Combined Transcriptomic and Proteomic Profiling Uncovers Developmental Dynamics of Autophagy in the Cortex

Background/Objectives: Autophagy is an evolutionarily conserved degradation and recycling pathway through which cells deliver cytoplasmic components, including toxic or damaged proteins and organelles, to lysosomes for clearance. In neurons, which are largely post-mitotic, degradative pathways are essential to prevent the accumulation of cellular waste and to maintain nutrient and energy homeostasis. Increasing evidence suggests that autophagy plays a critical role during early brain development, when neuronal circuits are established, synaptic connections are refined, and activity-dependent mechanisms shape network architecture. However, the developmental regulation of autophagy-related genes and the composition of the autophagic machinery at synapses remain poorly understood. This study aimed to characterize the maturation-dependent dynamics of autophagy–lysosomal genes and to investigate the synaptic autophagy-associated proteome during cortical development. Methods: Genome-wide transcriptomic analyses were performed in the cortical brain region across developmental stages to assess changes in the expression of autophagy–lysosomal genes. In parallel, synaptosomes were isolated and subjected to proteomic analysis to identify autophagy-related proteins associated with synaptic compartments. Results: Transcriptomic profiling revealed stage-dependent regulation of autophagy–lysosomal genes during cortical maturation. Proteomic analysis of synaptosomes identified multiple autophagy-associated proteins enriched at synaptic sites, suggesting that components of the autophagic machinery are present at synapses and may participate in synaptic remodeling and function during key phases of neuronal network formation. Conclusions: These findings provide new insights into the developmental regulation of autophagy in the brain and highlight the potential contribution of synaptic autophagy to neuronal circuit maturation. Understanding these mechanisms may help identify novel therapeutic targets for neurological disorders associated with impaired synaptic and cellular homeostasis.