Genome-scale metabolic modeling uncovers cell-type specific signatures associated with APOE variants

Metabolic dysregulation is a key feature of Alzheimer's disease (AD) pathogenesis, with the APOE ε4 variant (APOE4) representing the strongest genetic risk factor. In this study, we utilized a metabolite-centric approach to investigate how APOE4 reshapes cellular metabolism across brain cell types. Transcriptomic data from isogenic iPSC-derived neurons, astrocytes, and microglia were integrated into a human genome-scale metabolic model to identify genotype-specific alterations. These findings were validated using metabolomics data from the same cell types. In addition to cholesterol and fatty acid dysregulation, we identified alterations in bile acid biosynthesis, folate metabolism, and thyroid hormone metabolism. Similar metabolic signatures were also detected in human postmortem transcriptomic data. Integrating transcriptomic and metabolomic data enhances the understanding of biological mechanisms underlying APOE4-associated metabolic dysregulation in AD.