Rapid Design and Development of CRISPR-Cas13a Targeting SARS-CoV-2 Spike Protein

Overview

Journal Theranostics

Date 2021 Jan 4

PMID 33391497

Citations 32

Authors

Lin Wang

Junhu Zhou

Qixue Wang

Yunfei Wang

Chunsheng Kang

Affiliations

Soon will be listed here.

Abstract

The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a worldwide epidemic of the lethal respiratory coronavirus disease (COVID-19), necessitating urgent development of specific and effective therapeutic tools. Among several therapeutic targets of coronaviruses, the spike protein is of great significance due to its key role in host invasion. Here, we report a potential anti-SARS-CoV-2 strategy based on the CRISPR-Cas13a system. : A comprehensive set of bioinformatics methods, including sequence alignment, structural comparison, and molecular docking, was utilized to identify a SARS-CoV-2-spike(S)-specific segment. A tiling crRNA library targeting this specific RNA segment was designed, and optimal crRNA candidates were selected using methods. The efficiencies of the crRNA candidates were tested in human HepG2 and AT2 cells. : The most effective crRNA sequence inducing a robust cleavage effect on S and a potent collateral cleavage effect were identified. : This study provides a rapid design pipeline for a CRISPR-Cas13a-based antiviral tool against SARS-CoV-2. Moreover, it offers a novel approach for anti-virus study even if the precise structures of viral proteins are indeterminate.

Citing Articles

Advances in CRISPR-Cas technology and its applications: revolutionising precision medicine.

Azeez S, Hamad R, Hamad B, Shekha M, Bergsten P Front Genome Ed. 2024; 6:1509924.

PMID: 39726634 PMC: 11669675. DOI: 10.3389/fgeed.2024.1509924.

Decoding the genome of SARS-CoV-2: a pathway to drug development through translation inhibition.

Wu S, Xiao T, Chen H, Li X RNA Biol. 2024; 21(1):1-18.

PMID: 39630134 PMC: 11632750. DOI: 10.1080/15476286.2024.2433830.

Advancing CRISPR-Based Solutions for COVID-19 Diagnosis and Therapeutics.

Hadi R, Poddar A, Sonnaila S, Bhavaraju V, Agrawal S Cells. 2024; 13(21.

PMID: 39513901 PMC: 11545109. DOI: 10.3390/cells13211794.

Structures, mechanisms and applications of RNA-centric CRISPR-Cas13.

Yang H, Patel D Nat Chem Biol. 2024; 20(6):673-688.

PMID: 38702571 PMC: 11375968. DOI: 10.1038/s41589-024-01593-6.

Suppression of Borna Disease Virus Replication during Its Persistent Infection Using the CRISPR/Cas13b System.

Sasaki S, Ogawa H, Katoh H, Honda T Int J Mol Sci. 2024; 25(6).

PMID: 38542493 PMC: 10971351. DOI: 10.3390/ijms25063523.

References

Aman R, Ali Z, Butt H, Mahas A, Aljedaani F, Khan M . RNA virus interference via CRISPR/Cas13a system in plants. Genome Biol. 2018; 19(1):1. PMC: 5755456. DOI: 10.1186/s13059-017-1381-1. View

Ackerman C, Myhrvold C, Thakku S, Freije C, Metsky H, Yang D . Massively multiplexed nucleic acid detection with Cas13. Nature. 2020; 582(7811):277-282. PMC: 7332423. DOI: 10.1038/s41586-020-2279-8. View

Wang M, Cao R, Zhang L, Yang X, Liu J, Xu M . Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro. Cell Res. 2020; 30(3):269-271. PMC: 7054408. DOI: 10.1038/s41422-020-0282-0. View

Jing X, Xie B, Chen L, Zhang N, Jiang Y, Qin H . Implementation of the CRISPR-Cas13a system in fission yeast and its repurposing for precise RNA editing. Nucleic Acids Res. 2018; 46(15):e90. PMC: 6125684. DOI: 10.1093/nar/gky433. View

Wang Y, Zhang D, Du G, Du R, Zhao J, Jin Y . Remdesivir in adults with severe COVID-19: a randomised, double-blind, placebo-controlled, multicentre trial. Lancet. 2020; 395(10236):1569-1578. PMC: 7190303. DOI: 10.1016/S0140-6736(20)31022-9. View

Chen F, Alphonse M, Liu Q . Strategies for nonviral nanoparticle-based delivery of CRISPR/Cas9 therapeutics. Wiley Interdiscip Rev Nanomed Nanobiotechnol. 2019; 12(3):e1609. DOI: 10.1002/wnan.1609. View

Chu C, Cheng V, Hung I, Wong M, Chan K, Chan K . Role of lopinavir/ritonavir in the treatment of SARS: initial virological and clinical findings. Thorax. 2004; 59(3):252-6. PMC: 1746980. DOI: 10.1136/thorax.2003.012658. View

Li W, Zhang C, Sui J, Kuhn J, Moore M, Luo S . Receptor and viral determinants of SARS-coronavirus adaptation to human ACE2. EMBO J. 2005; 24(8):1634-43. PMC: 1142572. DOI: 10.1038/sj.emboj.7600640. View

Baum A, Fulton B, Wloga E, Copin R, Pascal K, Russo V . Antibody cocktail to SARS-CoV-2 spike protein prevents rapid mutational escape seen with individual antibodies. Science. 2020; 369(6506):1014-1018. PMC: 7299283. DOI: 10.1126/science.abd0831. View

10.

Meeske A, Marraffini L . RNA Guide Complementarity Prevents Self-Targeting in Type VI CRISPR Systems. Mol Cell. 2018; 71(5):791-801.e3. PMC: 7955661. DOI: 10.1016/j.molcel.2018.07.013. View

11.

Shin J, Lee N, Cho S, Cho B . Targeted Genome Editing Using DNA-Free RNA-Guided Cas9 Ribonucleoprotein for CHO Cell Engineering. Methods Mol Biol. 2018; 1772:151-169. DOI: 10.1007/978-1-4939-7795-6_8. View

12.

Russell C, Millar J, Baillie J . Clinical evidence does not support corticosteroid treatment for 2019-nCoV lung injury. Lancet. 2020; 395(10223):473-475. PMC: 7134694. DOI: 10.1016/S0140-6736(20)30317-2. View

13.

Towler P, Staker B, Prasad S, Menon S, Tang J, Parsons T . ACE2 X-ray structures reveal a large hinge-bending motion important for inhibitor binding and catalysis. J Biol Chem. 2004; 279(17):17996-8007. PMC: 7980034. DOI: 10.1074/jbc.M311191200. View

14.

Kuba K, Imai Y, Rao S, Gao H, Guo F, Guan B . A crucial role of angiotensin converting enzyme 2 (ACE2) in SARS coronavirus-induced lung injury. Nat Med. 2005; 11(8):875-9. PMC: 7095783. DOI: 10.1038/nm1267. View

15.

Myhrvold C, Freije C, Gootenberg J, Abudayyeh O, Metsky H, Durbin A . Field-deployable viral diagnostics using CRISPR-Cas13. Science. 2018; 360(6387):444-448. PMC: 6197056. DOI: 10.1126/science.aas8836. View

16.

Du L, He Y, Zhou Y, Liu S, Zheng B, Jiang S . The spike protein of SARS-CoV--a target for vaccine and therapeutic development. Nat Rev Microbiol. 2009; 7(3):226-36. PMC: 2750777. DOI: 10.1038/nrmicro2090. View

17.

Yang L, Wang Y, Li S, Yao R, Luan P, Wu H . Dynamic Imaging of RNA in Living Cells by CRISPR-Cas13 Systems. Mol Cell. 2019; 76(6):981-997.e7. DOI: 10.1016/j.molcel.2019.10.024. View

18.

Abbott T, Dhamdhere G, Liu Y, Lin X, Goudy L, Zeng L . Development of CRISPR as an Antiviral Strategy to Combat SARS-CoV-2 and Influenza. Cell. 2020; 181(4):865-876.e12. PMC: 7189862. DOI: 10.1016/j.cell.2020.04.020. View

19.

Abudayyeh O, Gootenberg J, Essletzbichler P, Han S, Joung J, Belanto J . RNA targeting with CRISPR-Cas13. Nature. 2017; 550(7675):280-284. PMC: 5706658. DOI: 10.1038/nature24049. View

20.

Chen L, Xiong J, Bao L, Shi Y . Convalescent plasma as a potential therapy for COVID-19. Lancet Infect Dis. 2020; 20(4):398-400. PMC: 7128218. DOI: 10.1016/S1473-3099(20)30141-9. View