Fig. 5: IMC reveals single-cell spatial proteomic changes in AD.

a, IMC was performed in postmortem human cortical tissue (n = 2 control, n = 6 late-stage AD and n = 6 DSAD) using the Hyperion Imaging System (Standard BioTools). Illustrations were created with Biorender.com. b, Representative IMC images from control, late-stage AD and DSAD samples with select targets from the panel. c, Images as in b at higher magnification and focused around amyloid plaques. d, UMAP plot showing the unbiased clustering of segmented nuclei from the IMC dataset based on their protein intensity values. Each dot represents a segmented nucleus, colored by cluster assignment. e, Stacked bar plots showing the proportion of segmented nuclei assigned to each cluster stratified by disease groups. f, Heatmap showing the relative protein intensity of each protein in each IMC cluster. Dendrograms depict hierarchical clustering results based on these relative intensities. g–l, Violin plots showing the distribution of protein intensities for selected proteins in IMC clusters Neuron (Aβ+, MAP2+) (g), Neuron (NeuN+, MAP2+) (h), ASC (GFAP+) (i), ASC (GFAP+, Tau+) (j), MG (CD44+) (k), MG (CD68+) (l), stratified by disease groups. For box and whisker plots, box boundaries and lines correspond to the IQR and median, respectively. Whiskers extend to the lowest or highest data points that are no further than 1.5 times the IQR from the box boundaries. Two-sided Wilcoxon rank-sum test results are overlaid on each plot. NS, P > 0.05; **P ≤ 0.01; ***P ≤ 0.001, ****P ≤ 0.0001. IQR, interquartile range; NS, not significant; ECM, extracellular matrix.