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Chaves LCS, Orr-Burks N, Vanover D, Mosur VV, Hosking SR, Kumar E. K. P, Jeong H, Jung Y, Assumpção JAF, Peck HE, Nelson SL, Burke KN, Garrison MA, Arthur RA, Claussen H, Heaton NS, Lafontaine ER, Hogan RJ, Zurla C, Santangelo PJ. mRNA-encoded Cas13 treatment of Influenza via site-specific degradation of genomic RNA. PLoS Pathog 2024; 20:e1012345. [PMID: 38968329 PMCID: PMC11253931 DOI: 10.1371/journal.ppat.1012345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 07/17/2024] [Accepted: 06/13/2024] [Indexed: 07/07/2024] Open
Abstract
The CRISPR-Cas13 system has been proposed as an alternative treatment of viral infections. However, for this approach to be adopted as an antiviral, it must be optimized until levels of efficacy rival or exceed the performance of conventional approaches. To take steps toward this goal, we evaluated the influenza viral RNA degradation patterns resulting from the binding and enzymatic activity of mRNA-encoded LbuCas13a and two crRNAs from a prior study, targeting PB2 genomic and messenger RNA. We found that the genome targeting guide has the potential for significantly higher potency than originally detected, because degradation of the genomic RNA is not uniform across the PB2 segment, but it is augmented in proximity to the Cas13 binding site. The PB2 genome targeting guide exhibited high levels (>1 log) of RNA degradation when delivered 24 hours post-infection in vitro and maintained that level of degradation over time, with increasing multiplicity of infection (MOI), and across modern influenza H1N1 and H3N2 strains. Chemical modifications to guides with potent LbuCas13a function, resulted in nebulizer delivered efficacy (>1-2 log reduction in viral titer) in a hamster model of influenza (Influenza A/H1N1/California/04/09) infection given prophylactically or as a treatment (post-infection). Maximum efficacy was achieved with two doses, when administered both pre- and post-infection. This work provides evidence that mRNA-encoded Cas13a can effectively mitigate Influenza A infections opening the door to the development of a programmable approach to treating multiple respiratory infections.
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Affiliation(s)
- Lorena C. S. Chaves
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Nichole Orr-Burks
- Department of Infectious Diseases, College of Veterinary Medicine University of Georgia, Athens, Georgia, United States of America
| | - Daryll Vanover
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Varun V. Mosur
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Sarah R. Hosking
- Department of Infectious Diseases, College of Veterinary Medicine University of Georgia, Athens, Georgia, United States of America
| | - Pramod Kumar E. K.
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Hyeyoon Jeong
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Younghun Jung
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - José A. F. Assumpção
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Hannah E. Peck
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Sarah L. Nelson
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Kaitlyn N. Burke
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - McKinzie A. Garrison
- Emory Integrated Computational Core, Emory University, Atlanta, Georgia, United States of America
| | - Robert A. Arthur
- Emory Integrated Computational Core, Emory University, Atlanta, Georgia, United States of America
| | - Henry Claussen
- Emory Integrated Computational Core, Emory University, Atlanta, Georgia, United States of America
| | - Nicholas S. Heaton
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, United States of America
- Duke Human Vaccine Institute Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Eric R. Lafontaine
- Department of Infectious Diseases, College of Veterinary Medicine University of Georgia, Athens, Georgia, United States of America
| | - Robert J. Hogan
- Department of Infectious Diseases, College of Veterinary Medicine University of Georgia, Athens, Georgia, United States of America
| | - Chiara Zurla
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Philip J. Santangelo
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, Georgia, United States of America
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Recinos Y, Ustianenko D, Yeh YT, Wang X, Jacko M, Yesantharao LV, Wu Q, Zhang C. CRISPR-dCas13d-based deep screening of proximal and distal splicing-regulatory elements. Nat Commun 2024; 15:3839. [PMID: 38714659 PMCID: PMC11076525 DOI: 10.1038/s41467-024-47140-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 03/16/2024] [Indexed: 05/10/2024] Open
Abstract
Pre-mRNA splicing, a key process in gene expression, can be therapeutically modulated using various drug modalities, including antisense oligonucleotides (ASOs). However, determining promising targets is hampered by the challenge of systematically mapping splicing-regulatory elements (SREs) in their native sequence context. Here, we use the catalytically inactive CRISPR-RfxCas13d RNA-targeting system (dCas13d/gRNA) as a programmable platform to bind SREs and modulate splicing by competing against endogenous splicing factors. SpliceRUSH, a high-throughput screening method, was developed to map SREs in any gene of interest using a lentivirus gRNA library that tiles the genetic region, including distal intronic sequences. When applied to SMN2, a therapeutic target for spinal muscular atrophy, SpliceRUSH robustly identifies not only known SREs but also a previously unknown distal intronic SRE, which can be targeted to alter exon 7 splicing using either dCas13d/gRNA or ASOs. This technology enables a deeper understanding of splicing regulation with applications for RNA-based drug discovery.
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Affiliation(s)
- Yocelyn Recinos
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Dmytro Ustianenko
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
- Flagship Pioneering, Cambridge, MA, 02142, USA
| | - Yow-Tyng Yeh
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Xiaojian Wang
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Martin Jacko
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
- Aperture Therapeutics, Inc., San Carlos, CA, 94070, USA
| | - Lekha V Yesantharao
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
- Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Qiyang Wu
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Chaolin Zhang
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA.
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA.
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Shi P, Wu X. Programmable RNA targeting with CRISPR-Cas13. RNA Biol 2024; 21:1-9. [PMID: 38764173 PMCID: PMC11110701 DOI: 10.1080/15476286.2024.2351657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/01/2024] [Indexed: 05/21/2024] Open
Abstract
The RNA-targeting CRISPR-Cas13 system has enabled precise engineering of endogenous RNAs, significantly advancing our understanding of RNA regulation and the development of RNA-based diagnostic and therapeutic applications. This review aims to provide a summary of Cas13-based RNA targeting tools and applications, discuss limitations and challenges of existing tools and suggest potential directions for further development of the RNA targeting system.
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Affiliation(s)
- Peiguo Shi
- Department of Medicine and Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Xuebing Wu
- Department of Medicine and Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
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Chen Y, Jiang H, Liu X, Wang X. Engineered Electrochemiluminescence Biosensors for Monitoring Heavy Metal Ions: Current Status and Prospects. BIOSENSORS 2023; 14:9. [PMID: 38248386 PMCID: PMC10813191 DOI: 10.3390/bios14010009] [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: 11/04/2023] [Revised: 12/14/2023] [Accepted: 12/20/2023] [Indexed: 01/23/2024]
Abstract
Metal ion contamination has serious impacts on environmental and biological health, so it is crucial to effectively monitor the levels of these metal ions. With the continuous progression of optoelectronic nanotechnology and biometrics, the emerging electrochemiluminescence (ECL) biosensing technology has not only proven its simplicity, but also showcased its utility and remarkable sensitivity in engineered monitoring of residual heavy metal contaminants. This comprehensive review begins by introducing the composition, advantages, and detection principles of ECL biosensors, and delving into the engineered aspects. Furthermore, it explores two signal amplification methods: biometric element-based strategies (e.g., HCR, RCA, EDC, and CRISPR/Cas) and nanomaterial (NM)-based amplification, including quantum dots, metal nanoclusters, carbon-based nanomaterials, and porous nanomaterials. Ultimately, this review envisions future research trends and engineered technological enhancements of ECL biosensors to meet the surging demand for metal ion monitoring.
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Affiliation(s)
| | | | | | - Xuemei Wang
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China; (Y.C.); (H.J.); (X.L.)
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