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Thornton BW, Weissman RF, Tran RV, Duong BT, Rodriguez JE, Terrace CI, Groover ED, Park JU, Tartaglia J, Doudna JA, Savage DF. Latent activity in TnpB revealed by mutational scanning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.11.637750. [PMID: 39990302 PMCID: PMC11844463 DOI: 10.1101/2025.02.11.637750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/25/2025]
Abstract
TnpB is an evolutionarily diverse family of RNA-guided endonucleases associated with prokaryotic transposons. Due to their small size and putative evolutionary relationship to Cas12s, TnpB holds significant potential for genome editing and mechanistic exploration. However, most TnpBs lack robust gene-editing activity, and unbiased profiling of mutational effects on editing activity has not been experimentally explored. Here, we mapped comprehensive sequence-function landscapes of a TnpB ribonucleoprotein and discovered many activating mutations in both the protein and RNA. Single-position changes in the RNA outperform existing variants, highlighting the utility of systematic RNA scaffold mutagenesis. Leveraging the mutational landscape of the TnpB protein, we identified enhanced protein variants from a combinatorial library of activating mutations. These variants increased editing in human cells and N. benthamiana by over two-fold and fifty-fold relative to wild-type TnpB, respectively. In total, this study highlights unknown elements critical for regulation of endonuclease activity in both the TnpB protein and the RNA, and reveals a surprising amount of latent activity accessible through mutation.
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Affiliation(s)
- Brittney W. Thornton
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Rachel F. Weissman
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Ryan V. Tran
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720, US
- Scribe Therapeutics, Alameda, CA, 94501, USA
| | - Brenda T. Duong
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720, US
| | - Jorge E. Rodriguez
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Cynthia I. Terrace
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Evan D. Groover
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Jung-Un Park
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Julia Tartaglia
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Jennifer A. Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, 94720, USA
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720, US
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, US
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David F. Savage
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, 94720, USA
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Karp H, Zoltek M, Wasko K, Vazquez AL, Brim J, Ngo W, Schepartz A, Doudna J. Packaged delivery of CRISPR-Cas9 ribonucleoproteins accelerates genome editing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.18.619117. [PMID: 39464099 PMCID: PMC11507943 DOI: 10.1101/2024.10.18.619117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/29/2024]
Abstract
Effective genome editing requires a sufficient dose of CRISPR-Cas9 ribonucleoproteins (RNPs) to enter the target cell while minimizing immune responses, off-target editing and cytotoxicity. Clinical use of Cas9 RNPs currently entails electroporation into cells ex vivo, but no systematic comparison of this method to packaged RNP delivery has been made. Here we compared two delivery strategies, electroporation and enveloped delivery vehicles (EDVs), to investigate the Cas9 dosage requirements for genome editing. Using fluorescence correlation spectroscopy (FCS), we determined that >1300 Cas9 RNPs per nucleus are typically required for productive genome editing. EDV-mediated editing was >30-fold more efficient than electroporation, and editing occurs at least two-fold faster for EDV delivery at comparable total Cas9 RNP doses. We hypothesize that differences in efficacy between these methods result in part from the increased duration of RNP nuclear residence resulting from EDV delivery. Our results directly compare RNP delivery strategies, showing that packaged delivery could dramatically reduce the amount of CRISPR-Cas9 RNPs required for experimental or clinical genome editing.
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Affiliation(s)
- Hannah Karp
- Department of Chemistry, University of California, Berkeley, California 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, California 94720, USA
| | - Madeline Zoltek
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
| | - Kevin Wasko
- Innovative Genomics Institute, University of California, Berkeley, California 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
| | - Angel Luis Vazquez
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Jinna Brim
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
| | - Wayne Ngo
- Innovative Genomics Institute, University of California, Berkeley, California 94720, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, USA
- Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, California 94158
| | - Alanna Schepartz
- Department of Chemistry, University of California, Berkeley, California 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, USA
- Innovation Investigator, ARC Institute, Palo Alto, CA 94304, USA
- Chan Zuckerberg Biohub, San Francisco, California 94158, United States
| | - Jennifer Doudna
- Department of Chemistry, University of California, Berkeley, California 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, California 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, USA
- Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, California 94158
- Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA
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3
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Kim M, Hwang Y, Lim S, Jang HK, Kim HO. Advances in Nanoparticles as Non-Viral Vectors for Efficient Delivery of CRISPR/Cas9. Pharmaceutics 2024; 16:1197. [PMID: 39339233 PMCID: PMC11434874 DOI: 10.3390/pharmaceutics16091197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2024] [Revised: 09/05/2024] [Accepted: 09/09/2024] [Indexed: 09/30/2024] Open
Abstract
The clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 system is a gene-editing technology. Nanoparticle delivery systems have attracted attention because of the limitations of conventional viral vectors. In this review, we assess the efficiency of various nanoparticles, including lipid-based, polymer-based, inorganic, and extracellular vesicle-based systems, as non-viral vectors for CRISPR/Cas9 delivery. We discuss their advantages, limitations, and current challenges. By summarizing recent advancements and highlighting key strategies, this review aims to provide a comprehensive overview of the role of non-viral delivery systems in advancing CRISPR/Cas9 technology for clinical applications and gene therapy.
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Affiliation(s)
- Minse Kim
- Division of Chemical Engineering and Bioengineering, College of Art, Culture and Engineering, Kangwon National University, Chuncheon 24341, Republic of Korea
- Department of Smart Health Science and Technology, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Youngwoo Hwang
- Department of Smart Health Science and Technology, Kangwon National University, Chuncheon 24341, Republic of Korea
- Department of Systems Immunology, Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Seongyu Lim
- Division of Chemical Engineering and Bioengineering, College of Art, Culture and Engineering, Kangwon National University, Chuncheon 24341, Republic of Korea
- Department of Smart Health Science and Technology, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Hyeon-Ki Jang
- Division of Chemical Engineering and Bioengineering, College of Art, Culture and Engineering, Kangwon National University, Chuncheon 24341, Republic of Korea
- Department of Smart Health Science and Technology, Kangwon National University, Chuncheon 24341, Republic of Korea
- Multidimensional Genomics Research Center, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Hyun-Ouk Kim
- Division of Chemical Engineering and Bioengineering, College of Art, Culture and Engineering, Kangwon National University, Chuncheon 24341, Republic of Korea
- Department of Smart Health Science and Technology, Kangwon National University, Chuncheon 24341, Republic of Korea
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Ferreira da Silva J, Tou CJ, King EM, Eller ML, Rufino-Ramos D, Ma L, Cromwell CR, Metovic J, Benning FMC, Chao LH, Eichler FS, Kleinstiver BP. Click editing enables programmable genome writing using DNA polymerases and HUH endonucleases. Nat Biotechnol 2024:10.1038/s41587-024-02324-x. [PMID: 39039307 PMCID: PMC11751136 DOI: 10.1038/s41587-024-02324-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 06/24/2024] [Indexed: 07/24/2024]
Abstract
Genome editing technologies based on DNA-dependent polymerases (DDPs) could offer several benefits compared with other types of editors to install diverse edits. Here, we develop click editing, a genome writing platform that couples the advantageous properties of DDPs with RNA-programmable nickases to permit the installation of a range of edits, including substitutions, insertions and deletions. Click editors (CEs) leverage the 'click'-like bioconjugation ability of HUH endonucleases with single-stranded DNA substrates to covalently tether 'click DNA' (clkDNA) templates encoding user-specifiable edits at targeted genomic loci. Through iterative optimization of the modular components of CEs and their clkDNAs, we demonstrate the ability to install precise genome edits with minimal indels in diverse immortalized human cell types and primary fibroblasts with precise editing efficiencies of up to ~30%. Editing efficiency can be improved by rapidly screening clkDNA oligonucleotides with various modifications, including repair-evading substitutions. Click editing is a precise and versatile genome editing approach for diverse biological applications.
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Affiliation(s)
- Joana Ferreira da Silva
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Connor J Tou
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Biological Engineering Program, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Emily M King
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Biological and Biomedical Sciences Program, Harvard University, Boston, MA, USA
| | - Madeline L Eller
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - David Rufino-Ramos
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Linyuan Ma
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Christopher R Cromwell
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Jasna Metovic
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Friederike M C Benning
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Luke H Chao
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Florian S Eichler
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Benjamin P Kleinstiver
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.
- Department of Pathology, Harvard Medical School, Boston, MA, USA.
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Eggers AR, Chen K, Soczek KM, Tuck OT, Doherty EE, Thornton BW, Xu B, Trinidad MI, Doudna JA. Rapid DNA unwinding accelerates genome editing by engineered CRISPR-Cas9. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.14.571777. [PMID: 38168238 PMCID: PMC10760125 DOI: 10.1101/2023.12.14.571777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Thermostable CRISPR-Cas9 enzymes could improve genome editing efficiency and delivery due to extended protein lifetimes. However, initial experimentation demonstrated Geobacillus stearothermophilus Cas9 (GeoCas9) to be virtually inactive when used in cultured human cells. Laboratory-evolved variants of GeoCas9 overcome this natural limitation by acquiring mutations in the wedge (WED) domain that produce >100-fold higher genome editing levels. Cryo-EM structures of the wildtype and improved GeoCas9 (iGeoCas9) enzymes reveal extended contacts between the WED domain of iGeoCas9 and DNA substrates. Biochemical analysis shows that iGeoCas9 accelerates DNA unwinding to capture substrates under the magnesium-restricted conditions typical of mammalian but not bacterial cells. These findings enabled rational engineering of other Cas9 orthologs to enhance genome editing levels, pointing to a general strategy for editing enzyme improvement. Together, these results uncover a new role for the Cas9 WED domain in DNA unwinding and demonstrate how accelerated target unwinding dramatically improves Cas9-induced genome editing activity.
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