L-Serine Deficiency Elicits Intracellular Accumulation of Cytotoxic Deoxysphingolipids and Lipid Body Formation

Disturbed sphingolipid metabolism with elevated 1-deoxysphingolipids in glycogen storage disease type I - A link to metabolic control

BACKGROUND

1-Deoxysphingolipids (1-deoxySLs) are atypical sphingolipids. They are formed during sphingolipid de novo synthesis by the enzyme serine palmitoyltransferase, due to the alternate use of alanine over its canonical substrate serine. Pathologically elevated 1-deoxySL are involved in several neurological and metabolic disorders. The objective of this study was to investigate the role of 1-deoxySL in glycogen storage disease type I (GSDI).

METHODS

In this prospective, longitudinal observational study (median follow-up 1.8y), the plasma 1-deoxySL profile was analyzed in 15 adult GSDI patients (12 GSDIa, 3 GSDIb), and 31 healthy controls, along with standard parameters for monitoring GSDI.

RESULTS

1-Deoxysphinganine (1-deoxySA) concentrations were elevated in GSDI compared to controls (191 ± 129 vs 35 ± 14 nmol/l, p < 0.0001). Concordant with the mechanism of 1-deoxySL synthesis, plasma alanine was higher (625 ± 182 vs 398 ± 90 μmol/l, p < 0.0001), while serine was lower in GSDI than in controls (88 ± 22 vs 110 ± 18 μmol/l. p < 0.001). Accordingly, serine, alanine and triglycerides were determinants of 1-deoxySA in the longitudinal analysis of GSDIa. 1-deoxySA concentrations correlated with the occurrence of low blood glucose (area under the curve below 4 mmol/l) in continuous glucose monitoring. The 1-deoxySL profile in GSDIb was distinct from GSDIa, with a different ratio of saturated to unsaturated 1-deoxySL.

CONCLUSION

In addition to the known abnormalities of lipoproteins, GSDI patients also have a disturbed sphingolipid metabolism with elevated plasma 1-deoxySL concentrations. 1-DeoxySA relates to the occurrence of low blood glucose, and may constitute a potential new biomarker for assessing metabolic control. GSDIa and Ib have distinct 1-deoxySL profiles indicating that both GSD subtypes have diverse phenotypes regarding lipid metabolism.

Deoxysphingolipid precursors indicate abnormal sphingolipid metabolism in individuals with primary and secondary disturbances of serine availability

Patients with primary serine biosynthetic defects manifest with intellectual disability, microcephaly, ichthyosis, seizures and peripheral neuropathy. The underlying pathogenesis of peripheral neuropathy in these patients has not been elucidated, but could be related to a decrease in the availability of certain classical sphingolipids, or to an increase in atypical sphingolipids. Here, we show that patients with primary serine deficiency have a statistically significant elevation in specific atypical sphingolipids, namely deoxydihydroceramides of 18-22 carbons in acyl length. We also show that patients with aberrant plasma serine and alanine levels secondary to mitochondrial disorders also display peripheral neuropathy along with similar elevations of atypical sphingolipids. We hypothesize that the etiology of peripheral neuropathy in patients with primary mitochondrial disorders is related to this elevation of deoxysphingolipids, in turn caused by increased availability of alanine and decreased availability of serine. These findings could have important therapeutic implications for the management of these patients.

Enhanced vulnerability to oxidative stress and induction of inflammatory gene expression in 3-phosphoglycerate dehydrogenase-deficient fibroblasts

l‐Serine (l‐Ser) is a necessary precursor for the synthesis of proteins, lipids, glycine, cysteine, d‐serine, and tetrahydrofolate metabolites. Low l‐Ser availability activates stress responses and cell death; however, the underlying molecular mechanisms remain unclear. l‐Ser is synthesized de novo from 3‐phosphoglycerate with 3‐phosphoglycerate dehydrogenase (Phgdh) catalyzing the first reaction step. Here, we show that l‐Ser depletion raises intracellular H₂O₂ levels and enhances vulnerability to oxidative stress in Phgdh‐deficient mouse embryonic fibroblasts. These changes were associated with reduced total glutathione levels. Moreover, levels of the inflammatory markers thioredoxin‐interacting protein and prostaglandin‐endoperoxide synthase 2 were upregulated under l‐Ser‐depleted conditions; this was suppressed by the addition of N‐acetyl‐l‐cysteine. Thus, intracellular l‐Ser deficiency triggers an inflammatory response via increased oxidative stress, and de novo l‐Ser synthesis suppresses oxidative stress damage and inflammation when the external l‐Ser supply is restricted.

Re-evaluation of Culture Condition of PC12 and SH-SY5Y Cells Based on Growth Rate and Amino Acid Consumption

BACKGROUND/AIM

Most of the previous investigators have used various types of media for the culture of nerve cells. In order to optimize the culture conditions, we compared the growth rate and amino acid consumption by two popular neuron models, rat PC12 and human SH-SY5Y, grown in DMEM or DMEM: Ham's F-12 (1:1): non-essential amino acids, supplemented with 10% fetal bovine serum (referred to DMEM and Mix, respectively).

MATERIALS AND METHODS

Cell growth was monitored by the MTT method. Amino acids in the culture medium were quantitated by amino acid analysis after deproteinization.

RESULTS

Efficient cell attachment could be achieved even if PC12 cells were inoculated at extreme lower cell density in a non-coated plain dish, without addition of its condition medium. Both PC12 and SH-SY5Y cells proliferated up to slightly higher cell density in DMEM than in Mix. Approximately 2-fold higher utilization rate of glutamine and essential amino acids was observed in DMEM. Amyloid peptides such as Aβ_1-42 and Aβ_25-35 suppressed their growth nearly by 50%.

CONCLUSION

The present study suggests the usefulness of DMEM for the study of searching neuroprotective substances, based on its favorable effects on cell attachment, cell growth and amino acid utilization as well as amyloid peptide sensitivity.

D-serine, a novel uremic toxin, induces senescence in human renal tubular cells via GCN2 activation

The prevalence of chronic kidney disease (CKD), characterized by progressive renal dysfunction with tubulointerstitial fibrosis, is increasing because of societal aging. Uremic toxins, accumulated during renal dysfunction, cause kidney damage, leading to renal deterioration. A recent metabolomic analysis revealed that plasma D-serine accumulation is associated with faster progression of renal dysfunction in CKD patients. However, the causal relationship and the underlying mechanisms remain unclear. Herein, we demonstrated that D-serine markedly induced cellular senescence and apoptosis in a human proximal tubular cell line, HK-2, and primary culture of human renal tubular cells. The former was accompanied by G2/M cell cycle arrest and senescence-associated secretory phenotype, including pro-fibrotic and pro-inflammatory factors, contributing to tubulointerstitial fibrosis. Integrated stress response mediated by the general control nonderepressible 2 played an important role in D-serine-induced tubular cell toxicity and pro-fibrotic phenotypes, accelerating CKD progression and kidney aging. D-serine upregulated the L-serine synthesis pathway. Furthermore, D-serine-induced suppression of tubular cell proliferation was ameliorated by L-serine administration, indicating that D-serine exposure induced an L-serine-deprived state in tubular cells, compensated by L-serine synthesis. Thus, this study unveils molecular mechanisms underlying D-serine-induced tubular damage and pro-fibrotic phenotypes, suggesting that D-serine is a uremic toxin involved in CKD pathogenesis.

Infantile Serine Biosynthesis Defect Due to Phosphoglycerate Dehydrogenase Deficiency: Variability in Phenotype and Treatment Response, Novel Mutations, and Diagnostic Challenges

Serine biosynthesis defects can present in a broad phenotypic spectrum ranging from Neu-Laxova syndrome, a lethal disease with multiple congenital anomalies at the severe end, to an infantile disease with severe psychomotor retardation and seizures as an intermediate phenotype, to a childhood disease with intellectual disability at the mild end. In this report we present 6 individuals from 3 families with infantile phosphoglycerate dehydrogenase (PGDH) deficiency who presented with psychomotor delay, growth failure, microcephaly, and spasticity. The phenotype was variable with absence of seizures in 2 sisters in family 1 and 1 infant in family 2 and seizures with pronounced happy affect in 3 sisters in family 3. The initiation of serine treatment had pronounced effect on seizures and spasticity in the sisters in family 3, but minimal developmental effects on the children in families 1 and 2. With such phenotypic variability, the diagnosis of PGDH deficiency can be challenging.

Correlation of the plasma sphingoid base profile with results from oral glucose tolerance tests in gestational diabetes mellitus

Oral glucose tolerance test (OGTT) is usually insufficient to accurately predict the risk for type 2 diabetes mellitus (T2DM), it is therefore necessary to identify an additional biomarker that would most likely improve the accuracy of OGTT. The current OGTT was performed in 53 volunteers after ingestion of 75 g glucose in 250 ml water to each volunteer. Similarly the sphingoid base profile of these volunteers was explored using liquid-chromatography linked with mass spectrometer (LC-MS) and correlated with the different time-points glucose values of OGTT as well as with total area under the curve (tAUC), incremental area under the curve (iAUC), and positive incremental area under the curve (pAUC). The findings showed that 1-deoxysphinganine (1-deoxySA) was significantly positively correlated with the 1-hour, 2-hour, and 3-hour plasma glucose level as well as with total, incremental, and positive incremental AUC while 1-deoxysphingosine (1-deoxySO) was correlated only with 1-hour, 2-hour glucose levels and tAUC of OGTT. The C18SAdiene was negatively correlated with all-time points glucose values and AUCs followed by negative correlation of C18SO, C16SO and C17SO with 2-hour glucose and tAUC of OGTT. The ratios of 1-deoxySA and 1-deoxySO with respect to C18SAdiene have shown significant correlation with 2-hour and AUCs. These ratios were higher in subjects with gestational diabetes in comparison with normal subjects. These findings underlined that 1-deoxysphingolipids (1-deoxySLs) and their ratios with C18SAdiene could be significantly correlated with the glucose load of OGTT and might be used as predictive biomarkers along with OGTT for the risk assessment of diabetes.

Localization of 1-deoxysphingolipids to mitochondria induces mitochondrial dysfunction

1-Deoxysphingolipids (deoxySLs) are atypical sphingolipids that are elevated in the plasma of patients with type 2 diabetes and hereditary sensory and autonomic neuropathy type 1 (HSAN1). Clinically, diabetic neuropathy and HSAN1 are very similar, suggesting the involvement of deoxySLs in the pathology of both diseases. However, very little is known about the biology of these lipids and the underlying pathomechanism. We synthesized an alkyne analog of 1-deoxysphinganine (doxSA), the metabolic precursor of all deoxySLs, to trace the metabolism and localization of deoxySLs. Our results indicate that the metabolism of these lipids is restricted to only some lipid species and that they are not converted to canonical sphingolipids or fatty acids. Furthermore, exogenously added alkyne-doxSA [(2S,3R)-2-aminooctadec-17-yn-3-ol] localized to mitochondria, causing mitochondrial fragmentation and dysfunction. The induced mitochondrial toxicity was also shown for natural doxSA, but not for sphinganine, and was rescued by inhibition of ceramide synthase activity. Our findings therefore indicate that mitochondrial enrichment of an N-acylated doxSA metabolite may contribute to the neurotoxicity seen in diabetic neuropathy and HSAN1. Hence, we provide a potential explanation for the characteristic vulnerability of peripheral nerves to elevated levels of deoxySLs.

Adaptive response to l-serine deficiency is mediated by p38 MAPK activation via 1-deoxysphinganine in normal fibroblasts

Reduced availability of l‐serine limits cell proliferation and leads to an adaptation to l‐serine‐deficient environment, the underlying molecular mechanism of which remain largely unexplored. Genetic ablation of 3‐phosphoglycerate dehydrogenase (Phgdh), which catalyzes the first step of de novo l‐serine synthesis, led to diminished cell proliferation and the activation of p38 MAPK and stress‐activated protein kinase/Jun amino‐terminal kinase in mouse embryonic fibroblasts under l‐serine depletion. The resultant l‐serine deficiency induced cyclin‐dependent kinase inhibitor 1a (Cdkn1a; p21) expression, which was mediated by p38 MAPK. Survival of the Phgdh‐deficient mouse embryonic fibroblasts was markedly reduced by p38 MAPK inhibition under l‐serine depletion, whereas p38 MAPK could be activated by 1‐deoxysphinganine, an atypical alanine‐derived sphingoid base that was found to accumulate in l‐serine‐depleted mouse embryonic fibroblasts. These observations provide persuasive evidence that when the external l‐serine supply is limited, l‐serine synthesized de novo in proliferating cells serves as a metabolic gatekeeper to maintain cell survival and the functions necessary for executing cell cycle progression.

Database

Gene Expression Omnibus, accession number GSE55687.

Introduction to Thematic Minireview Series: Novel Bioactive Sphingolipids

Sphingosine was named by J. L. W. Thudichum for its enigmatic properties. This descriptor has applied to sphingolipids for over a century because new enigmas continue to surface. This JBC minireview series presents articles about three novel subspecies of sphingolipids, α-galactosylceramides, 4,5-dihydroceramides, and 1-deoxysphingolipids, that have important activities but, until recently, remained undetected (or at least understudied) in the shadow of very closely related compounds. They also serve as a reminder that important metabolites still lie "off the radar screen" in reports of global and comprehensive metabolomic profiling.

1-Deoxysphingolipids Encountered Exogenously and Made de Novo: Dangerous Mysteries inside an Enigma

The traditional backbones of mammalian sphingolipids are 2-amino, 1,3-diols made by serine palmitoyltransferase (SPT). Many organisms additionally produce non-traditional, cytotoxic 1-deoxysphingoid bases and, surprisingly, mammalian SPT biosynthesizes some of them, too (e.g. 1-deoxysphinganine from l-alanine). These are rapidly N-acylated to 1-deoxy-“ceramides” with very uncommon biophysical properties. The functions of 1-deoxysphingolipids are not known, but they are certainly dangerous as contributors to sensory and autonomic neuropathies when elevated by inherited SPT mutations, and they are noticeable in diabetes, non-alcoholic steatohepatitis, serine deficiencies, and other diseases. As components of food as well as endogenously produced, these substances are mysteries within an enigma.