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Engineering a photoactivatable A-to-I RNA base editor for gene therapy in vivo

Nature Biotechnology (2025)Cite this article

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Abstract

Tunable and reversible regulation of exogenous and endogenous gene expression would be useful for improving the safety and efficacy of gene therapy. Current chemically inducible systems are limited by the rapid diffusion and extended metabolism of small molecules, and associated side effects. Here we develop a photoactivatable RNA adenosine base editor (PA-rABE) by harnessing a compact Cas13 variant and a split ADAR2 deaminase fused with the Magnets system, which is activated through blue-light-induced dimerization. PA-rABE achieves highly efficient editing on endogenous RNA with minimal bystander editing and off-target effects. By editing a phosphorylation site of the endogenous CTNNB1 gene, PA-rABE stabilizes the β-catenin protein and activates Wnt signaling in vivo. Using adeno-associated virus vectors to deliver PA-rABE along with an hF9 variant containing a premature termination codon, we show amelioration of clotting defects in hemophilia B mice upon illumination. In summary, PA-rABE offers a controlled RNA base-editing technology for diverse biomedical applications, enabling reversible and spatiotemporally specific modulation.

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Fig. 1: Engineered PA-rABE.
Fig. 2: Optimization of PA-rABE.
Fig. 3: Characterization of the PA-rABE system performance.
Fig. 4: Application of PA-rABE in endogenous targets.
Fig. 5: Performance of PA-rABE in vivo.
Fig. 6: PA-rABE-mediated optogenetic therapy for HB.

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Data availability

All NGS data have been deposited in the NCBI Sequence Read Archive database under BioProject numbers PRJNA1194220, PRJNA1197542 and PRJNA1194292 (refs. 58,59,60). Whole-transcriptome RNA-seq are available under BioProject numbers PRJNA1194549, PRJNA1207784 and PRJNA1207789 (refs. 61,62,63).

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Acknowledgements

We extend our gratitude to H. Yang (HuidaGene Therapeutics Co. Ltd.) and T. Chi (School of Life Sciences and Technology, ShanghaiTech University) for providing mxABE and REPAIRx plasmids, respectively. We are grateful to the Laboratory Animal Center (Minhang Campus) ECNU Multifunctional Platform for Innovation and the East China Normal University Public Platform for Innovation (011). We thank Y. Zhang from the Flow Cytometry Core Facility of School of Life Sciences in the East China Normal University, and Shanghai Decode Biotech Co., Ltd. for technical support. This study was partially supported by grants from the National Natural Science Foundation of China (numbers 32025023, 32230064, 32101194, 32311530111 and 32271485), National Key R&D Program of China (2023YFC3403400 and 2023YFE0209200), China Postdoctoral Science Foundation (BX2021104), Shanghai Municipal Commission for Science and Technology (21JC1402200, 24J22800400), the Fundamental Research Funds for the Central Universities and Swedish Research Council (Vetenskapsrådet, 2020-03543). D.L. is a SANS Exploration Scholar.

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Author notes

  1. These authors contributed equally: Huiying Li, Yuhao Qiu, Bowen Song, Xinyi Quan.

Authors and Affiliations

  1. Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology and School of Life Sciences, East China Normal University, Shanghai Academy of Natural Sciences (SANS), Shanghai, China

    Huiying Li, Yuhao Qiu, Bowen Song, Xinyi Quan, Dan Zhang, Xinru Li, Jingyun Yang, Xiaohong Liu, Shuming Yin, Liren Wang, Honghui Han, Haifeng Ye, Yiyun Cheng, Bing Du, Mingyao Liu & Dali Li

  2. Southern Medical University Affiliated Fengxian Hospital, Shanghai, China

    Huiying Li, Zhiyang Zeng, Zhenliang Sun & Xueli Zhang

  3. Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, China

    Ji Jing

  4. Department of Molecular Bioscience, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden

    Qi Dai

  5. BRL Medicine Inc., Shanghai, China

    Mingyao Liu

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Contributions

H.L., M.L. and D.L. designed the experiments. H.L., Y.Q., B.S., X.Q., X. Li., J.Y., X. Liu., Z.Z., H.H. and S.Y. performed the experiments. H.L., D.L., D.Z., J.J., L.W., B.D., M.L., H.Y., Z.S., Y.C. and X.Z. analyzed the data. H.L., Q.D. and D.L. wrote the paper with input from all the authors. D.L. supervised the research.

Corresponding authors

Correspondence to Bing Du, Mingyao Liu or Dali Li.

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Competing interests

A patent application (application number PCT/CN2024/124011) based on the results reported in this study has been submitted but not yet authorized. The patent applicant is East China Normal University, and D.L., H.L., Y.Q., B.S., X.Q. and M.L. are the inventors. The other authors declare no competing interests.

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Nature Biotechnology thanks Yuan Ping, Yi Yang and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Li, H., Qiu, Y., Song, B. et al. Engineering a photoactivatable A-to-I RNA base editor for gene therapy in vivo. Nat Biotechnol (2025). https://doi.org/10.1038/s41587-025-02610-2

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