Loss of CLN7 results in depletion of soluble lysosomal proteins and impaired mTOR reactivation

Abstract

Defects in the MFSD8 gene encoding the lysosomal membrane protein CLN7 lead to CLN7 disease, a neurodegenerative lysosomal storage disorder belonging to the group of neuronal ceroid lipofuscinoses. Here, we have performed a SILAC-based quantitative analysis of the lysosomal proteome using Cln7-deficient mouse embryonic fibroblasts (MEFs) from a Cln7 knockout (ko) mouse model. From 3335 different proteins identified, we detected 56 soluble lysosomal proteins and 29 highly abundant lysosomal membrane proteins. Quantification revealed that the amounts of 12 different soluble lysosomal proteins were significantly reduced in Cln7 ko MEFs compared with wild-type controls. One of the most significantly depleted lysosomal proteins was Cln5 protein that underlies another distinct neuronal ceroid lipofuscinosis disorder. Expression analyses showed that the mRNA expression, biosynthesis, intracellular sorting and proteolytic processing of Cln5 were not affected, whereas the depletion of mature Cln5 protein was due to increased proteolytic degradation by cysteine proteases in Cln7 ko lysosomes. Considering the similar phenotypes of CLN5 and CLN7 patients, our data suggest that depletion of CLN5 may play an important part in the pathogenesis of CLN7 disease. In addition, we found a defect in the ability of Cln7 ko MEFs to adapt to starvation conditions as shown by impaired mammalian target of rapamycin complex 1 reactivation, reduced autolysosome tubulation and increased perinuclear accumulation of autolysosomes compared with controls. In summary, depletion of multiple soluble lysosomal proteins suggest a critical role of CLN7 for lysosomal function, which may contribute to the pathogenesis and progression of CLN7 disease.

Clinical implementation of gene panel testing for lysosomal storage diseases

“…The neuronal ceroid lipofuscinoses are a group of diseases caused by mutations in 13 genes ( CLN1‐8 , CLN10‐14 ) and display an overlapping disease spectrum. For instance, recent proteomics analysis has revealed that one of the proteins which is markedly downregulated in neuronal ceroid lipofuscinosis type 7, is, besides MFSD8 itself, CLN5 (Danyukova et al, ). Moreover, while for instance the CLN1 , CLN2, and CLN10 genes encode for proteins with an enzymatic activity, this has currently not been demonstrated for CLN3 and MFSD8 , which give rise to endosomal/lysosomal transmembrane proteins, consequently making the development of biochemical assays for these latter two challenging (Mohammed, O'Hare, Warley, Tear, & Tuxworth, ).…”

NPC1-mTORC1 signaling Couples Cholesterol Sensing to Organelle Homeostasis and is a Targetable Pathway in Niemann-Pick type C

“…The observation that hydrolases mutated in other lysosomal storage disorders, such as acid lipase, betaglucosidase and galactosidase are depleted from NPC lysosomes suggests the intriguing possibility that NPC compounds the pathogenic consequences of cholesterol storage with those of other diseases such as Wolman, Krabbe and Mucopolysaccharidosis III (Ballabio and Gieselmann, 2009), and could provide a mechanistic basis for the accumulation of neurofibrillary tangles, a pathogenic trait of Alzheimer Disease, in NPC brains (Walkley and Suzuki, 2004). More generally, hydrolase loss may be a common trait of several LSDs (Danyukova et al, 2018;Platt et al, 2018), a possibility that can be tested through the use of lysosomal profiling in cellular models of those diseases.…”

Neuronal Ceroid Lipofuscinoses: Connecting Calcium Signalling through Calmodulin

“…These 13 genes encode enzymes (CLN1, CLN2, CLN5, CLN10, and CLN13), transmembrane proteins (CLN3, CLN7, and CLN12), membrane proteins that localize to the endoplasmic reticulum (CLN6 and CLN8), cytoplasmic proteins (CLN11 and CLN14), and a protein found on synaptic vesicles (CLN4) [ 2 ]. Along with distinct localizations, the NCL proteins have been linked to fundamental cellular processes, including sphingolipid metabolism, protein degradation, and lysosomal pH homeostasis, among others [ 5 , 6 , 7 , 8 , 9 , 10 ]. Since mutations in NCL proteins cause nearly identical clinical phenotypes, they are thought to participate in shared or convergent biological pathways [ 11 ].…”