Engineering precise adenine base editor with infinitesimal rates of bystander mutations and off-target editing

Abstract

Adenine base editors (ABEs) catalyze A-to-G transitions showing broad applications, but their bystander mutations and off-target editing effects raise the concerns of safety issues. Through structure-guided engineering, we found ABE8e with an N108Q mutation reduced both adenine and cytosine bystander editing, and introduction of an additional L145T mutation (ABE9), further refined the editing window to 1-2nt with eliminated cytosine editing. Importantly, ABE9 induced very minimal RNA and undetectable Cas9-independent DNA off-target effects, which mainly installed desired single A-to-G conversion in mouse and rat embryos to efficiently generate disease models. Moreover, ABE9 accurately edited A5 position of the protospacer sequence in pathogenic homopolymeric adenosine sites (up to 342.5-fold precision than ABE8e) and was further confirmed through a library of guide RNA-target sequence pairs. Due to the minimized editing window, ABE9 could further broaden the targeting scope for precise correction of pathogenic SNVs when fused to Cas9 variants with expanded PAM compatibility.