SNAC: A Single-Nuclei Atlas of Capsid Distribution in Nonhuman Primate Eye

Adeno-associated virus (AAV) vectors have emerged as the leading gene therapy vehicle due to their favorable safety profile and sustained payload expression. Approved therapies such as voretigene neparvovec (Luxturna) and omnasemnogene abeparvovec (Zolgensma) rely on the tropism of natural AAV variants. The majority of discovered natural AAVs and engineered AAV capsids have not been comprehensively profiled for their biodistribution, especially at single-cell resolution. Recent advances in single nuclei sequencing can enable further refinement of AAV cell-type specificity and reduce off-target effects. However, low levels of transduction and muted sensitivity of current single-cell detection methods make screening pooled capsids at single-cell resolution challenging. Here, we develop SNAC (Single-Nuclei Atlas of Capsid distribution), an improved method for single-nuclei profiling of AAV transduction at multiplex scale. We provide proof of concept using the nonhuman primate eye as a model system, showing that we can accurately identify and quantify vector expression in all major retinal cell types. Furthermore, the ranking of capsids by SNAC agrees with that from pre-established tissue sampling protocols. Our method promises to reduce the time, effort, and cost of accurate cell-type-specific profiling of AAV capsids.