Role for NF-kB in herpes encephalitis pathology in mice genocopying an inborn error of IRF3-IFN immunity

Herpes simplex encephalitis (HSE) is a devastating disease with high mortality and serious sequelae. Genetic defects in the interferon (IFN-I) pathway predispose individuals to HSE, but underlying mechanisms remain unclear. Using transgenic mice with the IRF3 R278Q mutation, orthologue to HSE-associated IRF3 R285Q, and iPSC-derived CNS cells from a pediatric patient carrying the variant, we investigated mechanisms in HSE. IRF3 R278Q transgenic mice exhibited aggravated HSV-1 brain disease and elevated CNS viral loads. Accordingly, microglia from the IRF3 R278Q mice showed reduced HSV-1-induced IFN-I expression. Surprisingly, unaltered Ifnb levels along with elevated levels of inflammatory cytokines were detected in infected transgenic mouse brains, correlating with higher viral load. This was successfully modelled in patient microglia. Multiomics-based immune profiling revealed an inflammatory monocyte population in the infected IRF3 R278Q mouse brain, which was enriched for NF-κB activation. NF-κB inhibition improved disease outcomes, surpassing the effect of acyclovir. These findings suggest that IFN-I defects lead to elevated levels of HSV-1 replication in the brain, which subsequently enables NF-κB-driven immunopathology, offering insights with therapeutic potential. Brain stems from IRF3 full knockout mice, transgenic mice homozygous for an IRF3 R278Q aminoacid substitution and WT mice were harvested on day 5 post ocular HSV-1 infection. Two to three brain stems were pooled per sample. Single-cell suspensions were used to generate barcoded single-cell RNA-seq libraries according to the manufacturer’s protocol. Library quality control was performed, and sequencing was carried out on a high-throughput sequencer.