SPNS1 is required for the transport of lysosphingolipids and lysoglycerophospholipids from lysosomes

Accumulation of sphingolipids, especially sphingosines, in the lysosomes is attributed to the pathogenesis of several lysosomal storage diseases. In search for a lysosomal protein that mediates the release of sphingosines, we identified SPNS1 which shares the highest homology to SPNS2, a sphingosine-1-phosphate (S1P) transporter. We generated knockout cells and mice for Spns1 and employed lipidomics and metabolomics to identify SPNS1 ligands. We found that knockouts of Spns1 resulted in the accumulation of sphingolipids, including sphingosines in embryonic brains and cell lines. These results suggest that deficiency of SPNS1 affects the clearance of sphingolipids in lysosomes. Biochemical assays demonstrated that sphingosines released from lysosomes required SPNS1. Furthermore, by performing a comprehensive analysis of metabolites from livers of postnatal Spns1 knockout mice (gSpns1-cKO), we detected a striking accumulation of lysoglycerophospholipids including LPC, LPE, LPG, and lysoplasmalogens. Interestingly, the release of these lysoglycerophospholipids also required SPNS1. Global knockout of Spns1 (gSpns1-KO) resulted in embryonic lethality between E12.5-E13.5 with developmental defects. Postnatal deletion of Spns1 in mice caused lipid accumulation in the lysosomes and pathological conditions reminiscent of lysosomal storage diseases. These results reveal a critical molecular role of SPNS1 as a transporter for lysosphingolipids and lysoglyerophospholipids from the lysosomes and link its physiological functions with lysosomal storage diseases. Significance Phospholipids, including glycerophospholipids and sphingolipids, are delivered to the lysosomes for recycling. The hydrolysis of these lipids by lysosomal enzymes generates the corresponding lysoglycerophospholipids, such as lysophosphatidylcholine and lysosphingolipids, such as sphingosine, which are believed to be exported out of the lysosomes for recycling in the cytoplasm. However, it is unknown how these lysophospholipids are released from the lysosomes. The current study utilized genetic knockout models in combination with mass spectrometry analysis of complex phospholipids and sphingolipids to characterize the roles of an orphan lysosomal transporter, namely SPNS1. These findings show that deficiency of SPNS1 results in the accumulation of lysophospholipids in cells and animal tissues and that the transporter is required to transport both lysoglycerophospholipids and lysosphingolipids out of the lysosomes. SPNS1 is critical for early development in mice. Ablation of SPNS1 at postnatal life causes pathological conditions reminiscent of lysosomal storage diseases in mice. These findings reveal the molecular functions of SPNS1 as a lysophospholipid transporter and provide a foundation for studying the transport of these lysolipids in lysosomal storage diseases.