1
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Sinan S, Appleby NM, Chou CW, Finkelstein IJ, Russell R. Kinetic dissection of pre-crRNA binding and processing by CRISPR-Cas12a. RNA (NEW YORK, N.Y.) 2024; 30:1345-1355. [PMID: 39009379 PMCID: PMC11404446 DOI: 10.1261/rna.080088.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Accepted: 06/24/2024] [Indexed: 07/17/2024]
Abstract
CRISPR-Cas12a binds and processes a single pre-crRNA during maturation, providing a simple tool for genome editing applications. Here, we constructed a kinetic and thermodynamic framework for pre-crRNA processing by Cas12a in vitro, and we measured the contributions of distinct regions of the pre-crRNA to this reaction. We find that the pre-crRNA binds rapidly and extraordinarily tightly to Cas12a (K d = 0.6 pM), such that pre-crRNA binding is fully rate limiting for processing and therefore determines the specificity of Cas12a for different pre-crRNAs. The guide sequence contributes 10-fold to the binding affinity of the pre-crRNA, while deletion of an upstream sequence has no significant effect. After processing, the mature crRNA remains very tightly bound to Cas12a with a comparable affinity. Strikingly, the affinity contribution of the guide region increases to 600-fold after processing, suggesting that additional contacts are formed and may preorder the crRNA for efficient DNA target recognition. Using a direct competition assay, we find that pre-crRNA-binding specificity is robust to changes in the guide sequence, addition of a 3' extension, and secondary structure within the guide region. However, stable secondary structure in the guide region can strongly inhibit DNA targeting, indicating that care should be taken in crRNA design. Together, our results provide a quantitative framework for pre-crRNA binding and processing by Cas12a and suggest strategies for optimizing crRNA design in genome editing applications.
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Affiliation(s)
- Selma Sinan
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA
| | - Nathan M Appleby
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA
| | - Chia-Wei Chou
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA
| | - Rick Russell
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA
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2
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Jaybhaye SG, Chavhan RL, Hinge VR, Deshmukh AS, Kadam US. CRISPR-Cas assisted diagnostics of plant viruses and challenges. Virology 2024; 597:110160. [PMID: 38955083 DOI: 10.1016/j.virol.2024.110160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 06/04/2024] [Accepted: 06/21/2024] [Indexed: 07/04/2024]
Abstract
Plant viruses threaten global food security by infecting commercial crops, highlighting the critical need for efficient virus detection to enable timely preventive measures. Current techniques rely on polymerase chain reaction (PCR) for viral genome amplification and require laboratory conditions. This review explores the applications of CRISPR-Cas assisted diagnostic tools, specifically CRISPR-Cas12a and CRISPR-Cas13a/d systems for plant virus detection and analysis. The CRISPR-Cas12a system can detect viral DNA/RNA amplicons and can be coupled with PCR or isothermal amplification, allowing multiplexed detection in plants with mixed infections. Recent studies have eliminated the need for expensive RNA purification, streamlining the process by providing a visible readout through lateral flow strips. The CRISPR-Cas13a/d system can directly detect viral RNA with minimal preamplification, offering a proportional readout to the viral load. These approaches enable rapid viral diagnostics within 30 min of leaf harvest, making them valuable for onsite field applications. Timely identification of diseases associated with pathogens is crucial for effective treatment; yet developing rapid, specific, sensitive, and cost-effective diagnostic technologies remains challenging. The current gold standard, PCR technology, has drawbacks such as lengthy operational cycles, high costs, and demanding requirements. Here we update the technical advancements of CRISPR-Cas in viral detection, providing insights into future developments, versatile applications, and potential clinical translation. There is a need for approaches enabling field plant viral nucleic acid detection with high sensitivity, specificity, affordability, and portability. Despite challenges, CRISPR-Cas-mediated pathogen diagnostic solutions hold robust capabilities, paving the way for ideal diagnostic tools. Alternative applications in virus research are also explored, acknowledging the technology's limitations and challenges.
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Affiliation(s)
- Siddhant G Jaybhaye
- Vilasrao Deshmukh College of Agricultural Biotechnology, Nanded Road, Latur, Vasantrao Naik Marathwada Krishi Vidyapeeth, Maharashtra, India
| | - Rahul L Chavhan
- Vilasrao Deshmukh College of Agricultural Biotechnology, Nanded Road, Latur, Vasantrao Naik Marathwada Krishi Vidyapeeth, Maharashtra, India
| | - Vidya R Hinge
- Vilasrao Deshmukh College of Agricultural Biotechnology, Nanded Road, Latur, Vasantrao Naik Marathwada Krishi Vidyapeeth, Maharashtra, India
| | - Abhijit S Deshmukh
- Vilasrao Deshmukh College of Agricultural Biotechnology, Nanded Road, Latur, Vasantrao Naik Marathwada Krishi Vidyapeeth, Maharashtra, India
| | - Ulhas S Kadam
- Plant Molecular Biology and Biotechnology Research Centre (PMBBRC), Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Gyeongsangnam-do, South Korea.
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3
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Storz U. The CRISPR Cas patent files, part 2: Is Cpf1/Cas12a a less conflict- prone alternative to Cas9? J Biotechnol 2024; 381:67-75. [PMID: 38181979 DOI: 10.1016/j.jbiotec.2023.12.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/11/2023] [Accepted: 12/30/2023] [Indexed: 01/07/2024]
Abstract
CRISPR Cpf1/Cas12a has been discussed as a less conflict prone alternative, patent-wise, to Cas9. This article investigates whether or not this assumption is correct, and comes to the conclusion that the promise that CRISPR Cpf1/Cas12 would make things easier, and be less conflict-prone, is fragile.
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Affiliation(s)
- Ulrich Storz
- Michalski Hüttermann & Partner Patentanwälte mbB Düsseldorf, München, Germany.
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4
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Vlassis A, Jensen TL, Mohr M, Jedrzejczyk DJ, Meng X, Kovacs G, Morera-Gómez M, Barghetti A, Muyo Abad S, Baumgartner RF, Natarajan KN, Nielsen LK, Warnecke T, Gill RT. CRISPR-Cas12a-integrated transgenes in genomic safe harbors retain high expression in human hematopoietic iPSC-derived lineages and primary cells. iScience 2023; 26:108287. [PMID: 38034357 PMCID: PMC10682145 DOI: 10.1016/j.isci.2023.108287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 04/23/2023] [Accepted: 10/18/2023] [Indexed: 12/02/2023] Open
Abstract
Discovery of genomic safe harbor sites (SHSs) is fundamental for multiple transgene integrations, such as reporter genes, chimeric antigen receptors (CARs), and safety switches, which are required for safe cell products for regenerative cell therapies and immunotherapies. Here we identified and characterized potential SHS in human cells. Using the CRISPR-MAD7 system, we integrated transgenes at these sites in induced pluripotent stem cells (iPSCs), primary T and natural killer (NK) cells, and Jurkat cell line, and demonstrated efficient and stable expression at these loci. Subsequently, we validated the differentiation potential of engineered iPSC toward CD34+ hematopoietic stem and progenitor cells (HSPCs), lymphoid progenitor cells (LPCs), and NK cells and showed that transgene expression was perpetuated in these lineages. Finally, we demonstrated that engineered iPSC-derived NK cells retained expression of a non-virally integrated anti-CD19 CAR, suggesting that several of the investigated SHSs can be used to engineer cells for adoptive immunotherapies.
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Affiliation(s)
- Arsenios Vlassis
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Tanja L. Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Marina Mohr
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Dominika J. Jedrzejczyk
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Xiangyou Meng
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Gergo Kovacs
- DTU Bioengineering, Technical University of Denmark, Søltofts Plads 224, 2800 Kongens Lyngby, Denmark
| | - Martí Morera-Gómez
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Andrea Barghetti
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
- Artisan Bio, 363 Centennial Parkway, Suite 310, Louisville, CO 80027, USA
| | - Sergi Muyo Abad
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Roland F. Baumgartner
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
- Artisan Bio, 363 Centennial Parkway, Suite 310, Louisville, CO 80027, USA
| | - Kedar N. Natarajan
- DTU Bioengineering, Technical University of Denmark, Søltofts Plads 224, 2800 Kongens Lyngby, Denmark
| | - Lars K. Nielsen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia
| | - Tanya Warnecke
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
- Artisan Bio, 363 Centennial Parkway, Suite 310, Louisville, CO 80027, USA
| | - Ryan T. Gill
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
- Artisan Bio, 363 Centennial Parkway, Suite 310, Louisville, CO 80027, USA
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5
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Sinan S, Appleby NM, Russell R. Kinetic dissection of pre-crRNA binding and processing by CRISPR-Cas12a. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.25.550589. [PMID: 37546762 PMCID: PMC10402064 DOI: 10.1101/2023.07.25.550589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
CRISPR-Cas12a binds and processes a single pre-crRNA during maturation, providing a simple tool for genome editing applications. Here, we constructed a kinetic and thermodynamic framework for pre-crRNA processing by Cas12a in vitro, and we measured the contributions of distinct regions of the pre-crRNA to this reaction. We find that the pre-crRNA binds rapidly and extraordinarily tightly to Cas12a (Kd = 0.6 pM), such that pre-crRNA binding is fully rate limiting for processing and therefore determines the specificity of Cas12a for different pre-crRNAs. The guide sequence contributes 10-fold to the affinities of both the precursor and mature forms of the crRNA, while deletion of an upstream sequence had no significant effect on affinity of the pre-crRNA. After processing, the mature crRNA remains very tightly bound to Cas12a, with a half-life of ~1 day and a Kd value of 60 pM. Addition of a 5'-phosphoryl group, which is normally lost during the processing reaction as the scissile phosphate, tightens binding of the mature crRNA by ~10-fold by accelerating binding and slowing dissociation. Using a direct competition assay, we found that pre-crRNA binding specificity is robust to other changes in RNA sequence, including tested changes in the guide sequence, addition of a 3' extension, and secondary structure within the guide region. Together our results provide a quantitative framework for pre-crRNA binding and processing by Cas12a and suggest strategies for optimizing crRNA design in some genome editing applications.
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Affiliation(s)
- Selma Sinan
- Department of Molecular Biosciences, University of Texas at Austin, Austin TX 78712
| | - Nathan M. Appleby
- Department of Molecular Biosciences, University of Texas at Austin, Austin TX 78712
| | - Rick Russell
- Department of Molecular Biosciences, University of Texas at Austin, Austin TX 78712
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6
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Mohr M, Damas N, Gudmand-Høyer J, Zeeberg K, Jedrzejczyk D, Vlassis A, Morera-Gómez M, Pereira-Schoning S, Puš U, Oliver-Almirall A, Lyholm Jensen T, Baumgartner R, Tate Weinert B, Gill RT, Warnecke T. The CRISPR-Cas12a Platform for Accurate Genome Editing, Gene Disruption, and Efficient Transgene Integration in Human Immune Cells. ACS Synth Biol 2023; 12:375-389. [PMID: 36750230 PMCID: PMC9942205 DOI: 10.1021/acssynbio.2c00179] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Indexed: 02/09/2023]
Abstract
CRISPR-Cas12a nucleases have expanded the toolbox for targeted genome engineering in a broad range of organisms. Here, using a high-throughput engineering approach, we explored the potential of a novel CRISPR-MAD7 system for genome editing in human cells. We evaluated several thousand optimization conditions and demonstrated accurate genome reprogramming with modified MAD7. We identified crRNAs that allow for ≤95% non-homologous end joining (NHEJ) and 66% frameshift mutations in various genes and observed the high-cleavage fidelity of MAD7 resulting in undetectable off-target activity. We explored the dsDNA delivery efficiency of CRISPR-MAD7, and by using our optimized transfection protocol, we obtained ≤85% chimeric antigen receptor (CAR) insertions in primary T cells, thus exceeding the baseline integration efficiencies of therapeutically relevant transgenes using currently available virus-free technologies. Finally, we evaluated multiplex editing efficiency with CRISPR-MAD7 and demonstrated simultaneous ≤35% CAR transgene insertions and ≤80% gene disruption efficiencies. Both the platform and our transfection procedure are easily adaptable for further preclinical studies and could potentially be used for clinical manufacturing of CAR T cells.
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Affiliation(s)
- Marina Mohr
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Nkerorema Damas
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Johanne Gudmand-Høyer
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Katrine Zeeberg
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Dominika Jedrzejczyk
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Arsenios Vlassis
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Martí Morera-Gómez
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Sara Pereira-Schoning
- Artisan
Bio, 363 Centennial Parkway,
Suite 310, Louisville, Colorado 80027, United States
| | - Urška Puš
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Anna Oliver-Almirall
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Tanja Lyholm Jensen
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Roland Baumgartner
- Artisan
Bio, 363 Centennial Parkway,
Suite 310, Louisville, Colorado 80027, United States
| | - Brian Tate Weinert
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Ryan T. Gill
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
- Artisan
Bio, 363 Centennial Parkway,
Suite 310, Louisville, Colorado 80027, United States
| | - Tanya Warnecke
- Artisan
Bio, 363 Centennial Parkway,
Suite 310, Louisville, Colorado 80027, United States
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7
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Kuzmin AA, Tomilin AN. Building Blocks of Artificial CRISPR-Based Systems beyond Nucleases. Int J Mol Sci 2022; 24:ijms24010397. [PMID: 36613839 PMCID: PMC9820447 DOI: 10.3390/ijms24010397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/19/2022] [Accepted: 12/19/2022] [Indexed: 12/28/2022] Open
Abstract
Tools developed in the fields of genome engineering, precise gene regulation, and synthetic gene networks have an increasing number of applications. When shared with the scientific community, these tools can be used to further unlock the potential of precision medicine and tissue engineering. A large number of different genetic elements, as well as modifications, have been used to create many different systems and to validate some technical concepts. New studies have tended to optimize or improve existing elements or approaches to create complex synthetic systems, especially those based on the relatively new CRISPR technology. In order to maximize the output of newly developed approaches and to move from proof-of-principle experiments to applications in regenerative medicine, it is important to navigate efficiently through the vast number of genetic elements to choose those most suitable for specific needs. In this review, we have collected information regarding the main genetic elements and their modifications, which can be useful in different synthetic systems with an emphasis of those based on CRISPR technology. We have indicated the most suitable elements and approaches to choose or combine in planning experiments, while providing their deeper understanding, and have also stated some pitfalls that should be avoided.
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