Design of antiviral AGO2-dependent short hairpin RNAs

Yuanyuan Bie; Jieling Zhang; Jiyao Chen; Yumin Zhang; Muhan Huang; Leike Zhang; Xi Zhou; Yang Qiu

doi:10.1016/j.virs.2024.05.001

August 2024

Citation: Yuanyuan Bie, Jieling Zhang, Jiyao Chen, Yumin Zhang, Muhan Huang, Leike Zhang, Xi Zhou, Yang Qiu. Design of antiviral AGO2-dependent short hairpin RNAs .VIROLOGICA SINICA, 2024, 39(4) : 645-654. http://dx.doi.org/10.1016/j.virs.2024.05.001

Design of antiviral AGO2-dependent short hairpin RNAs

Yuanyuan Bie ^a,b,c ,
Jieling Zhang ^a,b,d ,
Jiyao Chen ^a,b ,
Yumin Zhang ^a,b ,
Muhan Huang ^a,b ,
Leike Zhang ^a,b,c ,
Xi Zhou ^{a,b,c,d
,,} ,
Yang Qiu ^{a,b,c,d
,,}

a. Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China;
b. State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China;
c. University of Chinese Academy of Sciences, Beijing 100049, China;
d. School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China

Corresponding author: Xi Zhou, zhouxi@wh.iov.cn
Yang Qiu, yangqiu@wh.iov.cn
Received Date: 11 March 2024
Accepted Date: 06 May 2024
Available online: 09 May 2024

Abstract

The increasing emergence and re-emergence of RNA virus outbreaks underlines the urgent need to develop effective antivirals. RNA interference (RNAi) is a sequence-specific gene silencing mechanism that is triggered by small interfering RNAs (siRNAs) or short hairpin RNAs (shRNAs), which exhibits significant promise for antiviral therapy. AGO2-dependent shRNA (agshRNA) generates a single-stranded guide RNA and presents significant advantages over traditional siRNA and shRNA. In this study, we applied a logistic regression algorithm to a previously published chemically siRNA efficacy dataset and built a machine learning-based model with high predictive power. Using this model, we designed siRNA sequences targeting diverse RNA viruses, including human enterovirus A71 (EV71), Zika virus (ZIKV), dengue virus 2 (DENV2), mouse hepatitis virus (MHV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and transformed them into agshRNAs. We validated the performance of our agshRNA design by evaluating antiviral efficacies of agshRNAs in cells infected with different viruses. Using the agshRNA targeting EV71 as an example, we showed that the anti-EV71 effect of agshRNA was more potent compared with the corresponding siRNA and shRNA. Moreover, the antiviral effect of agshRNA is dependent on AGO2-processed guide RNA, which can load into the RNA-induced silencing complex (RISC). We also confirmed the antiviral effect of agshRNA in vivo. Together, this work develops a novel antiviral strategy that combines machine learning-based algorithm with agshRNA design to custom design antiviral agshRNAs with high efficiency.
- AgshRNA
- , Antiviral strategy
- , Machine learning model

Electronic Supplementary Material

10.1016j.virs.2024.05.001-ESM.docx
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