Additional file 1 of MAVS signaling of long-lived brain-resident myeloid cells is needed during viral encephalitis to adjust the transcriptome of CNS infiltrating CD8+ T cells

Supplementary Material 1: Extended Data Fig. 1. MAVS signaling is not required to control VSV dissemination to peripheral organs upon intranasal virus instillation. C57BL/6 and Mavs−/− mice were i.n. VSV infected with 103 PFU of VSV and liver, spleen, and lung was prepared at the indicated days. (A) Virus titers were determined by plaque assay in liver, spleen, and lung homogenates (N = 2, n ≥ 5 per genotype, combined data). (B) Virus titers were determined by plaque assay in olfactory bulb (OB), cerebrum (CR), brain stem (BS), cerebellum (CRBL), liver (LI), and spleen (SPL) homogenates dissected at the end of the experiment (30 dpi) or at the time point of exclusion criteria from one of the two survival experiments (Fig. 1F). Two-tailed Mann–Whitney test * < 0.05, ** < 0.01, ***P < 0.001, ****P < 0.0001. Extended Data Fig. 2. MAVS signaling within the infected CNS is essential for viral restriction and host protection. (A) Virus titers were determined by plaque assay in olfactory bulb (OB), cerebrum (CR), brain stem (BS), cerebellum (CRBL), liver (LI), spleen (SPL) and lung (LU) homogenates dissected at the time point of exclusion criteria from the survival experiment (Fig. 2A) from i.n. VSV infected MAVS−/−, Syn1-Cre± MAVSfl/fl and CX3CR1-CreER± MAVSfl/fl. (B) The OB of infected mice was prepared 4 days post infection and IFN-α was determined from lysates by an ELISA method (N = 2, n ≥ 5 per genotype, combined data). (C) Primary data in dot plot graphs per cytokine as shown in the heat map of Fig. 2D. (D) Mavs−/− mice were intranasally infected with 103 PFU of VSV-eGFP and 6 days later histological analysis was performed from the olfactory bulb, VSV-eGFP (green) and P2RY12+ (red) within the glomerular and granular cell layer of the OB (representative data from n = 2). Extended Data Fig. 3. Mavs deficiency in microglia does not affect leukocyte recruitment into the infected OB. (A) Flow cytometry density plots (B) and quantification of immune cell subsets within the OB of C57BL/6 (WT) and CX3CR1-CreER± MAVSfl/fl mice i.n. instilled with 103 PFU of VSV at 6 dpi (n = 3 per genotype). Extended Data Fig. 4. Depletion of Mavs in microglia affects the microglia transcriptomic profile during infection. (A) Heat map of relative expression of differentially expressed genes with a log2-fold change cut-off between microglia from C57BL/6 (WT) and CX3CR1-CreER±MAVSfl/fl mice i.n. infected with 103 PFU of VSV. (B) Comparative pathway analysis of the top 10 differentially enriched pathways of microglia from C57BL/6 (WT) and CX3CR1-CreER± MAVSfl/fl mice infected with 103 PFU of VSV.