High-Throughput 5' UTR Engineering for Enhanced Protein Production in Non-Viral Gene Therapies

Abstract

Despite significant clinical progress in cell and gene therapies, maximizing protein expression in order to enhance potency remains a major challenge. One approach to increase protein expression is by optimizing translation through the engineering of 5 untranslated regions (5 UTRs). Here, we developed a high-throughput strategy to design, screen, and optimize novel 5UTRs that enhance protein expression from a strong human cytomegalovirus (CMV) promoter. We first identified naturally occurring 5 UTRs with high translation efficiencies and used this information with in silico genetic algorithms to generate synthetic 5 UTRs. A total of [~]12,000 5 UTRs were then screened using a recombinase-mediated integration strategy that greatly enhances the sensitivity of high-throughput screens by eliminating copy number and position effects that limit lentiviral approaches. Using this approach, we identified three synthetic 5 UTRs that outperformed commonly used non-viral gene therapy plasmids in expressing protein payloads. Furthermore, combinatorial assembly of these 5 UTRs enabled even higher protein expression than obtained with each individual 5 UTR. In summary, we demonstrate that high-throughput screening of 5 UTR libraries with recombinase-mediated integration can identify genetic elements that enhance protein expression, which should have numerous applications for engineered cell and gene therapies.