Abstract
One hundred and fifty years ago, Johann Thudichum described sphingolipids as unusual “Sphinx-like” lipids from the brain. Today, we know that thousands of sphingolipid molecules mediate many essential functions in embryonic development and normal physiology. In addition, sphingolipid metabolism and signaling pathways are dysregulated in a wide range of pathologies, and therapeutic agents that target sphingolipids are now used to treat several human diseases. However, our understanding of sphingolipid regulation at cellular and organismal levels and their functions in developmental, physiological, and pathological settings is rudimentary. In this Review, we discuss recent advances in sphingolipid pathways in different organelles, how secreted sphingolipid mediators modulate physiology and disease, progress in sphingolipid-targeted therapeutic and diagnostic research, and the trans-cellular sphingolipid metabolic networks between microbiota and mammals. Advances in sphingolipid biology have led to a deeper understanding of mammalian physiology and may lead to progress in the management of many diseases.
Keywords: Sphingolipids, Subcellular Organelles, Lipoproteins, Microbiome, Sphingosine-1-phosphate
eTOC
Sphingolipids are a heterogenous group of lipids with important roles in membrane form and function, cell signalling and development. This Review discusses the regulation of sphingolipid metabolism at the subcellular and organismal levels, and explores the therapeutic potential of targeting sphingolipids in human diseases.
Introduction
Sphingolipids, a major class of lipids found in all eukaryotic cells, were initially isolated in the late 19th century by Johann Thudicum, who named them after the Greek mythical creature the Sphinx for their “enigmatic nature”1. Subsequent biochemical studies uncovered sphingosine (one of the sphingoid bases)2, as the fundamental building block of sphingolipids. Since then, structures of complex sphingolipids such as glycosphingolipids have been elucidated3. Concomitantly, sphingolipids accumulation in human genetic diseases, collectively known as sphingolipidoses, were noted4. In the past few decades, the structures of thousands of sphingolipid species, as well as several dozen enzymes involved in sphingolipid metabolism and their association with various diseases, have been identified (for a summary of the metabolic pathways, see Fig. 1 and below). Since then, deepening our understanding of the regulation of sphingolipid metabolic enzymes to control sphingolipid homeostasis and investigating the functions of different classes of sphingolipids has been the central focus in the field.
Fig. 1: Overview of sphingolipid structures and metabolic pathways.

Sphingolipid metabolism is separated into several pathways that branch from the central metabolite ceramide. a, The de novo synthesis pathway is initiated by the action of the serine palmitoyltransferase (SPT) complex, which uses palmitoyl-CoA and serine to form 3-ketodihydrosphingosine. 3-Ketodihydrosphingosine reductase (KDSR) reduces 3-ketodihydrosphingosine to form dihydrosphingosine. Ceramide synthases (CERSs) further convert dihydrosphingosine into dihydroceramide by N-acylation. Finally, a Δ4 double bond is introduced by the dihydroceramide sphingolipid Δ4-desaturase DES1 (DEGS1), forming ceramide, the central hub of sphingolipid metabolism. b, Ceramide can be hydrolysed by ceramidase (CDase), releasing sphingosine and free fatty acids. In the salvage pathway, sphingosine can be hexadecenal is converted to palmitoyl-CoA, and ethanolamine phosphate is utilized to form phospholipids. d, Ceramide can be converted into sphingomyelin by sphingomyelin synthases (SMSs), in which a phosphocholine (PC) head group is added to the 1-hydroxyl group of ceramide. Degradation of sphingomyelin is mediated by various classes of sphingomyelinases (SMases), generating ceramide to be utilized in other pathways. e, Ceramide can be used to synthesize glycosphingolipids by the sequential addition of sugar groups to the 1-hydroxyl group of ceramide. As an example, glucosylceramide is synthesized by UDP-glucose ceramide glucosyltransferase (UGCG). Glucosylceramide provides the core structure for more complex glycosphingolipids containing additional sugar groups mediated by a family of glycosyltransferases. Sugar moieties of glycosphingolipids are mostly removed in the lysosome by various glycosidases, releasing ceramide. f, Ceramide can be phosphorylated by ceramide kinase (CERK) to form ceramide-1-phosphate, which acts as a second messenger and regulates many biological functions. The reverse reaction is catalysed by PLPPs to generate ceramide. g, Alternatively, O-acylation of ceramide can be catalysed by diacylglycerol O-acyltransferases (DGATs), forming 1-O-acylceramides, which are incorporated into lipid droplets.
For a long time, sphingolipids were mainly considered as structural components of membranes5. Investigations since the 1980s revealed that specific sphingolipid species, such as ceramide, sphingosine, and sphingosine-1-phosphate (S1P), are involved in the regulation of many biological processes, and these species have been referred to as bioactive sphingolipids. For example, sphingolipid metabolites were found to function in the regulation of protein kinase C (PKC) and PKC-dependent turnover of sphingomyelin in 1987 (refs.6,7). Second, ceramide as a participant in tumor necrosis factor (TNF)-α-induced apoptosis was reported in 1993 (ref. 8). S1P was initially reported to be a second messenger that regulates intracellular calcium levels910,11. With the discovery of its first G protein-coupled receptor, sphingosine 1-phosphate receptor 1 (S1PR1)12,13, a variety of biological functions of S1P have been revealed, including cell survival, vascular development, and immune cell trafficking14. The FDA approval of the therapeutic Fingolimod that targets S1P receptors to treat autoimmune disease15 further underscored the therapeutic significance of the sphingolipid signaling pathway. These emerging roles in various aspects of fundamental processes and pathophysiology marked sphingolipids as a bona fide class of bioactive lipids.
In this Review, we will first discuss the regulation of sphingolipid metabolism in subcellular compartments. The second part of the Review will cover sphingolipid homeostasis at the organismal level. We will discuss the role of dietary sphingolipids, the interactions between mammalian hosts and gut microbiota through sphingolipid metabolites, and the regulation of circulatory sphingolipids with their contributions to human diseases. Lastly, we will cover recent progress in the therapeutic targeting of the S1P signaling axis.
Intracellular sphingolipid homeostasis
Sphingolipids regulate a wide range of biological processes and thus their levels are tightly controlled. Genetic ablation of the rate-limiting enzyme for sphingolipid biosynthesis, namely, serine palmitoyl transferase (SPT), causes embryonic lethality in mice16 and growth and sporulation defects in yeast17. In contrast, sphingolipid accumulation causes ER stress, mitochondrial defects, and lysosomal defects (for more details, see18-20). Identifying most of the enzymes in the sphingolipid metabolic pathway and their subcellular localization has provided us with a holistic understanding of this lipid family at the level of individual cells. Due to their hydrophobic nature, sphingolipids are associated with membranes and distributed through vesicles and membrane contact sites [G] (MCS), where many regulatory mechanisms of sphingolipid homeostasis occur. In this section, we will discuss the key features of enzymes involved in sphingolipid metabolism (Fig. 1) and highlight the regulation of sphingolipid distribution in different organelles (Fig. 2). Furthermore, we will provide examples of dysregulation of cellular sphingolipid metabolism that contributes to metabolic, cardiovascular, and neurodegenerative diseases. A more detailed description, including additional references to human diseases, is provided in Supplementary Table 1.
Fig. 2: Intracellular sphingolipid biosynthesis and distribution in organelles.

Sphingolipid metabolism is compartmentalized in cells, where each organelle has a unique sphingolipid signature due to the presence of specific enzymes and regulatory proteins. Details for individual organelles are found in the text. a, The de novo biosynthesis pathway occurs in the endoplasmic reticulum (ER), forming ceramide as the central hub for other sphingolipid pathways. ORM1-like proteins (ORMDLs) are sensors of ceramide levels and negatively regulate the activity of the serine palmitoyltransferase (SPT) complex, which catalyses the first step of ceramide synthesis using serine and palmitoyl-CoA as substrates (see Fig. 1 and Box 1 for details). b, Ceramide is rapidly transported to the Golgi through both transporter-dependent and vesicular-dependent mechanisms. Ceramide transfer protein (CERT) transports ceramide to the trans-Golgi complex. Here, sphingomyelin synthase 1 (SMS1) transfers the phosphocholine group from phosphatidylcholines to ceramide, generating sphingomyelin and diacylglycerol (DAG). DAG, in turn, activates protein kinase D (PKD), which serves as a negative feedback loop by inhibiting CERT activity. This mechanism ensures proper regulation of sphingolipid flux from the ER to the Golgi. Ceramide at the ER–cis-Golgi contact site is shuttled via vesicular transport and converted to glucosylceramide by UDP-glucose ceramide glucosyltransferase (UGCG) in the cytosolic side of the Golgi. It is then transported to the trans-Golgi by transporter protein phosphoinositol 4-phosphate adapter protein 2 (FAPP2; also known as PLEKHA8), for synthesis of lactosylceramide by β-1,4-galactosyltransferase 5 (B4GALT5) or B4GALT6, allowing subsequent formation of various glycosphingolipids such as gangliosides and globosides. c, Sphingomyelin and glycosphingolipids reach the plasma membrane through vesicular transport and become enriched in the outer leaflet of the plasma membrane and clustered with other lipids such as cholesterol. Sphingomyelin in the plasma membrane can be degraded by neutral sphingomyelinase (nSMase) to generate ceramide, which is subsequently used to generate sphingosine-1-phosphate (S1P). d, Sphingomyelin and glycosphingolipids are transported to lysosomes by endocytic and/or pinocytic pathways and are metabolized into ceramide by the action of acid sphingomyelinase (aSMase) and glycosidases, respectively. Ceramide is further degraded by acid ceramidase (aCDase), releasing sphingosine (Sph) and free fatty acid. Sph can exit the lysosome via transporters, such as NPC intracellular cholesterol transporter 1 (NPC1), StAR-related lipid transfer protein 3 (STARD3) and protein spinster homologue 1 (SPNS1), at ER–lysosome contact sites. Lysosomal Sph can also flip to the outer leaflet of the lysosome and be phosphorylated by sphingosine kinase 1 (SPHK1) to form S1P. S1P transfer from the lysosome to the ER may take place at contact sites between these two organelles. At the ER, Sph can be recycled to form ceramide (catalysed by ceramide synthases (CERSs)) or converted to S1P by SPHKs. S1P can then be degraded by S1P lyase 1 to hexadecenal and ethanolamine phosphate in the degradation pathway or dephosphorylated into Sph by S1P phosphatase 1 and 2 (SGPP1 and SGPP2). e, Some sphingolipid metabolic enzymes have been identified in association with mitochondria, including SMase, CDase, CERS and SPHK2. Although sphingolipid metabolic enzymes involved in the de novo synthesis pathway, including SPT complex and dihydroceramide sphingolipid Δ4-desaturase DES1 (DEGS1), are also identified at ER–mitochondria contact sites, it remains unclear whether de novo synthesis of sphingolipid occurs in mitochondria itself or only at mitochondria–ER contact sites, supplying sphingolipids to the mitochondria. f, At ER–lipid droplet contact sites, ceramide can be O-acylated by diacylglycerol O-acyltransferases (DGATs) in coordination with long-chain fatty acid CoA ligase 5 (ACSL5) for fatty acid synthesis, forming acylceramide, which is stored in lipid droplets.
Endoplasmic Reticulum
Like other classes of membrane lipids (phospholipids and sterols), de novo synthesis of sphingolipids occurs in the endoplasmic reticulum (ER)21. Sphingolipid biosynthetic enzymes located in the cytoplasmic side of the ER utilise the substrates L-serine (an amino acid) and palmitoyl-CoA (a fatty acid) to synthesize sphingoid bases (Figs. 1A and 2A)22,23. The mammalian heterotrimeric SPT complex, consisting of SPTLC1, SPTLC2 or SPTLC3, and SPT small subunit A (SPTSSA) or SPTSSB, catalyses the first and rate-limiting step of the pathway24-26. Elevated sphingolipid levels as a negative regulator of SPT activity was first described in cultured cells27. The mechanism involves sensing of high ceramide levels by the SPT complex, which was demonstrated in both intact cells and isolated membranes28. The key sensors are a family of ER membrane proteins, ORM1-like proteins 1-3 (ORMDL 1-3) (ref.29), which we discuss further in Box 1. The importance of this regulatory mechanism was revealed by recent human genetic studies, which identified mutations in the SPT complex as the cause of childhood Amyotrophic Lateral Sclerosis [G] (ALS) and hereditary spastic paraplegia [G] (HSP)30,31. Childhood ALS-associated SPTLC1 mutations and HSP-associated SPTSSA mutations prevent ORMDL-mediated suppression of SPT enzymatic activity, leading to abnormal accumulation of several sphingolipid species32. The analysis of ALS mutations that cause motor neuronal symptoms is likely due to the abnormal accumulation of sphingolipid species in the cells of the central nervous system (CNS), even though precise molecular mechanisms and affected cell types are still under investigation. It is likely that perturbation of sphingolipid content and diversity in organelle membranes is a major pathogenic mechanism. SPT mutations in other neurodegenerative diseases have also uncovered connections between amino acid metabolism (important substrates for SPT complex) and de novo sphingolipid synthesis, which we discuss in Box 2.
Box 1 ∣. Structure of the mammalian SPT complex across regulatory states.
The serine palmitoyl transferase (SPT) complex has been crystalized in various organisms, revealing very conserved structures265-268. SPTLC1 and SPTLC2 form a heterodimer with the transmembrane domain of SPTLC1 inserted into another heterodimer, forming a heterotetramer resembling a dimeric chicken leg structure266,267. This helix-swapped configuration is not observed in the yeast SPT complex (SPOTS) and does not affect activity and stability of the complex269. The coenzyme of the SPT complex, pyridoxal phosphate, is accommodated in a polar pocket through an aldimine linkage to SPTLC2266,267. SPTLC1 assists in stabilizing the phosphate group in pyridoxal phosphate through hydrogen bonding266,267. The hydroxyl head group of the substrate, l-serine, is essential for its binding to the active sites of SPTLC2 through hydrogen bonds. The long acyl chain of palmitoyl-CoA lies in a tunnel formed mainly by SPTLC2266,267. SPT small subunit A (SPTSSA) resides below the SPTLC1–SPTLC2 complex with one vertical transmembrane helix and the other parallel to the endoplasmic reticulum (ER) membrane266,267. SPTSSA brings SPTLC2 closer to the ER membrane, stabilizing the complex and stimulating its enzymatic activity266,267. Notably, the side chain in SPTSSA extends into SPTLC2 and seals the substrate-binding tunnel limiting the size of the substrate accommodated in the tunnel266,267. In SPTSSB, Val25 with a smaller side chain replaces Met28 in SPTSSA to accommodate longer acyl chains266,267. Hence, the presence of SPTSSA or SPTSSB influences substrate specificity of the complex.
It has been demonstrated that SPT activity is negatively regulated by a family of ER membrane proteins, the ORM1-like proteins (ORMDL1–ORMDL3)29. The structure of the SPT–ORMDL3 complex has been solved for human and plant orthologues, providing insights into this inhibitory mechanism267,268. ORMDL3 sits in the centre of the complex, contains four transmembrane helices, and is positioned between SPTSSA and SPTLC1266,267. The amino terminus of ORMDL3 interferes with substrate entry, where Met1 occupies the substrate-binding tunnel of SPTLC2 and Asn2 interacts with SPTLC1 through a hydrogen bond266,267. When ceramide levels are low, the amino terminus of ORMDL3 is flexible, allowing for substrate entry. High ceramide levels in the ER membrane can lead to binding of ceramide to Asn13 of ORMDL3 and lock it into an inhibitory conformation, inhibiting substrate entry266,267. A recent study revealed that, in the yeast SPT complex, the amino terminus of Orm1 (the yeast orthologue of ORMDL proteins) is extended and facing away from the active site of Lcb2 (the yeast orthologue of SPTLC2)269. It is possible that phosphorylation of Orm1 at the amino terminus by kinases, such as the serine/threonine kinase Ypk, regulates the activity of SPT270,271 through rearrangement of the amino terminus of Orm1.
Additional regulators of ORMDLs have been reported. In cultured endothelial cells, ORMDL levels are regulated by sphingosine-1-phosphate (S1P)–S1P receptor-mediated ORMDL degradation by ubiquitination272. An ER structural protein, Nogo-B (also known as reticulon 4), was reported to bind ORMDLs and negatively regulate SPT activity273, yet the structural basis of this interaction is not known. Collectively, these studies indicate that ORMDLs are the ceramide-sensitive regulatory subunits of the SPT complex rather than a general inhibitor of the SPT complex.
Box 2 ∣. SPT mutations and non-canonical sphingolipids.
Mutations in SPTLC1 and SPTLC2 have been mapped in hereditary sensory and autonomic neuropathy type 1274,275 and macular telangiectasia type 2276. These mutations are located outside of the ORM1-like protein (ORMDL)-interaction domain of serine palmitoyl transferase (SPT)277, which enables the mutant enzymes to use alternative substrates (alanine and glycine instead of serine), leading to the formation of deoxy sphingoid bases (missing a C1-OH group)278,279. Such 1-deoxy-sphingolipids cannot be further metabolized into complex sphingolipids and cannot be recycled in the canonical catabolic pathways, leading to cellular toxicity. Administration of high doses of l-serine lowers 1-deoxy-sphingolipid levels and improves motor performances and demyelination of sciatic nerve in both mice and humans carrying SPT mutations associated with hereditary sensory and autonomic neuropathy type 1, highlighting the significance of substrate availability to SPT complex280,281. Moreover, the pathological relevance of 1-deoxy-sphingolipids may be broad, as such sphingolipid species were found to be elevated in other pathological conditions such as diabetes282. In a genetic mouse model of type 2 diabetes, in which plasma 1-deoxy-sphingolipid levels are raised, serine supplementation normalized 1-deoxy-sphingolipid levels and slowed the progression of diabetic neuropathy283. A recent publication also demonstrated that a serine-deficient and glycine-deficient diet in mice results in 1-deoxy-sphingolipid synthesis in tumours, which reduced tumour progression284. Together, substrate-mediated correction of abnormal 1-deoxy-sphingolipids synthesis by SPT could be a potential strategy for modulating numerous diseases in which sphingolipid metabolism is abnormal.
Mechanisms by which deoxy-sphingolipids cause cell stress and pathological phenotypes are not fully understood. 1-Deoxy-sphingolipids may affect biophysical properties of membranes and/or induce their effects through specific protein transducers. Indeed, long-term exposure to 1-deoxy-sphingolipids, which are normally formed in the endoplasmic reticulum (ER), alters ER morphology and induces ER stress285. A transcriptomics profiling study of 1-deoxy-sphingolipid toxicity in human retinal organoids revealed sustained activation of pro-apoptotic PKR-like endoplasmic reticulum kinase (PERK) signalling and diminished protective signalling of activating transcription factor 6 (ATF6), suggesting induction of the unfolded protein response286. In macrophages, 1-deoxy-sphingolipid accumulation leads to mitochondria fragmentation and dysfunction, resulting in autophagosome and lysosomal mislocalization, suppression of cell proliferation, and inflammasome activation285,287. Whether such mechanisms contribute to 1-deoxy-sphingolipid-induced pathology in vivo is unclear at present.
Despite their resistance to canonical sphingolipid catabolism, 1-deoxy-sphingolipids are nevertheless detoxified by alternative pathways. Although poorly understood, recent studies have shed light on the involvement of cytochrome P450288 and a sphingoid base desaturase (FADS3)289. The latter converts 1-deoxy-sphinganine to the less toxic 1-deoxy-sphingosine, potentially reducing the pathological phenotypes289. In addition, recent findings suggested that 1-deoxy-sphingolipids may participate in lymphatic and cardiac development during embryogenesis290. Through unbiased screening, 1-deoxy-sphingosine was identified as an activator for nuclear transcriptional factors NR2F1 and NR2F2290. Supplementation of 1-deoxy-sphingosine promoted human cardiomyocyte maturation ex vivo290, unveiling the role of 1-deoxy-sphingolipids during development. Although it is not clear if 1-deoxy-sphingolipids are normally produced during embryogenesis and activate nuclear transcriptional factors to regulate cardiac development (physiological relevance), this study suggested the potential role for these non-canonical sphingolipid metabolites in normal vertebrate embryogenesis.
The product synthesised by the SPT complex, 3-keto-dihydrosphingosine (3-KDS), is further reduced into dihydrosphingosine by 3-keto-dihydrosphingosine reductase (KDSR)33,34 (Fig…1A). This intermediate step controls the proper metabolic flux as loss of KDSR caused substrate accumulation and disrupted the ER structure in leukemic cells35. 3-KDS downregulates ER stress proteins, including protein kinase R-like ER kinase (PERK), and activates transcription factor 6 (ATF6), rendering increased sensitivity to ER stress inducers such as tunicamycin35. Moreover, a recent report demonstrated that patients carrying mutations in KDSR exhibited palmoplantar keratoderma, a group of disorders characterized by epidermal thickening, which may be due to ectopic formation of atypical sphingolipids, 3-ketodihydroceramide, from 3-KDS in the epidermis36.
Dihydrosphingosine, as one of the sphingoid bases, is further processed by ceramide synthase (CERS) enzymes to form dihydroceramides with various acyl chain lengths37,38 (Fig. 1A). Mammalian CERSs exist in six isoforms (CERS1-6), with preferences for distinct fatty acid chain lengths39. Multiple species of (dihydro-)ceramides show different subcellular localization, tissue-specificity, and physiological function (reviewed in40). For example, loss of C24-ceramides synthesized by CERS2 limited gut inflammation41 and impaired insulin production42, whereas loss of C16-ceramides synthesized by CERS5 and CERS6 had the opposite42.
Formation of ceramide, the central species in sphingolipid metabolism, requires the introduction of a double bond between carbon 4 and 5 of dihydrosphingosine, which is generated by the delta 4-desaturase, sphingolipid 1 (DEGS1) (Fig. 1A). Several reports have implicated the importance of this double bond as dihydroceramides have unique biological functions compared to ceramides (reviewed in43). Interestingly, a recent mouse study showed that ceramide, not dihydroceramide, causes insulin resistance and hepatic steatosis44, implicating DEGS1 targeting as a potential therapeutic approach.
Due to its hydrophobicity, ceramide accumulation induces ER stress through direct binding of the unfolded protein response [G] (UPR) regulatory protein, BiP, and disruption of calcium homeostasis45,46. Consequently, ceramide is rapidly transported to the Golgi complex. It can also be converted into galactosylceramide by ceramide UDP-galactosyltransferase (CGT) on the luminal side of the ER47. Galactosylceramide is further converted to produce sulfatide, which is particularly abundant in neurons (for details see review 48).
Interestingly, five out of six CERS isoenzymes contain a homeodomain [G] , which is not required for the catalytic activity of ceramide synthesis49, suggesting its role as a transcriptional factor. Both the Drosophila melanogaster CERS enzyme shlank50 and the zebrafish CERS2b isoform51 were shown to affect gene expression. In the first case, Shlank regulates gene expression in response to feeding status by binding to the promoter regions of lipases. In the latter case, Cers2b can sense increased sphingosine levels and induce its transcription via the homeodomain-dependent autoinduction of its mRNA and protein, thereby reducing sphingosine-induced oocyte and embryonic toxicity51. However, the divergence of the putative DNA binding domain of mammalian CERS isoforms from the bona fide DNA binding motifs of homeobox transcription factors has led some researchers to suggest that CERS enzymes are not transcription factors39. Moreover, since the ER membrane is contiguous with the nuclear membrane, the transmembrane topology of the CERS isoforms with potential nuclear functions in the ER or nuclear membrane domains needs to be defined. This controversy needs further investigation to resolve.
In addition to ceramide biosynthesis, the ER also orchestrates essential steps in sphingoid base recycling and degradation, referred to as the salvage pathway and the degradation pathway, respectively (Fig. 1B, C and 2A). Within the salvage pathway, S1P, originating from various organelles and translocated to the ER, undergoes dephosphorylation by sphingosine-1-phosphate phosphatase 1 or 2 (SGPP1 and SGPP2)52,53. Subsequently, the resulting sphingosine can be converted to ceramide by CERSs to ultimately result in sphingomyelin and glycosphingolipids in the Golgi (Fig. 1D and 1E, discussed below in the Golgi section). Alternatively, S1P degradation, catalyzed by sphingosine-1-phosphate lyase (SGPL1), yields hexadecenal and ethanolamine phosphate54-56, constituting the degradation pathway (Fig. 1B). This irreversible breakdown of sphingolipids ultimately generates fatty acids (palmitate) and phospholipid head groups, representing the only exit point in the sphingolipid metabolism (Fig. 1B). Notably, the degradation pathway is crucial for maintaining sphingolipid homeostasis, as SGPL1 plays a critical role in embryogenesis, neonatal development, and adult homeostasis57.
Golgi Complex
Ceramide transported to the Golgi complex undergoes conversion into complex sphingolipids such as sphingomyelin and glycosphingolipids (Fig. 1D, E and 2B). Alternatively, it can be phosphorylated by ceramide kinase (CERK) into ceramide-1-phosphate (C1P), which regulates unique biological processes (Fig. 1F, for more details see reviews in58,59). Ceramide transfer protein (CERT) is essential to move ceramide from the ER to the trans-Golgi network (TGN)60, where the sphingomyelin synthases (SMS1 or 2)61 transfer the phosphocholine group of phosphatidylcholine to ceramide, generating sphingomyelin and diacylglycerol in the lumen (Figure 1D and 2B, ER–trans-Golgi contact site)61. Ceramide can also be transported to cis-Golgi membranes through vesicle-mediated mechanisms (Fig. 2B). In this scenario, ceramide on the cytosolic side of the cis-Golgi membrane is converted into glucosylceramide by the action of UDP-glucose ceramide glycosyltransferase (UGCG) (Fig. 1E and 2B). Glucosylceramide is further transported by the glucosylceramide-transfer protein phosphatidylinositol-four-phosphate adapter protein 2 (FAPP2, also known as PLEKHA8) to the TGN, where glucosylceramide is flipped into the luminal side of the membrane (Fig. 2B)62. Subsequently, a galactose group is transferred to glucosylceramide by glycosyltransferases, β-1,4 galactosyltransferases V and VI (BAGALT5 and 6), forming lactosylceramide (Fig. 2B)63. Lactosylceramides act as the precursor molecules for the biosynthesis of various classes of glycosphingolipids, such as globosides [G] and gangliosides [G] (Fig. 2B) (see ref. 20 for further details on metabolic pathways for glycosphingolipid synthesis).
Gain-of-function mutations in CERT have been linked to intellectual disability in humans64,65. Constitutively active CERT increases sphingolipid flux, causing neurotoxicity66,67. Interestingly, a long isoform of CERT (CERTL) can be co-immunoprecipitated with amyloid precursor protein and decreases amyloid Aβ formation and brain inflammation68, suggesting that CERT isoforms may be coupled to amyloid Aβ pathology. However, the underlying mechanisms need to be explored further. Interestingly, replication of the hepatitis C virus69 and infection with Chlamydia trachomatis70 were attenuated in CERT knockout cells or by pharmacological inhibition of CERT activity. These studies underscored the importance of sphingolipid fluxes at MCS as key cellular regulatory hubs and highlighted the disruption of these structures in diseases.
Enrichment of sphingomyelin and other lipids at the Golgi and post-Golgi organellar membranes increases membrane thickness and alters the biophysical properties of the membrane, both of which are critical for proper Golgi function71. Altered sphingolipid flux changes the morphology of the Golgi complex, leading to inhibition of cargo sorting and defects in the formation of transmembrane proteins72,73,74. Moreover, differential sphingolipid distribution throughout the secretory pathway from the ER to the TGN to the plasma membrane (PM) controls protein secretion and signaling: Recent studies reported that mutant SMS2 mislocated to the ER alters sphingolipid distribution and causes retention of secretory proteins75,76. Development of new tools to accurately measure and visualize sphingolipid distribution between the Golgi and associated subcellular compartments (i.e. ER–Golgi contact sites and Golgi-post Golgi membrane) is needed to better understand sphingolipid functions in cell physiology.
Plasma Membrane
Sphingomyelin and glycosphingolipids synthesized in the lumenal side of the Golgi complex are moved to the outer leaflet of the PM by vesicle-mediated transport77 (Fig 2C). SMS2, located on the extracellular surface of the PM, also contributes to sphingomyelin abundance on the extracellular leaflet of the PM, where it catalyses the reverse reaction of neutral sphingomyelinase (nSMase). nSMase acts at an optimal pH of 7.4 and is thus active extracellularly, whereas other sphingomyelinases show different pH optima, such as acid SMase (aSMase), which is active at low pH in the lysosome (Fig. 1D and 2C)61. Sphingolipids are abundant in the PM, accounting for about 10% of total phospholipids78. Sphingomyelin in the PM is associated with various critical functions. First, sphingomyelin on the outer leaflet of the PM interacts with other lipids to create a rigid mechanical barrier and structural integrity79. A recent study demonstrated that sphingomyelin on the extracellular leaflet of the PM can be moved to the cytosolic leaflet in a phosphatidylinositol 4,5-bisphosphate (PIP2)-dependent manner80. This trans-bilayer movement may be important as altered sphingomyelin distribution in the PM causes myelination defects of Schwann cells [G] 81. Second, sphingomyelin in the PM directly affects cholesterol homeostasis by sequestering cholesterol in the PM (Fig. 2C). Cholesterol in the PM can be divided into different compartments based on its association with sphingomyelin8283. A recent study demonstrated that sphingomyelin binds to cholesterol, causing sphingomyelin to assume a unique conformation compared to unbound sphingomyelin, thereby retaining it in the PM84. This sphingomyelin–cholesterol complex remains constant even when cholesterol levels in the PM fluctuate84. When free cholesterol (not bound to sphingomyelin) levels rise, it is transported to the ER to inhibit Sterol regulatory element-binding proteins [G] (SREBPs), which are essential for de novo synthesis of cholesterol85. Reciprocally, cholesterol depletion can increase sphingomyelin abundance in the PM by inducing ceramide synthesis86, indicating that cholesterol and sphingomyelin are co-regulated to maintain PM lipid homeostasis. Third, sphingomyelin–cholesterol-enriched domains, which are associated with caveolae [G] and lipid rafts [G] , act as platforms for diverse cellular functions, including shuttling molecules on the cell surface, signal transduction pathways, and entry for pathogens and toxins87. In the brain, cognitive decline that occurs during aging and neurodegenerative diseases is associated with alterations in the composition and structure of lipid rafts88. Major facilitator superfamily domain-containing protein 2A (MFSD2A, also known as NLS1), a transporter responsible for uptake of lysophospholipids containing omega-3 fatty acids such as docosahexaenoic acid [G] (DHA), regulates fatty acid uptake and inhibits caveolae-mediated transcytosis across the blood-brain barrier89. It is possible that sphingomyelin contained in the lipid rafts, together with cholesterol and raft-resident caveolin, maintains the optimal transport function of MFSD2A, which is important for the uptake of omega-3 fatty acid-containing lipids from the periphery into the CNS89. Lastly, the sphingomyelin pool in the plasma membrane acts as a storage to generate lipid signaling molecules, including ceramide and S1P (Fig. 2C, discussed below in the systemic and cellular functions of S1P section). The ability of sphingomyelin to function as a precursor of bioactive molecules in a wide array of biological processes is reviewed elsewhere90.
Like sphingomyelin, glycosphingolipids are found in lipid microdomains, such as lipid rafts and caveolae, and provide rigidity and resistance to the PM (Fig. 2C)79. The complex saccharide groups of glycosphingolipids allow them to interact with neighboring membrane components or various extracellular ligands to regulate cell growth, differentiation, morphogenesis, cell–matrix interaction, cell–cell interactions, and pathogen recognition (for more details see review in91). For instance, ganglioside GM1, the most common brain ganglioside enriched in lipid rafts, may interact with amyloid-β isoforms and regulate the formation and metabolism of amyloid-β-containing complexes92,93. In the heart, cardiac glycosphingolipids are required to maintain β-adrenergic receptor signaling and contractile capacity in cardiomyocytes, which is important for normal heart function94. Cell surface glycosphingolipids have also been shown to be involved in immunity. It has been reported that cell surface glycosphingolipid repertoire determines effective Human leukocyte antigen (HLA) class I [G] presentation and is involved in anti-tumor immune activation95. Recent work examining the sphingolipidome at single-cell resolution revealed that globo- and ganglio-series of glycosphingolipids act as positive and negative regulators for fibroblast growth factor (FGF)-2 signaling respectively, impacting dermal fibroblast proliferation and differentiation processes96. This study suggests that glycosphingolipid and sphingolipid heterogeneity may lead to unique cellular identities. Whether such mechanisms have a role in differential sensitivity to inflammation and its resolution, host defense, cancer, development etc. is not known but is worthy of future investigations.
Lysosome
The lysosome is the key organelle responsible for catabolism of proteins and recycling of amino acids, carbohydrates, nucleic acids, and lipids, including sphingolipids. Sphingomyelin and glycosphingolipid catabolism in the lysosome is initiated by internalization and recycling of membranes through the endolysosomal and pinocytotic pathways (Fig. 2D). Sphingomyelin is degraded by aSMase to release ceramide and phosphorylcholine, termed as the sphingomyelinase pathway (Fig. 1D and 2D)97. In contrast, glycosphingolipids that reach the lysosome interact with specific proteins such as the ganglioside GM2-activator and prosaposins, enabling a family of glycosidases to remove the sugar moiety, generating ceramide (Figure 1E and 2D)98,99(for a detailed review on different glycosidases, see100). The resulting ceramides are degraded by acid ceramidase (aCDase), generating sphingosine and fatty acids (Fig. 1E and 2D)101. Sphingosine accumulation is toxic to the lysosome due to its positive charge at low pH102 and causes lysosomal defects through disruption of calcium homeostasis103,104. Consequently, sphingosine is removed from the lysosome by sphingosine kinase 1 (SPHK1), which forms S1P on the cytosolic surface of lysosomes and enters the ER through MCS105 (Fig. 2D). As a consequence, S1P can be recycled through the salvage pathway or be degraded by the degradation pathway (Fig. 1C). Alternatively, sphingosine can enter the ER and be phosphorylated by sphingosine kinase 2 (SPHK2) to form S1P106. A highly debated question in the field is whether lysosome sphingosine entry into the ER requires carriers similar to CERT-mediated ceramide transport into the Golgi complex at the MCS. Recent studies have identified proteins that shuttle sphingosine from the lysosome to the ER including NPC intracellular cholesterol transporter 1 (NPC1)107,, StAR-related lipid transfer protein 3 (STARD3)108 and protein spinster homolog 1 (SPNS1)109 (Fig. 2D). However, ablation of STARD3 has led only to mild lysosomal defects107, suggesting other mechanisms, such as diffusion of sphingosine at MCS, may be involved. Some of these potential sphingosine transporter proteins are also involved in sterol transport and regulate MCS between the lysosome and the ER110. Conversely, a recent study demonstrated that lysosome–ER MCS and cholesterol flux can be affected by sphingosine accumulation caused by genetic deletion of SPHK 1 and SPHK2 (ref.111). These reports suggest that the co-regulation of sphingolipid and cholesterol transport and metabolism occurs not only at the Golgi complex but also at the lysosome.
Defects in lysosomal hydrolases or sphingolipid activator proteins cause the accumulation of nondegradable glycosphingolipid intermediates, resulting in lysosomal storage disorders (LSDs)112. Consequently, the non-metabolized substrates accumulate as lamellar structures, which can be identified by light or electron microscopy. Most LSDs exhibit neurodegenerative pathology and myelination defects, which reflects the significance of sphingolipid homeostasis in the CNS. The pathological accumulation of lysosomal sphingosine can also lead to aberrant storage of cholesterol in Niemann–Pick disease [G] 103,104,113. Detailed information on molecular mechanisms of lysosomal degradation and pathological effects leading to storage diseases can be found in this comprehensive review114.
Mitochondria
Mitochondria possess a unique lipid composition, which is required for its metabolic needs and membrane morphology. Although sphingolipids are the minor components of mitochondrial lipids115, dysregulation of sphingolipid homeostasis impacts mitochondria functions and affects regulation of cellular apoptosis116. Early studies showed that short-chain ceramides could bind and stimulate serine-threonine-protein phosphatase 2A (PP2A), which de-phosphorylates and inactivates the anti-apoptotic function of Bcl2 (refs.117,118,119). Simultaneously, substrates of PP2A such as protein kinase C and Akt are inhibited, resulting in the activation of pro-apoptotic Bcl-2-family proteins such as BAD120. Alternatively, studies suggested that ceramides act locally in mitochondria to induce apoptosis. For example, targeted overexpression of bacterial sphingomyelinase in mitochondria induced apoptosis121. Exogenous ceramide can form channels on isolated mitochondria to increase the permeability of the mitochondrial outer membrane, causing cytochrome c release120,122. Upon irradiation, ceramides may form macrodomains on the mitochondria membrane to regulate the functions of apoptosis regulator BAX123.
Subsequently, an emerging important question in the field is whether ceramides are locally produced within mitochondria or transferred from the ER through MCS. In support of the former hypothesis, enzymes crucial for sphingolipid metabolism including CERS124, neutral ceramidase125, neutral sphingomyelinase126, glucocerebrosidase127, and SPHK2 (ref.128) have been found in the mitochondria (Fig. 2E). Notably, the source of sphingomyelin used to generate ceramide in mitochondria remains elusive as SMSs have not been reported in the mitochondria. As subcellular fractionation technology of mitochondria cannot fully exclude contamination with other membranes, improved imaging methods such as visualizing endogenous enzyme by state-of-the-art microscopy should be performed to ascertain mitochondrial localization of these enzymes. Nevertheless, it is possible that some sphingolipids, including ceramide, are generated locally in mitochondria.
The second hypothesis suggests that sphingolipids are transferred through mitochondria-associated membrane (MAM) of the ER (Fig. 2E). These ER–mitochondria contact sites are important for lipid transfer and Ca2+ exchange between the two organelles, e.g., regulating mitochondria-dependent apoptosis129,130. Ceramide and other sphingolipids may be transferred by similar mechanisms. MAM-dependent ceramide flux is sufficient to induce cytochrome c release across the outer mitochondria membrane to drive apoptosis129. It has been reported that SPT complexes may be formed at ER–mitochondria contact sites where mitochondrial outer membrane-localized SPTLC2 interacts in trans with ER-localized SPTLC1 (ref.131). DEGS1, which acts in the last step of the de novo synthesis pathway of sphingolipids (Fig. 1A), is also found at MAM132. Moreover, SMS-related protein 1 (SMSr), which is located in the ER, can regulate mitochondrial sphingolipid homeostasis through preventing ceramide accumulation in the mitochondria133. As discussed above, it is likely that mitochondrial sphingolipids are derived from multiple sources. Further studies are needed to decipher the mechanisms of ER–mitochondria ceramide transfer and to achieve a more holistic principle of sphingolipid regulation in the mitochondria.
Lipid Droplets
Lipid droplets (LDs) are organelles that consist of a phospholipid monolayer with a core of neutral lipids (mostly triglyceride and sterol esters), providing energy for metabolic needs134. They are synthesized at the ER when neutral lipids accumulate between the leaflets of the ER134. As de novo synthesis of sphingolipids also occurs in the ER, recent work demonstrated that ceramide can be converted to acylceramide by diacylglycerol O-acyltransferase 2 (DGAT2) and stored in LDs135 (Fig. 1G and 2F). Since ceramide accumulation in the ER causes ER stress, the ceramide-to-acylceramide flux may serve as a detoxification route to shunt excessive ceramide to prevent toxicity. The significance of this sphingolipid flux in vivo requires further investigation.
Systemic regulation of sphingolipids in vertebrates
Sphingolipid composition and abundance are also tightly regulated at the systemic level in multicellular organisms. In mammals, extracellular sphingolipids are associated with circulating lipoproteins136, extracellular vesicles (EVs)137 and are produced by the commensal microbiota in the gut138. In fact, dysregulated systemic sphingolipid metabolism is observed in many pathophysiological conditions, serves as a biomarker for human diseases and may be therapeutically tractable. In this section, we will review how the diet impacts systemic sphingolipid metabolism, how sphingolipid metabolism within the microbiome impacts the host, and the regulation and functions of circulating sphingolipids associated with lipoproteins and extracellular vesicles (EVs). Finally, we will provide a concise overview of recent advances in the biology of S1P.
Dietary Sphingolipids
In the United States, sphingolipid intake through the diet, mainly derived from egg, milk, meat and fish products, is estimated to be 300–400 mg/day139. Sphingomyelin, as the major dietary sphingolipid species, is poorly absorbed in the small intestine140. Instead, it is first broken down by alkaline sphingomyelinase (alk-SMase) into ceramide and phosphorylcholine (ChoP)140(Fig. 3). Ceramide species, which remain poorly absorbed, are further hydrolyzed by neutral ceramidase (ASAH2) at the brush border [G] of enterocytes into sphingosine and free fatty acids141 (Fig. 1B and 3). As sphingosine enters the enterocyte142, it is phosphorylated to S1P by SPHK2 (ref.143) (Fig 3). S1P is then metabolized by the degradation pathway (Fig 1C), and the resulting reactive aldehyde hexadecenal is rapidly converted to palmitic acid by hexadecenal dehydrogenase (Fig 3)144. Palmitic acid is incorporated into triglycerides, packed into chylomicrons [G] , and enters the circulatory system (Fig 3). A fraction of absorbed sphingosine is converted into ceramide and other complex sphingolipids through the salvage pathway (Fig 1B)145. In addition, a small fraction of sphingomyelin and ceramide are absorbed directly140,146.
Fig. 3: Systemic regulation of sphingolipids.

Dietary sphingolipids, mostly enriched in sphingomyelin (SM), are broken down into the website functhis may affect how tions. Please view our privacy policy for further details on ceramide in the gut by alkhow we aline sphingprocess omyoyur inelinasformae (tioAlkn. Di-SMassmisse). Subsequently, ceramide is metabolized by neutral ceramidase (ASAH2) at the brush border of enterocytes, releasing sphingosine (Sph) and free fatty acids (FAs). Extracellular Sph and ceramide in the intestine can impact microbiome function in the gut. Conversely, microbiota-derived sphingolipids can regulate host gut health by regulating enterocytes and immune cells in the gut. Sph and free FAs can also be absorbed by enterocytes. The majority of Sph is converted to sphingosine-1-phosphate (S1P) in the endoplasmic reticulum (ER) and enters the degradation pathway, generating palmitic acid (PA), which can be incorporated into triglycerides (TGs) along with other FAs in the ER. Only a small portion of Sph is converted to ceramide. Both ceramide and TGs can then be transferred onto nascent apolipoprotein B48 (APOB48) by microsomal transfer protein (MTP) during pre-chylomicron formation. Pre-chylomicrons are transported via pre-chylomicron transport vesicles (PCTV) and reach the Golgi complex, where ceramide-derived sphingomyelin can be further incorporated. Subsequently, sphingolipids are secreted along with chylomicrons from the enterocytes via exocytosis of secretory vesicles. In the circulation, sphingolipids are present within various lipoproteins, including chylomicron, very-low-density lipoprotein (VLDL), low-density lipoprotein (LDL) and high-density lipoprotein (HDL). Whereas sphingomyelins are present in all lipoproteins, ceramide content is high in VLDL and LDL, and S1P is enriched in HDL. Sphingolipid transfer between lipoproteins can occur through spontaneous exchange and phospholipid transporter (PLTP)-dependent mechanisms. In addition to lipoproteins, many cells generate extracellular vesicles (EVs), which are enriched with sphingolipids such as sphingomyelin and glycosphingolipids. Sphingolipids in EVs can regulate EV biosynthesis and are involved in intercellular communication events that regulate pathophysiological conditions. In many disease conditions, such as cardiovascular, metabolic and neurodegenerative diseases, changes in circulatory sphingolipid profiles can serve as biomarkers or may be targeted for therapeutic purposes. CERS, ceramide synthase; SGPL1, S1P lyase 1; SPHKs, sphingosine kinases.
Although there is no known nutritional requirements for sphingolipids, dietary supplementation of sphingomyelin has been reported to have beneficial effects on the prevention of colon cancer, intestinal inflammatory disease and cardiovascular disease (for more details see147). Our understanding of the cholesterol-lowering effect of dietary sphingomyelin in humans is still limited and remains preliminary (see review in148). A recent clinical study in overweight postmenopausal women demonstrated that 4 weeks of milk polar lipid supplementation [G] (containing >25% of sphingomyelin) reduced cholesterol absorption and improved lipid markers of cardiovascular disease, including the ratio of total cholesterol to HDL-cholesterol and the ratio of the apolipoprotein B (ApoB) to ApoA1 (ref. 149). This evidence is complemented by another clinical study in which milk polar lipid supplementation decreased sphingolipid metabolism in humans, resulting in reduced atherogenic [G] sphingomyelin and ceramide levels, underscoring the beneficial effects of dietary sphingolipids150. Additional clinical studies and better knowledge of mechanisms are needed to develop nutritional guidelines for sphingolipid intake in the diet.
Microbiota-derived Sphingolipids
Sphingolipids produced from commensal microbiota have been found to impact host physiology (Fig 3). Glycosphingolipids produced by soil-dwelling Sphingomonas species were first identified to activate invariant natural killer T (iNKT) cells [G] in the gut151. Subsequently, sphingolipids derived from the intestinal microbe Bacteroides fragilis were shown to suppress the activation of host iNKT cells, protect mice from colitis, and maintain normal intestinal musical homeostasis152,153. Bacterial-derived sphingolipids likely pass the epithelial barrier in the gut and impact host metabolic pathways. One murine study showed that bacterial-derived sphingolipids increased ceramide levels in the liver, whereas de novo sphingolipid biosynthesis was reduced154. Oral supplementation of sphingolipid-producing bacteria could ameliorate hepatic lipid accumulation in a mouse model of hepatic steatosis, demonstrating the therapeutic potential in targeting sphingolipid interaction between the host and microbiota155. There are still many unidentified sphingolipid metabolites produced by microbiota, which may have significant influences on host physiology. Microbial sphingolipids exhibit distinctive structural features characterized by non-canonical double bonds, hydroxyl groups, branched fatty acids, and odd chain lengths153,154,156. It is likely that such atypical sphingolipid species regulate immune cell–cell interactions, alter host sphingolipid metabolism, and modulate cell signaling pathways.
Conversely, dietary sphingolipids in the lumen of the intestine can alter microbial populations in the gut. As sphingomyelin is broken down by the sphingomyelinases and ceramidases, bacteria in the gut are exposed to increased levels of sphingosine and ceramide derived from host and microbiome (Fig. 3). Sphingosine has antimicrobial activities157,158, whereassupplementation of milk sphingomyelin increases beneficial gut microbiota in mice and controls body weight159,160. A recent study reported that dietary sphinganine is metabolized by gut microbiota, illustrating the complex interactions between diet, microbiota and host161.
Circulatory Sphingolipids
Sphingolipids in the blood are either associated with circulating lipoprotein particles (chylomicron, very low-density lipoprotein [G] (VLDL), low-density lipoprotein [G] (LDL), and high-density lipoprotein [G] (HDL)), albumin, or circulating cells (i.e. leukocytes, erythrocytes and platelets). A comprehensive lipidomics study identified over 230 species of sphingolipids in human plasma, and sphingomyelin accounted for about 5% of total lipidome and 20% of total phospholipidome162. The most abundant sphingolipid in plasma is sphingomyelin (> 80%), followed by lactosylceramide, hexosylceramide [G] , ceramide, S1P and sphingosine in decreasing order163. Although sphingomyelin is associated with all circulating lipoproteins, S1P is enriched in HDL and ceramide is mostly found on LDL and VLDL163 (Fig. 3).
Circulatory sphingolipids are synthesized mainly by the cells of the liver and intestine, with only a minor proportion directly absorbed from the diet as discussed above (Fig. 3)140. The exact mechanisms of ceramide and sphingomyelin loading onto chylomicron and VLDL are not well understood. Several possible mechanisms have been proposed: For example, endogenous sphingolipids synthesized in the intestine and the liver may be exported along with triglycerides in chylomicron and VLDL by lipid transporter-dependent mechanisms164. Microsomal transfer protein (MTP) transfers lipids (triglycerides, cholesteryl esters, and phosphatidylcholine) into apoB-containing lipoproteins in the ER and the Golgi165. Sphingolipids such as ceramide and sphingomyelin can be incorporated into vesicular apoB-containing lipoproteins prior to their secretion as chylomicron and VLDL (Fig. 3). This is based on a study where MTP-deficient humans and liver- or intestine-specific knockout mice showed a marked reduction of ceramide and sphingomyelin in the plasma with concomitant accumulation of ceramide and sphingomyelin in the liver164. Similarly, attenuation of sphingolipid biosynthesis in the liver by deletion of Sptlc2 in mice showed a significant reduction of circulating lipoprotein-associated sphingomyelin, ceramide, and sphingosine166. In the case of HDL, nascent HDL in hepatocytes or intestinal enterocytes may acquire sphingomyelin at the Golgi during lipidation of ApoA-I167. Circulatory HDL may also take up sphingomyelin from cells in the vascular system. Reports have demonstrated that the phospholipid-transporting ATPase ABCA1 flips sphingomyelin and/or ceramide from the cytoplasmic leaflet to the extracellular leaflet to ApoA1 on HDL particles168,169.
While in circulation, triglycerides in mature ApoB-containing lipoproteins (chylomicron and VLDL) are hydrolyzed by lipoprotein lipase, shrinking the lipid-rich core of these lipoproteins170. Excess phospholipids such as phosphatidylcholine and sphingomyelin on the surface of lipoproteins need to be removed. Given the amphiphilic property of sphingomyelin, spontaneous transfer of sphingomyelin between different lipoproteins is possible171 (Fig. 3). Sphingomyelin can also be transferred by transporter proteins such as phospholipid transport protein (PLTP) 172,173. PTLP null mice showed reduced plasma sphingomyelin and altered sphingomyelin distribution in lipoproteins with accumulation in VLDL and LDL, suggesting that sphingomyelin fluxes between lipoproteins174. Additionally, a study utilizing labeled sphingomyelin in HDL demonstrated that it can be metabolized by tissues and transported to VLDL175. Indeed, scavenger receptor-B1 (SR-BI) and LDLR can be involved in the uptake of sphingomyelin from lipoproteins both in vitro142 and in vivo176 ,177. Reciprocally, a recent study reported that depletion of SMS activity in mice can impact LDL metabolism through downregulation of LDLR178. The physiological mechanisms by which lipoprotein-associated sphingomyelin is maintained and its functions in lipoprotein metabolism need to be further determined.
Sphingolipids are also present in EVs in the circulatory system (Fig. 3). EVs, i.e., heterogenous membrane vesicles released by many cell types, are formed by membrane shedding or through the extracellular release of multivesicular bodies [G]. They have roles in intercellular exchange of regulatory factors, elimination of cellular debris, and serve as biomarkers for diseases179. Glycosphingolipids, ceramide, sphingomyelin and amino-phospholipids are the most enriched lipids in EVs137. Increased ceramide levels in the PM and endosomal system promote the formation of extracellular vesicles through altering membrane curvature and fluidity180,181,182. Recent work described that CERT induces EV biogenesis through forming a complex with tumor susceptibility gene 101 protein (Tsg101), a component of endosomal sorting complex (ESCRT-I) involved in EV secretion183. In addition, S1P signaling through its GPCR, S1PR1, promotes multivesicular body (MVB)-derived EV formation184. These findings underscore the role of sphingolipids in EV biogenesis. Furthermore, sphingolipids in the membranes of EVs can impact recipient cells. For example, clustered glycosphingolipids on the EV surface bind to the amyloid Aβ peptide, leading to the aggregation of Aβ and fibril formation in vitro185. In the liver, FGF induces secretion of SPHK1-containing EVs that interact with hepatic stellate cells to induce cell migration and fibrosis186. Recent work from our group utilising Sptlc1 endothelial-specific knockout mice demonstrated that plasma ceramide, S1P and sphingosine is reduced significantly187. It is possible that a fraction of sphingolipids derived from the de novo biosynthetic pathway in the endothelium is released into the circulation along with EVs.
Circulatory sphingolipids in the plasma and EV are biomarkers of several pathological conditions, including neurodegenerative, metabolic, cardiovascular diseases and aging (reviewed in188-190) (Fig. 3C). Notably, it has been proposed that ceramide levels in plasma could potentially serve as a cardiovascular disease marker, possibly surpassing LDL-cholesterol 191. Numerous studies have demonstrated elevated ceramide in coronary artery diseases (CAD) patients192-194. Furthermore, ceramide species with certain acyl chain lengths, including C16:0, C18:0, and C24:1, have shown correlations with the risk of CAD in clinical studies195. However, protective effects of ceramides on the vasculature such as stimulation of endothelial nitric oxide synthesis have also been noted196,197. Based on the extensive body of studies that has implicated the pathogenic roles of ceramide in CAD (review in198), it is important to determine whether and how elevated plasma ceramide species impact CAD pathology.
Systemic and cellular functions of S1P
In vertebrates, S1P is secreted and acts on its G protein-coupled receptors sphingosine 1-phosphate receptor 1-5 (S1PR1-5) to mediate many physiological processes199. S1P has been studied extensively as a circulating lipid mediator, intracellular metabolite and organelle-specific regulator of various cell types. It is produced by two enzymes, SPHK1 and SPHK2, where SPHK1 resides largely in the cytosol, and SPHK2 is found in the nucleus200, the inner mitochondrial membrane128, and the ER201. SPHK1, which is thought to act downstream of neutral sphingomyelinase and neutral ceramidase, is translocated to the PM for S1P synthesis upon stimulation202-204 (Fig. 4). A unique isoform of SPHK1 is secreted in an isoform-specific manner both in vitro and in vivo205,206. The physiological significance of circulating SPHK1 is not clear, but it may be needed to reduce free sphingosine levels in the plasma, or associated with lipoproteins, or EVs. As S1P is hydrophilic, transporters are needed for its secretion. So far, two S1P transporters have been identified, including the sphingosine-1-phosphate transporters SPNS2 in the endothelium and MFSD2B in the erythrocytes and platelets, contributing 20% and 50% of S1P levels in the blood, respectively207-210 (Fig. 4A). Following export, S1P associates with S1P chaperones (defined as carriers that facilitate receptor signaling), namely apolipoprotein M (ApoM) in the HDL and albumin in the lipoprotein-free compartment, respectively (Fig. 4B). S1P chaperones enable its transport to target cells, where S1P activates S1PRs, hence regulating downstream signaling and biological processes such as cell migration, survival, fate determination and gene expression211,212 (Fig 4C). The unique S1P distribution (termed S1P gradient) constructed by its transporters, chaperones, and metabolic enzymes is tightly regulated and controls various physiological processes such as vascular development and lymphocyte trafficking. More details on regulation of circulatory S1P are discussed in Box 3.
Fig. 4: S1P metabolism and its therapeutic strategies.

a, Circulatory sphingosine-1-phosphate (S1P) is mostly provided by erythrocytes, endothelial cells and platelets. In the endothelium, sphingomyelin (SM) in the plasma membrane can be converted by neutral sphingomyelinase (nSMase), generating ceramide (Cer). Ceramide can be converted back to sphingomyelin by sphingomyelin synthase 2 (SMS2) or be degraded by ceramidase (CDase) into sphingosine (Sph). Sph can be converted back to Cer by ceramide synthases (CERSs) or flip to the inner leaflet of the plasma membrane. By the action of sphingosine kinase 1 (SPHK1), S1P can be formed and released extracellularly by the S1P transporter protein spinster homologue 2 (SPNS2). Erythrocytes and platelets utilize exogenous Sph to form S1P by sphingosine kinase 1 (SPHK1) or SPHK2 and export it through the S1P transporter major facilitator superfamily domain-containing protein 2B (MFSD2B). b, Once released, S1P is bound to chaperones such as apolipoprotein M (APOM) and albumin, whereby the affinity to APOM on high-density lipoprotein (HDL) is higher than the affinity to albumin. The S1P chaperone system stabilizes S1P in the circulation to facilitate its action in autocrine and paracrine manners. Our group developed engineered APOM conjugated with the Fc domain of IgG (APOM-Fc) to restore depleted S1P in circulation247, which is seen in diabetes and cardiovascular diseases. This approach may be useful in these pathological conditions. c, S1P binds to its Gprotein-coupled receptors S1P receptors 1–5 (S1PR1–S1PR5) on the same cells or other cells, activating various downstream signalling pathways and regulating many biological processes, including cell migration, survival, cell fate and gene expression. d, Extracellular S1P can be dephosphorylated by phospholipid phosphatase 3 (PLPP3) into Sph, which can flip into the inner leaflet of the plasma membrane. Sph is re-phosphorylated by SPHK1 into S1P and reaches the endoplasmic reticulum (ER) for imidazole (THI), 4-deoxypyridoxine (DOP), LX2931, LX2932, LX3305 and A6770 264. An inhibitor for SPNS2, 16d, has been developed recently251. The development of inhibitors or activators targeting MFSD2B is still under investigation.
Box 3 ∣. Regulation of circulatory S1P.
Earlier work suggested ATP-binding cassette sub-family C member 1 (ABCC1; also known as MRP1) and ABCA1 as transporters of sphingosine-1-phosphate (S1P) based on the evidence that nonspecific inhibitors of ABC transporters blocked S1P release291,292. However, since the discovery of specific S1P transporters, protein spinster homologue 2 (SPNS2) and major facilitator superfamily domain-containing protein 2B (MFSD2B), the physiological significance of S1P transport by ABC transporters has been questioned. The first S1P transporter, SPNS2, was identified in zebrafish216. Deletion of the spns2 gene in the murine lymphatic endothelial cell reduces S1P levels in the lymph and blocks lymphocyte egress from secondary lymphoid organs such as lymph nodes217,293. A distinct S1P transporter, MFSD2B, was later identified in red blood cells (RBCs) and platelets218. Deletion of the Mfsd2b gene in mice reduced circulatory S1P by over 50%, which further confirmed the role of RBCs as a major source of circulatory S1P218. It has been demonstrated that RBCs take up exogenous sphingosine as a source for S1P formation294. Global deletion of both Spns2 and Mfsd2b genes caused embryonic lethality with a vascular haemorrhagic phenotype similar to that of S1P receptor (S1PR) compound knockout mice295, indicating that S1P transporters are needed for receptor activation during embryogenesis. The search for S1P transporter inhibitors is motivated by the apparent role of these transporters in the regulation of immune, vascular and cancer phenotypes251. The crystal structure of SPNS2 revealed that SPNS2 is a uniporter that exports SIP through facilitated diffusion, possibly regulated by membrane phosphoinositides such as phosphatidylinositol 4,5-bisphosphate296. By contrast, MFSD2B uses the proton gradient for S1P transport294 and its high-resolution ultra-structure is not resolved.
In blood plasma, 65% of S1P is bound to apolipoprotein M (APOM) on high-density lipoprotein, and the remaining is found in the lipoprotein-free fraction, bound mostly to serum albumin297 (Fig. 4). Mice lacking APOM showed a 50% reduction in plasma S1P and exhibited enhanced vascular leak and hypertension298,299. Upon injury, these mice showed defective liver regeneration and enhanced fibrosis248. By contrast, albumin knockout mice have a mild reduction in blood S1P300 and have not been reported to have a vascular leakage phenotype. This can be explained by the fact that APOM is bound to S1P with higher affinity221-301 and provides stable activation of the endothelial receptors302. At the same time, albumin binds weakly to S1P and induces activation of the receptors transiently302. Notably, APOM and albumin double-knockout mice are viable and were found to retain 20% S1P in the blood, in which proteins such as APOA4 can substitute as an S1P carrier300. This points to the important and redundant roles of circulatory proteins for sufficient activation of S1PR. Interestingly, the APOM gene is located in the MHC III region of the genome, which is dense in coding genes relevant to immune response and host defence303, implying important functions of APOM in immunity and inflammation. Moreover, this region is highly conserved in vertebrate genomes. Overall, the intricate chaperone system is constructed to ensure the functionality of this bioactive lipid messenger during development and proper organ function.
The levels of circulatory S1P are highly compartmentalized: in general, S1P concentration is high in the blood (−1μM), low in the lymph (−0.1μM) and the lowest in interstitial fluids of tissues (<1nM)304. This S1P gradient is described to be essential for the trafficking of naive lymphocytes from the thymus and secondary lymphoid organs305. S1PR1 is internalized upon binding to S1P, and naive lymphocytes use this interaction as a ‘stay or go’ signal: disrupting the S1P gradient either by deleting SPNS2 in lymphatic endothelial cells or by knocking out S1P lyase caused failure of T cell egress in the thymus owing to altered thymic S1P levels306,307. Stimulation with polyinosinic-polycytidylic acid, which mimics viral infection-induced nucleic acid, in mouse monocytes leads to S1P secretion and disrupts the gradient, keeping T cells in the lymph node308. A novel function of S1P produced from lymphatic endothelial cells has been described recently. S1P provides T cell survival via S1PR1, dependent on its role in egress309. Nevertheless, internalization of S1PR1 is required to restrict JNK phosphorylation and maintain BCL-2 family expression, limiting apoptosis310. These findings suggest that S1PR1 internalization is vital in maintaining the naive T cell repertoire. This could explain poor antibody responses after prolonged treatment with S1PR1 antagonists310 Future work defining the role of the S1P gradient in the lymph node will be pivotal to improving our current use of S1PR1-targeted drugs.
In vivo studies indicated that S1P in blood, especially when bound to albumin, is rapidly dephosphorylated and recycled in the liver, suggesting an important role for the liver in S1P homeostasis213,214,215. Extracellular S1P is de-phosphorylated at the cell surface, for example by phospholipid phosphate phosphatase 3 (PLPP3), to form sphingosine, which is taken up by cells and is re-phosphorylated by SPHK1 in the cytosolic leaflet215 (Fig 4D). Resynthesized S1P can enter the salvage pathway for recycling or the degradation pathway to exit sphingolipid metabolism (Fig 1B)215. This mode of sphingolipid uptake is conserved in evolution, as the wunen gene of D. melanogaster (PLPP3 homologue) carries out its developmental function in a similar manner216,217.
S1P may have additional organelle-specific roles, some of which are controversial and/or not fully elucidated. Building on the well-accepted finding of SPHK2 localization in the nucleus201,205,218, it was proposed that SPHK2-mediated S1P is an inhibitor of histone deacetyase-1 (HDAC-1) and thus an epigenetic regulator and modulator of nuclear transcription219. This hypothesis has been examined by various groups in many cells and tissue-specific contexts. Several studies reported that nuclear S1P and a phosphorylated form of the S1P analog (called FTY720P), regulate histone acetylation in cells220-222. In a D. melanotaster model, amyloid-induced neurotoxicity is attenuated by FTY720 in a SPHK2-dependent manner, suggesting a nuclear function of SPHK2 in epigenetic modification and neuronal plasticity 223. In a mammalian model of heart regeneration, nuclear function of SPHK2 appeared to be required for cardiomyocyte proliferation, an essential step in heart repair of neonatal mice224. These studies suggest a unique nuclear function of S1P, which needs further exploration.
In the cytosol, S1P was proposed to be a missing co-factor for the ubiquitin ligase, TNF receptor-associated factor 2 (TRAF2), an essential signaling protein in inflammatory cytokine signaling pathways225. In addition, SPHK1 was reported to bind to TRAF2 following TNFα signaling226. However, the genetic knockout mouse model of TRAF2 exhibited distinct phenotypes, including epidermal hyperplasia and psoriatic skin inflammation, which were not observed in SPHK1-deficient mice227. These findings do not support the notion that S1P is required for TRAF2-mediated inflammatory events.
Targeting S1P using therapeutics
Dysregulated S1P signaling pathways contribute to several cardiovascular, autoimmune, inflammatory, neurological, oncologic and fibrotic diseases199. S1PR-targeted small molecule drugs have found widespread utility in the treatment of several autoimmune conditions199. The first approved drug of this class was Fingolimod, Which induces ß-arrestin-dependent internalization and degradation of S1PR1 in adaptive immune cells (T- and B-cells), thus reducing autoreactive inflammatory cell infiltration into target organs199,15. Currently, four drugs in this class have been approved to treat relapsing remitting multiple sclerosis (RRMS), progressive forms of multiple sclerosis and ulcerative colitis199,228 (Figure 4C). In addition, several clinical trials are underway to determine the utility of S1PR1 inhibitors in other autoimmune diseases such as atopic dermatitis, systemic lupus erythematosus and inflammatory bowel disease229. A detailed discussion of S1PR targeting in autoimmune therapeutics can be obtained from the following recent review229. Recently, detailed molecular structures of S1P receptor isotypes in active and inactive conformations have been solved by cryo-EM techniques230,231,232. The availability of high-resolution three-dimensional structures of S1PRs is anticipated to further advance the development of novel pharmacological tools for therapeutic modulation of S1P signaling pathways in various diseases.
Other targets of sphingolipid metabolism and signaling have also been explored for therapeutic applications. S1P chaperones, which are depleted in several pathological conditions, could provide opportunities for treatment of diseases. For example, the HDL constituent ApoM that is reduced in several pathological conditions such as diabetes233, sepsis234, coronary artery disease235, heart failure236 and acute respiratory distress syndrome induced by SARS-CoV2 (ref.237), could be replenished by therapeutic administration of ApoM-bound S1P to enhance vascular function and tissue repair and resolution responses. To address this, our group has developed a novel biologic, ApoM-Fc, that binds S1P and activates endothelial S1PRs selectively238 (Fig 4B). ApoM-Fc administration suppresses deleterious phenotypes in preclinical mouse models of cardiac ischemia or reperfusion injury, brain stroke, lung and kidney fibrosis, abnormal vascular proliferation in the retina and vascular permeability in immune complex-mediated lung injury239-241. ApoM-mediated S1PR activation in the endothelium may be a viable therapeutic strategy to suppress abnormal vascular leak, enable endothelial survival and increase vascular function in a wide range of diseases. Since ApoM-Fc administration does not lead to lymphopenia or bradycardia238, this therapeutic approach may provide some advantages over FDA-approved small molecules that target S1PR1.
The potential in targeting S1P transporters to manipulate S1P metabolism has also been investigated (Fig 4B). A small molecule, 16d, which inhibits SPNS2 activity, reduces plasma S1P and induces lymphopenia242. Activation of S1P transporters may also have beneficial effects in treating anemia and cancer metastasis209,243.
Enzymes regulating S1P metabolism can also be considered for therapeutics, yet their adverse effects must be considered due to the ubiquitous nature of sphingolipid metabolism in all cell types that impact general cell structure and function. The use of SPHK inhibitors in pathological conditions such as cancer has been discussed in references244,245(Fig. 4A). S1P lyase inhibitors have shown benefits in many in vitro and animal model studies (reviewed in246, Fig. 4D). Recent studies suggested beneficial effects of S1P lyase inhibition in Huntington’s disease and cancer by altering sphingolipid metabolism247,248. Current efforts are ongoing to replace the enzyme in S1P lyase insufficiency syndrome249 and Fabry’s disease250, which causes renal and adrenal pathology. Sphingosine itself has antibacterial activities and it has been suggested that its use may be beneficial for the treatment of infectious diseases251,252. In addition, ceramidases have also been suggested to have therapeutic utility253. In summary, a large body of work has supported the idea that S1P dysregulation in diseases provides opportunities for novel therapeutic interventions.
Conclusions and perspectives
It is clear that sphingolipids regulate almost every aspect of biology, from membrane homeostasis, organelle function, cell–cell interactions, cell fate determination to microbiome-dependent processes. The fundamental steps of sphingolipid metabolism, trafficking, and functions have been discovered in recent decades. In addition, the discovery of S1P as an extracellular lipid mediator that signals via GPCRs has led to improved understanding of vascular and immune systems and paved the way for the launch of new drugs to treat immune system disorders. This Review has summarized some salient aspects of sphingolipid biology. However, our understanding of sphingolipid metabolism, trafficking, and regulation at both cellular and organismal levels in multicellular eukaryotes is still limited. In addition, general principles of how these lipids regulate membranes structure and dynamics is an area that needs further study. Given the importance of sphingolipids in embryonic development, physiology and diseases that range from neurodegeneration, CAD, diabetes and inflammatory conditions, increasing this knowledge base is important. Further discoveries in sphingolipid research promise to lead to new insights in cell biology, physiology, and therapeutic approaches for a plethora of human diseases.
Supplementary Material
Acknowledgements
AK is supported in part by a postdoctoral fellowship from AHA. TH acknowledges the support of NIH grants (R01EY031715, R01AI173377, R01AG078602 and R35HL135821).
Glossary
- Atherogenic
Substances or conditions that promote the development of atherosclerosis, a disease characterized by the buildup of plaque in arterial walls, leading to narrowing and potential blockages in blood vessels.
- Brush border
A dense layer of microvilli on the surface of enterocytes, increasing their surface area for absorption of nutrients from the digestive tract.
- Caveolae
Small invaginations in the plasma membrane of cells, serving as specialized lipid rafts involved in various cellular processes such as signal transduction and vesicular trafficking.
- Childhood Amyotrophic Lateral Sclerosis (ALS)
A rare neurodegenerative disorder that affects motor neurons in children, leading to progressive muscle weakness and loss of motor function.
- Chylomicron
Large lipoprotein particles with a diameter typically ranging from 75 to 1200 nm, primarily composed of apoB-48, responsible for transporting dietary triglycerides from the intestine to various tissues throughout the body.
- Docosahexaenoic Acid (DHA)
A type of omega-3 essential fatty acid with a double bond at C3 and C4 that is enriched in the brain, retina, and skin, and is crucial for brain development, cognitive function, and overall health.
- Gangliosides
A class of glycosphingolipids primarily found in cell membranes, particularly abundant in nerve cells, containing one or more sialic acids on their sugar moiety. These have essential roles in cell signaling and neuronal development.
- Globosides
A class of glycosphingolipids characterized by a common tetrasaccharide core structure containing a terminal Galα1-4Galβ1-4Glcβ1-1Cer motif, frequently observed in biological membranes and involved in various physiological functions.
- Hereditary Spastic Paraplegia (HSP)
A group of genetic disorders characterized by progressive stiffness and weakness in the lower limbs due to degeneration of the nerves controlling muscle movement.
- Hexosylceramide
A class of glycosphingolipids consisting of a hexose linked to the 1-OH group of the ceramide as the monosaccharide, playing essential roles in cell structure and signaling.
- High-density lipoprotein (HDL)
A lipoprotein particle with a diameter ranging from 5 to 12 nm, primarily composed of apolipoprotein A-I, transporting cholesterol from tissues back to the liver for excretion, and is known to reduce the risk of cardiovascular disease.
- Homeodomain
A protein motif that binds to specific DNA sequences, regulating gene expression and playing crucial roles in embryonic development and cell differentiation.
- Human leukocyte antigen (HLA) Class I
A class of proteins on the cell surface that play a critical role in immune system recognition and response by presenting antigenic peptides to cytotoxic T cells.
- Invariant natural killer T cells
A distinct population of T cells that express an invariant T cell receptor and recognize glycosphingolipids such as α–galactosylceramide to modulate immune responses.
- Lipid rafts
Cholesterol-enriched lipid microdomains in cell membranes that play key roles in organizing signaling molecules and facilitating various cellular processes such as signal transduction and membrane trafficking.
- Low-density lipoprotein (LDL)
A lipoprotein particle with a diameter ranging from 18 to 25 nm, primarily composed of apoB-100, carrying cholesterol from the liver to tissues, high levels of which are associated with an increased risk of cardiovascular disease.
- Milk polar lipid supplementation
A dietary supplementation of specific polar lipids derived from milk, including enriched glycerophospholipids and sphingolipids, may confer various health benefits such as improved lipid metabolism and gut health.
- Membrane contact sites (MCS)
specialized regions where the membranes of two organelles come into close proximity, facilitating direct communication and transfer of lipids, ions, and other molecules between them.
- Multivesicular Bodies
A cellular structure involved in the sorting and trafficking of proteins and lipids, characterized by multiple internal vesicles enclosed within a single membrane.
- Niemann-Pick Disease
A group of disorders caused by acid sphingomyelinase deficiency, where abnormal amounts of sphingolipids are accumulated in the lysosome, damaging various tissues.
- Schwann cells
Specialized glial cells in the peripheral nervous system that wrap around axons to form myelin sheaths, facilitating rapid conduction of nerve impulses.
- Sterol regulatory element-binding proteins (SREBPs)
A family of membrane-bound proteins that act as transcription factors to regulate cholesterol and fatty acid synthesis.
- Unfolded protein response
A cellular mechanism that regulates the folding capacity of the ER and manages unfolded or misfolded proteins, aiming to restore protein homeostasis.
- Very low-density lipoprotein
A lipoprotein particle with a diameter ranging from 30 to 80 nm, primarily responsible for transporting triglycerides synthesized in the liver to peripheral tissues, and is metabolized to form LDL particles.
Footnotes
Competing interests
T.H. is an inventor on patents and patent application on S1P cheparones and S1PR modulations.
Supplementary information
Supplementary information is available for this paper at https://doi.org/10.1038/s415XX-XXX-XXXX-X
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