Mutations in DNAJC5 (encoding the J domain-containing HSP70 co-chaperone CSP) are associated with adult neuronal ceroid lipofuscinosis (ANCL), a dominant-inherited neurodegenerative disease featuring lysosome-derived autofluorescent storage material (AFSM) termed lipofuscin. Functionally, CSP has been implicated in chaperoning synaptic proteins and in misfolding-associated protein secretion (MAPS), but how CSP dysfunction causes lipofuscinosis and neurodegeneration is unclear. Here we report two distinct protein quality control functions of CSP at endolysosomes and perinuclear vesicles, respectively. We show that the endolysosome-associated CSP promotes microautophagy of misfolded clients, but is dispensable for MAPS. By contrast, the perinuclear-localized CSP, regulated by a previously unknown CSP interactor named CD98hc, is critical for MAPS but unneeded for microautophagy. Importantly, these processes are coupled by CSP in a J-domain regulated manner. Uncoupling these two processes, as seen in cells lacking CD98hc or expressing ANCL-associated CSP mutants, generates CSP-containing AFSMs resembling NCL patient-derived lipofuscin, and also induces neurodegeneration in a Drosophila ANCL model. These findings suggest that blocking MAPS while allowing CSP-mediated microautophagy disrupts lysosome homeostasis, causing CSP-associated lipofuscinosis and neurodegeneration.
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