Effective in vivo RNA base editing via engineered cytidine deaminase APOBECs fused with PUF proteins

Wenjian Han (), Bo Yuan, Xiaojuan Fan, Weike Li, Yiting Yuan, Yuefang Zhang, Shu Wang, Shifang Shan, Markus Hafner, Zefeng Wang () and Zilong Qiu ()
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Wenjian Han: Shanghai Jiao Tong University School of Medicine
Bo Yuan: Fudan University
Xiaojuan Fan: National Institute of Arthritis and Musculoskeletal and Skin Disease
Weike Li: Chinese Academy of Sciences
Yiting Yuan: Shanghai Jiao Tong University School of Medicine
Yuefang Zhang: Shanghai Jiao Tong University School of Medicine
Shu Wang: Shanghai Jiao Tong University School of Medicine
Shifang Shan: Chinese Academy of Sciences
Markus Hafner: National Institute of Arthritis and Musculoskeletal and Skin Disease
Zefeng Wang: Southern University of Science and Technology
Zilong Qiu: Shanghai Jiao Tong University School of Medicine

Nature Communications, 2025, vol. 16, issue 1, 1-17

Abstract: Abstract Base editing stands at the forefront of genetic engineering, heralding precise genetic modifications with broad implications. While CRISPR-based DNA and RNA base editing systems capitalize on sgRNA-guided specificity and diverse deaminase functionalities, the pursuit of efficient C-to-U RNA editing has been hampered by the inherent constraints of cytidine deaminases. Here, we report an RNA base editing platform by refining cytidine deaminases, termed professional APOBECs (ProAPOBECs), through systematic enhancements and AI-driven protein engineering. ProAPOBECs demonstrate unprecedented catalytic versatility, particularly fused with RNA-recognizing Pumilio and FBF (PUF) proteins. We demonstrate that in vivo RNA base editing of Pcsk9 using ProAPOBECs effectively lowers cholesterol levels in mice. Additionally, AAV-mediated RNA base editing with ProAPOBECs in the brain of an autism mouse model not only corrects point mutations in Mef2c mRNAs but also significantly alleviates disease-associated phenotypes. This work introduces a pioneering collection of RNA base editing instruments, emphasizing their therapeutic potential in combatting genetic disorders.

Date: 2025
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DOI: 10.1038/s41467-025-64748-6

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