Comprehensive mutagenesis maps the effect of all single codon mutations in the AAV2 rep gene on AAV production

Joint Public Review:

In this work, Jain and colleagues have created two libraries of the AAV2 rep gene - either expressed separately from a strong heterologous promoter or embedded in the viral wild-type context - containing all possible single codon mutations. The libraries were cleverly made through a cloning process that ensured each mutant was attached to an exactly known 20-nt barcode included in each mutagenic oligo. This allowed the authors to confidently observe nearly all rep variants in their experiments, resulting in a comprehensive map between Rep protein variants and AAV production. Interrogation of these libraries identified several variants that improved AAV production, including mutations not observed in natural AAV isolates thus far, as independently verified through a conventional AAV vector production protocol. These benefits were also conserved across multiple natural AAV capsid variants including the heterologous AAV5 serotype.

While many other groups have previously created and interrogated individual point mutants of the AAV rep gene/protein or domain swapping mutants, this study is distinguished and excels by its degree of comprehensiveness and the complexity of the two complementary libraries. This reflects the next step in the field's efforts to better understand the natural biology of AAV and, as a result, to improve the production of recombinant AAV gene transfer vectors. Considering the rapidly increasing momentum of these vectors in the clinics and as approved drugs on the gene therapy market, and considering that the individual validation experiments reported in this work support the conclusions, this work including the reported resources and technologies is likely to have a critical impact on current and future research on AAV biology and vector development.

However, there are a few areas in which the study could be expanded for even greater impact. For instance, the authors may consider testing the selected rep variants in the context of a self-complementary AAV genome, which has different biology compared to the single-stranded genomes used in this study, and which is widely used granted its compatibility with the transgene of choice (which should be <2.5 kb). Likewise, it would be important to study the functionality of the selected rep variants with at least one AAV genome of regular size, considering that the two tested here seem rather unusual in length (2.9 kb, which is very small, or 5.0 kb, which is borderline large). Last but not least, despite the fact that the AAV2 ITRs are by far most commonly used in the field, it will also be interesting to test these rep variants in combination with ITRs derived from other AAV serotypes, considering that numerous groups have previously cloned and analyzed them, and that they can provide several benefits over the AAV2 ITRs.

Furthermore, in interpreting the results of this study, the reader should bear in mind that what has been measured and validated in this work is the production of intact genome-containing AAVs. Production is a precondition to functional AAVs that can transduce cells but is not equivalent to it. While the two are likely well correlated, further studies are needed to determine how well the effects of Rep protein variants on AAV production translate to their ability to then transduce cells. The more relevant property for gene therapy is the efficiency by which an AAV preparation transduces cells. For example, might production-enhancing Rep protein variants change the ratio of empty capsids to genome-containing capsids in a way that influences transduction efficiency of the corresponding AAV preparations? Does this influence reduce or enhance the production benefit? This particular scenario of empty capsid ratios influencing transduction represents a population effect that is not possible to capture in the multiplex assay, but it seems like a good idea to at least test transduction of some individual variants because transduction is the important function of AAV for gene therapy.

One additional aspect that may warrant further consideration is the assumption, as mentioned in Figure 2's legend, that synonymous mutations are neutral and can serve as controls for normalizing the production rate. However, Figures S5-6 and Figures S11-12 suggest that synonymous mutations are not necessarily neutral, as their distribution is similar to that of nonsynonymous mutations. Thus, a deeper examination of the impacts of synonymous mutations on the genotype-phenotype landscape could provide more nuanced insights into AAV2 rep gene function.