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Kong D, Zhou Y, Wei Y, Wang X, Huang Q, Gao X, Wan H, Liu M, Kang L, Yu G, Yin J, Guan N, Ye H. Exploring plant-derived phytochrome chaperone proteins for light-switchable transcriptional regulation in mammals. Nat Commun 2024; 15:4894. [PMID: 38849338 PMCID: PMC11161646 DOI: 10.1038/s41467-024-49254-5] [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: 01/04/2024] [Accepted: 05/30/2024] [Indexed: 06/09/2024] Open
Abstract
Synthetic biology applications require finely tuned gene expression, often mediated by synthetic transcription factors (sTFs) compatible with the human genome and transcriptional regulation mechanisms. While various DNA-binding and activation domains have been developed for different applications, advanced artificially controllable sTFs with improved regulatory capabilities are required for increasingly sophisticated applications. Here, in mammalian cells and mice, we validate the transactivator function and homo-/heterodimerization activity of the plant-derived phytochrome chaperone proteins, FHY1 and FHL. Our results demonstrate that FHY1/FHL form a photosensing transcriptional regulation complex (PTRC) through interaction with the phytochrome, ΔPhyA, that can toggle between active and inactive states through exposure to red or far-red light, respectively. Exploiting this capability, we develop a light-switchable platform that allows for orthogonal, modular, and tunable control of gene transcription, and incorporate it into a PTRC-controlled CRISPRa system (PTRCdcas) to modulate endogenous gene expression. We then integrate the PTRC with small molecule- or blue light-inducible regulatory modules to construct a variety of highly tunable systems that allow rapid and reversible control of transcriptional regulation in vitro and in vivo. Validation and deployment of these plant-derived phytochrome chaperone proteins in a PTRC platform have produced a versatile, powerful tool for advanced research and biomedical engineering applications.
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Affiliation(s)
- Deqiang Kong
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, 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
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, 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
- Wuhu Hospital, Health Science Center, East China Normal University, Middle Jiuhua Road 263, Wuhu City, China
| | - Yu Wei
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, 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
| | - Xinyi Wang
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, 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
| | - Qin Huang
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, 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
| | - Xianyun Gao
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, 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
| | - Hang Wan
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, 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
| | - Mengyao Liu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, 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
| | - Liping Kang
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, 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
| | - Guiling Yu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, 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
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, 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
- Chongqing Key Laboratory of Precision Optics, Chongqing Institute of East China Normal University, Chongqing, 401120, China
| | - Ningzi Guan
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, 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.
| | - Haifeng Ye
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, 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.
- Wuhu Hospital, Health Science Center, East China Normal University, Middle Jiuhua Road 263, Wuhu City, China.
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2
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Allemailem KS, Almatroudi A, Rahmani AH, Alrumaihi F, Alradhi AE, Alsubaiyel AM, Algahtani M, Almousa RM, Mahzari A, Sindi AAA, Dobie G, Khan AA. Recent Updates of the CRISPR/Cas9 Genome Editing System: Novel Approaches to Regulate Its Spatiotemporal Control by Genetic and Physicochemical Strategies. Int J Nanomedicine 2024; 19:5335-5363. [PMID: 38859956 PMCID: PMC11164216 DOI: 10.2147/ijn.s455574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 05/30/2024] [Indexed: 06/12/2024] Open
Abstract
The genome editing approach by clustered regularly interspaced short palindromic repeats (CRISPR)/associated protein 9 (CRISPR/Cas9) is a revolutionary advancement in genetic engineering. Owing to its simple design and powerful genome-editing capability, it offers a promising strategy for the treatment of different infectious, metabolic, and genetic diseases. The crystal structure of Streptococcus pyogenes Cas9 (SpCas9) in complex with sgRNA and its target DNA at 2.5 Å resolution reveals a groove accommodating sgRNA:DNA heteroduplex within a bilobate architecture with target recognition (REC) and nuclease (NUC) domains. The presence of a PAM is significantly required for target recognition, R-loop formation, and strand scission. Recently, the spatiotemporal control of CRISPR/Cas9 genome editing has been considerably improved by genetic, chemical, and physical regulatory strategies. The use of genetic modifiers anti-CRISPR proteins, cell-specific promoters, and histone acetyl transferases has uplifted the application of CRISPR/Cas9 as a future-generation genome editing tool. In addition, interventions by chemical control, small-molecule activators, oligonucleotide conjugates and bioresponsive delivery carriers have improved its application in other areas of biological fields. Furthermore, the intermediation of physical control by using heat-, light-, magnetism-, and ultrasound-responsive elements attached to this molecular tool has revolutionized genome editing further. These strategies significantly reduce CRISPR/Cas9's undesirable off-target effects. However, other undesirable effects still offer some challenges for comprehensive clinical translation using this genome-editing approach. In this review, we summarize recent advances in CRISPR/Cas9 structure, mechanistic action, and the role of small-molecule activators, inhibitors, promoters, and physical approaches. Finally, off-target measurement approaches, challenges, future prospects, and clinical applications are discussed.
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Affiliation(s)
- Khaled S Allemailem
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
| | - Ahmad Almatroudi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
| | - Arshad Husain Rahmani
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
| | - Faris Alrumaihi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
| | - Arwa Essa Alradhi
- General Administration for Infectious Disease Control, Ministry of Health, Riyadh 12382, Saudi Arabia
| | - Amal M Alsubaiyel
- Department of Pharmaceutics, College of Pharmacy, Qassim University, Buraydah 51452, Saudi Arabia
| | - Mohammad Algahtani
- Department of Laboratory & Blood Bank, Security Forces Hospital, Mecca 21955, Saudi Arabia
| | - Rand Mohammad Almousa
- Department of Education, General Directorate of Education, Qassim 52361, Saudi Arabia
| | - Ali Mahzari
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Al-Baha University, Al-Baha 65527, Saudi Arabia
| | - Abdulmajeed A A Sindi
- Department of Basic Medical Sciences, Faculty of Applied Medical Sciences, Al-Baha University, Al-Baha 65527, Saudi Arabia
| | - Gasim Dobie
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, Jazan University, Gizan 82911, Saudi Arabia
| | - Amjad Ali Khan
- Department of Basic Health Sciences, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
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3
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Chen Y, Ping Y. Development of CRISPR/Cas Delivery Systems for In Vivo Precision Genome Editing. Acc Chem Res 2023; 56:2185-2196. [PMID: 37525893 DOI: 10.1021/acs.accounts.3c00279] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
ConspectusClustered, regularly interspaced, short palindromic repeat (CRISPR)/associated protein 9 (CRISPR/Cas9) is emerging as a powerful genome-editing tool, enabling precise and targeted modifications of virtually any genomic sequence in living cells. These technologies have potential therapeutic applications for cancers, metabolic diseases, and genetic disorders. However, several major challenges hinder the full realization of their potential. Specifically, CRISPR-Cas9 gene editors, whether delivered as plasmid DNA, mRNA/sgRNA, or ribonucleoprotein (RNP), exhibit poor membrane permeability, restricting their access to the intracellular genome, where the editing occurs. Additionally, these editors lack tissue or organ specificity, raising concerns about off-target editing at the tissue level that causes unwanted genotoxicity. Though a range of delivery carriers has been developed to deliver Cas9 editors, their effectiveness is often limited by a number of barriers at both the extracellular and intracellular levels. Moreover, the prolonged activity of Cas9 increases the risk of off-target editing at the genomic level. Therefore, it is crucial to develop efficient delivery vectors, along with molecular switches to safely regulate Cas9 activity.In this Account, we summarize our recent achievements in developing different types of materials that can efficiently deliver the plasmid DNA encoding Cas9 protein and single-guide RNA (sgRNA), or Cas9 RNP into cells to highlight the design considerations of carriers for safe and efficient delivery in vitro and in vivo. After elucidating the chemical and physical factors that are responsible for encapsulating and delivering these biomacromolecules, we further elucidate how we design the biodegradable polymeric carriers using dynamic disulfide chemistry, emphasize their safe and efficient delivery features for genome-editing biomacromolecules, and also introduce the integration of the intracellular delivery of genome-editing biomacromolecules with microneedle-based transdermal delivery to promote therapeutic genome editing for inflammatory skin disorders. Finally, we review how we exploit optical, chemical, and genetic switches to control the Cas9 activity in conjunction with targeted delivery to address the spatiotemporal specificity of gene editing in vivo and demonstrate their precision therapy against cancer and colitis treatment as proof-of-concept examples. In the final part, we will summarize the progress we have made and propose the future directions that may impact the field based on our own research outcomes.
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Affiliation(s)
- Yuxuan Chen
- College of Pharmaceutical Science, Zhejiang University, Hangzhou 310058, China
| | - Yuan Ping
- College of Pharmaceutical Science, Zhejiang University, Hangzhou 310058, China
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Allemailem KS, Almatroodi SA, Almatroudi A, Alrumaihi F, Al Abdulmonem W, Al-Megrin WAI, Aljamaan AN, Rahmani AH, Khan AA. Recent Advances in Genome-Editing Technology with CRISPR/Cas9 Variants and Stimuli-Responsive Targeting Approaches within Tumor Cells: A Future Perspective of Cancer Management. Int J Mol Sci 2023; 24:7052. [PMID: 37108214 PMCID: PMC10139162 DOI: 10.3390/ijms24087052] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/06/2023] [Accepted: 04/09/2023] [Indexed: 04/29/2023] Open
Abstract
The innovative advances in transforming clustered regularly interspaced short palindromic repeats-associated protein 9 (CRISPR/Cas9) into different variants have taken the art of genome-editing specificity to new heights. Allosteric modulation of Cas9-targeting specificity by sgRNA sequence alterations and protospacer adjacent motif (PAM) modifications have been a good lesson to learn about specificity and activity scores in different Cas9 variants. Some of the high-fidelity Cas9 variants have been ranked as Sniper-Cas9, eSpCas9 (1.1), SpCas9-HF1, HypaCas9, xCas9, and evoCas9. However, the selection of an ideal Cas9 variant for a given target sequence remains a challenging task. A safe and efficient delivery system for the CRISPR/Cas9 complex at tumor target sites faces considerable challenges, and nanotechnology-based stimuli-responsive delivery approaches have significantly contributed to cancer management. Recent innovations in nanoformulation design, such as pH, glutathione (GSH), photo, thermal, and magnetic responsive systems, have modernized the art of CRISPR/Cas9 delivery approaches. These nanoformulations possess enhanced cellular internalization, endosomal membrane disruption/bypass, and controlled release. In this review, we aim to elaborate on different CRISPR/Cas9 variants and advances in stimuli-responsive nanoformulations for the specific delivery of this endonuclease system. Furthermore, the critical constraints of this endonuclease system on clinical translations towards the management of cancer and prospects are described.
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Affiliation(s)
- Khaled S. Allemailem
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
| | - Saleh A. Almatroodi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
| | - Ahmad Almatroudi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
| | - Faris Alrumaihi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
| | - Waleed Al Abdulmonem
- Department of Pathology, College of Medicine, Qassim University, Buraydah 51452, Saudi Arabia
| | - Wafa Abdullah I. Al-Megrin
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | | | - Arshad Husain Rahmani
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
| | - Amjad Ali Khan
- Department of Basic Health Sciences, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
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5
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LeBlanc N, Charles TC. Bacterial genome reductions: Tools, applications, and challenges. Front Genome Ed 2022; 4:957289. [PMID: 36120530 PMCID: PMC9473318 DOI: 10.3389/fgeed.2022.957289] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/29/2022] [Indexed: 11/16/2022] Open
Abstract
Bacterial cells are widely used to produce value-added products due to their versatility, ease of manipulation, and the abundance of genome engineering tools. However, the efficiency of producing these desired biomolecules is often hindered by the cells’ own metabolism, genetic instability, and the toxicity of the product. To overcome these challenges, genome reductions have been performed, making strains with the potential of serving as chassis for downstream applications. Here we review the current technologies that enable the design and construction of such reduced-genome bacteria as well as the challenges that limit their assembly and applicability. While genomic reductions have shown improvement of many cellular characteristics, a major challenge still exists in constructing these cells efficiently and rapidly. Computational tools have been created in attempts at minimizing the time needed to design these organisms, but gaps still exist in modelling these reductions in silico. Genomic reductions are a promising avenue for improving the production of value-added products, constructing chassis cells, and for uncovering cellular function but are currently limited by their time-consuming construction methods. With improvements to and the creation of novel genome editing tools and in silico models, these approaches could be combined to expedite this process and create more streamlined and efficient cell factories.
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Affiliation(s)
- Nicole LeBlanc
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
- *Correspondence: Nicole LeBlanc,
| | - Trevor C. Charles
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
- Metagenom Bio Life Science Inc., Waterloo, ON, Canada
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6
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Gao ZF, Zheng LL, Dong LM, Li JZ, Shen Y, Chen P, Xia F. Label-Free Resonance Rayleigh Scattering Amplification for Lipopolysaccharide Detection and Logical Circuit by CRISPR/Cas12a-Driven Guanine Nanowire Assisted Non-Cross-Linking Hybridization Chain Reaction. Anal Chem 2022; 94:6371-6379. [DOI: 10.1021/acs.analchem.2c00848] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Zhong Feng Gao
- Advanced Materials Institute, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250014, People’s Republic of China
- Collaborative Innovation Center of Tumor Marker Detection Technology, Equipment and Diagnosis-Therapy Integration in Universities of Shandong, Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Feixian Campus, Linyi University, Linyi 276005, People’s Republic of China
| | - Lin Lin Zheng
- Advanced Materials Institute, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250014, People’s Republic of China
- Collaborative Innovation Center of Tumor Marker Detection Technology, Equipment and Diagnosis-Therapy Integration in Universities of Shandong, Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Feixian Campus, Linyi University, Linyi 276005, People’s Republic of China
| | - Lu Ming Dong
- Collaborative Innovation Center of Tumor Marker Detection Technology, Equipment and Diagnosis-Therapy Integration in Universities of Shandong, Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Feixian Campus, Linyi University, Linyi 276005, People’s Republic of China
| | - Jin Ze Li
- Collaborative Innovation Center of Tumor Marker Detection Technology, Equipment and Diagnosis-Therapy Integration in Universities of Shandong, Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Feixian Campus, Linyi University, Linyi 276005, People’s Republic of China
| | - Yizhong Shen
- School of Food & Biological Engineering, Key Laboratory for Agricultural Products Processing of Anhui Province, Hefei University of Technology, Hefei 230009, People’s Republic of China
| | - Pu Chen
- Department of Chemical Engineering and Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L3G1, Canada
| | - Fan Xia
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, People’s Republic of China
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7
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Liu X, Kang X, Lei C, Ren W, Liu C. Programming the trans-cleavage Activity of CRISPR-Cas13a by Single-Strand DNA Blocker and Its Biosensing Application. Anal Chem 2022; 94:3987-3996. [PMID: 35193353 DOI: 10.1021/acs.analchem.1c05124] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The precise and controllable programming of the trans-cleavage activity of the CRISPR-Cas13a systems is significant but challenging for fabricating high-performance biosensing systems toward various kinds of biomolecule targets. In this work, we have demonstrated that under a critical low Mg2+ concentration, a simple and short single-stranded DNA (ssDNA) probe free of any modification can efficiently prevent the assembly of crRNA and LwaCas13a only by partially binding with the crRNA repeat region, thereby blocking the trans-cleavage activity of the LwaCas13a system. Furthermore, we have demonstrated that the blocked trans-cleavage activity of the LwaCas13a system can be recovered by various kinds of biologically important substances as long as they could specifically release the blocker DNA from the crRNA in a target-responsive manner, providing a facile route for the quantification of diverse biomarkers such as enzymes, antigens/proteins, and exosomes. To the best of our knowledge, this is reported for the first time that a simple ssDNA can be employed as the switch element to control the crRNA structure and regulate the trans-cleavage activity of Cas13a, which has enriched the CRISPR-Cas13a sensing toolbox and will greatly expand its application scope.
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Affiliation(s)
- Xiaoling Liu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, Shaanxi, P. R. China
| | - Xinyue Kang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, Shaanxi, P. R. China
| | - Chao Lei
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, Shaanxi, P. R. China
| | - Wei Ren
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, Shaanxi, P. R. China
| | - Chenghui Liu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, Shaanxi, P. R. China
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8
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Yan X, Pan Q, Xin H, Chen Y, Ping Y. Genome-editing prodrug: Targeted delivery and conditional stabilization of CRISPR-Cas9 for precision therapy of inflammatory disease. SCIENCE ADVANCES 2021; 7:eabj0624. [PMID: 34878850 PMCID: PMC8654308 DOI: 10.1126/sciadv.abj0624] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Regulation of CRISPR-Cas9 functions in vivo is conducive to developing precise therapeutic genome editing. Here, we report a CRISPR-Cas9 prodrug nanosystem (termed NanoProCas9), which combines the targeted delivery and the conditional activation of CRISPR-Cas9 for the precision therapy of inflammatory bowel disease. NanoProCas9 is composed of (i) cationic poly(β-amino ester) (PBAE) capable of complexing plasmid DNA encoding destabilized Cas9 (dsCas9) nuclease, (ii) a layer of biomimetic cell membrane coated on PBAE/plasmid nanocomplexes for the targeted delivery of PBAE/dsCas9 complexes, and (iii) the stimuli-responsive precursory molecules anchored on the exofacial membrane. The systemic administration of NanoProCas9 enables the targeted delivery of dsCas9 plasmid into inflammatory lesions, where the precursory small molecule can be activated by ROS signals to stabilize expressed dsCas9, thereby activating Cas9 function for inflammatory genome editing. The proposed “genome-editing prodrug” presents a proof-of-concept example to precisely regulate CRISPR-Cas9 functions by virtue of particular pathological stimuli in vivo.
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Affiliation(s)
- Xiaojie Yan
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qi Pan
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Huhu Xin
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yuxuan Chen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yuan Ping
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, China
- Corresponding author.
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9
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Li X, Pan Y, Chen C, Gao Y, Liu X, Yang K, Luan X, Zhou D, Zeng F, Han X, Song Y. Hypoxia‐Responsive Gene Editing to Reduce Tumor Thermal Tolerance for Mild‐Photothermal Therapy. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202107036] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Xueqing Li
- College of Engineering and Applied Sciences Jiangsu Key Laboratory of Artificial Functional Materials State Key Laboratory of Analytical Chemistry for Life Science Nanjing University Nanjing 210023 China
| | - Yongchun Pan
- College of Engineering and Applied Sciences Jiangsu Key Laboratory of Artificial Functional Materials State Key Laboratory of Analytical Chemistry for Life Science Nanjing University Nanjing 210023 China
| | - Chao Chen
- School of Medicine & Holistic Integrative Medicine Jiangsu Collaborative Innovation Canter of Chinese Medicinal Resources Industrialization Nanjing University of Chinese Medicine Nanjing 210023 China
| | - Yanfeng Gao
- College of Engineering and Applied Sciences Jiangsu Key Laboratory of Artificial Functional Materials State Key Laboratory of Analytical Chemistry for Life Science Nanjing University Nanjing 210023 China
| | - Xinli Liu
- College of Engineering and Applied Sciences Jiangsu Key Laboratory of Artificial Functional Materials State Key Laboratory of Analytical Chemistry for Life Science Nanjing University Nanjing 210023 China
| | - Kaiyong Yang
- School of Medicine & Holistic Integrative Medicine Jiangsu Collaborative Innovation Canter of Chinese Medicinal Resources Industrialization Nanjing University of Chinese Medicine Nanjing 210023 China
| | - Xiaowei Luan
- College of Engineering and Applied Sciences Jiangsu Key Laboratory of Artificial Functional Materials State Key Laboratory of Analytical Chemistry for Life Science Nanjing University Nanjing 210023 China
| | - Dongtao Zhou
- College of Engineering and Applied Sciences Jiangsu Key Laboratory of Artificial Functional Materials State Key Laboratory of Analytical Chemistry for Life Science Nanjing University Nanjing 210023 China
| | - Fei Zeng
- College of Engineering and Applied Sciences Jiangsu Key Laboratory of Artificial Functional Materials State Key Laboratory of Analytical Chemistry for Life Science Nanjing University Nanjing 210023 China
| | - Xin Han
- School of Medicine & Holistic Integrative Medicine Jiangsu Collaborative Innovation Canter of Chinese Medicinal Resources Industrialization Nanjing University of Chinese Medicine Nanjing 210023 China
| | - Yujun Song
- College of Engineering and Applied Sciences Jiangsu Key Laboratory of Artificial Functional Materials State Key Laboratory of Analytical Chemistry for Life Science Nanjing University Nanjing 210023 China
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10
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Li X, Pan Y, Chen C, Gao Y, Liu X, Yang K, Luan X, Zhou D, Zeng F, Han X, Song Y. Hypoxia-Responsive Gene Editing to Reduce Tumor Thermal Tolerance for Mild-Photothermal Therapy. Angew Chem Int Ed Engl 2021; 60:21200-21204. [PMID: 34297462 DOI: 10.1002/anie.202107036] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Indexed: 01/17/2023]
Abstract
Near-infrared (NIR)-light-triggered photothermal therapy (PTT) is usually associated with undesirable damage to healthy organs nearby due to the high temperatures (>50 °C) available for tumor ablation. Low-temperature PTT would therefore have tremendous value for clinical application. Here, we construct a hypoxia-responsive gold nanorods (AuNRs)-based nanocomposite of CRISPR-Cas9 for mild-photothermal therapy via tumor-targeted gene editing. AuNRs are modified with azobenzene-4,4'-dicarboxylic acid (p-AZO) to achieve on-demand release of CRISPR-Cas9 using hypoxia-responsive azo bonds. In the hypoxic tumor microenvironment, the azo groups of the hypoxia-activated CRISPR-Cas9 nanosystem based on gold nanorods (APACPs) are selectively reduced by the overexpression of reductases, leading to the release of Cas9 and subsequent gene editing. Owing to the knockout of HSP90α for reducing the thermal resistance of cancer cells, highly effective tumor ablation both in vitro and in vivo was achieved with APACPs under mild PTT.
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Affiliation(s)
- Xueqing Li
- College of Engineering and Applied Sciences, Jiangsu Key Laboratory of Artificial Functional Materials, State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing, 210023, China
| | - Yongchun Pan
- College of Engineering and Applied Sciences, Jiangsu Key Laboratory of Artificial Functional Materials, State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing, 210023, China
| | - Chao Chen
- School of Medicine & Holistic Integrative Medicine, Jiangsu Collaborative Innovation Canter of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Yanfeng Gao
- College of Engineering and Applied Sciences, Jiangsu Key Laboratory of Artificial Functional Materials, State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing, 210023, China
| | - Xinli Liu
- College of Engineering and Applied Sciences, Jiangsu Key Laboratory of Artificial Functional Materials, State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing, 210023, China
| | - Kaiyong Yang
- School of Medicine & Holistic Integrative Medicine, Jiangsu Collaborative Innovation Canter of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Xiaowei Luan
- College of Engineering and Applied Sciences, Jiangsu Key Laboratory of Artificial Functional Materials, State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing, 210023, China
| | - Dongtao Zhou
- College of Engineering and Applied Sciences, Jiangsu Key Laboratory of Artificial Functional Materials, State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing, 210023, China
| | - Fei Zeng
- College of Engineering and Applied Sciences, Jiangsu Key Laboratory of Artificial Functional Materials, State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing, 210023, China
| | - Xin Han
- School of Medicine & Holistic Integrative Medicine, Jiangsu Collaborative Innovation Canter of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Yujun Song
- College of Engineering and Applied Sciences, Jiangsu Key Laboratory of Artificial Functional Materials, State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing, 210023, China
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11
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Zhuo C, Zhang J, Lee JH, Jiao J, Cheng D, Liu L, Kim HW, Tao Y, Li M. Spatiotemporal control of CRISPR/Cas9 gene editing. Signal Transduct Target Ther 2021; 6:238. [PMID: 34148061 PMCID: PMC8214627 DOI: 10.1038/s41392-021-00645-w] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 04/09/2021] [Accepted: 05/13/2021] [Indexed: 02/06/2023] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)/associated protein 9 (CRISPR/Cas9) gene editing technology, as a revolutionary breakthrough in genetic engineering, offers a promising platform to improve the treatment of various genetic and infectious diseases because of its simple design and powerful ability to edit different loci simultaneously. However, failure to conduct precise gene editing in specific tissues or cells within a certain time may result in undesirable consequences, such as serious off-target effects, representing a critical challenge for the clinical translation of the technology. Recently, some emerging strategies using genetic regulation, chemical and physical strategies to regulate the activity of CRISPR/Cas9 have shown promising results in the improvement of spatiotemporal controllability. Herein, in this review, we first summarize the latest progress of these advanced strategies involving cell-specific promoters, small-molecule activation and inhibition, bioresponsive delivery carriers, and optical/thermal/ultrasonic/magnetic activation. Next, we highlight the advantages and disadvantages of various strategies and discuss their obstacles and limitations in clinical translation. Finally, we propose viewpoints on directions that can be explored to further improve the spatiotemporal operability of CRISPR/Cas9.
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Grants
- the Guangdong Province Science and Technology Innovation Special Fund (International Scientific Cooperation, 2018A050506035), the National Natural Science Foundation of China (51903256).
- the National Key Research and Development Program of China (2016YFE0117100), the National Natural Science Foundation of China (21875289 and U1501243), the Guangdong-Hong Kong Joint Innovation Project (2016A050503026), the Major Project on the Integration of Industry, Education and Research of Guangzhou City (201704030123), the Science and Technology Program of Guangzhou (201704020016), the Guangdong Innovative and Entrepreneurial Research Team Program (2013S086)
- National Research Foundation, Republic of Korea (2015K1A1A2032163, 2018K1A4A3A01064257, 2018R1A2B3003446)
- the National Key Research and Development Program of China (2019YFA0111300, 2016YFE0117100), the National Natural Science Foundation of China (21907113), the Guangdong Provincial Pearl River Talents Program (2019QN01Y131), the Thousand Talents Plan.
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Affiliation(s)
- Chenya Zhuo
- Laboratory of Biomaterials and Translational Medicine, Center for Nanomedicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jiabin Zhang
- Laboratory of Biomaterials and Translational Medicine, Center for Nanomedicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jung-Hwan Lee
- Institute of Tissue Regeneration Engineering (ITREN), Dankook University, Cheonan, South Korea
| | - Ju Jiao
- Department of Nuclear Medicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Du Cheng
- PCFM Lab of Ministry of Education, School of Materials Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Li Liu
- Department of Gynecology and Obstetrics, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Hae-Won Kim
- Institute of Tissue Regeneration Engineering (ITREN), Dankook University, Cheonan, South Korea.
| | - Yu Tao
- Laboratory of Biomaterials and Translational Medicine, Center for Nanomedicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
| | - Mingqiang Li
- Laboratory of Biomaterials and Translational Medicine, Center for Nanomedicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
- Guangdong Provincial Key Laboratory of Liver Disease Research, Guangzhou, China.
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12
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Jain S, Xun G, Abesteh S, Ho S, Lingamaneni M, Martin TA, Tasan I, Yang C, Zhao H. Precise Regulation of Cas9-Mediated Genome Engineering by Anti-CRISPR-Based Inducible CRISPR Controllers. ACS Synth Biol 2021; 10:1320-1327. [PMID: 34006094 DOI: 10.1021/acssynbio.0c00548] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
CRISPR/Cas9 is a powerful genome editing tool, but its off-target cleavage activity can result in unintended adverse outcomes for therapeutic applications. Here we report the design of a simple tunable CRISPR controller in which a chemically inducible anti-CRISPR protein AcrIIA4 is engineered to disable Cas9 DNA binding upon the addition of trimethoprim. Dose-dependent control over Cas9 editing and dCas9 induction was achieved, which drastically improved the specificity and biosafety of the CRISPR/Cas9 system. We utilized the anti-CRISPR protein AcrIIA4 as a means to interfere with Cas9 DNA binding activity. By fusing AcrIIA4 to a ligand-inducible destabilization domain DHFR(DD), we show significantly reduced off-target activity in mammalian cells. Furthermore, we describe a new inducible promoter system Acr-OFF based on CRISPR controllers, which is regulated by an FDA-approved ligand trimethoprim.
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Affiliation(s)
- Surbhi Jain
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Guanhua Xun
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Shireen Abesteh
- School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Sherri Ho
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Manasi Lingamaneni
- School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Teresa A Martin
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ipek Tasan
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Che Yang
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Huimin Zhao
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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13
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Hochrein LM, Li H, Pierce NA. High-Performance Allosteric Conditional Guide RNAs for Mammalian Cell-Selective Regulation of CRISPR/Cas. ACS Synth Biol 2021; 10:964-971. [PMID: 33930275 DOI: 10.1021/acssynbio.1c00037] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The activity of a conditional guide RNA (cgRNA) is dependent on the presence or absence of an RNA trigger, enabling cell-selective regulation of CRISPR/Cas function. cgRNAs are programmable at two levels, with the target-binding sequence controlling the target of Cas activity (edit, silence, or induce a gene of choice) and the trigger-binding sequence controlling the scope of Cas activity (subset of cells expressing the trigger RNA). Allosteric cgRNA mechanisms enable independent design of the target and trigger sequences, providing the flexibility to select the regulatory target and scope independently. Building on prior advances in dynamic RNA nanotechnology that demonstrated the cgRNA concept, here we set the goal of engineering high-performance allosteric cgRNA mechanisms for the mammalian setting, pursuing both ON → OFF logic (conditional inactivation by an RNA trigger) and OFF → ON logic (conditional activation by an RNA trigger). For each mechanism, libraries of orthogonal cgRNA/trigger pairs were designed using NUPACK. In HEK 293T cells expressing cgRNAs, triggers, and inducing dCas9: (1) a library of four ON → OFF "terminator switch" cgRNAs exhibit a median fold-change of ≈50×, a median fractional dynamic range of ≈20%, and a median crosstalk modulus of ≈9%; (2) a library of three OFF → ON "split-terminator switch" cgRNAs exhibit a median fold-change of ≈150×, a median fractional dynamic range of ≈50%, and a median crosstalk modulus of ≈4%. Further, we demonstrate that xrRNA elements that protect viral RNAs from degradation by exoribonucleases can dramatically enhance the performance of RNA synthetic biology. The high-performance allosteric cgRNAs demonstrated here for ON → OFF and OFF → ON logic in mammalian cells provide a foundation for pursuing applications of programmable cell-selective regulation.
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Affiliation(s)
- Lisa M Hochrein
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Heyun Li
- Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Niles A Pierce
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, California 91125, United States
- Division of Engineering & Applied Science, California Institute of Technology, Pasadena, California 91125, United States
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14
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Zhang Y, Ling X, Su X, Zhang S, Wang J, Zhang P, Feng W, Zhu YY, Liu T, Tang X. Optical Control of a CRISPR/Cas9 System for Gene Editing by Using Photolabile crRNA. Angew Chem Int Ed Engl 2020; 59:20895-20899. [DOI: 10.1002/anie.202009890] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Indexed: 12/28/2022]
Affiliation(s)
- Yu Zhang
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38, Xueyuan Rd. Beijing 100191 China
| | - Xinyu Ling
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38, Xueyuan Rd. Beijing 100191 China
| | - Xiaoxuan Su
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38, Xueyuan Rd. Beijing 100191 China
| | - Shilin Zhang
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38, Xueyuan Rd. Beijing 100191 China
| | - Jing Wang
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38, Xueyuan Rd. Beijing 100191 China
| | - Pingjing Zhang
- Biomics Biotechnologies Co. Ltd. Nantong 226016 Jiangsu Province China
| | - Wenjian Feng
- Biomics Biotechnologies Co. Ltd. Nantong 226016 Jiangsu Province China
| | - York Yuanyuan Zhu
- Biomics Biotechnologies Co. Ltd. Nantong 226016 Jiangsu Province China
| | - Tao Liu
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38, Xueyuan Rd. Beijing 100191 China
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38, Xueyuan Rd. Beijing 100191 China
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15
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Zhang Y, Ling X, Su X, Zhang S, Wang J, Zhang P, Feng W, Zhu YY, Liu T, Tang X. Optical Control of a CRISPR/Cas9 System for Gene Editing by Using Photolabile crRNA. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202009890] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Yu Zhang
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38, Xueyuan Rd. Beijing 100191 China
| | - Xinyu Ling
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38, Xueyuan Rd. Beijing 100191 China
| | - Xiaoxuan Su
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38, Xueyuan Rd. Beijing 100191 China
| | - Shilin Zhang
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38, Xueyuan Rd. Beijing 100191 China
| | - Jing Wang
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38, Xueyuan Rd. Beijing 100191 China
| | - Pingjing Zhang
- Biomics Biotechnologies Co. Ltd. Nantong 226016 Jiangsu Province China
| | - Wenjian Feng
- Biomics Biotechnologies Co. Ltd. Nantong 226016 Jiangsu Province China
| | - York Yuanyuan Zhu
- Biomics Biotechnologies Co. Ltd. Nantong 226016 Jiangsu Province China
| | - Tao Liu
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38, Xueyuan Rd. Beijing 100191 China
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38, Xueyuan Rd. Beijing 100191 China
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16
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A non-invasive far-red light-induced split-Cre recombinase system for controllable genome engineering in mice. Nat Commun 2020; 11:3708. [PMID: 32709899 PMCID: PMC7381682 DOI: 10.1038/s41467-020-17530-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 07/03/2020] [Indexed: 12/19/2022] Open
Abstract
The Cre-loxP recombination system is a powerful tool for genetic manipulation. However, there are widely recognized limitations with chemically inducible Cre-loxP systems, and the UV and blue-light induced systems have phototoxicity and minimal capacity for deep tissue penetration. Here, we develop a far-red light-induced split Cre-loxP system (FISC system) based on a bacteriophytochrome optogenetic system and split-Cre recombinase, enabling optogenetical regulation of genome engineering in vivo solely by utilizing a far-red light (FRL). The FISC system exhibits low background and no detectable photocytotoxicity, while offering efficient FRL-induced DNA recombination. Our in vivo studies showcase the strong organ-penetration capacity of FISC system, markedly outperforming two blue-light-based Cre systems for recombination induction in the liver. Demonstrating its strong clinical relevance, we successfully deploy a FISC system using adeno-associated virus (AAV) delivery. Thus, the FISC system expands the optogenetic toolbox for DNA recombination to achieve spatiotemporally controlled, non-invasive genome engineering in living systems. Current light-inducible Cre-loxP systems have minimal capacity for deep tissue penetration. Here, the authors present a far-red light-induced split Cre-loxP system for in vivo genome engineering.
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17
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Wu Y, Yang L, Chang T, Kandeel F, Yee JK. A Small Molecule-Controlled Cas9 Repressible System. MOLECULAR THERAPY-NUCLEIC ACIDS 2020; 19:922-932. [PMID: 32000033 PMCID: PMC7063486 DOI: 10.1016/j.omtn.2019.12.026] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 12/21/2019] [Indexed: 12/26/2022]
Abstract
CRISPR-Cas9 has been developed into a powerful molecular tool for genome engineering, and it has revolutionized the field of biomedical research. Despite the tremendous potential of CRISPR-Cas9 in biomedical research, precise control of CRISPR-Cas9 over the dose and exposure time is important to expand its applications. In this study, we fused Cas9 with a peptide termed small molecule-assisted shut-off (SMASh) consisting of a protease domain and a degron domain derived from hepatitis C virus (HCV). The presence of SMASh allows tight control of the Cas9 stability via a clinically approved HCV protease inhibitor asunaprevir (ASV). We showed that the engineered Cas9 responded to ASV administration and rapidly degraded in a dose- and time-dependent manner. Cas9 degradation was reversible upon ASV removal that restored the gene editing activity. We also showed that limiting the level of Cas9 in cells increased the specificity of gene editing. The SMASh tag therefore provides an effective tool to control Cas9 stability, allowing an improvement in the accuracy, safety, and versatility of the CRISPR-Cas9 system for genome editing and gene regulation studies.
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Affiliation(s)
- Youjun Wu
- Department of Translational Research and Cellular Therapeutics, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Lu Yang
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
| | - Tammy Chang
- Department of Translational Research and Cellular Therapeutics, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Fouad Kandeel
- Department of Translational Research and Cellular Therapeutics, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Jiing-Kuan Yee
- Department of Translational Research and Cellular Therapeutics, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA.
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18
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Lin B, An Y, Meng L, Zhang H, Song J, Zhu Z, Liu W, Song Y, Yang C. Control of CRISPR-Cas9 with small molecule-activated allosteric aptamer regulating sgRNAs. Chem Commun (Camb) 2019; 55:12223-12226. [PMID: 31552919 DOI: 10.1039/c9cc05531b] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The CRISPR-Cas9 system enables facile and efficient genome engineering in living cells and organisms. Small molecule control of CRISPR-Cas9 would allow precise temporal control in applications of the technology. In this work, we developed s[combining low line]mall m[combining low line]olecule-activated allosteric a[combining low line]ptamer r[combining low line]egulat[combining low line]ing (SMART)-sgRNAs as general strategies to control programmable genome editing. With SMART-sgRNAs, temporal control of the CRISPR-Cas9 system against different targets can be achieved, which should facilitate its application in various fields, such as biomedical genome editing, drug screening and chromosome imaging.
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Affiliation(s)
- Bingqian Lin
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
| | - Yuan An
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
| | - Lingyan Meng
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
| | - Huimin Zhang
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Jia Song
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Zhi Zhu
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
| | - Wen Liu
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China.
| | - Yanling Song
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China. and Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Chaoyong Yang
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China. and Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
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19
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Chylinski K, Hubmann M, Hanna RE, Yanchus C, Michlits G, Uijttewaal ECH, Doench J, Schramek D, Elling U. CRISPR-Switch regulates sgRNA activity by Cre recombination for sequential editing of two loci. Nat Commun 2019; 10:5454. [PMID: 31784531 PMCID: PMC6884486 DOI: 10.1038/s41467-019-13403-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 11/07/2019] [Indexed: 01/20/2023] Open
Abstract
CRISPR-Cas9 is an efficient and versatile tool for genome engineering in many species. However, inducible CRISPR-Cas9 editing systems that regulate Cas9 activity or sgRNA expression often suffer from significant limitations, including reduced editing capacity, off-target effects, or leaky expression. Here, we develop a precisely controlled sgRNA expression cassette that can be combined with widely-used Cre systems, termed CRISPR-Switch (SgRNA With Induction/Termination by Cre Homologous recombination). Switch-ON facilitates controlled, rapid induction of sgRNA activity. In turn, Switch-OFF-mediated termination of editing improves generation of heterozygous genotypes and can limit off-target effects. Furthermore, we design sequential CRISPR-Switch-based editing of two loci in a strictly programmable manner and determined the order of mutagenic events that leads to development of glioblastoma in mice. Thus, CRISPR-Switch substantially increases the versatility of gene editing through precise and rapid switching ON or OFF sgRNA activity, as well as switching OVER to secondary sgRNAs.
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Affiliation(s)
- Krzysztof Chylinski
- Vienna Biocenter Core Facilities, Vienna Biocenter (VBC), Dr. Bohr Gasse 3, Vienna, Austria
| | - Maria Hubmann
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna Biocenter (VBC), Dr. Bohr Gasse 3, 1030, Vienna, Austria
| | - Ruth E Hanna
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Connor Yanchus
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Georg Michlits
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna Biocenter (VBC), Dr. Bohr Gasse 3, 1030, Vienna, Austria
| | - Esther C H Uijttewaal
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna Biocenter (VBC), Dr. Bohr Gasse 3, 1030, Vienna, Austria
| | - John Doench
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daniel Schramek
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Ulrich Elling
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna Biocenter (VBC), Dr. Bohr Gasse 3, 1030, Vienna, Austria.
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20
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Mills EM, Barlow VL, Luk LYP, Tsai YH. Applying switchable Cas9 variants to in vivo gene editing for therapeutic applications. Cell Biol Toxicol 2019; 36:17-29. [PMID: 31418127 PMCID: PMC7051928 DOI: 10.1007/s10565-019-09488-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 07/29/2019] [Indexed: 12/20/2022]
Abstract
Progress in targeted gene editing by programmable endonucleases has paved the way for their use in gene therapy. Particularly, Cas9 is an endonuclease with high activity and flexibility, rendering it an attractive option for therapeutic applications in clinical settings. Many disease-causing mutations could potentially be corrected by this versatile new technology. In addition, recently developed switchable Cas9 variants, whose activity can be controlled by an external stimulus, provide an extra level of spatiotemporal control on gene editing and are particularly desirable for certain applications. Here, we discuss the considerations and difficulties for implementing Cas9 to in vivo gene therapy. We put particular emphasis on how switchable Cas9 variants may resolve some of these barriers and advance gene therapy in the clinical setting.
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Affiliation(s)
- Emily M Mills
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK
| | | | - Louis Y P Luk
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK
| | - Yu-Hsuan Tsai
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK.
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21
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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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22
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Hanewich-Hollatz MH, Chen Z, Hochrein LM, Huang J, Pierce NA. Conditional Guide RNAs: Programmable Conditional Regulation of CRISPR/Cas Function in Bacterial and Mammalian Cells via Dynamic RNA Nanotechnology. ACS CENTRAL SCIENCE 2019; 5:1241-1249. [PMID: 31403072 PMCID: PMC6661866 DOI: 10.1021/acscentsci.9b00340] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Indexed: 05/18/2023]
Abstract
A guide RNA (gRNA) directs the function of a CRISPR protein effector to a target gene of choice, providing a versatile programmable platform for engineering diverse modes of synthetic regulation (edit, silence, induce, bind). However, the fact that gRNAs are constitutively active places limitations on the ability to confine gRNA activity to a desired location and time. To achieve programmable control over the scope of gRNA activity, here we apply principles from dynamic RNA nanotechnology to engineer conditional guide RNAs (cgRNAs) whose activity is dependent on the presence or absence of an RNA trigger. These cgRNAs are programmable at two levels, with the trigger-binding sequence controlling the scope of the effector activity and the target-binding sequence determining the subject of the effector activity. We demonstrate molecular mechanisms for both constitutively active cgRNAs that are conditionally inactivated by an RNA trigger (ON → OFF logic) and constitutively inactive cgRNAs that are conditionally activated by an RNA trigger (OFF → ON logic). For each mechanism, automated sequence design is performed using the reaction pathway designer within NUPACK to design an orthogonal library of three cgRNAs that respond to different RNA triggers. In E. coli expressing cgRNAs, triggers, and silencing dCas9 as the protein effector, we observe a median conditional response of ≈4-fold for an ON → OFF "terminator switch" mechanism, ≈15-fold for an ON → OFF "splinted switch" mechanism, and ≈3-fold for an OFF → ON "toehold switch" mechanism; the median crosstalk within each cgRNA/trigger library is <2%, ≈2%, and ≈20% for the three mechanisms. To test the portability of cgRNA mechanisms prototyped in bacteria to mammalian cells, as well as to test generalizability to different effector functions, we implemented the terminator switch in HEK 293T cells expressing inducing dCas9 as the protein effector, observing a median ON → OFF conditional response of ≈4-fold with median crosstalk of ≈30% for three orthogonal cgRNA/trigger pairs. By providing programmable control over both the scope and target of protein effector function, cgRNA regulators offer a promising platform for synthetic biology.
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Affiliation(s)
- Mikhail H Hanewich-Hollatz
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Zhewei Chen
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Lisa M Hochrein
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Jining Huang
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Niles A Pierce
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, California 91125, United States
- Division of Engineering & Applied Science, California Institute of Technology, Pasadena, California 91125, United States
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
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23
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24
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Barriers to genome editing with CRISPR in bacteria. J Ind Microbiol Biotechnol 2019; 46:1327-1341. [PMID: 31165970 DOI: 10.1007/s10295-019-02195-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 05/23/2019] [Indexed: 02/08/2023]
Abstract
Genome editing is essential for probing genotype-phenotype relationships and for enhancing chemical production and phenotypic robustness in industrial bacteria. Currently, the most popular tools for genome editing couple recombineering with DNA cleavage by the CRISPR nuclease Cas9 from Streptococcus pyogenes. Although successful in some model strains, CRISPR-based genome editing has been slow to extend to the multitude of industrially relevant bacteria. In this review, we analyze existing barriers to implementing CRISPR-based editing across diverse bacterial species. We first compare the efficacy of current CRISPR-based editing strategies. Next, we discuss alternatives when the S. pyogenes Cas9 does not yield colonies. Finally, we describe different ways bacteria can evade editing and how elucidating these failure modes can improve CRISPR-based genome editing across strains. Together, this review highlights existing obstacles to CRISPR-based editing in bacteria and offers guidelines to help achieve and enhance editing in a wider range of bacterial species, including non-model strains.
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25
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Qi F, Tan B, Ma F, Zhu B, Zhang L, Liu X, Li H, Yang J, Cheng B. A Synthetic Light-switchable System based on CRISPR Cas13a Regulates the Expression of LncRNA MALAT1 and Affects the Malignant Phenotype of Bladder Cancer Cells. Int J Biol Sci 2019; 15:1630-1636. [PMID: 31360106 PMCID: PMC6643210 DOI: 10.7150/ijbs.33772] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 04/10/2019] [Indexed: 12/19/2022] Open
Abstract
DNA sequences drive their various functions through post-transcriptional processes, using mRNA or lncRNA (long non-coding RNA), and this accommodates the gene network by using various RNA types. However, the tools necessary to regulate RNA molecules are few. Likewise, RNA knockdown techniques that can be artificially controlled have not been extensively explored. Here, we investigated a novel light-inducible synthetic system based on CRISPR-Cas13a that can be used for RNA knockdown and binding in cancer cells. Based on the techniques of synthetic molecular biology, we constructed a light sensor, which efficiently induced Cas13a protein expression after blue light illumination. We also chose a lncRNA, Metastasis-associated Lung Adenocarcinoma Transcript 1 (MALAT1), as the functional target and detected it in bladder cancer 5637 and T24 cells in order to demonstrate the application of our synthetic system. Fluorescence reporter assays and real-time quantitative PCR (qRT-PCR) were used to detect the expression of the target gene. Phenotypic experiments were also used to test the effects of our synthetic system in bladder cancers. The results showed that our synthetic light-switchable system could inhibit the expression of MALAT1, and the fluorescence activity of enhanced green fluorescent protein. Our novel system provides a new technique to study RNA functions in gene networks and for precise tumor treatments.
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Affiliation(s)
- Fuming Qi
- Urology and Andrology Department, Shengli OilFiled Central Hospital, Dongying, 257034, Shandong, China
| | - Bo Tan
- Urology and Andrology Department, Shengli OilFiled Central Hospital, Dongying, 257034, Shandong, China
| | - Fujun Ma
- Urology and Andrology Department, Shengli OilFiled Central Hospital, Dongying, 257034, Shandong, China
| | - Bo Zhu
- Urology and Andrology Department, Shengli OilFiled Central Hospital, Dongying, 257034, Shandong, China
| | - Li Zhang
- Burn and Plastic surgery Department, Shengli OilFiled Central Hospital, Dongying, 257034, Shandong, China
| | - Xiaoyun Liu
- Urology and Andrology Department, Shengli OilFiled Central Hospital, Dongying, 257034, Shandong, China
| | - Honglei Li
- Medical Department, Shengli OilFiled Central Hospital, Dongying, 257034, Shandong, China
| | - Jinhui Yang
- Urology and Andrology Department, Shengli OilFiled Central Hospital, Dongying, 257034, Shandong, China
| | - Bo Cheng
- Urology and Andrology Department, Shengli OilFiled Central Hospital, Dongying, 257034, Shandong, China
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26
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Nandy S, Pathak B, Zhao S, Srivastava V. Heat-shock-inducible CRISPR/Cas9 system generates heritable mutations in rice. PLANT DIRECT 2019; 3:e00145. [PMID: 31404128 PMCID: PMC6603394 DOI: 10.1002/pld3.145] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 05/08/2019] [Accepted: 05/13/2019] [Indexed: 05/22/2023]
Abstract
Transient expression of CRISPR/Cas9 is an effective approach for limiting its activities and improving its precision in genome editing. Here, we describe the heat-shock-inducible CRISPR/Cas9 for controlled genome editing, and demonstrate its efficiency in the model crop, rice. Using the soybean heat-shock protein gene promoter and the rice U3 promoter to express Cas9 and sgRNA, respectively, we developed the heat-shock (HS)-inducible CRISPR/Cas9 system, and tested its efficacy in targeted mutagenesis. Two loci were targeted in rice, and the presence of targeted mutations was determined before and after the HS treatment. Only a low rate of targeted mutagenesis was detected before HS (~16%), but an increased rate of mutagenesis was observed after the HS treatment among the transgenic lines (50-63%). Analysis of regenerated plants harboring HS-CRISPR/Cas9 revealed that targeted mutagenesis was suppressed in the plants but induced by HS, which was detectable by Sanger sequencing after a few weeks of HS treatments. Most importantly, the HS-induced mutations were transmitted to the progeny at a high rate, generating monoallelic and biallelic mutations that independently segregated from the Cas9 gene. Additionally, off-target mutations were either undetectable or found at a lower rate in HS-CRISPR/Cas9 lines as compared to the constitutive-overexpression CRISPR/Cas9 lines. Taken together, this work shows that HS-CRISPR/Cas9 is a controlled and reasonably efficient platform for genome editing, and therefore, a promising tool for limiting genome-wide off-target effects and improving the precision of genome editing.
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Affiliation(s)
- Soumen Nandy
- Department of Crop, Soil & Environmental Sciences University of Arkansas Fayetteville Arkansas
| | - Bhuvan Pathak
- Department of Crop, Soil & Environmental Sciences University of Arkansas Fayetteville Arkansas
- Cell and Molecular Biology Program University of Arkansas Fayetteville Arkansas
| | - Shan Zhao
- Department of Crop, Soil & Environmental Sciences University of Arkansas Fayetteville Arkansas
| | - Vibha Srivastava
- Department of Crop, Soil & Environmental Sciences University of Arkansas Fayetteville Arkansas
- Cell and Molecular Biology Program University of Arkansas Fayetteville Arkansas
- Department of Horticulture University of Arkansas Fayetteville Arkansas
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27
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Li Y, Teng X, Zhang K, Deng R, Li J. RNA Strand Displacement Responsive CRISPR/Cas9 System for mRNA Sensing. Anal Chem 2019; 91:3989-3996. [PMID: 30810036 DOI: 10.1021/acs.analchem.8b05238] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
CRISPR/Cas9 has already become a powerful tool for genomic manipulation, and further engineering of the system allows it to be precisely regulated in response to external signals, thus, broadening its application possibilities, such as biosensing or bioimaging. However, most stimuli-responsive CRISPR systems are built based on elaborately designed and engineered inducible Cas9 proteins, and external stimuli are still mostly limited as small molecules and light. To construct more precise and easy-to-build responsive CRISPR systems and broaden their responsive species, we seek to engineer conditional guide RNA, rather than Cas9 protein, to mediate conditional CRISPR corresponding to logic operation. Here, we construct mRNA-sensing CRISPR by gRNA reconfiguration and toehold mediated strand displacement, in which each target site could be independently controlled. We show that switches can be embedded into the gRNA and used as RNA sensors, capable of detecting multiple mRNA inputs orthogonally and providing CRISPR/Cas9 response outputs. NOR and NAND logical gates are also constructed, demonstrating its orthogonality and programmability. This strategy promises potential uses in constructing genetic circuits to detect endogenous mRNAs and initiate cellular responses.
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Affiliation(s)
- Yue Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology , Tsinghua University , Beijing 100084 , China
| | - Xucong Teng
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology , Tsinghua University , Beijing 100084 , China
| | - Kaixiang Zhang
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology , Tsinghua University , Beijing 100084 , China
- School of Pharmaceutical Sciences , Zhengzhou University , Zhengzhou 450001 , China
| | - Ruijie Deng
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology , Tsinghua University , Beijing 100084 , China
| | - Jinghong Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology , Tsinghua University , Beijing 100084 , China
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28
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Gangopadhyay SA, Cox KJ, Manna D, Lim D, Maji B, Zhou Q, Choudhary A. Precision Control of CRISPR-Cas9 Using Small Molecules and Light. Biochemistry 2019; 58:234-244. [PMID: 30640437 PMCID: PMC6586488 DOI: 10.1021/acs.biochem.8b01202] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The CRISPR (clustered regularly interspaced short palindromic repeat)-Cas system is an adaptive immune system of bacteria that has furnished several RNA-guided DNA endonucleases (e.g., Cas9) that are revolutionizing the field of genome engineering. Cas9 is being used to effect genomic alterations as well as in gene drives, where a particular trait may be propagated through a targeted species population over several generations. The ease of targeting catalytically impaired Cas9 to any genomic loci has led to development of technologies for base editing, chromatin imaging and modeling, epigenetic editing, and gene regulation. Unsurprisingly, Cas9 is being developed for numerous applications in biotechnology and biomedical research and as a gene therapy agent for multiple pathologies. There is a need for precise control of Cas9 activity over several dimensions, including those of dose, time, and space in these applications. Such precision controls, which are required of therapeutic agents, are particularly important for Cas9 as off-target effects, chromosomal translocations, immunogenic response, genotoxicity, and embryonic mosaicism are observed at elevated levels and with prolonged activity of Cas9. Here, we provide a perspective on advances in the precision control of Cas9 over aforementioned dimensions using external stimuli (e.g., small molecules or light) for controlled activation, inhibition, or degradation of Cas9.
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Affiliation(s)
- Soumyashree A. Gangopadhyay
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
- Divisions of Renal Medicine and Engineering, Brigham and Women’s Hospital, Boston, Massachusetts 02115, United States
| | - Kurt J. Cox
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Debasish Manna
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
- Divisions of Renal Medicine and Engineering, Brigham and Women’s Hospital, Boston, Massachusetts 02115, United States
| | - Donghyun Lim
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Basudeb Maji
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
- Divisions of Renal Medicine and Engineering, Brigham and Women’s Hospital, Boston, Massachusetts 02115, United States
| | - Qingxuan Zhou
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Amit Choudhary
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
- Divisions of Renal Medicine and Engineering, Brigham and Women’s Hospital, Boston, Massachusetts 02115, United States
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29
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Baaske J, Mühlhäuser WWD, Yousefi OS, Zanner S, Radziwill G, Hörner M, Schamel WWA, Weber W. Optogenetic control of integrin-matrix interaction. Commun Biol 2019; 2:15. [PMID: 30652127 PMCID: PMC6325061 DOI: 10.1038/s42003-018-0264-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 12/12/2018] [Indexed: 12/17/2022] Open
Abstract
Optogenetic approaches have gathered momentum in precisely modulating and interrogating cellular signalling and gene expression. The use of optogenetics on the outer cell surface to interrogate how cells receive stimuli from their environment, however, has so far not reached its full potential. Here we demonstrate the development of an optogenetically regulated membrane receptor-ligand pair exemplified by the optically responsive interaction of an integrin receptor with the extracellular matrix. The system is based on an integrin engineered with a phytochrome-interacting factor domain (OptoIntegrin) and a red light-switchable phytochrome B-functionalized matrix (OptoMatrix). This optogenetic receptor-ligand pair enables light-inducible and -reversible cell-matrix interaction, as well as the controlled activation of downstream mechanosensory signalling pathways. Pioneering the application of optogenetic switches in the extracellular environment of cells, this OptoMatrix-OptoIntegrin system may serve as a blueprint for rendering matrix-receptor interactions amendable to precise control with light.
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Affiliation(s)
- Julia Baaske
- Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
- Signalling Research Centers BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany
| | - Wignand W. D. Mühlhäuser
- Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
- Signalling Research Centers BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany
| | - O. Sascha Yousefi
- Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
- Signalling Research Centers BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstr. 19A, 79104 Freiburg, Germany
- Center for Chronic Immunodeficiency, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Sebastian Zanner
- Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Gerald Radziwill
- Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
- Signalling Research Centers BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany
| | - Maximilian Hörner
- Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
- Signalling Research Centers BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstr. 19A, 79104 Freiburg, Germany
| | - Wolfgang W. A. Schamel
- Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
- Signalling Research Centers BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstr. 19A, 79104 Freiburg, Germany
- Center for Chronic Immunodeficiency, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Wilfried Weber
- Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
- Signalling Research Centers BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstr. 19A, 79104 Freiburg, Germany
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30
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Suzuki T, Asami M, Patel SG, Luk LYP, Tsai YH, Perry ACF. Switchable genome editing via genetic code expansion. Sci Rep 2018; 8:10051. [PMID: 29968790 PMCID: PMC6030211 DOI: 10.1038/s41598-018-28178-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 06/11/2018] [Indexed: 01/07/2023] Open
Abstract
Multiple applications of genome editing by CRISPR-Cas9 necessitate stringent regulation and Cas9 variants have accordingly been generated whose activity responds to small ligands, temperature or light. However, these approaches are often impracticable, for example in clinical therapeutic genome editing in situ or gene drives in which environmentally-compatible control is paramount. With this in mind, we have developed heritable Cas9-mediated mammalian genome editing that is acutely controlled by the cheap lysine derivative, Lys(Boc) (BOC). Genetic code expansion permitted non-physiological BOC incorporation such that Cas9 (Cas9BOC) was expressed in a full-length, active form in cultured somatic cells only after BOC exposure. Stringently BOC-dependent, heritable editing of transgenic and native genomic loci occurred when Cas9BOC was expressed at the onset of mouse embryonic development from cRNA or Cas9BOC transgenic females. The tightly controlled Cas9 editing system reported here promises to have broad applications and is a first step towards purposed, spatiotemporal gene drive regulation over large geographical ranges.
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Affiliation(s)
- Toru Suzuki
- Laboratory of Mammalian Molecular Embryology, Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, England
| | - Maki Asami
- Laboratory of Mammalian Molecular Embryology, Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, England
| | - Sanjay G Patel
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, Wales
| | - Louis Y P Luk
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, Wales
| | - Yu-Hsuan Tsai
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, Wales.
| | - Anthony C F Perry
- Laboratory of Mammalian Molecular Embryology, Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, England.
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