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Li YJ, Chien SH, Huang R, Herrmann A, Zhao Q, Li PC, Zhang C, Martincuks A, Santiago NL, Zong K, Swiderski P, Okimoto RA, Song M, Rodriguez L, Forman SJ, Wang X, Yu H. A platform to deliver single and bi-specific Cas9/guide RNA to perturb genes in vitro and in vivo. Mol Ther 2024:S1525-0016(24)00480-5. [PMID: 39091030 DOI: 10.1016/j.ymthe.2024.07.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 06/20/2024] [Accepted: 07/29/2024] [Indexed: 08/04/2024] Open
Abstract
Although CRISPR-Cas9 technology is poised to revolutionize the treatment of diseases with underlying genetic mutations, it faces some significant issues limiting clinical entry. They include low-efficiency in vivo systemic delivery and undesired off-target effects. Here, we demonstrate, by modifying Cas9 with phosphorothioate-DNA oligos (PSs), that one can efficiently deliver single and bi-specific CRISPR-Cas9/guide RNA (gRNA) dimers in vitro and in vivo with reduced off-target effects. We show that PS-Cas9/gRNA-mediated gene knockout preserves chimeric antigen receptor T cell viability and expansion in vitro and in vivo. PS-Cas9/gRNA mediates gene perturbation in patient-derived tumor organoids and mouse xenograft tumors, leading to potent tumor antitumor effects. Further, HER2 antibody-PS-Cas9/gRNA conjugate selectively perturbs targeted genes in HER2+ ovarian cancer xenografts in vivo. Moreover, we created bi-specific PS-Cas9 with two gRNAs to target two adjacent sequences of the same gene, leading to efficient targeted gene disruption ex vivo and in vivo with markedly reduced unintended gene perturbation. Thus, the cell-penetrating PS-Cas9/gRNA can achieve efficient systemic delivery and precision in gene disruption.
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Affiliation(s)
- Yi-Jia Li
- Department of Immuno-Oncology, Beckman Research Institute and City of Hope Medical Center, Duarte, CA 91010, USA.
| | - Sheng-Hsuan Chien
- Cellular Immunotherapy Center, Department of Hematology and Hematopoietic Cell Transplantation, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA; Division of Transfusion Medicine, Department of Medicine, Taipei Veterans General Hospital, and Institute of Clinical Medicine, National Yang-Ming Chiao Tung University, Taipei 11201, Taiwan
| | - Rui Huang
- Department of Immuno-Oncology, Beckman Research Institute and City of Hope Medical Center, Duarte, CA 91010, USA
| | - Andreas Herrmann
- Department of Immuno-Oncology, Beckman Research Institute and City of Hope Medical Center, Duarte, CA 91010, USA
| | - Qianqian Zhao
- Department of Immuno-Oncology, Beckman Research Institute and City of Hope Medical Center, Duarte, CA 91010, USA
| | - Pei-Chuan Li
- Department of Immuno-Oncology, Beckman Research Institute and City of Hope Medical Center, Duarte, CA 91010, USA
| | - Chunyan Zhang
- Cellular Immunotherapy Center, Department of Hematology and Hematopoietic Cell Transplantation, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Antons Martincuks
- Department of Immuno-Oncology, Beckman Research Institute and City of Hope Medical Center, Duarte, CA 91010, USA
| | - Nicole Lugo Santiago
- Department of Surgery, Division of Gynecologic Oncology, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Katherine Zong
- Department of Immuno-Oncology, Beckman Research Institute and City of Hope Medical Center, Duarte, CA 91010, USA
| | - Piotr Swiderski
- DNA/RNA Synthesis Laboratory, Beckman Research Institute at City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Ross A Okimoto
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94115, USA
| | - Mihae Song
- Department of Surgery, Division of Gynecologic Oncology, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Lorna Rodriguez
- Department of Surgery, Division of Gynecologic Oncology, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Stephen J Forman
- Cellular Immunotherapy Center, Department of Hematology and Hematopoietic Cell Transplantation, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Xiuli Wang
- Cellular Immunotherapy Center, Department of Hematology and Hematopoietic Cell Transplantation, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Hua Yu
- Department of Immuno-Oncology, Beckman Research Institute and City of Hope Medical Center, Duarte, CA 91010, USA.
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2
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Małecka EM, Woodson SA. RNA compaction and iterative scanning for small RNA targets by the Hfq chaperone. Nat Commun 2024; 15:2069. [PMID: 38453956 PMCID: PMC10920880 DOI: 10.1038/s41467-024-46316-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 02/18/2024] [Indexed: 03/09/2024] Open
Abstract
RNA-guided enzymes must quickly search a vast sequence space for their targets. This search is aided by chaperones such as Hfq, a protein that mediates regulation by bacterial small RNAs (sRNAs). How RNA binding proteins enhance this search is little known. Using single-molecule Förster resonance energy transfer, we show that E. coli Hfq performs a one-dimensional scan in which compaction of the target RNA delivers sRNAs to sites distant from the location of Hfq recruitment. We also show that Hfq can transfer an sRNA between different target sites in a single mRNA, favoring the most stable duplex. We propose that compaction and segmental transfer, combined with repeated cycles of base pairing, enable the kinetic selection of optimal sRNA targets. Finally, we show that RNA compaction and sRNA transfer require conserved arginine patches. We suggest that arginine patches are a widespread strategy for enabling the movement of RNA across protein surfaces.
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Affiliation(s)
- Ewelina M Małecka
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St.,5, Baltimore, MD, 21218, USA.
- Laboratory of Single-Molecule Biophysics, International Institute of Molecular and Cell Biology in Warsaw, Trojdena 4, Warsaw, 02-109, Poland.
| | - Sarah A Woodson
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St.,5, Baltimore, MD, 21218, USA.
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3
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Kovalev MA, Davletshin AI, Karpov DS. Engineering Cas9: next generation of genomic editors. Appl Microbiol Biotechnol 2024; 108:209. [PMID: 38353732 PMCID: PMC10866799 DOI: 10.1007/s00253-024-13056-y] [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: 06/13/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/16/2024]
Abstract
The Cas9 endonuclease of the CRISPR/Cas type IIA system from Streptococcus pyogenes is the heart of genome editing technology that can be used to treat human genetic and viral diseases. Despite its large size and other drawbacks, S. pyogenes Cas9 remains the most widely used genome editor. A vast amount of research is aimed at improving Cas9 as a promising genetic therapy. Strategies include directed evolution of the Cas9 protein, rational design, and domain swapping. The first generation of Cas9 editors comes directly from the wild-type protein. The next generation is obtained by combining mutations from the first-generation variants, adding new mutations to them, or refining mutations. This review summarizes and discusses recent advances and ways in the creation of next-generation genomic editors derived from S. pyogenes Cas9. KEY POINTS: • The next-generation Cas9-based editors are more active than in the first one. • PAM-relaxed variants of Cas9 are improved by increased specificity and activity. • Less mutagenic and immunogenic variants of Cas9 are created.
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Affiliation(s)
- Maxim A Kovalev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991, Moscow, Russia
- Department of Biology, Lomonosov Moscow State University, 119234, Moscow, Russia
| | - Artem I Davletshin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991, Moscow, Russia
| | - Dmitry S Karpov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991, Moscow, Russia.
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991, Moscow, Russia.
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4
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Chen Z, Li X, Zhang Q, Sun W, Song X, Zhang X, Huang X, Sun B. Enlarged DNA unwinding by Nme2Cas9 permits a broadened base editing window beyond the protospacer. SCIENCE CHINA. LIFE SCIENCES 2024; 67:424-427. [PMID: 37606848 DOI: 10.1007/s11427-023-2384-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 06/05/2023] [Indexed: 08/23/2023]
Affiliation(s)
- Ziting Chen
- School of Life Science and Technology and Gene Editing Center, ShanghaiTech University, Shanghai, 201210, China
| | - Xiangyang Li
- School of Life Science and Technology and Gene Editing Center, ShanghaiTech University, Shanghai, 201210, China
- Zhejiang Lab, Hangzhou, Zhejiang, 311121, China
| | - Qian Zhang
- School of Life Science and Technology and Gene Editing Center, ShanghaiTech University, Shanghai, 201210, China
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenjun Sun
- School of Life Science and Technology and Gene Editing Center, ShanghaiTech University, Shanghai, 201210, China
| | - Xiaoxuan Song
- School of Life Science and Technology and Gene Editing Center, ShanghaiTech University, Shanghai, 201210, China
| | - Xia Zhang
- School of Life Science and Technology and Gene Editing Center, ShanghaiTech University, Shanghai, 201210, China
| | - Xingxu Huang
- School of Life Science and Technology and Gene Editing Center, ShanghaiTech University, Shanghai, 201210, China.
- Zhejiang Lab, Hangzhou, Zhejiang, 311121, China.
| | - Bo Sun
- School of Life Science and Technology and Gene Editing Center, ShanghaiTech University, Shanghai, 201210, China.
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5
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Ham DT, Browne TS, Banglorewala PN, Wilson TL, Michael RK, Gloor GB, Edgell DR. A generalizable Cas9/sgRNA prediction model using machine transfer learning with small high-quality datasets. Nat Commun 2023; 14:5514. [PMID: 37679324 PMCID: PMC10485023 DOI: 10.1038/s41467-023-41143-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 08/24/2023] [Indexed: 09/09/2023] Open
Abstract
The CRISPR/Cas9 nuclease from Streptococcus pyogenes (SpCas9) can be used with single guide RNAs (sgRNAs) as a sequence-specific antimicrobial agent and as a genome-engineering tool. However, current bacterial sgRNA activity models struggle with accurate predictions and do not generalize well, possibly because the underlying datasets used to train the models do not accurately measure SpCas9/sgRNA activity and cannot distinguish on-target cleavage from toxicity. Here, we solve this problem by using a two-plasmid positive selection system to generate high-quality data that more accurately reports on SpCas9/sgRNA cleavage and that separates activity from toxicity. We develop a machine learning architecture (crisprHAL) that can be trained on existing datasets, that shows marked improvements in sgRNA activity prediction accuracy when transfer learning is used with small amounts of high-quality data, and that can generalize predictions to different bacteria. The crisprHAL model recapitulates known SpCas9/sgRNA-target DNA interactions and provides a pathway to a generalizable sgRNA bacterial activity prediction tool that will enable accurate antimicrobial and genome engineering applications.
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Affiliation(s)
- Dalton T Ham
- Department of Biochemistry, Schulich School of Medicine and Dentistry, London, ON, N6A5C1, Canada
| | - Tyler S Browne
- Department of Biochemistry, Schulich School of Medicine and Dentistry, London, ON, N6A5C1, Canada
| | - Pooja N Banglorewala
- Department of Biochemistry, Schulich School of Medicine and Dentistry, London, ON, N6A5C1, Canada
| | | | | | - Gregory B Gloor
- Department of Biochemistry, Schulich School of Medicine and Dentistry, London, ON, N6A5C1, Canada.
| | - David R Edgell
- Department of Biochemistry, Schulich School of Medicine and Dentistry, London, ON, N6A5C1, Canada.
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6
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Full-Length Model of SaCas9-sgRNA-DNA Complex in Cleavage State. Int J Mol Sci 2023; 24:ijms24021204. [PMID: 36674715 PMCID: PMC9867433 DOI: 10.3390/ijms24021204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/24/2022] [Accepted: 12/27/2022] [Indexed: 01/10/2023] Open
Abstract
Staphylococcus aureus Cas9 (SaCas9) is a widely used genome editing tool. Understanding its molecular mechanisms of DNA cleavage could effectively guide the engineering optimization of this system. Here, we determined the first cryo-electron microscopy structure of the SaCas9-sgRNA-DNA ternary complex. This structure reveals that the HNH nuclease domain is tightly bound to the cleavage site of the target DNA strand, and is in close contact with the WED and REC domains. Moreover, it captures the complete structure of the sgRNA, including the previously unresolved stem-loop 2. Based on this structure, we build a full-length model for the ternary complex in cleavage state. This model enables identification of the residues for the interactions between the HNH domain and the WED and REC domains. Moreover, we found that the stem-loop 2 of the sgRNA tightly binds to the PI and RuvC domains and may also regulate the position shift of the RuvC domain. Further mutagenesis and molecular dynamics simulations supported the idea that the interactions of the HNH domain with the WED and REC domains play an important role in the DNA cleavage. Thus, this study provides new mechanistic insights into the DNA cleavage of SaCas9 and is also useful for guiding the future engineering of SaCas9-mediated gene editing systems.
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7
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Jia X, Li Y, Wang T, Bi L, Guo L, Chen Z, Zhang X, Ye S, Chen J, Yang B, Sun B. Discrete RNA-DNA hybrid cleavage by the EXD2 exonuclease pinpoints two rate-limiting steps. EMBO J 2023; 42:e111703. [PMID: 36326837 PMCID: PMC9811613 DOI: 10.15252/embj.2022111703] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 10/17/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022] Open
Abstract
EXD2 is a recently identified exonuclease that cleaves RNA and DNA in double-stranded (ds) forms. It thus serves as a model system for investigating the similarities and discrepancies between exoribonuclease and exodeoxyribonuclease activities and for understanding the nucleic acid (NA) unwinding-degradation coordination of an exonuclease. Here, using a single-molecule fluorescence resonance energy transfer (smFRET) approach, we show that despite stable binding to both substrates, EXD2 barely cleaves dsDNA and yet displays both exoribonuclease and exodeoxyribonuclease activities toward RNA-DNA hybrids with a cleavage preference for RNA. Unexpectedly, EXD2-mediated hybrid cleavage proceeds in a discrete stepwise pattern, wherein a sudden 4-bp duplex unwinding increment and the subsequent dwell constitute a complete hydrolysis cycle. The relatively weak exodeoxyribonuclease activity of EXD2 partially originates from frequent hybrid rewinding. Importantly, kinetic analysis and comparison of the dwell times under varied conditions reveal two rate-limiting steps of hybrid unwinding and nucleotide excision. Overall, our findings help better understand the cellular functions of EXD2, and the cyclic coupling between duplex unwinding and exonucleolytic degradation may be generalizable to other exonucleases.
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Affiliation(s)
- Xinshuo Jia
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Yanan Li
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Teng Wang
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Lulu Bi
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Lijuan Guo
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Ziting Chen
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Xia Zhang
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Shasha Ye
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
- Present address:
ZJU‐Hangzhou Global Scientific and Technological Innovation CenterZhejiang UniversityHangzhouChina
| | - Jia Chen
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Bei Yang
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghaiChina
| | - Bo Sun
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
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8
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Liu H, Zhou Y, Song Y, Zhang Q, Kan Y, Tang X, Xiao Q, Xiang Q, Liu H, Luo Y, Bao R. Structural and Dynamics Studies of the Spcas9 Variant Provide Insights into the Regulatory Role of the REC1 Domain. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01804] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Huayi Liu
- Frontiers Science Center of Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Yi Zhou
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yingjie Song
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Qianqian Zhang
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Yeyi Kan
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xinyue Tang
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Qingjie Xiao
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute (Zhangjiang Laboratory), Chinese Academy of Sciences, Shanghai 200135, China
| | - Qianyin Xiang
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Huanxiang Liu
- Faculty of Applied Science, Macao Polytechnic University, Macao, SAR 999078, China
| | - Yunzi Luo
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
- Frontiers Science Center of Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Rui Bao
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
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