Extended Data Figure 6. DAAs express signatures of reactive astrocytes and are found across brain regions.
(a-b) Signatures of inflammatory reactive astrocytes found in AD. Ridge plots showing the distribution of expression scores across each astrocyte cluster, for previously defined signature genes of: pan-reactive, A1, and A2 (from Liddelow et al.17, left), or of: pan-reactive, inflammation (LPS-induced), and ischemia (MCAO-induced) (from Zamanian et al.18 right). Expression score per cell is the geometric mean normalized expression level (TPMs) across all signature genes, corrected by subtraction of the geometric mean expression of a random set of genes of similar expression levels. (b) Violin plots showing the distribution of expression scores across WT (3,831 cells, n=4 animals) and AD (3,514 cells, n=4 animals), for signature genes for: A1 and A2 astrocytes (as defined in Liddelow et al.17). Scores computed as in (a). (c) Expression of genes from reactive, A1, and A2 signatures, showing diversity of gene patterns across astrocyte clusters. 2-D umap3 embedding of 7,345 single nuclei RNA profiles of astrocytes in the hippocampus of WT and 5xFAD mice (as in Extended Data Fig. 3a), colored by the gene expression level. Area of the graph with highest expression is marked in dotted black lines. Gene name on top of each graph. The signature the gene is associate with (pan reactive, A1 or A2) on the right side of each panel. (d) Astrocytes expressing DAA markers are present in AD brains, enriched in the subiculum and in proximity to Aβ plaques. Representative immunofluorescence images (staining repeated over n=4 AD and WT mice, with 4 brain slices per animal) in sagittal sections of 7–8-month old 5XFAD mice (with Figure 2f-h). From top to Bottom: Subiculum, stained for GFAP (green), VIM (red), and serpinA3N (gray), (as in Fig. 2f). Dentate gyrus (in Figure 2g, left) and subiculum (in Figure 2g, right), stained for GFAP (green), VIM (red), and Aβ (gray). Subiculum, stained for GFAP (green), serpinA3N (red), and Aβ (gray) (as in Figure 2h). Cell nuclei are shown in blue (Hoechst). Scale bar, 50μm.