TLR5 versus TLR7/8 agonist-dependent modulation of the early gene expression response to inactivated influenza virus vaccine in newborn nonhuman primates.

There is an urgent need for strategies that can improve vaccine immunogenicity, especially for vulnerable populations such as newborns and young infants. Growing evidence supports Toll-Like Receptor agonists (TLRa) as potent stimulatory molecules to increase vaccine efficacy. We have previously demonstrated that the inclusion of either flagellin (TLR5a) or R848 (TLR7/8a) in an inactivated influenza virus vaccine can improve responses in newborn NHP, with R848 being superior at providing protection upon challenge. This study aimed to identify early immune events triggered by either inactivated virus alone or in combination with R848 or flagellin using scRNA-seq analysis of draining lymph nodes (dLN) collected 24 h after vaccination. Our study reveals that globally, R848 enhanced gene expression associated with B cell activation, while flagellin was a stronger modulator of T cells. Analysis of distinct lymph node populations showed that surprisingly, while APCs had a potent transcriptional response to inactivated virus, we observed minimal additional changes in transcriptional activity with addition of a TLRa. In contrast, R848 had a potent effect on cellular translation, while flagellin resulted in increased expression of type I interferon genes in B cells. All vaccines resulted in a population of T cells bearing an interferon response signature that was further modified by TLRa inclusion. R848 uniquely increased the expression of genes involved with cellular migration and inflammation in this population, while flagellin increased genes involved in vesicular trafficking, cAMP responsiveness, and calcium signaling. Together, these results suggest R848 promotes newborn B cell activation and enhanced migration/retention in the dLN. In contrast, flagellin amplifies the type I interferon signature of B cells and had broad impacts on the responding T cell population. Our findings provide new insights into the modulation of early vaccine responses in newborns following administration of inactivated influenza virus, R848 and flagellin.