VPS41recessive mutation causes ataxia and dystonia with retinal dystrophy and mental retardation by inhibiting HOPS function and mTORC1 signaling

Abstract

The vacuolar protein sorting protein 41 (VPS41) is a neuroprotective protein in models of Parkinson's disease (PD). As part of the HOPS (Homotypic fusion and Protein Sorting) complex, VPS41 regulates fusion of lysosomes with late endosomes and autophagosomes. Independent of HOPS, VPS41 regulates transport of newly synthesized lysosomal membrane proteins and secretory proteins. Here we report two brothers with compound heterozygous mutations in VPS41 (VPS41 R662* and VPS41 S285P ), born to healthy and non-consanguineous parents. Both patients displayed transient retinal dystrophy, ataxia and dystonia, with brain MRI findings of cerebellar atrophy and a thin saber-shape corpus callosum. Patient-derived fibroblasts contained enzymatically active lysosomes that were poorly reached by endocytic cargo and failed to attract the mTORC1 complex. Consequently, transcription factor TFE3, a driver of autophagy and lysosomal genes, showed continuous nuclear localization which resulted in elevated LC3-II levels and an impaired response to nutrient starvation. CRISPR/CAS VPS41 HeLa knockout cells showed a similar phenotype that could be rescued by wildtype VPS41 but not by VPS41 S285P or VPS41 R662* . mTORC1 inhibition was also seen after knockout of HOPS subunits VPS11 or VPS18. Regulated neuropeptide secretion in PC12 VPS41 knockout cells was rescued by VPS41 S285P expression, indicating that this HOPS-independent function was preserved. Co-expression of the VPS41 S285P and VPS41 R662* variants in a C. elegans model of PD abolished the protective effect of VPS41 against α-synuclein-induced neurodegeneration. We conclude that both disease-associated VPS41 variants specifically abrogate HOPS function, which leads to a delay in endocytic cargo delivery to lysosomes, mTORC1 inhibition and irresponsiveness to autophagic clues. Our studies signify a link between HOPS function and mTORC1 signaling and imply that HOPS function is required for the neuroprotective effect of VPS41 in PD.

Loss‐of‐Function Variants in HOPS Complex Genes VPS16 and VPS41 Cause Early Onset Dystonia Associated with Lysosomal Abnormalities

“…Corroborating our findings, we note that a paper not yet published but recently deposited with bioRxiv describes an additional family where 2 siblings with homozygous missense variants in VPS41 were affected by dystonia and ataxia, with similar MRI findings to our proband, and lysosomal abnormalities in patient-derived fibroblasts. 16 Thus, our study further supports the emerging role of biallelic LOF VPS41 mutations in early-onset movement disorders. The microscopic vacuolar changes we observed in both VPS16 and VPS41-patient-derived cells are consistent with lysosomal dysfunction.…”

Pancreatic β-Cell–Specific Deletion of VPS41 Causes Diabetes Due to Defects in Insulin Secretion

“…In contrast, HA-VPS41 S284P –expressing cells displayed a defect in EGF degradation similar to VPS41 KO cells, indicating a defect in HOPS ( Fig. 2 B ) as observed in other cell types ( 20 ). Strikingly, we observed that this mutant rescued insulin secretion and insulin content ( Fig.…”

“…We also find that the S285P human mutation, which is unable to rescue HOPS function ( 20 ), restores insulin secretion completely, indicating that it is actually possible to isolate HOPS-dependent and -independent functions of VPS41. Furthermore, this observation also helps explain why patients bearing this mutation have no observable endocrine-associated defects.…”

“…Human patients carrying a point mutation within VPS41 (VPS41 S285P ) exhibit neurological defects without any endocrine dysregulation ( 20 ). As this point-mutant results in impaired HOPS function ( 20 ), we reasoned that this could be a helpful tool to distinguish between HOPS-dependent and -independent effects of VPS41. Thus, we stably expressed an HA-tagged rat VPS41 S284P (S285P equivalent in rat) in VPS41 KO INS-1 cells ( Fig.…”

“…Lack of VPS41 decreases SG number and affects their ability to undergo regulated exocytosis, which is concomitant with a defect in sorting of SG transmembrane proteins. We show that a patient mutation of VPS41, which is deficient for HOPS function ( 20 ), rescues insulin-regulated secretion in VPS41 knockout (KO) INS-1 cells, indicating VPS41 function in insulin-regulated secretion is independent of HOPS. Finally, we report that mice with a targeted deletion of VPS41 in β-cells develop diabetes due to a defect in insulin SG biogenesis and secretion.…”