N1-methylpseudouridylation of mRNA causes +1 ribosomal frameshifting

TLDR

In vitro‑transcribed mRNAs are used as therapeutics, and while modified nucleotides reduce immunogenicity, their impact on translation fidelity remains largely unexplored. We show that N1‑methylpseudouridine incorporation induces +1 ribosomal frameshifting during translation, elicits immune responses to frameshifted products, and that synonymous sequence changes can mitigate this effect, underscoring potential off‑target consequences for mRNA vaccines.

Abstract

Abstract In vitro-transcribed (IVT) mRNAs are modalities that can combat human disease, exemplified by their use as vaccines for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). IVT mRNAs are transfected into target cells, where they are translated into recombinant protein, and the biological activity or immunogenicity of the encoded protein exerts an intended therapeutic effect 1,2 . Modified ribonucleotides are commonly incorporated into therapeutic IVT mRNAs to decrease their innate immunogenicity 3–5 , but their effects on mRNA translation fidelity have not been fully explored. Here we demonstrate that incorporation of N 1 -methylpseudouridine into mRNA results in +1 ribosomal frameshifting in vitro and that cellular immunity in mice and humans to +1 frameshifted products from BNT162b2 vaccine mRNA translation occurs after vaccination. The +1 ribosome frameshifting observed is probably a consequence of N 1 -methylpseudouridine-induced ribosome stalling during IVT mRNA translation, with frameshifting occurring at ribosome slippery sequences. However, we demonstrate that synonymous targeting of such slippery sequences provides an effective strategy to reduce the production of frameshifted products. Overall, these data increase our understanding of how modified ribonucleotides affect the fidelity of mRNA translation, and although there are no adverse outcomes reported from mistranslation of mRNA-based SARS-CoV-2 vaccines in humans, these data highlight potential off-target effects for future mRNA-based therapeutics and demonstrate the requirement for sequence optimization.