Pathogenic variants of sphingomyelin synthase SMS2 disrupt lipid landscapes in the secretory pathway

Sphingomyelin is a dominant sphingolipid in mammalian cells. Its production in the trans-Golgi traps cholesterol synthesized in the ER to promote formation of a sphingomyelin/sterol gradient along the secretory pathway. This gradient marks a fundamental transition in physical membrane properties that help specify organelle identify and function. We previously identified mutations in sphingomyelin synthase SMS2 that cause osteoporosis and skeletal dysplasia. Here, we show that SMS2 variants linked to the most severe bone phenotypes retain full enzymatic activity but fail to leave the ER owing to a defective autonomous ER export signal. Cells harboring pathogenic SMS2 variants accumulate sphingomyelin in the ER and display a disrupted transbilayer sphingomyelin asymmetry. These aberrant sphingomyelin distributions also occur in patient-derived fibroblasts and are accompanied by imbalances in cholesterol organization, glycerophospholipid profiles, and lipid order in the secretory pathway. We postulate that pathogenic SMS2 variants undermine the capacity of osteogenic cells to uphold nonrandom lipid distributions that are critical for their bone forming activity.Peer reviewe

Impact of pathogenic SMS2 variants on lipid landscapes and membrane properties along the secretory pathway

Sphingomyelin (SM) is a major component of mammalian cell membranes. Its bulk production in the trans-Golgi provides a thermodynamic trap for cholesterol synthesized in the ER to promote the formation of a SM/sterol concentration gradient along the secretory pathway. This gradient marks a fundamental transition in physical membrane properties that helps specify organelle identity and function. A previous study identified mutations in SM synthase SMS2 as the underlying cause of a hereditary form of osteoporosis and skeletal dysplasia. This work shows that two missense SMS2 variants linked to the most severe bone phenotype, p.I62S and p.M64R, retain full enzymatic activity but are unable to leave the ER owing to a defective autonomous ER export signal. Consequently, bulk production of SM is mistargeted to the ER, the site for de novo synthesis of the SM precursor ceramide. Combining organellar lipidomics with the application of lipid reporters, I find that cells harboring these pathogenic SMS2 variants accumulate plasma membrane-like SM levels in the ER and display a disrupted SM asymmetry at the plasma membrane, presumably due to a constitutive SM scrambling in the ER. These aberrant SM distributions also occur in patient-derived fibroblasts and are accompanied by significant imbalances in cholesterol organization and lipid order along the secretory pathway. Moreover, I find that a more common nonsense SMS2 variant associated with a milder bone phenotype, p.R50X, yields a truncated but catalytically active enzyme that is mistargeted to an early Golgi compartment. Collectively, these data indicate that pathogenic SMS2 variants undermine the capacity of cells to uphold nonrandom lipid distributions in the secretory pathway that may be critical for the bone forming activity of osteogenic cells

Ca2+-activated sphingomyelin scrambling and turnover mediate ESCRT-independent lysosomal repair

Lysosomes are vital organelles vulnerable to injuries from diverse materials. Failure to repair or sequester damaged lysosomes poses a threat to cell viability. Here we report that cells exploit a sphingomyelin-based lysosomal repair pathway that operates independently of ESCRT to reverse potentially lethal membrane damage. Various conditions perturbing organelle integrity trigger a rapid calcium-activated scrambling and cytosolic exposure of sphingomyelin. Subsequent metabolic conversion of sphingomyelin by neutral sphingomyelinases on the cytosolic surface of injured lysosomes promotes their repair, also when ESCRT function is compromised. Conversely, blocking turnover of cytosolic sphingomyelin renders cells more sensitive to lysosome-damaging drugs. Our data indicate that calcium-activated scramblases, sphingomyelin, and neutral sphingomyelinases are core components of a previously unrecognized membrane restoration pathway by which cells preserve the functional integrity of lysosomes