Fig. 3: Lipidomic analysis of human isogenic APOE3/3 and APOE4/4 iAstrocytes.

a, Schematic overview of isogenic iPS cell lines and experimental design. This image was created using BioRender.com. b–e, Volcano plot presents a typical example of log₂ fold change of altered lipid species in Kolf2.1J set 1 (b) and BIONi037 (d) ApoE4 versus ApoE3 iAstrocytes. Also shown are heat maps of most differentiating lipid species between ApoE4 and ApoE3 iAstrocytes in Kolf2.1J set 1 (c) and BIONi037 (e). f, Summary data of changes in all detected lipid classes in ApoE4 versus ApoE3 iAstrocytes (N = 9; three independent experiments from three isogenic sets). Data are shown as the median and IQR; whiskers indicate the furthest data point within 1.5× the IQR. *P < 0.05 (two-sided paired t-test or Mann–Whitney U-test with BH correction). g, Fold change in TGs with indicated number of double bonds (unsaturation) in ApoE4 versus ApoE3 iAstrocytes. All experiments presented in f are included here. Data are shown as the mean. h, Representative images and quantification of the average lipid droplet number per astrocyte based on Plin2 staining (N = 6; three independent experiments from two isogenic sets). Data are shown as the mean. **P < 0.01 (two-sided t-test). Scale bar, 25 μm. Open circles and triangles indicate the mean per experiment, while solid dots represent all independent wells.