Loss of spatacsin impairs cholesterol trafficking and calcium homeostasis

Mutations in SPG11, leading to loss of spatacsin function, impair the formation of membrane tubules in lysosomes and cause the accumulation of lipids in lysosome compartment. However, the full nature of lipids accumulating in lysosomes and the physiological consequences of such accumulation are not known. Here we show that loss of spatacsin, but also downregulation of clathrin, inhibited the formation of tubules on late endosomes/lysosomes and prevented the clearance of cholesterol from this subcellular compartment. Using spatacsin-deficient cells, we evaluated the consequences of impaired cholesterol clearance from late endosomes/lysosomes. The accumulation of cholesterol in late endosomes/lysosomes led to lower cholesterol levels in the plasma membrane, enhancing the entry of extracellular calcium by store-operated calcium entry and increasing resting cytosolic calcium levels. Higher cytosolic calcium levels promoted the nuclear translocation of the master regulator of lysosomes TFEB. Downregulation of TFEB or decrease in resting calcium levels in absence of spatacsin partially corrected the formation of tubules and the accumulation of cholesterol in lysosomes, suggesting that spatacsin could be indirectly implicated in the formation of tubules. Our work reveals a homeostatic balance between cholesterol trafficking and cytosolic calcium levels and shows that loss of spatacsin impairs this homeostatic equilibrium.