1
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Yong J, Wu M, Carroll BJ, Xu ZP, Zhang R. Enhancing plant biotechnology by nanoparticle delivery of nucleic acids. Trends Genet 2024; 40:352-363. [PMID: 38320883 DOI: 10.1016/j.tig.2024.01.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/12/2024] [Accepted: 01/12/2024] [Indexed: 02/08/2024]
Abstract
Plant biotechnology plays a crucial role in developing modern agriculture and plant science research. However, the delivery of exogenous genetic material into plants has been a long-standing obstacle. Nanoparticle-based delivery systems are being established to address this limitation and are proving to be a feasible, versatile, and efficient approach to facilitate the internalization of functional RNA and DNA by plants. The nanoparticle-based delivery systems can also be designed for subcellular delivery and controlled release of the biomolecular cargo. In this review, we provide a concise overview of the recent advances in nanocarriers for the delivery of biomolecules into plants, with a specific focus on applications to enhance RNA interference, foreign gene transfer, and genome editing in plants.
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Affiliation(s)
- Jiaxi Yong
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia; Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Miaomiao Wu
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Bernard J Carroll
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Zhi Ping Xu
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia; Institute of Biomedical Health Technology and Engineering and Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, P. R. China 518107
| | - Run Zhang
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia; Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Indooroopilly, Queensland 4068, Australia.
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2
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Henn D, Zhao D, Sivaraj D, Trotsyuk A, Bonham CA, Fischer KS, Kehl T, Fehlmann T, Greco AH, Kussie HC, Moortgat Illouz SE, Padmanabhan J, Barrera JA, Kneser U, Lenhof HP, Januszyk M, Levi B, Keller A, Longaker MT, Chen K, Qi LS, Gurtner GC. Cas9-mediated knockout of Ndrg2 enhances the regenerative potential of dendritic cells for wound healing. Nat Commun 2023; 14:4729. [PMID: 37550295 PMCID: PMC10406832 DOI: 10.1038/s41467-023-40519-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 07/26/2023] [Indexed: 08/09/2023] Open
Abstract
Chronic wounds impose a significant healthcare burden to a broad patient population. Cell-based therapies, while having shown benefits for the treatment of chronic wounds, have not yet achieved widespread adoption into clinical practice. We developed a CRISPR/Cas9 approach to precisely edit murine dendritic cells to enhance their therapeutic potential for healing chronic wounds. Using single-cell RNA sequencing of tolerogenic dendritic cells, we identified N-myc downregulated gene 2 (Ndrg2), which marks a specific population of dendritic cell progenitors, as a promising target for CRISPR knockout. Ndrg2-knockout alters the transcriptomic profile of dendritic cells and preserves an immature cell state with a strong pro-angiogenic and regenerative capacity. We then incorporated our CRISPR-based cell engineering within a therapeutic hydrogel for in vivo cell delivery and developed an effective translational approach for dendritic cell-based immunotherapy that accelerated healing of full-thickness wounds in both non-diabetic and diabetic mouse models. These findings could open the door to future clinical trials using safe gene editing in dendritic cells for treating various types of chronic wounds.
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Affiliation(s)
- Dominic Henn
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University, Stanford, CA, USA
- Department of Plastic Surgery, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Surgery, University of Arizona, Tucson, AZ, USA
| | - Dehua Zhao
- Department of Bioengineering, Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Dharshan Sivaraj
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University, Stanford, CA, USA
- Department of Surgery, University of Arizona, Tucson, AZ, USA
| | - Artem Trotsyuk
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University, Stanford, CA, USA
- Department of Surgery, University of Arizona, Tucson, AZ, USA
| | - Clark Andrew Bonham
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University, Stanford, CA, USA
| | - Katharina S Fischer
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University, Stanford, CA, USA
- Department of Surgery, University of Arizona, Tucson, AZ, USA
| | - Tim Kehl
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, Saarbrücken, Germany
| | - Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland University, Saarbruecken, Germany
| | - Autumn H Greco
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University, Stanford, CA, USA
| | - Hudson C Kussie
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University, Stanford, CA, USA
- Department of Burn, Trauma, Acute and Critical Care Surgery, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sylvia E Moortgat Illouz
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University, Stanford, CA, USA
| | - Jagannath Padmanabhan
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University, Stanford, CA, USA
| | - Janos A Barrera
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University, Stanford, CA, USA
| | - Ulrich Kneser
- Department of Hand, Plastic, and Reconstructive Surgery, BG Trauma Center Ludwigshafen, Ruprecht-Karls-University of Heidelberg, Heidelberg, Germany
| | - Hans-Peter Lenhof
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, Saarbrücken, Germany
| | - Michael Januszyk
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University, Stanford, CA, USA
| | - Benjamin Levi
- Department of Burn, Trauma, Acute and Critical Care Surgery, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Andreas Keller
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, Saarbrücken, Germany
| | - Michael T Longaker
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University, Stanford, CA, USA
| | - Kellen Chen
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University, Stanford, CA, USA
- Department of Surgery, University of Arizona, Tucson, AZ, USA
| | - Lei S Qi
- Department of Bioengineering, Sarafan ChEM-H, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub - San Francisco, San Francisco, CA, USA.
| | - Geoffrey C Gurtner
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University, Stanford, CA, USA.
- Department of Surgery, University of Arizona, Tucson, AZ, USA.
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3
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LaBauve AE, Saada EA, Jones IKA, Mosesso R, Noureddine A, Techel J, Gomez A, Collette N, Sherman MB, Serda RE, Butler KS, Brinker CJ, Schoeniger JS, Sasaki D, Negrete OA. Lipid-coated mesoporous silica nanoparticles for anti-viral applications via delivery of CRISPR-Cas9 ribonucleoproteins. Sci Rep 2023; 13:6873. [PMID: 37105997 PMCID: PMC10133914 DOI: 10.1038/s41598-023-33092-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
Emerging and re-emerging viral pathogens present a unique challenge for anti-viral therapeutic development. Anti-viral approaches with high flexibility and rapid production times are essential for combating these high-pandemic risk viruses. CRISPR-Cas technologies have been extensively repurposed to treat a variety of diseases, with recent work expanding into potential applications against viral infections. However, delivery still presents a major challenge for these technologies. Lipid-coated mesoporous silica nanoparticles (LCMSNs) offer an attractive delivery vehicle for a variety of cargos due to their high biocompatibility, tractable synthesis, and amenability to chemical functionalization. Here, we report the use of LCMSNs to deliver CRISPR-Cas9 ribonucleoproteins (RNPs) that target the Niemann-Pick disease type C1 gene, an essential host factor required for entry of the high-pandemic risk pathogen Ebola virus, demonstrating an efficient reduction in viral infection. We further highlight successful in vivo delivery of the RNP-LCMSN platform to the mouse liver via systemic administration.
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Affiliation(s)
- Annette E LaBauve
- Department of Biotechnology and Bioengineering, Sandia National Laboratories, Livermore, USA
| | - Edwin A Saada
- Department of Systems Biology, Sandia National Laboratories, Livermore, USA
- Biotechnology and Biosciences Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, USA
| | - Iris K A Jones
- Department of Systems Biology, Sandia National Laboratories, Livermore, USA
| | - Richard Mosesso
- Department of Systems Biology, Sandia National Laboratories, Livermore, USA
| | - Achraf Noureddine
- Chemical and Biological Engineering, University of New Mexico, Albuquerque, USA
- Center for Micro-Engineered Materials, University of New Mexico, Albuquerque, USA
| | - Jessica Techel
- Department of Biotechnology and Bioengineering, Sandia National Laboratories, Livermore, USA
| | - Andrew Gomez
- Department of Active Ceramics Value Stream, Sandia National Laboratories, Albuquerque, USA
| | - Nicole Collette
- Biotechnology and Biosciences Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, USA
| | - Michael B Sherman
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, USA
| | - Rita E Serda
- Department of Internal Medicine, Health Sciences Center, University of New Mexico, Albuquerque, USA
| | - Kimberly S Butler
- Department of Molecular and Microbiology, Sandia National Laboratories, Albuquerque, USA
| | - C Jeffery Brinker
- Chemical and Biological Engineering, University of New Mexico, Albuquerque, USA
- Center for Micro-Engineered Materials, University of New Mexico, Albuquerque, USA
- Advanced Materials Laboratory, Sandia National Laboratories, Albuquerque, USA
| | | | - Darryl Sasaki
- Department of Biotechnology and Bioengineering, Sandia National Laboratories, Livermore, USA
| | - Oscar A Negrete
- Department of Systems Biology, Sandia National Laboratories, Livermore, USA.
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4
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Zhan Y, Cao C, Li A, Mei H, Liu Y. Enhanced RNA knockdown efficiency with engineered fusion guide RNAs that function with both CRISPR-CasRx and hammerhead ribozyme. Genome Biol 2023; 24:9. [PMID: 36650600 PMCID: PMC9843992 DOI: 10.1186/s13059-023-02852-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 01/06/2023] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND CRISPR-Cas13 is a newly emerging RNA knockdown technology that is comparable to RNAi. Among all members of Cas13, CasRx degrades RNA in human cells with high precision and effectiveness. However, it remains unclear whether the efficiency of this technology can be further improved and applied to gene therapy. RESULTS In this study, we fuse CasRx crRNA with an antisense ribozyme to construct a synthetic fusion guide RNA that can interact with both CasRx protein and ribozyme and tested the ability of this approach in RNA knockdown and cancer gene therapy. We show that the CasRx-crRNA-ribozyme system (CCRS) is more efficient for RNA knockdown of mRNAs and non-coding RNAs than conventional methods, including CasRx, shRNA, and ribozyme. In particular, CCRS is more effective than wild-type CasRx when targeting multiple transcripts simultaneously. We next use bladder cancer as a model to evaluate the anticancer effects of CCRS targeting multiple genes in vitro and in vivo. CCRS shows a higher anticancer effect than conventional methods, consistent with the gene knockdown results. CONCLUSIONS Thus, our study demonstrates that CCRS expands the design ideas and RNA knockdown capabilities of Cas13 technology and has the potential to be used in disease treatment.
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Affiliation(s)
- Yonghao Zhan
- grid.263488.30000 0001 0472 9649Shenzhen Institute of Translational Medicine, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen University, Shenzhen, 518035 China ,grid.412633.10000 0004 1799 0733Department of Urology, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou, 450052 China
| | - Congcong Cao
- grid.263488.30000 0001 0472 9649Shenzhen Institute of Translational Medicine, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen University, Shenzhen, 518035 China ,grid.9227.e0000000119573309Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 China
| | - Aolin Li
- grid.263488.30000 0001 0472 9649Shenzhen Institute of Translational Medicine, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen University, Shenzhen, 518035 China ,grid.263488.30000 0001 0472 9649Department of Urology, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University School of Medicine, Shenzhen, 518035 China
| | - Hongbing Mei
- grid.263488.30000 0001 0472 9649Department of Urology, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University School of Medicine, Shenzhen, 518035 China
| | - Yuchen Liu
- grid.263488.30000 0001 0472 9649Shenzhen Institute of Translational Medicine, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen University, Shenzhen, 518035 China
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5
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Shams A, Higgins SA, Fellmann C, Laughlin TG, Oakes BL, Lew R, Kim S, Lukarska M, Arnold M, Staahl BT, Doudna JA, Savage DF. Comprehensive deletion landscape of CRISPR-Cas9 identifies minimal RNA-guided DNA-binding modules. Nat Commun 2021; 12:5664. [PMID: 34580310 PMCID: PMC8476515 DOI: 10.1038/s41467-021-25992-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 09/10/2021] [Indexed: 11/28/2022] Open
Abstract
Proteins evolve through the modular rearrangement of elements known as domains. Extant, multidomain proteins are hypothesized to be the result of domain accretion, but there has been limited experimental validation of this idea. Here, we introduce a technique for genetic minimization by iterative size-exclusion and recombination (MISER) for comprehensively making all possible deletions of a protein. Using MISER, we generate a deletion landscape for the CRISPR protein Cas9. We find that the catalytically-dead Streptococcus pyogenes Cas9 can tolerate large single deletions in the REC2, REC3, HNH, and RuvC domains, while still functioning in vitro and in vivo, and that these deletions can be stacked together to engineer minimal, DNA-binding effector proteins. In total, our results demonstrate that extant proteins retain significant modularity from the accretion process and, as genetic size is a major limitation for viral delivery systems, establish a general technique to improve genome editing and gene therapy-based therapeutics.
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Affiliation(s)
- Arik Shams
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Sean A Higgins
- 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
- Scribe Therapeutics, Alameda, CA, 94501, USA
| | - Christof Fellmann
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
- Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Thomas G Laughlin
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
- Division of Biological Sciences, University of California, San Diego, San Diego, CA, 92093, USA
| | - Benjamin L Oakes
- 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
- Scribe Therapeutics, Alameda, CA, 94501, USA
| | - Rachel Lew
- Gladstone Institutes, San Francisco, CA, 94158, USA
| | - Shin Kim
- 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
| | - Maria Lukarska
- 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
| | - Madeline Arnold
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Brett T Staahl
- 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
- Scribe Therapeutics, Alameda, CA, 94501, 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
- Gladstone Institutes, San Francisco, CA, 94158, USA
- Graduate Group in Biophysics, University of California, Berkeley, Berkeley, CA, 94720, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720, 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.
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6
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Sun B, Chen H, Gao X. Versatile modification of the CRISPR/Cas9 ribonucleoprotein system to facilitate in vivo application. J Control Release 2021; 337:698-717. [PMID: 34364918 DOI: 10.1016/j.jconrel.2021.08.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 08/03/2021] [Accepted: 08/03/2021] [Indexed: 12/26/2022]
Abstract
The development of clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems has created a tremendous wave that is sweeping the world of genome editing. The ribonucleoprotein (RNP) method has evolved to be the most advantageous form for in vivo application. Modification of the CRISPR/Cas9 RNP method to adapt delivery through a variety of carriers can either directly improve the stability and specificity of the gene-editing tool in vivo or indirectly endow the system with high gene-editing efficiency that induces few off-target mutations through different delivery methods. The exploration of in vivo applications mediated by various delivery methods lays the foundation for genome research and variety improvements, which is especially promising for better in vivo research in the field of translational biomedicine. In this review, we illustrate the modifiable structures of the Cas9 nuclease and single guide RNA (sgRNA), summarize the latest research progress and discuss the feasibility and advantages of various methods. The highlighted results will enhance our knowledge, stimulate extensive research and application of Cas9 and provide alternatives for the development of rational delivery carriers in multiple fields.
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Affiliation(s)
- Bixi Sun
- Department of Biopharmacy, School of Pharmaceutical Sciences, Jilin University, 1266 Fujin Road, Changchun 130021, China
| | - Hening Chen
- Department of Biopharmacy, School of Pharmaceutical Sciences, Jilin University, 1266 Fujin Road, Changchun 130021, China
| | - Xiaoshu Gao
- Department of Biopharmacy, School of Pharmaceutical Sciences, Jilin University, 1266 Fujin Road, Changchun 130021, China.
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7
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Banerjee T, Takahashi H, Subekti DRG, Kamagata K. Engineering of the genome editing protein Cas9 to slide along DNA. Sci Rep 2021; 11:14165. [PMID: 34239016 PMCID: PMC8266852 DOI: 10.1038/s41598-021-93685-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 06/28/2021] [Indexed: 12/26/2022] Open
Abstract
The genome editing protein Cas9 faces engineering challenges in improving off-target DNA cleavage and low editing efficiency. In this study, we aimed to engineer Cas9 to be able to slide along DNA, which might facilitate genome editing and reduce off-target cleavage. We used two approaches to achieve this: reducing the sliding friction along DNA by removing the interactions of Cas9 residues with DNA and facilitating sliding by introducing the sliding-promoting tail of Nhp6A. Seven engineered mutants of Cas9 were prepared, and their performance was tested using single-molecule fluorescence microscopy. Comparison of the mutations enabled the identification of key residues of Cas9 to enhance the sliding along DNA in the presence and absence of single guide RNA (sgRNA). The attachment of the tail to Cas9 mutants enhanced sliding along DNA, particularly in the presence of sgRNA. Together, using the proposed approaches, the sliding ability of Cas9 was improved up to eightfold in the presence of sgRNA. A sliding model of Cas9 and its engineering action are discussed herein.
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Affiliation(s)
- Trishit Banerjee
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan
- Department of Chemistry, Graduate School of Science, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan
| | - Hiroto Takahashi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan
| | - Dwiky Rendra Graha Subekti
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan
- Department of Chemistry, Graduate School of Science, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan
| | - Kiyoto Kamagata
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan.
- Department of Chemistry, Graduate School of Science, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan.
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8
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CRISPR FokI Dead Cas9 System: Principles and Applications in Genome Engineering. Cells 2020; 9:cells9112518. [PMID: 33233344 PMCID: PMC7700487 DOI: 10.3390/cells9112518] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 11/05/2020] [Accepted: 11/19/2020] [Indexed: 12/18/2022] Open
Abstract
The identification of the robust clustered regularly interspersed short palindromic repeats (CRISPR) associated endonuclease (Cas9) system gene-editing tool has opened up a wide range of potential therapeutic applications that were restricted by more complex tools, including zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs). Nevertheless, the high frequency of CRISPR system off-target activity still limits its applications, and, thus, advanced strategies for highly specific CRISPR/Cas9-mediated genome editing are continuously under development including CRISPR–FokI dead Cas9 (fdCas9). fdCas9 system is derived from linking a FokI endonuclease catalytic domain to an inactive Cas9 protein and requires a pair of guide sgRNAs that bind to the sense and antisense strands of the DNA in a protospacer adjacent motif (PAM)-out orientation, with a defined spacer sequence range around the target site. The dimerization of FokI domains generates DNA double-strand breaks, which activates the DNA repair machinery and results in genomic edit. So far, all the engineered fdCas9 variants have shown promising gene-editing activities in human cells when compared to other platforms. Herein, we review the advantages of all published variants of fdCas9 and their current applications in genome engineering.
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9
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Kovač A, Miskey C, Menzel M, Grueso E, Gogol-Döring A, Ivics Z. RNA-guided retargeting of S leeping Beauty transposition in human cells. eLife 2020; 9:e53868. [PMID: 32142408 PMCID: PMC7077980 DOI: 10.7554/elife.53868] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 03/05/2020] [Indexed: 12/12/2022] Open
Abstract
An ideal tool for gene therapy would enable efficient gene integration at predetermined sites in the human genome. Here we demonstrate biased genome-wide integration of the Sleeping Beauty (SB) transposon by combining it with components of the CRISPR/Cas9 system. We provide proof-of-concept that it is possible to influence the target site selection of SB by fusing it to a catalytically inactive Cas9 (dCas9) and by providing a single guide RNA (sgRNA) against the human Alu retrotransposon. Enrichment of transposon integrations was dependent on the sgRNA, and occurred in an asymmetric pattern with a bias towards sites in a relatively narrow, 300 bp window downstream of the sgRNA targets. Our data indicate that the targeting mechanism specified by CRISPR/Cas9 forces integration into genomic regions that are otherwise poor targets for SB transposition. Future modifications of this technology may allow the development of methods for specific gene insertion for precision genetic engineering.
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Affiliation(s)
- Adrian Kovač
- Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich InstituteLangenGermany
| | - Csaba Miskey
- Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich InstituteLangenGermany
| | | | - Esther Grueso
- Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich InstituteLangenGermany
| | | | - Zoltán Ivics
- Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich InstituteLangenGermany
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10
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Desmarais JJ, Flamholz AI, Blikstad C, Dugan EJ, Laughlin TG, Oltrogge LM, Chen AW, Wetmore K, Diamond S, Wang JY, Savage DF. DABs are inorganic carbon pumps found throughout prokaryotic phyla. Nat Microbiol 2019; 4:2204-2215. [PMID: 31406332 PMCID: PMC10184468 DOI: 10.1038/s41564-019-0520-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 06/13/2019] [Accepted: 06/20/2019] [Indexed: 12/30/2022]
Abstract
Bacterial autotrophs often rely on CO2 concentrating mechanisms (CCMs) to assimilate carbon. Although many CCM proteins have been identified, a systematic screen of the components of CCMs is lacking. Here, we performed a genome-wide barcoded transposon screen to identify essential and CCM-related genes in the γ-proteobacterium Halothiobacillus neapolitanus. Screening revealed that the CCM comprises at least 17 and probably no more than 25 genes, most of which are encoded in 3 operons. Two of these operons (DAB1 and DAB2) contain a two-gene locus that encodes a domain of unknown function (Pfam: PF10070) and a putative cation transporter (Pfam: PF00361). Physiological and biochemical assays demonstrated that these proteins-which we name DabA and DabB, for DABs accumulate bicarbonate-assemble into a heterodimeric complex, which contains a putative β-carbonic anhydrase-like active site and functions as an energy-coupled inorganic carbon (Ci) pump. Interestingly, DAB operons are found in a diverse range of bacteria and archaea. We demonstrate that functional DABs are present in the human pathogens Bacillus anthracis and Vibrio cholerae. On the basis of these results, we propose that DABs constitute a class of energized Ci pumps and play a critical role in the metabolism of Ci throughout prokaryotic phyla.
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Affiliation(s)
- John J Desmarais
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Avi I Flamholz
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Cecilia Blikstad
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Eli J Dugan
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Thomas G Laughlin
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Luke M Oltrogge
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Allen W Chen
- Department of Chemistry, University of California, Berkeley, CA, USA
| | - Kelly Wetmore
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Spencer Diamond
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
| | - Joy Y Wang
- Department of Chemistry, University of California, Berkeley, CA, USA
| | - David F Savage
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
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11
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Pseudomonas putida in the quest of programmable chemistry. Curr Opin Biotechnol 2019; 59:111-121. [DOI: 10.1016/j.copbio.2019.03.012] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/15/2019] [Accepted: 03/12/2019] [Indexed: 11/19/2022]
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12
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Liu JJ, Orlova N, Oakes BL, Ma E, Spinner HB, Baney KLM, Chuck J, Tan D, Knott GJ, Harrington LB, Al-Shayeb B, Wagner A, Brötzmann J, Staahl BT, Taylor KL, Desmarais J, Nogales E, Doudna JA. CasX enzymes comprise a distinct family of RNA-guided genome editors. Nature 2019; 566:218-223. [PMID: 30718774 PMCID: PMC6662743 DOI: 10.1038/s41586-019-0908-x] [Citation(s) in RCA: 264] [Impact Index Per Article: 52.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 12/31/2018] [Indexed: 12/17/2022]
Abstract
The RNA-guided CRISPR-associated (Cas) proteins Cas9 and Cas12a provide adaptive immunity against invading nucleic acids, and function as powerful tools for genome editing in a wide range of organisms. Here we reveal the underlying mechanisms of a third, fundamentally distinct RNA-guided genome-editing platform named CRISPR-CasX, which uses unique structures for programmable double-stranded DNA binding and cleavage. Biochemical and in vivo data demonstrate that CasX is active for Escherichia coli and human genome modification. Eight cryo-electron microscopy structures of CasX in different states of assembly with its guide RNA and double-stranded DNA substrates reveal an extensive RNA scaffold and a domain required for DNA unwinding. These data demonstrate how CasX activity arose through convergent evolution to establish an enzyme family that is functionally separate from both Cas9 and Cas12a.
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Affiliation(s)
- Jun-Jie Liu
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Natalia Orlova
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
| | - Benjamin L Oakes
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Enbo Ma
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Hannah B Spinner
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | | | - Jonathan Chuck
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Dan Tan
- Clayton Foundation Laboratories of Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Gavin J Knott
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Lucas B Harrington
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Basem Al-Shayeb
- Department of Plant and Microbiology, University of California, Berkeley, CA, USA
| | | | - Julian Brötzmann
- Faculty of Chemistry and Pharmacy, Ludwig-Maximilians-University, Munich, Germany
| | - Brett T Staahl
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Kian L Taylor
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - John Desmarais
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Eva Nogales
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA.
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA.
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, CA, USA.
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA.
- Department of Chemistry, University of California, Berkeley, CA, USA.
- Gladstone Institutes, San Francisco, CA, USA.
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13
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Oakes BL, Fellmann C, Rishi H, Taylor KL, Ren SM, Nadler DC, Yokoo R, Arkin AP, Doudna JA, Savage DF. CRISPR-Cas9 Circular Permutants as Programmable Scaffolds for Genome Modification. Cell 2019; 176:254-267.e16. [PMID: 30633905 PMCID: PMC6414052 DOI: 10.1016/j.cell.2018.11.052] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 08/21/2018] [Accepted: 11/28/2018] [Indexed: 12/20/2022]
Abstract
The ability to engineer natural proteins is pivotal to a future, pragmatic biology. CRISPR proteins have revolutionized genome modification, yet the CRISPR-Cas9 scaffold is not ideal for fusions or activation by cellular triggers. Here, we show that a topological rearrangement of Cas9 using circular permutation provides an advanced platform for RNA-guided genome modification and protection. Through systematic interrogation, we find that protein termini can be positioned adjacent to bound DNA, offering a straightforward mechanism for strategically fusing functional domains. Additionally, circular permutation enabled protease-sensing Cas9s (ProCas9s), a unique class of single-molecule effectors possessing programmable inputs and outputs. ProCas9s can sense a wide range of proteases, and we demonstrate that ProCas9 can orchestrate a cellular response to pathogen-associated protease activity. Together, these results provide a toolkit of safer and more efficient genome-modifying enzymes and molecular recorders for the advancement of precision genome engineering in research, agriculture, and biomedicine.
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Affiliation(s)
- Benjamin L Oakes
- 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
| | - Christof Fellmann
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Gladstone Institutes, San Francisco, CA 94158, USA
| | - Harneet Rishi
- Graduate Group in Biophysics, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Kian L Taylor
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Shawn M Ren
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Dana C Nadler
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Rayka Yokoo
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Adam P Arkin
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 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; Gladstone Institutes, San Francisco, CA 94158, USA; Graduate Group in Biophysics, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - David F Savage
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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14
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Rouet R, de Oñate L, Li J, Murthy N, Wilson RC. Engineering CRISPR-Cas9 RNA–Protein Complexes for Improved Function and Delivery. CRISPR J 2018; 1:367-378. [DOI: 10.1089/crispr.2018.0037] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Affiliation(s)
- Romain Rouet
- Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia
- St Vincent's Clinical School, UNSW Medicine Sydney, Darlinghurst, New South Wales 2010, Australia
| | - Lorena de Oñate
- Innovative Genomics Institute, University of California, Berkeley, CA 94720
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720
| | - Jie Li
- Innovative Genomics Institute, University of California, Berkeley, CA 94720
- Department of Bioengineering, University of California, Berkeley, CA 94720
| | - Niren Murthy
- Innovative Genomics Institute, University of California, Berkeley, CA 94720
- Department of Bioengineering, University of California, Berkeley, CA 94720
| | - Ross C. Wilson
- Innovative Genomics Institute, University of California, Berkeley, CA 94720
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720
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15
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Rapid construction of metabolite biosensors using domain-insertion profiling. Nat Commun 2016; 7:12266. [PMID: 27470466 PMCID: PMC4974565 DOI: 10.1038/ncomms12266] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 06/15/2016] [Indexed: 12/15/2022] Open
Abstract
Single-fluorescent protein biosensors (SFPBs) are an important class of probes that enable the single-cell quantification of analytes in vivo. Despite advantages over other detection technologies, their use has been limited by the inherent challenges of their construction. Specifically, the rational design of green fluorescent protein (GFP) insertion into a ligand-binding domain, generating the requisite allosteric coupling, remains a rate-limiting step. Here, we describe an unbiased approach, termed domain-insertion profiling with DNA sequencing (DIP-seq), that combines the rapid creation of diverse libraries of potential SFPBs and high-throughput activity assays to identify functional biosensors. As a proof of concept, we construct an SFPB for the important regulatory sugar trehalose. DIP-seq analysis of a trehalose-binding-protein reveals allosteric hotspots for GFP insertion and results in high-dynamic range biosensors that function robustly in vivo. Taken together, DIP-seq simultaneously accelerates metabolite biosensor construction and provides a novel tool for interrogating protein allostery. In the construction of single fluorescent protein biosensors, selection of the insertion point of a fluorescent protein into a ligand-binding domain is a rate-limiting step. Here, the authors develop an unbiased, high-throughput approach, called domain insertion profiling with DNA sequencing (DIP-seq), to generate a novel trehalose biosensor.
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16
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Finnigan GC, Thorner J. mCAL: A New Approach for Versatile Multiplex Action of Cas9 Using One sgRNA and Loci Flanked by a Programmed Target Sequence. G3 (BETHESDA, MD.) 2016; 6:2147-56. [PMID: 27185399 PMCID: PMC4938667 DOI: 10.1534/g3.116.029801] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 05/10/2016] [Indexed: 02/06/2023]
Abstract
Genome editing exploiting CRISPR/Cas9 has been adopted widely in academia and in the biotechnology industry to manipulate DNA sequences in diverse organisms. Molecular engineering of Cas9 itself and its guide RNA, and the strategies for using them, have increased efficiency, optimized specificity, reduced inappropriate off-target effects, and introduced modifications for performing other functions (transcriptional regulation, high-resolution imaging, protein recruitment, and high-throughput screening). Moreover, Cas9 has the ability to multiplex, i.e., to act at different genomic targets within the same nucleus. Currently, however, introducing concurrent changes at multiple loci involves: (i) identification of appropriate genomic sites, especially the availability of suitable PAM sequences; (ii) the design, construction, and expression of multiple sgRNA directed against those sites; (iii) potential difficulties in altering essential genes; and (iv) lingering concerns about "off-target" effects. We have devised a new approach that circumvents these drawbacks, as we demonstrate here using the yeast Saccharomyces cerevisiae First, any gene(s) of interest are flanked upstream and downstream with a single unique target sequence that does not normally exist in the genome. Thereafter, expression of one sgRNA and cotransformation with appropriate PCR fragments permits concomitant Cas9-mediated alteration of multiple genes (both essential and nonessential). The system we developed also allows for maintenance of the integrated, inducible Cas9-expression cassette or its simultaneous scarless excision. Our scheme-dubbed mCAL for " M: ultiplexing of C: as9 at A: rtificial L: oci"-can be applied to any organism in which the CRISPR/Cas9 methodology is currently being utilized. In principle, it can be applied to install synthetic sequences into the genome, to generate genomic libraries, and to program strains or cell lines so that they can be conveniently (and repeatedly) manipulated at multiple loci with extremely high efficiency.
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Affiliation(s)
- Gregory C Finnigan
- Division of Biochemistry, Biophysics and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3202
| | - Jeremy Thorner
- Division of Biochemistry, Biophysics and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3202
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17
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Profiling of engineering hotspots identifies an allosteric CRISPR-Cas9 switch. Nat Biotechnol 2016; 34:646-51. [PMID: 27136077 PMCID: PMC4900928 DOI: 10.1038/nbt.3528] [Citation(s) in RCA: 152] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 03/07/2016] [Indexed: 01/02/2023]
Abstract
The CRISPR-associated protein Cas9 from Streptococcus
pyogenes is an RNA-guided DNA endonuclease with widespread utility
for genome modification. However, the structural constraints limiting the
engineering of Cas9 have not been determined. Here we experimentally profile
Cas9 using randomized insertional mutagenesis and delineate hotspots in the
structure capable of tolerating insertions of a PDZ domain without disrupting
the enzyme’s binding and cleavage functions. Orthogonal domains or
combinations of domains can be inserted into the identified sites with minimal
functional consequence. To illustrate the utility of the identified sites, we
construct an allosterically regulated Cas9 by insertion of the Estrogen Receptor
α Ligand Binding Domain. This protein displayed robust, ligand-dependent
activation in prokaryotic and eukaryotic cells, establishing a versatile
one-component system for inducible and reversible Cas9 activation. Thus, domain
insertion profiling facilitates the rapid generation of new Cas9 functionalities
and provides useful data for future engineering of Cas9.
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18
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Lee JS, Grav LM, Lewis NE, Faustrup Kildegaard H. CRISPR/Cas9-mediated genome engineering of CHO cell factories: Application and perspectives. Biotechnol J 2015; 10:979-94. [PMID: 26058577 DOI: 10.1002/biot.201500082] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 04/10/2015] [Accepted: 05/11/2015] [Indexed: 12/13/2022]
Abstract
Chinese hamster ovary (CHO) cells are the most widely used production host for therapeutic proteins. With the recent emergence of CHO genome sequences, CHO cell line engineering has taken on a new aspect through targeted genome editing. The bacterial clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) system enables rapid, easy and efficient engineering of mammalian genomes. It has a wide range of applications from modification of individual genes to genome-wide screening or regulation of genes. Facile genome editing using CRISPR/Cas9 empowers researchers in the CHO community to elucidate the mechanistic basis behind high level production of proteins and product quality attributes of interest. In this review, we describe the basis of CRISPR/Cas9-mediated genome editing and its application for development of next generation CHO cell factories while highlighting both future perspectives and challenges. As one of the main drivers for the CHO systems biology era, genome engineering with CRISPR/Cas9 will pave the way for rational design of CHO cell factories.
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Affiliation(s)
- Jae Seong Lee
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Lise Marie Grav
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Nathan E Lewis
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.,The Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego School of Medicine, CA, USA
| | - Helene Faustrup Kildegaard
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark.
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19
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Kiss A, Gong X, Kowalewski JM, Shafqat-Abbasi H, Strömblad S, Lock JG. Non-monotonic cellular responses to heterogeneity in talin protein expression-level. Integr Biol (Camb) 2015; 7:1171-85. [PMID: 26000342 DOI: 10.1039/c4ib00291a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Talin is a key cell-matrix adhesion component with a central role in regulating adhesion complex maturation, and thereby various cellular properties including adhesion and migration. However, knockdown studies have produced inconsistent findings regarding the functional influence of talin in these processes. Such discrepancies may reflect non-monotonic responses to talin expression-level variation that are not detectable via canonical "binary" comparisons of aggregated control versus knockdown cell populations. Here, we deployed an "analogue" approach to map talin influence across a continuous expression-level spectrum, which we extended with sub-maximal RNAi-mediated talin depletion. Applying correlative imaging to link live cell and fixed immunofluorescence data on a single cell basis, we related per cell talin levels to per cell measures quantitatively defining an array of cellular properties. This revealed both linear and non-linear correspondences between talin expression and cellular properties, including non-monotonic influences over cell shape, adhesion complex-F-actin association and adhesion localization. Furthermore, we demonstrate talin level-dependent changes in networks of correlations among adhesion/migration properties, particularly in relation to cell migration speed. Importantly, these correlation networks were strongly affected by talin expression heterogeneity within the natural range, implying that this endogenous variation has a broad, quantitatively detectable influence. Overall, we present an accessible analogue method that reveals complex dependencies on talin expression-level, thereby establishing a framework for considering non-linear and non-monotonic effects of protein expression-level heterogeneity in cellular systems.
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Affiliation(s)
- Alexa Kiss
- Center for Innovative Medicine, Department of Biosciences and Nutrition, Karolinska Institutet, Novum, Hälsov. 7-9, G-building floor 6, S-141 83 Huddinge, Sweden.
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