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

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 demonstrated 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 corrected point mutations in Mef2c mRNAs but also significantly alleviated disease-associated phenotypes. This work introduces a pioneering collection of RNA base editing instruments, emphasizing their therapeutic potential in combatting genetic disorders.