Drosophila Appl loss disrupts proteins in mitochondrial oxidative and glycosylation pathways conserved in Alzheimer's disease

The physiological functions of the amyloid precursor protein (APP) remain unclear due to genetic redundancy and complex phenotypes. For decades, Drosophila amyloid precursor protein-like (Appl) research has relied on Appl d, a presumed null allele generated by irradiation. Here, we show that Appl d contains complex chromosomal rearrangements and background mutations confounding the interpretation of gene function. To address this, we created a precise CRISPR toolkit, including a clean null and a reporter allele. Deep proteomic profiling reveals that true Appl loss affects proteins associated with N-linked glycosylation, mitochondrial, and metabolic functions in a distinct signature from the background of Appl d. This conserved metabolic signature mirrors alterations in human patients and mouse Alzheimer's models and is associated with disrupted sleep and locomotion in flies. Our findings correct the genetic understanding of Appl, establishing it as a conserved regulator of metabolic balance essential for neuronal function.