Fig. 3 ∣. Vascular enriched scRNA-Seq reveals reduced astrocytic endfeet and increased immune responses associated with liver-specific expression of apoE4.

Brain cortical tissues from iE3/Cre and iE4/Cre mice (n=4/genotype) at 12-13 months of age were subjected to vascular and glial cell-enriched single cell RNA-Sequencing (scRNA-Seq). a, Diagram showing an overview of the scRNA-seq experiment. b, The t-SNE plot showing the clusters of single cell events captured in scRNA-seq. c, Volcano plot depicting up- and down-regulated genes in astrocytic cell populations (AC1, AC2, AC3) in iE4/Cre⁺ mice compared to iE4/Cre⁻ control mice. Genes significant at the P value ≤ 0.05 and fold change ≥ 1.2 are denoted red in color. d, Heatmap revealing the scaled expression of differentially expressed genes in astrocytes from iE3/Cre and iE4/Cre mice. e, Brain sections from iE4/Cre⁻ or iE4/Cre⁺ mice (Cre⁻, n=11; Cre⁺, n=11) at 12-13 months of age were immunostained with anti-AQP4 (green) and anti-GFAP (red) antibodies. The AQP4 immunoreactivity with or without normalization to GFAP signal was quantified. Scale bar, 100 μm. Data represent mean ± s.e.m. AQP4: *, P = 0.036; AQP4/GFAP: *, P = 0.038, two-tailed Student's t-test. f, g, Violin plots showing the mean and variance differences between iE4/Cre⁻ and iE4/Cre⁺ astrocytes for genes regulating astrocyte endfeet (Aqp4 and Mlc1), innate immune response (H2-K1, Cxcl14 and Psmc6), and hypoxia/stress responses (Hsbp1).