Extended Data Fig. 4: Immune responses and pathology in the brain during chronic WT and Δbfd1 infection.

Brains were harvested from C57BL/6 J naïve mice and mice 30 dpi with WT or Δbfd1 parasites and analyzed as described. a, Detailed semiquantitative pathological scoring of brain histology sections. b, Cumulative pathology score based on the parameters shown in a (WT, n = 3 mice; Δbfd1, n = 4 mice.) c,d, Flow cytometry analysis of brains from naïve mice (n = 4 mice) and mice at 30 dpi with WT (n = 5 mice) or Δbfd1 (n = 3 mice) parasites (**p = 0.0093, *p = 0.0349, ****p = <0.0001; Data representative of 3 independent experiments). c, Quantification of CNS immune populations. d, Heatmaps displaying MFI of phenotypic markers used to identify UMAP clusters in Fig. 5e,f. e-g, Naive CD45.1⁺CD45.2⁺ OT-I T cells were transferred i.v. into mice 1 day prior to infection with WT (n = 3 mice) or Δbfd1 (n = 4 mice) parasites. Brains were harvested and analyzed by flow cytometry (Data representative of 2 independent experiments.) e, UMAP analysis of OT-I T cells at 14 and 30 dpi. f, Frequency of CD69⁺CD103⁺ OT-I T cells at 30 dpi (**p = 0.0053.) g, KLRG1 and CX3CR1 expression on OT-I T cells at 30 dpi (*p = 0.016035.). Data analyzed by two-sided Mann-Whitney test (b) or two-sided unpaired Student’s t-test (c,f,g); Bonferroni-Dunn correction for multiple comparisons was included in g; ns p > 0.05. Bar graphs depict the mean ± SD.

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