Extended Data 1. Contribution of AHR in CNS resident and infiltrating immune cells during EAE.

(a) qPCR of indicated genes from microglia, splenic macrophages, and astrocytes from control and CX3CR1-AHR mice on day 28 after EAE induction. Data are mean ± s.e.m. of n = 8 independent samples per group. P values were determined by two-sided Student’s t-test. (b) Flow cytometry analysis of AHR expression in microglia, monocytes and astrocytes from Control and CX3CR1-AHR mice 21 days after EAE induction. Thin line depicts isotype control, thick line AHR staining, and numbers indicate percentage of AHR positive cells. Representative of stainings of n=3 mice per group. (c) Spinal cord samples from naïve Control and CX3CR1-AHR mice were stained for Iba-1 and DAPI and Iba-1⁺ microglia/mm² were determined. n=5 mice per group. Data are mean ± s.e.m. and P value was determined by two-sided Student’s t-test. n.s. not significant. (d) TUNEL staining in Iba-1⁺ microglia in spinal cord sections of Control and CX3CR1-AHR mice as in (c). For the positive control, slides were cooked at 98°C in Citrate buffer during 60 minutes using a vapor cooker. Solid arrows show TUNEL positive microglia. Representative of n = 5 independent experiments. (e) Number of CNS-infiltrating (top) and splenic T-cells (bottom), and splenic pro-inflammatory monocytes (bottom) as determined by flow cytometry. n = 5 samples per group for CNS, n = 4 samples per group for spleen. Data are mean ± s.e.m. and P values were determined by two-sided Student’s t-test. (f) Proliferation assay from splenocytes isolated on day 28 of the experiment (Data are mean ± s.e.m. of n=4 biologically independent samples per group, representative of two independent experiments). (g) Bone marrow chimera were generated using WT mice irradiated as recipients, reconstituted with Control or CX3CR1-AHR bone marrow. Recipients of bone marrow were then rested for 3 weeks and thereafter treated with weekly tamoxifen gavages (4 mg) for another 3 weeks; after a total of 6 weeks, EAE was induced and tamoxifen administration continued weekly during EAE. Left, flow cytometry analysis of AHR expression in microglia and monocytes 21 days after EAE induction. Thin line depicts isotype control, thick line AHR staining, and numbers indicate percentage of AHR positive cells. Representative of stainings of n=3 independent mice per group. Right, EAE clinical course in bone marrow chimera mice. Data are mean ± s.e.m. and P values were determined by two-way ANOVA of n = 4 mice per group. (h) Control and CX3CR1-AHR mice were treated with with oral tamoxifen weekly starting from 5 weeks of age. EAE was induced at 8 weeks under continuation of weekly tamoxifen administration. Left, intracellular FACS staining for AHR in microglia and monocytes from at day 21 of EAE. Representative of stainings of n=3 independent mice per group. Right, clinical course of control and CX3CR1-AHR bone marrow chimera mice. Data are mean ± s.e.m. and P values were determined by two-way ANOVA of n = 4 mice per group.