Distinct lysosomal dysfunction patterns of GRN deficiency in the CNS implicate progranulin in cell type–specific protein sorting

Loss-of-function mutations in Progranulin ( GRN ) cause neuronal ceroid lipofuscinosis (NCL) and hereditary frontotemporal dementia, presumably through lysosomal dysfunction. Lysosomes are key metabolic organelles whose functions vary widely depending on their cell type of origin. These functional variations are driven by the lysosomal proteome, yet whether progranulin deficiency alters the lysosomal composition of the mammalian brain in a cell type-specific manner has not been tested. To answer this unknown, we used cell type-specific LysoIP to perform tandem-mass-tag mass-spectrometry and detected distinct aberrant proteomic signatures in progranulin-deficient astrocytes, neurons, and microglia, indicating cell type-specific dysregulation of key lysosomal proteins with crucial functions in sphingolipid metabolism and lysosome organization. These proteins markedly differed from progranulin-deficient RNAseq data sets, suggesting progranulin regulates lysosomal composition through post-translational mechanisms including the sorting of nascent proteins to the lysosome. Validation experiments confirmed that Mfsd8 and Ppt1, proteins whose mutations on their own cause NCL, were essentially absent from progranulin-deficient neuronal and microglial lysosomes, respectively. Our findings demonstrate the protein composition of lysosomes are uniquely sensitive to progranulin deficiency in a cell type-specific manner and that progranulin may function as an essential hub for endolysosomal homeostasis.