract
CRISPR-mediated gene activation (CRISPRa) is a promising therapeutic gene editing strategy without inducing DNA double-strand breaks (DSBs). However, in vivo implementation of these CRISPRa systems remains a challenge. Here, we report a compact and robust miniCas9 activator (termed miniCAFE) for in vivo activation of endogenous target genes. The system relies on recruitment of an engineered minimal nuclease-null Cas9 from Campylobacter jejuni and potent transcriptional activators to a target locus by a single guide RNA. It enables robust gene activation in human cells even with a single DNA copy and is able to promote lifespan of Caenorhabditis elegans through activation of longevity-regulating genes. As proof-of-concept, delivered within an all-in-one adeno-associated virus (AAV), miniCAFE can activate Fgf21 expression in the liver and regulate energy metabolism in adult mice. Thus, miniCAFE holds great therapeutic potential against human diseases.
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Affiliation(s)
- Xin Zhang
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Sihan Lv
- Department of Endocrinology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200072, China
| | - Zhenhuan Luo
- Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital Affiliated with Jinan University, Jinan University, Zhuhai 519000, China
- The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou 510632, China
| | - Yongfei Hu
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
| | - Xin Peng
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jie Lv
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Shanshan Zhao
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jianqi Feng
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Guanjie Huang
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Qin-Li Wan
- Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital Affiliated with Jinan University, Jinan University, Zhuhai 519000, China
- The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou 510632, China
| | - Jun Liu
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
| | - Hongxin Huang
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
| | - Bing Luan
- Department of Endocrinology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200072, China
| | - Dong Wang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
| | - Xiaoyang Zhao
- Department of Development, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Ying Lin
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Qinghua Zhou
- Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital Affiliated with Jinan University, Jinan University, Zhuhai 519000, China
- The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou 510632, China
| | - Zhen-Ning Zhang
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Zhili Rong
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China
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22
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Lek A, Ma K, Woodman KG, Lek M. Nuclease-Deficient Clustered Regularly Interspaced Short Palindromic Repeat-Based Approaches for In Vitro and In Vivo Gene Activation. Hum Gene Ther 2021; 32:260-274. [PMID: 33446040 DOI: 10.1089/hum.2020.241] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeat (CRISPR)-based technology has been adapted to achieve a wide range of genome modifications, including transcription regulation. The focus of this review is on the application of CRISPR-based platforms such as nuclease-deficient Cas9 and Cas12a, to achieve targeted gene activation. We review studies to date that have used CRISPR-based activation technology for the elucidation of biological mechanism and disease correction, as well as its application in genetic screens as a powerful tool for high-throughput genotype-phenotype mapping. In addition to our synthesis and critical analysis of published studies, we explore key considerations for the potential clinical translation of CRISPR-based activation technology.
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Affiliation(s)
- Angela Lek
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, USA
| | - Kaiyue Ma
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, USA
| | - Keryn G Woodman
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, USA
| | - Monkol Lek
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, USA
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23
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Martella A, Fisher DI. Regulation of Gene Expression and the Elucidative Role of CRISPR-Based Epigenetic Modifiers and CRISPR-Induced Chromosome Conformational Changes. CRISPR J 2021; 4:43-57. [PMID: 33616442 DOI: 10.1089/crispr.2020.0108] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In complex multicellular systems, gene expression is regulated at multiple stages through interconnected complex molecular pathways and regulatory networks. Transcription is the first step in gene expression and is subject to multiple layers of regulation in which epigenetic mechanisms such as DNA methylation, histone tail modifications, and chromosomal conformation play an essential role. In recent years, CRISPR-Cas9 systems have been employed to unearth this complexity and provide new insights on the contribution of chromatin dysregulation in the development of genetic diseases, as well as new tools to prevent or reverse this dysregulation. In this review, we outline the recent development of a variety of CRISPR-based epigenetic editors for targeted DNA methylation/demethylation, histone modification, and three-dimensional DNA conformational change, highlighting their relative performance and impact on gene regulation. Finally, we provide insights on the future developments aimed to accelerate our understanding of the causal relationship between epigenetic marks, genome organization, and gene regulation.
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Affiliation(s)
- Andrea Martella
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | - David I Fisher
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
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24
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Sgro A, Blancafort P. Epigenome engineering: new technologies for precision medicine. Nucleic Acids Res 2021; 48:12453-12482. [PMID: 33196851 PMCID: PMC7736826 DOI: 10.1093/nar/gkaa1000] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 10/10/2020] [Accepted: 10/16/2020] [Indexed: 02/07/2023] Open
Abstract
Chromatin adopts different configurations that are regulated by reversible covalent modifications, referred to as epigenetic marks. Epigenetic inhibitors have been approved for clinical use to restore epigenetic aberrations that result in silencing of tumor-suppressor genes, oncogene addictions, and enhancement of immune responses. However, these drugs suffer from major limitations, such as a lack of locus selectivity and potential toxicities. Technological advances have opened a new era of precision molecular medicine to reprogram cellular physiology. The locus-specificity of CRISPR/dCas9/12a to manipulate the epigenome is rapidly becoming a highly promising strategy for personalized medicine. This review focuses on new state-of-the-art epigenome editing approaches to modify the epigenome of neoplasms and other disease models towards a more 'normal-like state', having characteristics of normal tissue counterparts. We highlight biomolecular engineering methodologies to assemble, regulate, and deliver multiple epigenetic effectors that maximize the longevity of the therapeutic effect, and we discuss limitations of the platforms such as targeting efficiency and intracellular delivery for future clinical applications.
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Affiliation(s)
- Agustin Sgro
- Cancer Epigenetics Laboratory, The Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia.,School of Human Sciences, The University of Western Australia, Crawley, Perth, Western Australia 6009, Australia
| | - Pilar Blancafort
- Cancer Epigenetics Laboratory, The Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia.,School of Human Sciences, The University of Western Australia, Crawley, Perth, Western Australia 6009, Australia.,The Greehey Children's Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229, USA
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25
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Nakamura M, Gao Y, Dominguez AA, Qi LS. CRISPR technologies for precise epigenome editing. Nat Cell Biol 2021; 23:11-22. [PMID: 33420494 DOI: 10.1038/s41556-020-00620-7] [Citation(s) in RCA: 191] [Impact Index Per Article: 63.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 11/30/2020] [Indexed: 01/29/2023]
Abstract
The epigenome involves a complex set of cellular processes governing genomic activity. Dissecting this complexity necessitates the development of tools capable of specifically manipulating these processes. The repurposing of prokaryotic CRISPR systems has allowed for the development of diverse technologies for epigenome engineering. Here, we review the state of currently achievable epigenetic manipulations along with corresponding applications. With future optimization, CRISPR-based epigenomic editing stands as a set of powerful tools for understanding and controlling biological function.
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Affiliation(s)
- Muneaki Nakamura
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Yuchen Gao
- Department of Bioengineering, Stanford University, Stanford, CA, USA.,Cancer Biology Program, Stanford University, Stanford, CA, USA.,Mammoth Biosciences, South San Francisco, CA, USA
| | - Antonia A Dominguez
- Department of Bioengineering, Stanford University, Stanford, CA, USA.,Sana Biotechnology, South San Francisco, CA, USA
| | - Lei S Qi
- Department of Bioengineering, Stanford University, Stanford, CA, USA. .,Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA. .,Stanford ChEM-H Institute, Stanford University, Stanford, CA, USA.
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26
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Casas-Mollano JA, Zinselmeier MH, Erickson SE, Smanski MJ. CRISPR-Cas Activators for Engineering Gene Expression in Higher Eukaryotes. CRISPR J 2020; 3:350-364. [PMID: 33095045 PMCID: PMC7580621 DOI: 10.1089/crispr.2020.0064] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
CRISPR-Cas-based transcriptional activators allow genetic engineers to specifically induce expression of one or many target genes in trans. Here we review the many design variations of these versatile tools and compare their effectiveness in different eukaryotic systems. Lastly, we highlight several applications of programmable transcriptional activation to interrogate and engineer complex biological processes.
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Affiliation(s)
- J. Armando Casas-Mollano
- Department of Biochemistry, Molecular Biology, and Biophysics, BioTechnology Institute, University of Minnesota, Twin-Cities, Saint Paul, Minnesota, USA; and Cell Biology, and Development, University of Minnesota, Twin-Cities, Saint Paul, Minnesota, USA
| | - Matthew H. Zinselmeier
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Twin-Cities, Saint Paul, Minnesota, USA
| | - Samuel E. Erickson
- Department of Biochemistry, Molecular Biology, and Biophysics, BioTechnology Institute, University of Minnesota, Twin-Cities, Saint Paul, Minnesota, USA; and Cell Biology, and Development, University of Minnesota, Twin-Cities, Saint Paul, Minnesota, USA
| | - Michael J. Smanski
- Department of Biochemistry, Molecular Biology, and Biophysics, BioTechnology Institute, University of Minnesota, Twin-Cities, Saint Paul, Minnesota, USA; and Cell Biology, and Development, University of Minnesota, Twin-Cities, Saint Paul, Minnesota, USA
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27
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Tóth E, Varga É, Kulcsár PI, Kocsis-Jutka V, Krausz SL, Nyeste A, Welker Z, Huszár K, Ligeti Z, Tálas A, Welker E. Improved LbCas12a variants with altered PAM specificities further broaden the genome targeting range of Cas12a nucleases. Nucleic Acids Res 2020; 48:3722-3733. [PMID: 32107556 PMCID: PMC7144938 DOI: 10.1093/nar/gkaa110] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 02/07/2020] [Accepted: 02/24/2020] [Indexed: 12/26/2022] Open
Abstract
The widespread use of Cas12a (formerly Cpf1) nucleases for genome engineering is limited by their requirement for a rather long TTTV protospacer adjacent motif (PAM) sequence. Here we have aimed to loosen these PAM constraints and have generated new PAM mutant variants of the four Cas12a orthologs that are active in mammalian and plant cells, by combining the mutations of their corresponding RR and RVR variants with altered PAM specificities. LbCas12a-RVRR showing the highest activity was selected for an in-depth characterization of its PAM preferences in mammalian cells, using a plasmid-based assay. The consensus PAM sequence of LbCas12a-RVRR resembles a TNTN motif, but also includes TACV, TTCV CTCV and CCCV. The D156R mutation in improved LbCas12a (impLbCas12a) was found to further increase the activity of that variant in a PAM-dependent manner. Due to the overlapping but still different PAM preferences of impLbCas12a and the recently reported enAsCas12a variant, they complement each other to provide increased efficiency for genome editing and transcriptome modulating applications.
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Affiliation(s)
- Eszter Tóth
- Institute of Enzymology, Research Centre of Natural Sciences of the Hungarian Academy of Sciences, Budapest H-1117, Hungary
| | - Éva Varga
- Institute of Enzymology, Research Centre of Natural Sciences of the Hungarian Academy of Sciences, Budapest H-1117, Hungary.,Doctoral School of Multidisciplinary Medical Science, University of Szeged, Szeged H-6726, Hungary.,Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged H-6726, Hungary
| | - Péter István Kulcsár
- Institute of Enzymology, Research Centre of Natural Sciences of the Hungarian Academy of Sciences, Budapest H-1117, Hungary.,Doctoral School of Multidisciplinary Medical Science, University of Szeged, Szeged H-6726, Hungary.,Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged H-6726, Hungary
| | - Virág Kocsis-Jutka
- Institute of Enzymology, Research Centre of Natural Sciences of the Hungarian Academy of Sciences, Budapest H-1117, Hungary.,ProteoScientia Kft, Cserhátszentiván, H-3066, Hungary
| | - Sarah Laura Krausz
- Institute of Enzymology, Research Centre of Natural Sciences of the Hungarian Academy of Sciences, Budapest H-1117, Hungary.,School of Ph.D. Studies, Semmelweis University, Budapest, H-1085, Hungary
| | - Antal Nyeste
- Institute of Enzymology, Research Centre of Natural Sciences of the Hungarian Academy of Sciences, Budapest H-1117, Hungary.,Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged H-6726, Hungary.,ProteoScientia Kft, Cserhátszentiván, H-3066, Hungary
| | | | - Krisztina Huszár
- Institute of Enzymology, Research Centre of Natural Sciences of the Hungarian Academy of Sciences, Budapest H-1117, Hungary.,Biospirál-2006 Kft., Szeged, H-6726, Hungary
| | - Zoltán Ligeti
- Institute of Enzymology, Research Centre of Natural Sciences of the Hungarian Academy of Sciences, Budapest H-1117, Hungary.,Doctoral School of Multidisciplinary Medical Science, University of Szeged, Szeged H-6726, Hungary.,Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged H-6726, Hungary
| | - András Tálas
- Institute of Enzymology, Research Centre of Natural Sciences of the Hungarian Academy of Sciences, Budapest H-1117, Hungary.,School of Ph.D. Studies, Semmelweis University, Budapest, H-1085, Hungary
| | - Ervin Welker
- Institute of Enzymology, Research Centre of Natural Sciences of the Hungarian Academy of Sciences, Budapest H-1117, Hungary.,Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged H-6726, Hungary
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28
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Kunii A, Yamamoto T, Sakuma T. Various strategies of effector accumulation to improve the efficiency of genome editing and derivative methodologies. In Vitro Cell Dev Biol Anim 2020; 56:359-366. [PMID: 32514717 DOI: 10.1007/s11626-020-00469-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 05/21/2020] [Indexed: 12/30/2022]
Abstract
CRISPR-Cas9 is a sophisticated tool in which Cas9/sgRNA complexes bind to the programmed target sequences and induce DNA double-strand breaks (DSBs) enabling highly efficient genome editing. Moreover, when nuclease-inactive Cas9 (dCas9) is employed, its specific DNA-binding activity provides a variety of derivative technologies such as transcriptional activation/repression, epigenome editing, and chromosome visualization. In these derivative technologies, particular effector molecules are fused with dCas9 or recruited to the target site. However, there had been room for improvement, because both genome editing and derivative technologies require not only the DNA-binding tools but also the additional components for their efficient and flexible outcomes. For genome editing, DSB repair molecules and knock-in donor templates need to act at the DSB sites. Derivative technologies also require their various effector domains to be gathered onto the target sites. Recently, many groups have developed and utilized inventive platforms to accumulate these additional components to the target sequence by modifying Cas9 protein and/or sgRNA. Here, we summarize the strategies of CRISPR-based effector accumulation and the improved methodologies using these creative platforms.
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Affiliation(s)
- Atsushi Kunii
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Hiroshima, 739-8526, Japan
| | - Takashi Yamamoto
- Division of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
| | - Tetsushi Sakuma
- Division of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan.
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29
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Dai X, Blancafort P, Wang P, Sgro A, Thompson EW, Ostrikov K(K. Innovative Precision Gene-Editing Tools in Personalized Cancer Medicine. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:1902552. [PMID: 32596104 PMCID: PMC7312441 DOI: 10.1002/advs.201902552] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 02/08/2020] [Indexed: 05/07/2023]
Abstract
The development of clustered regularly interspaced short palindromic repeats (CRISPR) has spurred a successive wave of genome-engineering following zinc finger nucleases and transcription activator-like effector nucleases, and made gene-editing a promising strategy in the prevention and treatment of genetic diseases. However, gene-editing is not widely adopted in clinics due to some technical issues that challenge its safety and efficacy, and the lack of appropriate clinical regulations allowing them to advance toward improved human health without impinging on human ethics. By systematically examining the oncological applications of gene-editing tools and critical factors challenging their medical translation, genome-editing has substantial contributions to cancer driver gene discovery, tumor cell epigenome normalization, targeted delivery, cancer animal model establishment, and cancer immunotherapy and prevention in clinics. Gene-editing tools, epitomized by CRISPR, are predicted to represent a promising strategy toward the precise control of cancer initiation and development. However, some technical problems and ethical concerns are serious issues that need to be appropriately addressed before CRISPR can be incorporated into the next generation of molecular precision medicine. In this light, new technical developments to limit off-target effects are discussed herein, and the use of gene-editing approaches for treating otherwise incurable cancers is brought into focus.
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Affiliation(s)
- Xiaofeng Dai
- Wuxi School of MedicineJiangnan UniversityWuxi214122China
| | - Pilar Blancafort
- The Harry Perkins Institute of Medical ResearchNedlandsWestern Australia6009Australia
- School of Human SciencesThe University of Western AustraliaNedlandsWestern Australia6009Australia
- The Greehey Children's Cancer Research InstituteThe University of Texas Health Science Center at San AntonioSan AntonioTX78229USA
| | - Peiyu Wang
- Institute of Health and Biomedical InnovationQueensland University of TechnologyBrisbaneQueensland4059Australia
- School of Biomedical SciencesQueensland University of TechnologyBrisbaneQueensland4059Australia
- Translational Research InstituteWoolloongabbaQueensland4102Australia
| | - Agustin Sgro
- The Harry Perkins Institute of Medical ResearchNedlandsWestern Australia6009Australia
- School of Human SciencesThe University of Western AustraliaNedlandsWestern Australia6009Australia
| | - Erik W. Thompson
- Institute of Health and Biomedical InnovationQueensland University of TechnologyBrisbaneQueensland4059Australia
- School of Biomedical SciencesQueensland University of TechnologyBrisbaneQueensland4059Australia
- Translational Research InstituteWoolloongabbaQueensland4102Australia
| | - Kostya (Ken) Ostrikov
- Translational Research InstituteWoolloongabbaQueensland4102Australia
- School of Chemistry and PhysicsQueensland University of TechnologyBrisbaneQueensland4000Australia
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30
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The working dead: repurposing inactive CRISPR-associated nucleases as programmable transcriptional regulators in plants. ABIOTECH 2020; 1:32-40. [PMID: 36305006 PMCID: PMC9590457 DOI: 10.1007/s42994-019-00003-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 07/17/2019] [Indexed: 12/13/2022]
Abstract
Targeted gene manipulation is highly desirable for fundamental plant research, plant synthetic biology, and molecular breeding. The clustered regularly interspaced short palindromic repeats-associated (Cas) nuclease is a revolutionary tool for genome editing, and has received snowballing popularity for gene knockout applications in diverse organisms including plants. Recently, the nuclease-dead Cas (dCas) proteins have been repurposed as programmable transcriptional regulators through translational fusion with portable transcriptional repression or activation domains, which has paved new ways for flexible and multiplex control over the activities of target genes of interest without the need to generate DNA lesions. Here, we review the most important breakthroughs of dCas transcriptional regulators in non-plant organisms and recent accomplishments of this growing field in plants. We also provide perspectives on future development directions of dCas transcriptional regulators in plant research in hope to stimulate their quick evolution and broad applications.
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31
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Sajwan S, Mannervik M. Gene activation by dCas9-CBP and the SAM system differ in target preference. Sci Rep 2019; 9:18104. [PMID: 31792240 PMCID: PMC6888908 DOI: 10.1038/s41598-019-54179-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 11/08/2019] [Indexed: 12/21/2022] Open
Abstract
Gene overexpression through the targeting of transcription activation domains to regulatory DNA via catalytically defective Cas9 (dCas9) represents a powerful approach to investigate gene function as well as the mechanisms of gene control. To date, the most efficient dCas9-based activator is the Synergistic Activation Mediator (SAM) system whereby transcription activation domains are directly fused to dCas9 as well as tethered through MS2 loops engineered into the gRNA. Here, we show that dCas9 fused to the catalytic domain of the histone acetyltransferase CBP is a more potent activator than the SAM system at some loci, but less efficient at other locations in Drosophila cells. Our results suggest that different rate-limiting steps in the transcription cycle are affected by dCas9-CBP and the SAM system, and that comparing these activators may be useful for mechanistic studies of transcription as well as for increasing the number of hits in genome-wide overexpression screens.
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Affiliation(s)
- Suresh Sajwan
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691, Stockholm, Sweden.
| | - Mattias Mannervik
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691, Stockholm, Sweden.
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32
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Ghogare R, Williamson-Benavides B, Ramírez-Torres F, Dhingra A. CRISPR-associated nucleases: the Dawn of a new age of efficient crop improvement. Transgenic Res 2019; 29:1-35. [PMID: 31677059 DOI: 10.1007/s11248-019-00181-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 10/23/2019] [Indexed: 12/26/2022]
Abstract
The world stands at a new threshold today. As a planet, we face various challenges, and the key one is how to continue to produce enough food, feed, fiber, and fuel to support the burgeoning population. In the past, plant breeding and the ability to genetically engineer crops contributed to increasing food production. However, both approaches rely on random mixing or integration of genes, and the process can be unpredictable and time-consuming. Given the challenge of limited availability of natural resources and changing environmental conditions, the need to rapidly and precisely improve crops has become urgent. The discovery of CRISPR-associated endonucleases offers a precise yet versatile platform for rapid crop improvement. This review summarizes a brief history of the discovery of CRISPR-associated nucleases and their application in genome editing of various plant species. Also provided is an overview of several new endonucleases reported recently, which can be utilized for editing of specific genes in plants through various forms of DNA sequence alteration. Genome editing, with its ever-expanding toolset, increased efficiency, and its potential integration with the emerging synthetic biology approaches hold promise for efficient crop improvement to meet the challenge of supporting the needs of future generations.
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33
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Nihongaki Y, Otabe T, Ueda Y, Sato M. A split CRISPR-Cpf1 platform for inducible genome editing and gene activation. Nat Chem Biol 2019; 15:882-888. [PMID: 31406371 DOI: 10.1038/s41589-019-0338-y] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 07/04/2019] [Indexed: 12/31/2022]
Abstract
The CRISPR-Cpf1 endonuclease has recently been demonstrated as a powerful tool to manipulate targeted gene sequences. Here, we performed an extensive screening of split Cpf1 fragments and identified a pair that, combined with inducible dimerization domains, enables chemical- and light-inducible genome editing in human cells. We also identified another split Cpf1 pair that is spontaneously activated. The newly generated amino and carboxyl termini of the spontaneously activated split Cpf1 can be repurposed as de novo fusion sites of artificial effector domains. Based on this finding, we generated an improved split dCpf1 activator, which has the potential to activate endogenous genes more efficiently than a previously established dCas9 activator. Finally, we showed that the split dCpf1 activator can efficiently activate target genes in mice. These results demonstrate that the present split Cpf1 provides an efficient and sophisticated genome manipulation in the fields of basic research and biotechnological applications.
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Affiliation(s)
- Yuta Nihongaki
- Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan.,Department of Cell Biology and Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Takahiro Otabe
- Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Yoshibumi Ueda
- Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan.,Japan Agency for Medical Research and Development-PRIME, Tokyo, Japan
| | - Moritoshi Sato
- Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan. .,Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Saitama, Japan.
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34
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Zhang Y, Malzahn AA, Sretenovic S, Qi Y. The emerging and uncultivated potential of CRISPR technology in plant science. NATURE PLANTS 2019; 5:778-794. [PMID: 31308503 DOI: 10.1038/s41477-019-0461-5] [Citation(s) in RCA: 207] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 05/24/2019] [Indexed: 05/18/2023]
Abstract
The application of clustered regularly interspaced short palindromic repeats (CRISPR) for genetic manipulation has revolutionized life science over the past few years. CRISPR was first discovered as an adaptive immune system in bacteria and archaea, and then engineered to generate targeted DNA breaks in living cells and organisms. During the cellular DNA repair process, various DNA changes can be introduced. The diverse and expanding CRISPR toolbox allows programmable genome editing, epigenome editing and transcriptome regulation in plants. However, challenges in plant genome editing need to be fully appreciated and solutions explored. This Review intends to provide an informative summary of the latest developments and breakthroughs of CRISPR technology, with a focus on achievements and potential utility in plant biology. Ultimately, CRISPR will not only facilitate basic research, but also accelerate plant breeding and germplasm development. The application of CRISPR to improve germplasm is particularly important in the context of global climate change as well as in the face of current agricultural, environmental and ecological challenges.
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Affiliation(s)
- Yingxiao Zhang
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Aimee A Malzahn
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Simon Sretenovic
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA.
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, USA.
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Liu J, Srinivasan S, Li CY, Ho IL, Rose J, Shaheen M, Wang G, Yao W, Deem A, Bristow C, Hart T, Draetta G. Pooled library screening with multiplexed Cpf1 library. Nat Commun 2019; 10:3144. [PMID: 31316073 PMCID: PMC6637147 DOI: 10.1038/s41467-019-10963-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 05/31/2019] [Indexed: 12/26/2022] Open
Abstract
Capitalizing on the inherent multiplexing capability of AsCpf1, we developed a multiplexed, high-throughput screening strategy that minimizes library size without sacrificing gene targeting efficiency. We demonstrated that AsCpf1 can be used for functional genomics screenings and that an AsCpf1-based multiplexed library performs similarly as compared to currently available monocistronic CRISPR/Cas9 libraries, with only one vector required for each gene. We construct the smallest whole-genome CRISPR knock-out library, Mini-human, for the human genome (n = 17,032 constructs targeting 16,977 protein-coding genes), which performs favorably compared to conventional Cas9 libraries.
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Affiliation(s)
- Jintan Liu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Houston, Houston, TX, 77030, USA.
| | - Sanjana Srinivasan
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Houston, Houston, TX, 77030, USA
| | - Chieh-Yuan Li
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Houston, Houston, TX, 77030, USA
| | - I-Lin Ho
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Houston, Houston, TX, 77030, USA
| | - Johnathon Rose
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Houston, Houston, TX, 77030, USA
| | - MennatAllah Shaheen
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Houston, Houston, TX, 77030, USA
| | - Gang Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Wantong Yao
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Angela Deem
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Chris Bristow
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Traver Hart
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Giulio Draetta
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Houston, Houston, TX, 77030, USA.
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36
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Safari F, Zare K, Negahdaripour M, Barekati-Mowahed M, Ghasemi Y. CRISPR Cpf1 proteins: structure, function and implications for genome editing. Cell Biosci 2019; 9:36. [PMID: 31086658 PMCID: PMC6507119 DOI: 10.1186/s13578-019-0298-7] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 04/20/2019] [Indexed: 12/19/2022] Open
Abstract
CRISPR and CRISPR-associated (Cas) protein, as components of microbial adaptive immune system, allows biologists to edit genomic DNA in a precise and specific way. CRISPR-Cas systems are classified into two main classes and six types. Cpf1 is a putative type V (class II) CRISPR effector, which can be programmed with a CRISPR RNA to bind and cleave complementary DNA targets. Cpf1 has recently emerged as an alternative for Cas9, due to its distinct features such as the ability to target T-rich motifs, no need for trans-activating crRNA, inducing a staggered double-strand break and potential for both RNA processing and DNA nuclease activity. In this review, we attempt to discuss the evolutionary origins, basic architectures, and molecular mechanisms of Cpf1 family proteins, as well as crRNA designing and delivery strategies. We will also describe the novel Cpf1 variants, which have broadened the versatility and feasibility of this system in genome editing, transcription regulation, epigenetic modulation, and base editing. Finally, we will be reviewing the recent studies on utilization of Cpf1as a molecular tool for genome editing.
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Affiliation(s)
- Fatemeh Safari
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Khadijeh Zare
- Department of Basic Sciences, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Manica Negahdaripour
- Pharmaceutical Sciences Research Center, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mazyar Barekati-Mowahed
- Department of Physiology & Biophysics, School of Medicine, Case Western Reserve University, Ohio, USA
| | - Younes Ghasemi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
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37
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Nie Z, Gao W, Zhang Y, Hou Y, Liu J, Li Z, Xue W, Ye X, Jin A. STAG2 loss-of-function mutation induces PD-L1 expression in U2OS cells. ANNALS OF TRANSLATIONAL MEDICINE 2019; 7:127. [PMID: 31157248 DOI: 10.21037/atm.2019.02.23] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Background A tumor suppressor protein, stromal antigen 2 (STAG2), has recurrent mutations or loss of expression in many tumors including in bladder cancer, osteosarcoma (OS), and leukemia. However, the mechanism of STAG2 mutations promoting tumorigenesis is still unclear. Methods The distribution of STAG2 mutations in cancer was determined through the COSMIC database; we also generated a STAG2 truncating mutation in OS cell line U2OS cells to mimic a common mutation in OS. CCK-8 assay was employed to evaluate the effect of STAG2 on proliferation and chemo-resistance in OS cells. Cell apoptosis and cell cycle assays were used to assess the effect of STAG2 on apoptosis and the cycle of OS cells. A high throughput RNA sequencing (RNA-Seq) strategy using the Illumina Hiseq 2500 platform was applied to characterize the transcriptome profile from STAG2 knockout and STAG2 WT OS cell lines. Results We found that STAG2 deficient-cells exhibited reduced cell proliferation and growth; however, they enhanced cell metastasis and invasion, and increased tolerance to chemotherapeutic drugs. We also found that PD-L1, a molecule involved in tumor immune evasion, was up-regulated in the SATG2-lost cells. Expression profile analysis by RNA-seq revealed that there were changes in the expression of many immune-related genes. Conclusions Our findings indicated that STAG2 contributes to cell survival and chemo-resistance to cisplatin of OS, suggesting that deletion of STAG2 may promote tumorigenesis by enhancing the immune evasion capacity of cancer cells.
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Affiliation(s)
- Zhirui Nie
- Cancer Research Institute, Southern Medical University, Guangzhou 510515, China.,Department of Orthopedics, Zhu Jiang Hospital of Southern Medical University, Guangzhou 510282, China
| | - Wenwen Gao
- Cancer Research Institute, Southern Medical University, Guangzhou 510515, China
| | - Yan Zhang
- Cancer Research Institute, Southern Medical University, Guangzhou 510515, China
| | - Yuhe Hou
- Cancer Research Institute, Southern Medical University, Guangzhou 510515, China
| | - Jingxian Liu
- Cancer Research Institute, Southern Medical University, Guangzhou 510515, China
| | - Zhaoqiang Li
- Cancer Research Institute, Southern Medical University, Guangzhou 510515, China
| | - Wei Xue
- Cancer Research Institute, Southern Medical University, Guangzhou 510515, China
| | - Xidong Ye
- Cancer Research Institute, Southern Medical University, Guangzhou 510515, China
| | - Anmin Jin
- Department of Orthopedics, Zhu Jiang Hospital of Southern Medical University, Guangzhou 510282, China
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38
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Kleinstiver BP, Sousa AA, Walton RT, Tak YE, Hsu JY, Clement K, Welch MM, Horng JE, Malagon-Lopez J, Scarfò I, Maus MV, Pinello L, Aryee MJ, Joung JK. Engineered CRISPR-Cas12a variants with increased activities and improved targeting ranges for gene, epigenetic and base editing. Nat Biotechnol 2019; 37:276-282. [PMID: 30742127 PMCID: PMC6401248 DOI: 10.1038/s41587-018-0011-0] [Citation(s) in RCA: 386] [Impact Index Per Article: 77.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 12/21/2018] [Indexed: 02/08/2023]
Abstract
Broad use of CRISPR-Cas12a (formerly Cpf1) nucleases1 has been hindered by the requirement for
an extended TTTV protospacer adjacent motif (PAM)2. To address this limitation, we
engineered an enhanced Acidaminococcus sp. Cas12a variant
(enAsCas12a) that has a substantially expanded targeting range, enabling
targeting of many previously inaccessible PAMs. On average, enAsCas12a exhibits
two-fold higher genome editing activity on sites with canonical TTTV PAMs
compared to wild-type AsCas12a, and we successfully grafted a subset of
mutations from enAsCas12a onto other previously described AsCas12a
variants3 to enhance
their activities. enAsCas12a improves the efficiency of multiplex gene editing,
endogenous gene activation, and C-to-T base editing, and we engineered a
high-fidelity version of enAsCas12a (enAsCas12a-HF1) to reduce off-target
effects. Both enAsCas12a and enAsCas12a-HF1 function in HEK293T and primary
human T cells when delivered as ribonucleoprotein (RNP) complexes. Collectively,
enAsCas12a provides an optimized version of Cas12a that should enable wider
application of Cas12a enzymes for gene and epigenetic editing. [AU: Revised
abstract OK?]
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Affiliation(s)
- Benjamin P Kleinstiver
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA. .,Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA. .,Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA. .,Department of Pathology, Harvard Medical School, Boston, MA, USA. .,Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
| | - Alexander A Sousa
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA.,Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA
| | - Russell T Walton
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA.,Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA.,Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Y Esther Tak
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA.,Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA.,Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Jonathan Y Hsu
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA.,Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kendell Clement
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA.,Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA.,Department of Pathology, Harvard Medical School, Boston, MA, USA.,Cell Circuits and Epigenomics Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Moira M Welch
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA.,Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA
| | - Joy E Horng
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA.,Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA
| | - Jose Malagon-Lopez
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA.,Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA.,Department of Pathology, Harvard Medical School, Boston, MA, USA.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Advance Artificial Intelligence Research Laboratory, WuXi NextCODE, Cambridge, MA, USA
| | - Irene Scarfò
- Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA.,Cellular Immunotherapy Program, Cancer Center, Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Marcela V Maus
- Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA.,Cellular Immunotherapy Program, Cancer Center, Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Luca Pinello
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA.,Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA.,Department of Pathology, Harvard Medical School, Boston, MA, USA.,Cell Circuits and Epigenomics Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Martin J Aryee
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA.,Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA.,Department of Pathology, Harvard Medical School, Boston, MA, USA.,Cell Circuits and Epigenomics Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - J Keith Joung
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA. .,Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA. .,Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA. .,Department of Pathology, Harvard Medical School, Boston, MA, USA.
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Zhang Y, Zhang Y, Qi Y. Plant Gene Knockout and Knockdown by CRISPR-Cpf1 (Cas12a) Systems. Methods Mol Biol 2019; 1917:245-256. [PMID: 30610641 DOI: 10.1007/978-1-4939-8991-1_18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
CRISPR-Cpf1 (Cas12a) is a class II type V endonuclease, which has been used as a genome editing tool in different biological systems. Here we describe a fast, efficient, and user-friendly system for CRISPR-Cpf1 expression vector assembly. In this system, the Pol II promoter is used to drive the expression of both Cpf1 and its crRNA, with the crRNA flanked by hammerhead (HH) and hepatitis delta virus (HDV) ribozyme RNAs for precise crRNA processing. All the components of this system can be modified depending on plant species and experimental goals. Using this system, nearly 100% editing efficiency and 90% gene expression decrease were achieved in rice and Arabidopsis, respectively.
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Affiliation(s)
- Yingxiao Zhang
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Yong Zhang
- Department of Biotechnology, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA. .,Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, USA.
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40
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Liu H, Wang L, Luo Y. Blossom of CRISPR technologies and applications in disease treatment. Synth Syst Biotechnol 2018; 3:217-228. [PMID: 30370342 PMCID: PMC6199817 DOI: 10.1016/j.synbio.2018.10.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 10/09/2018] [Accepted: 10/10/2018] [Indexed: 02/05/2023] Open
Abstract
Since 2013, the CRISPR-based bacterial antiviral defense systems have revolutionized the genome editing field. In addition to genome editing, CRISPR has been developed as a variety of tools for gene expression regulations, live cell chromatin imaging, base editing, epigenome editing, and nucleic acid detection. Moreover, in the context of further boosting the usability and feasibility of CRISPR systems, novel CRISPR systems and engineered CRISPR protein mutants have been explored and studied actively. With the flourish of CRISPR technologies, they have been applied in disease treatment recently, as in gene therapy, cell therapy, immunotherapy, and antimicrobial therapy. Here we present the developments of CRISPR technologies and describe the applications of these CRISPR-based technologies in disease treatment.
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Affiliation(s)
- Huayi Liu
- Department of Gastroenterology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, PR China
| | - Lian Wang
- Department of Gastroenterology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, PR China
| | - Yunzi Luo
- Department of Gastroenterology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, PR China
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41
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Ma S, Lv J, Sun J, Tang P, Li H, Zhou H, Zhang Z, Lin Y, Rong Z. iKA-CRISPR hESCs for inducible and multiplex orthogonal gene knockout and activation. FEBS Lett 2018; 592:2238-2247. [PMID: 29869798 DOI: 10.1002/1873-3468.13127] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Revised: 05/26/2018] [Accepted: 05/28/2018] [Indexed: 11/08/2022]
Abstract
Human embryonic stem cells (hESCs) have a wide range of applications in early human embryonic development mimics, disease modeling, and cell therapy. To fulfill these applications, we established hESCs for inducible and multiplex orthogonal gene knockout and activation, which we named iKA-CRISPR hESCs. In cells, when complexed with a short guide RNA containing a 14-bp target sequence (14-bp gRNA) or a long 20-bp gRNA, the doxycycline-induced Cas9-p300 protein could activate gene transcription or cleave genomic DNA, respectively. We also demonstrate using iKA-CRISPR hESCs that knockout of OCT4 promoted differentiation, and developmentally relevant microRNAs and transcription factors could be efficiently activated. Thus, iKA-CRISPR hESCs provide a convenient platform to control gene expression networks and, therefore, facilitate the applications of hESCs in basic and translational biomedical research.
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Affiliation(s)
- Shufeng Ma
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Jie Lv
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Jing Sun
- State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Center for Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- Department of Cardiology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Pei Tang
- Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Huibin Li
- Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Hongwei Zhou
- Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Zhenhai Zhang
- State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Center for Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- Department of Cardiology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Ying Lin
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Zhili Rong
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
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42
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Schindele P, Wolter F, Puchta H. Transforming plant biology and breeding with CRISPR/Cas9, Cas12 and Cas13. FEBS Lett 2018; 592:1954-1967. [PMID: 29710373 DOI: 10.1002/1873-3468.13073] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 04/09/2018] [Accepted: 04/23/2018] [Indexed: 12/26/2022]
Abstract
Currently, biology is revolutionized by ever growing applications of the CRISPR/Cas system. As discussed in this Review, new avenues have opened up for plant research and breeding by the use of the sequence-specific DNases Cas9 and Cas12 (formerly named Cpf1) and, more recently, the RNase Cas13 (formerly named C2c2). Although double strand break-induced gene editing based on error-prone nonhomologous end joining has been applied to obtain new traits, such as powdery mildew resistance in wheat or improved pathogen resistance and increased yield in tomato, improved technologies based on CRISPR/Cas for programmed change in plant genomes via homologous recombination have recently been developed. Cas9- and Cas12- mediated DNA binding is used to develop tools for many useful applications, such as transcriptional regulation or fluorescence-based imaging of specific chromosomal loci in plant genomes. Cas13 has recently been applied to degrade mRNAs and combat viral RNA replication. By the possibility to address multiple sequences with different guide RNAs and by the simultaneous use of different Cas proteins in a single cell, we should soon be able to achieve complex changes of plant metabolism in a controlled way.
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Affiliation(s)
| | - Felix Wolter
- Botanical Institute, Karlsruhe Institute of Technology, Germany
| | - Holger Puchta
- Botanical Institute, Karlsruhe Institute of Technology, Germany
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