Fig. 3: Validation of T cell phenotypes in the SN.

a Uniform manifold approximation and projection (UMAP) graphs showing substantia nigra myeloid and T cell nuclei. b Feature plots showing the normalized expression of select T cell genes in the UMAP space. c Loadings (scores) of select T cell-related genes from scHPF performed on SN T cells. d Heatmap of average cell score of PD and control nuclei in each T cell scHPF factor. Columns represent factors; rows represent conditions. Blue indicates a low score; red indicates a high enrichment score. e Dotplots showing the normalized expression of select Factor 5 genes in PD and control T cells. f Boxplots of the donor contribution to each T cell factor. Wilcoxon test, two-tailed, p-values are indicated. Control-n = 12, PD-n = 9. The line indicates the median, and the bounds represent the 1st and 3rd quartile. The whiskers extend from the edges of the box to the smallest and largest values within 1.5 times the interquartile range. g Pre-ranked gene set enrichment analysis of the CD8 + T cell resident memory (TRM) gene set in T cell Factor 5 genes ranked by the gene loadings (left), CD8 + TRM gene set in T cell genes ranked by logFC in PD vs control (middle), and T cell Factor genes in T cell genes ranked by logFC in PD vs control (right). Normalized enrichment scores (NES) and adjusted two-sided p-values are indicated. h Immunohistochemical stains for CD103 (brown) in the SN. i Multiplex immunofluorescence of a PD SN showing colocalization between CD103 (red) and CD3 (green). Nuclei (DAPI) are shown in blue. Scale bar = 25 µm. Representative of colocalization from two donors (biological replicates). j Quantification of the density of CD103-positive cells per unit area in the SN. Unpaired one-tailed t-test with n = 4 for control and n = 5 for PD donors. P-value is indicated. Data is shown as mean +/- SEM.