Efficient AAV Mediated Transgenesis in Alveolar Stem Cells and Associated Niches.

Targeted delivery of transgenes to tissue resident stem cells and related niches offers avenues for interrogating pathways and editing endogenous alleles for therapeutic interventions. Here, we survey multiple AAV serotypes, administered via intranasal and retroorbital routes in mice, to target lung alveolar stem cell niche. We find that AAV5, AAV4, and AAV8 efficiently and preferentially transduce alveolar type-2 stem cells (AT2s), endothelial cells and PDGFRA+ fibroblasts, respectively. Interestingly, some AAVs show different cell tropism depending on the route of administration. Proof of concept experiments reveal the versatility of AAV5-mediated transgenesis for AT2-lineage labeling, clonal cell tracing following cell ablation, and conditional gene inactivation, in both postnatal and adult mouse lungs in vivo. AAV6, but not AAV5, efficiently transduces both mouse and human AT2s in alveolar organoids cultures. Furthermore, AAV5 and AAV6 can be used to deliver guide RNAs and transgene cassettes for homologous recombination in vivo and ex vivo, respectively. Using this system coupled with clonal derivation of AT2 organoids, we demonstrate efficient and simultaneous editing of multiple loci, including targeted insertion of a payload cassette in AT2s. Taken together, our studies highlight the powerful utility of AAVs for interrogating airway stem cells and other specific cell types both in vivo and ex vivo.