How modified RNA tricks the innate immune system

The innate immune system is the body’s first line of defense against pathogens and foreign substances. An essential component of this system are pattern recognition receptors, which recognize non-self RNA—such as that from viruses and bacteria—and trigger an immune response.

A team of LMU researchers led by immunologist Professor Veit Hornung and chemist Professor Thomas Carell has now deciphered the molecular mechanism by which certain RNA modifications evade these receptors—a key mechanism for the development of RNA therapeutics and mRNA vaccines. Their paper is published in the journal Cell.

The main pattern recognition receptors for identifying foreign RNA are the toll-like receptors TLR7 and TLR8, which are located in specific cell organelles called endolysosomes. However, the RNAs must first be broken down by certain enzymes in the endolysosomes before they can be recognized by the receptors—and this is why modified RNA is not recognized.

“We were able to show for the first time that modified RNA containing pseudouridine instead of uridine is less easily processed by lysosomal enzymes. At the same time, the receptors also fail to recognize the pseudouridine-containing fragments,” explains Marleen Bérouti, co-first author of the study alongside Mirko Wagner.

Pseudouridine is a modification of cellular RNAs that is widespread in nature, particularly in vertebrate RNA. Back in 2005, a groundbreaking study showed that pseudouridine in synthetic mRNA greatly reduces the immune response. This knowledge formed the basis for the development of RNA therapeutics and mRNA vaccines.

In certain mRNA vaccines against COVID-19, for example, a related modification called N1-methylpseudouridine was used, which, when incorporated into RNA, is also not recognized by the receptors. The mechanism identified by the researchers now explains mechanistically why modified mRNAs do not cause excessive inflammation, which is particularly important for the widespread application of this technology.

The new findings offer important starting points for the future targeted development of RNA-based drugs. “And, of course, it is also fundamentally important to understand why the body’s own RNA is not recognized,” says Hornung. “We are currently investigating in detail the role pseudouridine plays in this process.”