Extended Data Fig. 9: Brain T cells colocalize with microglia and Aβ plaques in 5xFAD mice and inhibit microglia proinflammatory activity.
From: CXCR6 orchestrates brain CD8+ T cell residency and limits mouse Alzheimer’s disease pathology
a, GSEA enrichment plot showing upregulation of inflammatory response signatures in microglia from 5xFAD mice versus Non-Tg mice. b, Violin plots showing expression of Tnf, Il1b and Tgfb1 in microglia from Non-Tg (n = 1,782 cells) and 5xFAD (n = 2,870 cells) mice. c, Relative percentages (normalized to Non-Tg mice) of TNF-α+ and pro-IL-1β+ microglia from 10-month-old Non-Tg (n = 15) and 5xFAD (n = 21) mice. d, Immunofluorescence images of brain CD3+ T cells in proximity to Aβ or Iba1+ microglia in 10-month-old 5xFAD mice. Scale bar, 20 μm. e, Immunofluorescence image of brain CD8+ T cells (red), Aβ (white) and Iba1+ microglia (green) in 10-month-old 5xFAD;Cxcr6–/– mice. Scale bar, 20 μm. f, g, Spatial colocalization index between CD8+ T cells (CD8) and activated microglia (Iba1) (f) or CD8 and Aβ plaques (g) within the brains of 5xFAD;Cxcr6+/+ (n = 105 scored interactions) and 5xFAD;Cxcr6–/– (n = 71 scored interactions) mice. The index values for each target–pair were compared by genotype (P values shown in black color) and against simulated random distribution (P values shown in red or green color) (see Methods). h, Immunofluorescence images of PD-1 (green) and CD8 (red) coexpressing T cells in proximity to Iba1+ microglia (white) in 10-month-old 5xFAD mice. Scale bar, 5 μm. i, Heatmap showing the differential interaction strength, predicted by CellChat, between T cell subsets and microglia in indicated mice. Row z score indicates the differential interaction strengths. j, k, Relative percentages (normalized to sex-matched controls) of pro-IL-1β+ microglia (j, k) and geometric mean fluorescence intensity (gMFI; j, k) from 10-month-old 5xFAD;B2m+/+ (percentage, n = 19 for female and 11 for male; gMFI, n = 19 for female and 9 for male) and 5xFAD;B2m–/– (percentage, n = 19 for female and 16 for male; gMFI, n = 19 for female and 13 for male) mice (j), or 5xFAD;Cxcr6+/+ (n = 10 for female and 16 for male) and 5xFAD;Cxcr6–/– (n = 14 for female and 24 for male) mice (k). l, m Frequencies of M0 and DAM subclusters from scRNA-seq analysis of microglia from indicated mice. n, Functional enrichment analysis of upregulated genes in M0 and DAM from 5xFAD;Cxcr6–/– versus 5xFAD;Cxcr6+/+ mice. Data were analyzed by two-tailed normalized weighted Kolmogorov–Smirnov test (NES for a), two-tailed Benjamini–Hochberg adjusted P value (FDR for a), two-tailed unpaired Student’s t-test (b, c, f, g, j, k), or two-tailed Fisher’s exact test (n). Data are shown as mean ± s.e.m. (c, j, k) or medians with quartiles (f, g); NS, not significant. Data were pooled from at least three (c, j, k) independent experiments or are representative of three (d, e) or two (f–h) independent experiments.
