Pseudouridine RNA avoids immune detection through impaired endolysosomal processing and TLR engagement

Recognition of exogenous RNA by Toll-like receptors (TLRs) is central to pathogen defense. Using two dis- tinct binding pockets, TLR7 and TLR8 recognize RNA degradation products generated by endolysosomal nu- cleases. RNA modifications present in endogenous RNA prevent TLR activation; notably, pseudouridine- containing RNA lacks immunostimulatory activity. Indeed, this property has been critical to the successful implementation of mRNA technology for medical purposes. However, the molecular mechanism for this im- mune evasion has remained elusive. Here, we report that RNase T2 and PLD exonucleases do not adequately process pseudouridine-containing RNA to generate TLR-agonistic ligands. As a second safety mechanism, TLR8 neglects pseudouridine as a ligand for its first binding pocket and TLR7 neglects pseudouridine-con- taining RNA as a ligand for its second pocket. Interestingly, the medically used N1-methylpseudouridine also evades RNase T2, PLD3, and PLD4 processing but is able to directly activate TLR8. Taken together, our find- ings provide a molecular basis for self-avoidance by RNA-sensing TLRs.