Extended Data Fig. 5: APOE expression is selectively elevated in APOE4 pericytes.
a, Quantification and representative image of APOE protein expression in brain vascular pericytes (NG2-positive cells) and non-pericytes (NG2-negative) cells in APOE4 knock-in mouse. Two-sided Student t test, p < 0.0001 Scale bar = 50 um. Center values and error bars are means from 150 APOE-positive cells for each genotype. b, anti-APOE antibody (Abcam, ab52607) is specific for human APOE protein and does not react with mouse Apoe protein or other proteins present in wild-type mouse hippocampus as reported by the manufacturer. The staining was repeated using 3 different mice c and d, Expression of APOE in isogenic iMural cells (c) and astrocyte (d) measured by RNA sequencing each condition represents three biological replicates pericyte, q = 0.0003 astrocyte, q = 0.0006 statistics performed by Dseq2, Center values and error bars are mean and SD from RNA prepared from 3 independent wells for each genotype. e Violin plots depicting APOE expression in pericytes/endothelial cells isolated from post-mortem prefrontal cortex of APOE4-carriers (n = 7) compared to non-carriers (n = 18). Differential expression was measured using a two-tailed Wilcoxon rank sum test, considering cells with detected expression of APOE (p = 0.0026). f, Images and quantification of APOE protein expression in post-mortem human prefrontal cortex from APOE4 carriers and non-carriers. Unpaired two-tailed t test (p = 0.023). Center values and error bars are mean and SD from staining of 4 prefrontal cortex sections from 4 different individuals. g, Differential plot of representative maker genes showing that pericytes and endothelial cells isolated from human hippocampus segregated into distinct cellular clusters (n = 82 individuals). h, Violin plots depicting APOE expression in endothelial cells isolated from post-mortem hippocampus APOE4-carriers (n = 16) compared to non-carriers (n = 46). Differential expression was measured using a two-tailed Wilcoxon rank sum test, considering cells with detected expression of APOE. Center lines are mean and dashed line are SD. i, Images and quantification of APOE protein expression α-SMA positive SMC in post-mortem human hippocampus from APOE4 carriers and non-carriers. Unpaired two-tailed t test (p = 0.5814). Center values are mean and SD of hippocampal sections from 6 individuals for each genotype. j, Western blot of APOE and GAPDH protein in a isogenic iPSC line in which the APOE gene was truncated via CRISPR-editing to yield a line that does not express of APOE protein and therefore is termed APOEKO line. The experiment was repeated at least 3 time with similar results.
