Extended Data Fig. 6: Clonal expansion of Pdcd1-expressing brain CD8⁺ T cells in 5xFAD mice.

a, Frequencies of clonally expanded (clonotype size > 1) versus non-expanded (clonotype size = 1) αβ⁺ T cells in brain and meninges from indicated mice. b, Subclustered brain and meninges αβ⁺ T cells colored by clonotype sizes and genotypes. c, Identification of CD4⁺ T cell, CD8⁺ T cell and NKT cell clusters among αβ⁺ T cells combined from both tissues and genotypes. d, TCR clones detected among CD8⁺ T cells, CD4⁺ T cells and NKT cells, grouped by their clonotype sizes. e, Top 5 GLIPH patterns with TRBV sequence and number of cells in clonally expanded CD8⁺ T cells in the brains of 5xFAD mice from scTCR-seq analysis. f, TCRMatch analysis for predicted antigen epitopes that are recognized by clonally expanded brain CD8⁺ T cells from 5xFAD mice. g, Bar plot showing Pearson correlation of gene expression with clonotype sizes, with Pdcd1 identified as the top-ranked gene. h, Heatmap depicting relative expression values of the top 10 differentially expressed genes in each brain CD8⁺ T cell subcluster shown in Fig. 4c, with selected genes labeled. i, Frequencies of clonotype sizes for brain CD8⁺ T cells from Fig. 4c cluster 2 (representing the highest expression of Pdcd1) in Non-Tg versus 5xFAD mice. j, Fold change (FC)/FC plot analysis of transcriptomes from clonally expanded versus non-expanded CD8⁺ T cells compared with Pdcd1⁺ versus Pdcd1^– CD8⁺ T cells. Red and blue dots indicate shared upregulated and downregulated genes, respectively. Data were analyzed by Pearson correlation coefficient (for r in j) and two-tailed F-test (for P value in j).