Genetically targeted proteomics identify compositional and phosphoproteome trajectories of corticostriatal projections across postnatal development

Axonal development in mammals begins in the embryonic stage and continues postnatally. During early postnatal period, proteomic landscape of axons changes rapidly, coordinated by transcription, protein turnover, and post-translational modifications. Studying axonal proteome across development in complex tissue remains challenging. Axonal compartments from the brain cannot be isolated without substantial losses. Axons from different circuits are intermingled; isolation techniques that do not resolve cell types likely mask neuronal class specific features. Here, we create a Cre-dependent APEX2 reporter mouse line and demonstrate its utility to map cell-type specific proteome of corticostriatal projections across postnatal development. We define temporal patterns of axonal proteome and phosphoproteome levels, and their relevance to neurodegenerative and psychiatric diseases. This analysis workflow also identifies proline-directed kinases and phosphosites as major regulators for corticostriatal development. Altogether, APEX2 transgenic reporter-based proximity labeling approach offers a flexible strategy for mapping subcellular proteome, with cell type specificity, across neurodevelopment.