Extended Data Fig. 2: Peripheral and cerebral metabolic profiling of APOE4s2 and ApoE-TR mice and ApoE colocalization with glia.
a, Allelic discrimination plot of mRNA analysis showing efficient and sustained expression of APOE2 in APOE4s2G mice at 72 h, 3 months, 6 months, and 12 months post switch compared to E2-TR, E4-TR, and APOE4s2 controls (nE2-TR = 6, nE4-TR = 6, nAPOE4s2 = 6, nAPOE4s2G = 6 for all timepoints).). b, Percent change in bodyweight recorded between mice on western diet (APOE4s2G: n = 12 total, n = 6 female, n = 6 male; APOE4s2: n = 13 total, n = 6 females, n = 7 males; E2-TR: n = 18 total, n = 10 females, n = 8 males; E4-TR: n = 12 total, n = 9 females, n = 3 males; no significance; 2way ANOVA with multiple comparisons). c, ApoE quantified in SEC fractions corresponding to VLDL, IDL/LDL and HDL lipoprotein classes. d,f,h, Triglycerides (d), total cholesterol (f), and phospholipids (h) quantified in plasma from E2-TR, E4-TR, APOE4s2, and APOE4s2G mice on normal chow (nE2-TR = 3, nE4-TR = 3, nAPOE4s2 = 5, nAPOE4s2G = 5; *p < 0.05, **p < 0.01, ****p < 0.0001; 2way ANOVA with multiple comparisons). e,g,i, Triglycerides (e), total cholesterol (g), and phospholipids (i) quantified in FPLC eluants corresponding to VLDL, LDL and HDL (nE2-TR = 3 pooled, nE4-TR = 3 pooled, nAPOE4s2 = 4 pooled, nAPOE4s2G = 4 pooled). j, Representative images of ApoE (red), NeuN (green), and DAPI (blue) staining in APOE4s2G and APOE4s2 controls. Scale is 100um. k, Representative images of ApoE (red) and NeuN (green) with DAPI nuclear stain (blue) in E4-TR and E2-TR brains. Scale is 100um. l, Representative images of ApoE (red), IBA1 (green), and DAPI (blue) in E4-TR and E2-TR mice. Scale is 100um. m, Representative images of ApoE (red), GFAP (green), and DAPI (blue) in E4-TR and E2-TR brains. Scale is 100um. n, Quantification of ApoE with astrocytes, microglia, and neurons in the hippocampus. *p < 0.05, ***p < 0.001, 2way ANOVA with multiple comparisons. o, Heatmap depicting top 10 most significantly changed lipids between E2-TR and E4-TR controls. p, Volcano plot showing differentially expressed lipids betweenE4-TR vs. E2-TR mice (nE2-TR = 8, nE4-TR = 8; all females). (FDR adjusted p < 0.05 (log10(P) > 1.3)). For detailed statistical information, see supplementary table 3. Data represent mean ± s.e.m. of biological replicates. Individual data points plotted. Box plots show center line, median; box limits, upper and lower quartiles; whiskers, minimum and maximum.
