Spatial Profiling of Base Editing by In Situ Sequencing in Mice and Macaques

Base editing allows for precise introduction of transition point mutations in dividing and non-dividing cells, making it a promising technology for correcting pathogenic mutations directly within organisms. However, efficient targeting of base editors to designated tissues remains a challenge, and accurately measuring editing rates with spatial resolution is necessary to harness the full potential of in vivo base editing. Here, we adapt imaging-based in situ sequencing (ISS) to map base editing events within tissues. We successfully employ the technology in murine brains treated with adeno-associated viral (AAV) vectors expressing adenine base editors (ABEs). By applying ISS to the liver, we further demonstrate that systemic delivery of ABEs into mice and macaques using lipid nanoparticle-RNA (LNP-RNA) results in effective editing across all metabolic zones of liver lobules. In addition, targeting two different genetic loci by repeated dosing suggests the absence of a specific hepatocyte population that is more receptive to LNP-RNA delivery or base editing. ISS could be instrumental in advancing the development of in vivo base editing treatments, potentially offering new therapeutic options for a wide range of genetic diseases.