ER-lysosome lipid transfer protein VPS13C/PARK23 prevents aberrant mtDNA-dependent STING signaling

Abstract

Mutations in VPS13C cause early onset, autosomal recessive Parkinsons Disease (PD). We have established that VPS13C encodes a lipid transfer protein localized to contact sites between the endoplasmic reticulum (ER) and late endosomes/lysosomes. In the current study, we demonstrate that depleting VPS13C in HeLa cells causes an accumulation of lysosomes with an altered lipid profile, including an accumulation of di-22:6 BMP, a biomarker of the PD-associated leucine-rich repeat kinase 2 (LRRK2) G2019S mutation. In addition, the DNA-sensing cGAS/STING pathway, which was recently implicated in PD pathogenesis, is activated in these cells. This activation results from a combination of elevated mitochondrial DNA in the cytosol and a defect in the degradation of activated STING, a lysosome-dependent process. These results suggest a link between ER-lysosome lipid transfer and innate immune activation and place VPS13C in pathways relevant to PD pathogenesis.

In situ architecture of the lipid transport protein VPS13C at ER-lysosomes membrane contacts

“…Overexpression of VPS13C^Halo and GFP-VAP (VAP-B) with or without Rab7 (possibly because Rab7 is not present at limiting concentration) is sufficient to produce a massive expansion of the normally occurring ER to endo/lysosome contacts (as represented schematically in Fig. 2A), resulting in endo/lysosomes completely surrounded by ER cisterns, as shown by fluorescence microscopy 17,21 (Fig. 2B) and electron microscopy (Fig.…”

“…The human genome comprises four VPS13 proteins, referred to as VPS13A, VPS13B, VPS13C and VPS13D, which have different localizations at membrane contact sites and whose mutations result in neurodevelopmental defects or neurodegenerative conditions [12][13][14][15] . A role of VPS13 family proteins in lipid transport, and more specifically at membrane contact sites, has now been supported by genetic, biochemical, imaging and structural studies 6,10,11,[16][17][18][19][20][21] . Fragments of VPS13 were shown to contain multiple lipids and to transfer lipids between artificial liposomes 17 .…”

“…Crystallographic studies of N-terminal region of VPS13 of Chaetomium thermophilum revealed a hydrophobic cavity 17 which cryo-EM studies of a longer rod-like fragment of the same protein subsequently suggested to continue as a hydrophobic groove along the entire length of the rod 19 . Moreover, binding sites for the ER and for other organelles have been identified in the Nterminal and C-terminal region of several VPS13 family members, respectively 17,18,[20][21][22] . Together, these results have suggested a bridge model of lipid transport ideally suited for the bulk delivery of lipids and in line with some of the proposed functions of VPS13 family members in membrane expansion 6 .…”

“…Our cryo-ET analysis of cell cryo-lamellae generated by cryo-FIB milling provides the first in situ structural evidence to support the bridge model of lipid transport and also suggests a dynamic interaction of VPS13C with the ER bilayer. VPS13C loss-of-function results in lysosomal dysfunction at the cellular level 21 and causes familial Parkinson's disease in human patients 14 . Moreover, as dysfunction of other VPS13 family also results in neurological diseases 28 , a better understanding of in situ architecture VPS13C has implications for both biology and medicine.…”

Inter-organellar Communication in Parkinson's and Alzheimer's Disease: Looking Beyond Endoplasmic Reticulum-Mitochondria Contact Sites

“…VPS13C contains motifs enabling it to bind to the ER, LE/Lys, and LD, so that it is positioned at the interface of ER-LE/Lys and ER-LDs (Kumar et al, 2018 ). Loss of VPS13C results in an increased number of lysosomes and accumulation of di-22:6-bis (monoacylglycerol) phosphate (di-22:6-BMP), a lipid enriched in endolysosomes and a biomarker for lipid storage disorders and neurodegeneration (Showalter et al, 2020 ; Hancock-Cerutti et al, 2021 ). On top, VPS13C knockout cells display a leakage of mitochondrial DNA into the cytosol and a lysosomal inability to degrade the consequently activated stimulator of interferon genes (STING), together culminating in the initiation of a cGAS/STING-induced inflammatory pathway (Motwani et al, 2019 ; Hancock-Cerutti et al, 2021 ).…”