Fig. 6

Cerebral organoids derived from ApoE3 ε3/ε3 and ApoE4 ε4/ε4 cerebral organoids show differences upon treatment with tramiprosate in metabolism, cholesterol storage and MAP kinase signaling pathway. (A) Morphology of cerebral organoids carrying ApoE3 ε3/ε3 and ApoE4 ε4/ε4 alleles. (B) Levels of tramiprosate (TRAMI) and 3-sulfopropanoic acid (SPA) in untreated (-) and treated (+) ApoE e3/e3 and e4/e4 organoids (N = 10). (C) Levels of carnitines (CAR), ether-linked lysophospholipid (LPC-O) and phospholipid species (PE-O), and cholesteryl esters (CE) in untreated (-) and treated (+) ApoE e3/e3 and e4/e4 organoids (N = 10). (D) Principal component analysis (PCA) of 64 dysregulated lipid species. (E) Levels of major mono-sialo-glycosphingolipid (GM1-3) and di-sialo-glycosphingolipid (GD1-3) species in untreated (-) and treated (+) ApoE e3/e3 and e4/e4 organoids (N = 10). (F and G) Levels of proteins involved in lipid transport (ApoE, NPC2, CLU), and neuronal protein markers (NEFM, NCAM1, MAP2) in untreated (-) and treated (+) ApoE e3/e3 and e4/e4 organoids (N = 10). (H) Western blot showing that ERK, but not AKT signaling pathway is downregulated upon treatment selectively in ApoE4 organoids. Targeted LC-MS-based proteomics and lipidomics analysis of cerebral organoids untreated (-) and treated (+) with tramiprosate (N = 10). Biological outliers have been presented as black dots (●). Statistical analysis was performed using the Kruskal-Wallis test, comparing the cerebral organoids treated with tramiprosate to the untreated, *p ≤ 0.05, **p ≤ 0.01, ***p ≤ 0.001, ****p ≤ 0.0001 (N = 10). A comprehensive list of abbreviations and nomenclature systems for lipids and proteins can be found in Supplementary Table 10.