The c-Rel transcription factor limits early interferon and neuroinflammatory responses to prevent herpes simplex encephalitis onset in mice

c-Rel is a transcription factor and a subunit of NF-kΒ encoded by the Rel gene. We previously demonstrated that a truncating cysteine to stop codon mutation at amino acid position 307 of c-Rel (RelC307X) results in susceptibility to herpes simplex virus type 1 (HSV-1). Approximately 60% of mutant RelC307X mice succumb to lethal herpes simplex encephalitis (HSE) in the hindbrain between days 6 and 9 postinfection, compared to resistant wild-type (Rel+/+) controls. Here, we performed dual host-pathogen RNA sequencing on Rel+/+ and RelC307X brainstems to measure differential viral and host gene expression that may underlie HSE susceptibility in mutant mice. Briefly, brainstems were harvested from Rel+/+ and RelC307X mice prior to HSE symptom onset at day 5 post-HSV-1 infection, compared to brainstems collected from non-infected control mice. Total RNA was isolated from bulk tissue using TRIzol (Invitrogen) and further column-purified using the RNeasy Mini Kit (Qiagen). RNA quality was assessed using Bioanalyzer RNA Pico chips (Agilent), and libraries were prepared following rRNA depletion. Libraries were sequenced on an Illumina HiSeq 2500 sequencer in paired-end 50bp configuration. Sequencing reads were aligned to both mouse and HSV-1 strain 17 reference genomes to obtain both host and viral gene expression counts. In total, 5 Rel+/+ and 6 RelC307X brainstem samples were analyzed at day 5 post-infection, and 4 Rel+/+ and 4 RelC307X independent non-infected samples as controls. Day 5 HSV-1-infected samples were further subdivided into high- or low-responder within both genotype groups based in part on the level of viral and host defence gene expression in each sample. Dual host-virus RNA sequencing was performed on bulk brainstem tissue to generate mRNA gene expression profiles of adult female wild-type (Rel+/+) and mutant (RelC307X) mice following intranasal HSV-1 infection, compared to non-infected control mice. HSV-1 infected mice are divided into high- and low-responders to HSV-1 infection.