Fig. 4

ApoeCh enhances microglial response to plaques confirmed by spatial transcriptomics. a Workflow for targeted 1000-plex single-cell spatial transcriptomics. FOVs were selected in hippocampus and cortex of each section, then imaged with DNA, rRNA, Histone, and GFAP markers for cell segmentation. Transcript counts for each gene were acquired per cell. b UMAP of 425,663 cells across 12 hemibrains (n = 3/genotype). Clustering at 1.0 resolution yielded 33 clusters, which were annotated manually based on gene expression and anatomical location in space. c 33 clusters plotted in XY space. d Proportion of the number of cells in each major cell type, grouped by genotype. Percentages normalized for the total number of cells in each genotype. e DAM cluster (black dots) plotted in XY space for each genotype. f Feature plot of Cst7 expression in UMAP space. g (top) Cst7-expressing cells (i.e., DAMs) surrounding an amyloid-beta plaque. (bottom) DAPI (grey) highlights the same plaque from top panel. Histone marker (green) highlights nucleosomes in cells surrounding the plaque. GFAP + (purple) cell processes surround the plaque. h Volcano plots showing DEGs between 5xFAD;ApoeCh and 5xFAD among major cell types. i Differential upregulation (DU) and differential downregulation (DD) scores for 5xFAD;ApoeCh vs. 5xFAD in each cluster plotted in space in a 5xFAD;ApoeCh brain. j Pseudo-bulk expression of top DEGs between 5xFAD;ApoeCh and 5xFAD across genotypes. k-m Microglial subclustering analysis. k UMAP of 33,808 subsetted microglia. (top) UMAP annotated with old labels from b. (bottom) Cells were re-clustered at 0.2 resolution to yield 7 new subclusters. l Proportion of the number of cells in each microglial subcluster, grouped by genotype. m Microglial subclusters in XY space in a 5xFAD;ApoeCh brain. (top) Amyloid-beta dense core plaques, shown by the presence of DAPI + aggregates (grey), circled in white. (bottom) Microglial subclusters plotted in space. Plaques from top panel circled in black