Adeno-associated virus (AAV) vectors are quickly becoming the “poster child” for therapeutic gene delivery. To this date, hundreds of naturally occurring isolates and synthetically engineered variants have been reported. While factors such as high production titre and low immunoreactivity are important to consider, the ability to deliver the genetic payload (physical transduction) and drive high transgene expression (functional transduction) remain the most important features when selecting AAV variants for (pre)clinical applications. Reporter expression assays are the most commonly used methods of determining vector fitness. However, such approaches are very time consuming and become impractical when evaluating large numbers of vector variants. Limited access to primary human tissues or challenging model systems, such as 3D organoids, further complicates vector testing. A convenient high-throughput method to determine AAVs’ transduction efficiencies would be beneficial.
We build a next-generation sequencing (NGS)-based AAV Testing Kit compatible with in vitro, ex vivo and in vivo applications. The AAV Testing Kit consists of a mix of 30 AAV variants that encode a CMV-eGFP cassette, that is identical between them apart from a unique 6-N barcode in the 3’ untranslated region of eGFP, allowing NGS barcode analysis at the DNA and RNA/cDNA levels. To validate the Kit, individually packaged barcoded variants were mixed at a 1:1:1 ratio and used to transduce cells/tissues of interest. DNA and RNA (cDNA) were extracted and subsequently analysed by NGS to determine the physical/ functional transduction efficiencies.
We were able to reliably assess the transduction efficiencies of immortalised cells, primary cells and iPSCs in vitro as well as in vivo tests in naïve mice and a xenograft liver mode. Our data is in agreement with previously reported transduction characteristics of individual capsids, validating our testing approach. More importantly, novel previously unknown tropisms were identified for some AAV variants.