Optimizing 5'UTRs for mRNA-delivered gene editing using deep learning

Abstract

mRNA therapeutics are revolutionizing the pharmaceutical industry, but methods to optimize the primary sequence for increased expression are still lacking. Here, we design 5UTRs for efficient mRNA translation using deep learning. We perform polysome profiling of fully or partially randomized 5UTR libraries in three cell types and find that UTR performance is highly correlated across cell types. We train models on all our datasets and use them to guide the design of high-performing 5UTRs using gradient descent and generative neural networks. We experimentally test designed 5UTRs with mRNA encoding megaTALTM gene editing enzymes for two different gene targets and in two different cell lines. We find that the designed 5UTRs support strong gene editing activity. Editing efficiency is correlated between cell types and gene targets, although the best performing UTR was specific to one cargo and cell type. Our results highlight the potential of model-based sequence design for mRNA therapeutics.