158. Cryptic ATG Removal from Synthetic Introns Increase the Therapeutic Efficacy of AAV Vector Mediated Gene Transfer

Abstract

Inclusion of synthetic introns in adeno-associated virus (AAV) vector expression cassettes is a commonly used maneuver to drive increased transgene expression, possibly via an increased stability and/or increased nuclear translocation of mRNA. Although the positive effect of intronic sequences on transgene expression has been demonstrated in several models, less clear is whether splicing in these synthetic expression cassettes occurs with 100% efficiency and if the presence of the unspliced intron can influence the efficiency of translation of the transgene. In an effort to optimize a liver gene transfer approach to treat Crigler-Najjar (CN) syndrome, an autosomal recessive disorder caused by mutations in the UDP-glucuronosyltransferase 1 isotype A1 (UGT1A1) gene, we analyzed the sequence of a synthetic intron derived from human beta-globin intron 2 (hBB2) for motifs that may affect the transgene expression levels. This analysis revealed the presence of out of frame and in frame ATG codons before the start site of the UGT1A1 transgene. Unexpectedly, the removal of these cryptic ATGs from the intronic sequence enhanced transgene expression, which resulted in stable, long-term correction of serum bilirubin levels in animal models of CN syndrome. These results demonstrate that intron optimization increases mRNA and protein levels in vitro and enhance the efficacy of the vector in vivo. Next, we conducted a similar analysis on other intronic sequences commonly used in AAV-mediated gene transfer, showing that the removal of cryptic ATGs in the intron at the 5’ of a transgene generally increases its expression. The scanning ribosome model may provide a solid explanation for our findings given that the intronic sequence is not completely removed by splicing. We thus analyzed the structure of the region at the 5’ of the transgene by RT-PCR and primer elongation assay and we observed the accumulation of unspliced forms of the mRNA. We also confirmed that the presence of cryptic ATGs has a critical impact on the translation efficiency of the transgene. In conclusion, our results confirm the positive effect of an intron fused to the 5’ of a transgene on its expression levels. On the other hand, our results provide evidence that the synthetic introns used in gene therapy are not spliced with 100% efficiency, thus the optimization of the sequence of the intron by removal of cryptic ATGs is important to increase the transgene expression in AAV vector-mediated gene transfer.