Rationally and in silico guided APOBEC3F-directed CBE for enhanced PDAC genetic therapy

Cytosine base editors (CBEs) mediate precise C-to-T conversion and hold considerable therapeutic promise, yet their editing function and utility in oncology remain underexplored. Here, we integrate evolutionary scale modeling (ESM) with structure-guided mutagenesis to remodel human APOBEC3F (A3F), yielding a panel of high-performance CBEs. Our high-efficiency A3F-CBEs achieve up to 1.9- and 3.3-fold higher on-target editing within the canonical editing window than A3A- and Anc689-BE4max, respectively. The high-accuracy A3F-CBEs deliver up to 3.0-fold improvement over haA3A-G at the majority of surveyed loci without compromising specificity. To demonstrate therapeutic potential, we deploy a dual-AAV platform packaging A3F-BE4max and dual gRNAs co-targeting KRAS and MYC in pancreatic ductal adenocarcinoma (PDAC) models. It elicits robust oncogene silencing and inhibited PDAC cell proliferation both in vitro and patient-derived organoids (PDOs). In a PDAC mouse model, it markedly suppresses tumor burden and extends survival. Our work establishes ESM-guided A3F-based CBEs as a versatile, precise platform for cancer genetic therapy.