Targeting C99-Mediated Metabolic Disruptions with Ketone Therapy in Alzheimer’s Disease

The role of ketone bodies in Alzheimer’s disease (AD) pathogenesis remains unclear, particularly regarding their effects on amyloid-driven toxicity. To address this, we developed a Drosophila model expressing human APP, BACE1, Aβ, and C99, and applied cryo-transmission electron microscopy, deep-learning-based phenotypic analysis, automated mitochondrial segmentation, and mass spectrometry proteomics to investigate disease mechanisms at cellular and molecular levels. We found that C99, rather than Aβ, acts as a primary driver of neurotoxicity, inducing lysosomal dysfunction, impaired autophagy, oxidative stress, and mitochondrial abnormalities. Treatment with β-hydroxybutyrate (BHB) corrected lysosomal acidification, restored autophagic flux, and ameliorated mitochondrial damage. Saracatinib, a kinase inhibitor, exhibited similar protective effects, suggesting convergence on shared regulatory pathways. Protein–protein interaction network analysis implicated activation of protein phosphatase methylesterase-1 (PPME1) as a contributor to autophagic impairment. Similarity network modeling suggested that BHB-mediated neuroprotection involves mTOR inhibition, linking metabolic regulation to autophagic rescue mechanisms. These findings reposition C99 as a critical pathogenic factor distinct from Aβ in AD and highlight lysosomal and autophagic dysfunction as central to disease progression. Our results suggest that modulation of ketone metabolism offers a promising therapeutic strategy for neurodegenerative diseases.