Introduction
Pyridoxal 5′-phosphate (PLP), the metabolically active form of vitamin B6, plays a pivotal role in brain metabolism and development (Surtees et al
2006). PLP is an essential cofactor in more than 100 metabolic reactions in humans (Clayton
2006). Most of the PLP-dependent reactions, such as transamination, decarboxylation, deamination, racemization and desulfhydration, are involved in amino acid metabolism (Ebadi
1981; Ueland et al
2015). PLP deficiency, either due to genetic or dietary causes, disrupts the metabolism of neurotransmitters (γ-aminobutyric acid (GABA), dopamine and serotonin), haeme, histamine, amino acids, carbohydrates and nucleotides (da Silva et al
2013; Ueland et al
2015).
Five inborn errors of metabolism are known to affect vitamin B6 concentrations: pyridoxine-dependent epilepsy (α-aminoadipic semialdehyde dehydrogenase (antiquitin) deficiency; OMIM #266100), hyperprolinemia type II (1-pyrroline-5-carboxylate dehydrogenase deficiency; OMIM #239510), pyridox(am)ine 5′-phosphate oxidase deficiency (PNPO deficiency; OMIM #610090), hypophosphatasia (tissue non-specific alkaline phosphatase (TNSALP) deficiency; OMIM #241500) and proline synthetase co-transcribed bacterial homologue deficiency (PROSC deficiency; OMIM #604436). These diseases, except for most cases of TNSALP, are characterized by seizures, often beginning in the first days of life, not responsive to anticonvulsants and only controlled by vitamin B6 supplementation (Baxter
1999; Stockler et al
2011). Besides neonatal seizures, many patients suffer from developmental delay or intellectual disability, despite the seizure control (Baxter
2001; van Karnebeek et al
2016; Darin et al
2016; Walker et al
2000; Mills et al
2005,
2014). Little is known about the specific biochemical changes that underlie the clinical symptoms of patients with vitamin B6 deficiency. Low GABA levels were thought to be the main reason for the epilepsy (Gospe et al
1994). GABA is the key inhibitory neurotransmitter in the central nervous system and is synthesized from glutamate (the main excitatory neurotransmitter) through the PLP-dependent enzyme glutamic acid decarboxylyase (GAD, EC 4.1.1.15). Animal studies performed in zebrafish larvae showed that upon exposure to ginkgotoxin (4′-O-methylpyridoxine, a pyridoxal 5′-phosphate antimetabolite) a seizure-like behaviour develops. The ginkgotoxin-induced seizures were reversed by the addition of GABA and/or PLP to the fish water, supporting the hypothesis that the seizures are caused by reduced PLP availability, which leads to an imbalance between GABA and glutamate (Lee et al
2012). However, conflicting data on glutamate and GABA levels in the CSF of patients suffering from vitamin B6 deficiency suggest that GABA deficiency may not be the sole cause of symptoms in pyridoxine-dependent epilepsy (Goto et al
2001; Baumeister et al
1994). Several studies have shown that vitamin B6-deficient patients may display biochemical features of aromatic L-amino acid decarboxylase (AADC) deficiency, with low CSF homovanillic acid (HVA) and 5-hydroxyindoleacetic acid (5-HIAA) (Clayton
2006; De Roo et al
2014; Darin et al
2016), raised tyrosine, 3-ortho-methyldopa, L-Dopa and 5-hydroxytryptophan (Darin et al
2016). Other studies report increased CSF and plasma concentrations of threonine (Mills et al
2005; Clayton
2006), and/or glycine (Darin et al
2016; Mills et al
2005) and/or branched chain amino acids (Darin et al
2016). Nevertheless, these results are not consistent in all studies (Levtova et al
2015), underlining the complexity of vitamin B6 deficiency. Many additional vitamin B6-dependent reactions may contribute to the clinical phenotype.
To elucidate the pathogenesis of brain vitamin B6 deficiency, we performed untargeted metabolomics on a neuronal cell model deprived of vitamin B6. Our observations indicate that additional factors next to GABA play a role in the pathogenesis of vitamin B6 deficiency.
Discussion
Vitamin B6 has an important role in development and functioning of the brain by catalyzing essential reactions in neurotransmitter and amino acid metabolism (Surtees et al
2006). To investigate the metabolic consequences of vitamin B6 deficiency in the brain, we employed a model system of Neuro-2a cells that were cultured in vitamin B6-deficient medium. Neuro-2a cells have a neuronal origin and are easily cultured in high amounts. In previous (yet unpublished) work we have investigated the presence of the enzymes involved in vitamin B6 metabolism and found that all are present in these cells, confirming that they provide a suitable model. This model mimics vitamin B6 deficiency as it results in strongly decreased intracellular concentrations of PLP (63% reduction at the latest time point) and PMP (50% reduction at the latest time point). The low PLP is a direct consequence of PL absence in the medium, whereas the decrease of PMP may reflect less transaminating activity secondary to the low PLP. It is unknown how the brain intracellular concentrations of vitamin B6 relate between B6-deficient and B6-proficient humans. However, some in vivo animal studies have documented vitamin B6 levels in the brain of B6-deficient animals. In Dakshinamurti et al, adult rats were fed PN-supplemented and PN-deficient diets and the PLP concentrations in the brains were documented. In the whole brain of B6-deficient rats, PLP concentrations were 28% reduced, while in their hypothalamus the reduction was 57% compared to PN-supplemented (control) rats (Dakshinamurti et al
1985). These results are in close accordance with the ones presented in this study. Thus, we successfully created a vitamin B6 deficiency model system.
Investigation of metabolism by untargeted metabolomics yielded a range of altered metabolites: amino acids, Krebs cycle intermediates, GABA and homovanillic acid. Among the most significantly changed metabolites were serine and glycine, which were both decreased as validated by targeted LC-MS/MS analysis. Flux studies clearly illustrated reduced serine biosynthesis in vitamin B6-deficient Neuro-2a cells and thus made evident that serine biosynthesis depends on vitamin B6. The PLP-dependent enzyme phosphoserine aminotransferase (PSAT, EC 2.6.1.52) cannot fully function in vitamin B6 deficient conditions, which is expected to result in less synthesis of phosphoserine and serine, as observed.
The low medium and intracellular serine concentrations are in contrast with reports on the effect of vitamin B6 deprivation on human plasma, in which the concentrations of glycine showed an increase of 28% after 2 weeks of vitamin B6 depletion and serine showed an increase of 47% after 1 week of depletion (Park and Linkswiler
1971). This behaviour was also observed in a 28-day vitamin B6 restriction diet study, where the plasma levels of healthy men and women for glycine and serine showed an increase of 15% and 12%, respectively (da Silva et al
2013). Furthermore, cerebrospinal fluid (CSF) studies of PNPO-deficient patients have reported elevated levels of glycine prior to B6 supplementation (Mills et al
2005). For the one individual in this study in whom CSF analysis was repeated after supplementation this normalized. Elevation of CSF glycine has been reported to occur secondary to a deficiency of the activity of the glycine cleavage system, which is PLP-dependent. It should be noted however that this does not occur in all PNPO-deficient patients, with some only showing a transient increase of glycine in CSF (Hoffmann et al
2007). Glycine levels have also been reported to be slightly raised in the CSF of patients with mutations in PROSC prior to B6-supplementation (Darin et al
2016). In patients with mutations in ALDH7A1, however, CSF glycine levels have been reported to be normal (Hoffmann et al
2007) or just slightly elevated (Mills et al
2010). Interestingly few studies report on serine levels leading us to assume that serine is kept within normal values in the CSF of vitamin B6 deficient patients. Additionally, in a B6-deprivation study in HepG2 cells, vitamin B6 deficiency yielded large increases in glycine concentrations and no effect on serine (da Silva et al
2014). However, our findings in the Neuro-2a model are in accordance with in vivo studies performed by Tews, in which mice fed on a PN-deficient diet for 4 weeks presented a progressive decrease in brain serine concentrations. Brain glycine concentrations significantly decreased during the first 2 weeks of PN-deprivation and increased after 4 weeks when compared to normal-PN fed mice. Upon reinstating a complete-PN diet, serine and glycine concentrations returned to control levels (Tews
1969). This suggests that a decrease in serine and concomitant decrease in glycine concentrations is tissue or cell type dependent.
Serine in brain originates from two sources: uptake and biosynthesis (de Koning et al
2003). Serine
de novo biosynthesis is a side-pathway of glycolysis. The first and rate-limiting step is the oxidation of 3-phosphoglycerate (3-PG) to 3-phosphohydroxypyruvate, by 3-phosphoglycerate dehydrogenase (PHGDH, EC 1.1.1.95). The conversion of 3-phosphohydroxypyruvate to 3-phosphoserine is catalyzed by phosphoserine aminotransferase, a PLP-dependent enzyme. Serine biosynthesis seems to be particularly important in the brain, as illustrated by the severe clinical symptoms in patients affected with a defect in serine synthesis, including congenital microcephaly, severe epilepsy and very little development (Jaeken et al
1996; Furuya
2008). In CSF of these patients, serine (both L- and D-serine) and glycine are decreased (van der Crabben et al
2013).
Glycine production depends on serine availability and on the PLP-dependent enzyme SHMT. SHMT catalyzes the transfer of the methyl group of serine to tetrahydrofolate (THF), allowing the formation of 5,10-methylenetetrahydrofolate (5,10-methyleneTHF) and glycine (de Koning et al
2003). 5,10-methyleneTHF is converted by the enzyme methylenetetrahydrofolate reductase (MTHFR, EC 1.5.1.20) to 5-mTHF, the main circulating form of folate which can serve as a methyl donor in the generation of S-adenosylmethionine (SAM). Indeed, the combination of less serine and PLP may lead to a lower activity of SHMT, explaining the decrease in the intracellular concentration of 5-mTHF in vitamin B6-deficient cells.
Our findings are important in considering pathogenesis and treatment of patients with vitamin B6-dependent epilepsy. Generally, it was thought that a reduction of GABA concentrations in the brain of these patients was the main cause of the epilepsy, due to suboptimal activity of the PLP-dependent enzyme glutamic acid decarboxylase. We demonstrate that low serine, glycine and 5-methyltetrahydrofolate may also contribute to pathogenesis. Probably, these amino acids are low in brain cells in vivo, as suggested by the B6-deficient mouse studies (Tews
1969). Although theoretically uptake of serine and glycine from blood to brain may compensate a lower serine biosynthetic capacity, two observations suggest clinical relevance of our findings. Patients with a defect in serine synthesis need high doses of serine to normalize serine in CSF (de Koning et al
2003; van der Crabben et al
2013). Furthermore, some patients with vitamin B6-dependent epilepsy clinically respond to supplementation of folinic acid, a 5-mTHF precursor (Nicolai et al
2006; Gallagher et al
2009; Stockler et al
2011; Dill et al
2011; van Karnebeek et al
2016). Our work provides an explanation for this hitherto puzzling observation.
Material and methods
Cell culture
Neuro-2a cells were purchased from ATCC Cell Biology Collection. Dulbecco’s modified eagle medium (DMEM) GlutaMAX™ (31966), B6 vitamer-free DMEM GlutaMAX™ (custom made 31966-like) medium, foetal bovine serum (FBS; 10270), penicillin-streptomycin (P/S; 15140) and trypsin-ethylenediaminetetraacetic acid (trypsin-EDTA, 0.5%) were purchased from Gibco (Invitrogen Life Technologies). Pyridoxal hydrochloride (PL-HCl) was purchased from Sigma-Aldrich (Steinheim, Germany). Cells were grown in 75 cm2 flasks and maintained in DMEM GlutaMAX™ supplemented with 10% heat-inactivated FBS and 1% P/S, in a humidified atmosphere of 5% CO2 at 37 °C. When cells reached optimal confluence (>70%) they were washed twice with PBS and passed into 6-well plates (1.5 × 105 cells per well) by trypsinization with 0.05% trypsin-EDTA. Confluent cells (>70%) were exposed to the experimental medium conditions: 1:1, PBS:B6 vitamer-free DMEM GlutaMAX™ (with 10% FBS and 1% P/S), with 100 nM of PL-HCl (content of vitamin B6: PL 97.4 ± 5.6 nM; PN 2.6 ± 2.6 nM; PM 1.4 ± 1.3 nM; PLP 1.9 ± 1.5; PNP and PMP are below the LOQ) or without vitamin B6 (residual content of vitamin B6: PL 4.7 ± 3.8 nM; PN 2.3 ± 0.4 nM; PM 1.1 ± 1.1 nM; PLP, PNP and PMP are below the LOQ).
Direct-infusion high-resolution mass spectrometry (DI-HRMS)
Direct-infusion was performed using chip-based infusion (400 nozzles, nominal internal Ø 5 μm) on the TriVersa NanoMate (Advion, Ithaca, NY, USA). High-resolution mass spectrometry (140,000) was performed using a Q-ExactivePlus (Thermo Scientific GmbH, Bremen, Germany) using a scan range of m/z 70 to 600 in positive and negative modes. Besides mass calibration of the instrument, internal lock masses were used for high mass accuracy. Cells were harvested in biological triplicates.
RAW data files were converted to mzXML format using MSConvert (Chambers et al
2012). The data were processed using an in-house developed untargeted metabolomics pipeline written in the R programming language (
http://www.r-project.org). First, the mzXML files were converted to readable format by the XCMS package (Smith et al
2006). For every sample, peak finding was done and peaks with the same
m/z (within 0.5*fwhm) were grouped over different samples. Peak groups that were not present in three out of three technical replicates in at least one biological sample were discarded. The intensities of the technical replicates were averaged. Peak groups were identified using all entries in the HMDB, including their most likely adducts (Na
+, K
+, NH
4
+ in positive mode and Cl
− and formate in negative mode) and isotopes, using an accuracy of 3 ppm or better. The statistical analysis was a t-test on the area under the curve (AUC) in a plot of intensities against time for every metabolite. Raw metabolomics data can be supplied upon request.
Amino acids
Amino acid concentrations were determined using the UPLC-MS/MS method described by Prinsen et al (
2016). Apart from adapting the range of the calibrators and quality control (QC) samples to resemble the concentrations in the samples, no further adaptations were needed for sample preparation or analysis of the amino acids.
Vitamin B6 vitamers
Vitamin B6 vitamers were quantified according to the method of van der Ham et al (
2012).
5-methyltetrahydrofolate (5-mTHF)
5-mTHF was purchased from Sigma-Aldrich (Steinheim, Germany). The internal standard 13C5–5-mTHF was purchased from Merck KGaA (Darmstadt, Germany). 5-mTHF analyses were performed on a Waters Micromass Quattro Ultima triple quadrupole mass spectrometer (Manchester, U.K.), using an Acquity UPLC® BEH C18 (130 Å, 17 μm 2.1 × 50 mm column) (Waters, Manchester, UK), which was kept at 30 °C, while the autosampler temperature was kept at 15 °C. The dwell time was set at 0.3 s. The capillary voltage was 3.00 kV and the cone voltage was 35 V. The source and desolvation temperatures were 120 and 450 °C respectively. The cone gas flow rate was 158 L/h. Quantitative analysis was achieved using a negative ion multiple reaction monitoring (MRM) mode with the m/z transitions of 460.2 > 313.2 and 465.2 > 313.2 with a collision energy of 17 and 18 V, for 5-mTHF and 13C5–5-mTHF respectively. The specific MRM transitions were determined by direct infusion of both standards and internal standards.
Neuro-2a cells were grown in 6-well plates and maintained in DMEM GlutaMAX™. When cells reached a confluence of >70%, they were washed twice with room temperature PBS and incubated with B6 vitamer-free DMEM GlutaMAX-I (supplemented with 10% FBS, 1% P/S, and with either 100 nM PL-HCl or without PL-HCl): PBS, 1:1. Cells were grown for 72 h in these media before collection. At 72 h the medium was refreshed with the exposition medium: B6 vitamer-free DMEM GlutaMAX-I (supplemented with 10% FBS, 1% P/S, and without or with 100 nM PL-HCl): PBS (
13C
6-glucose, 25 mM), 1:1. Cells were harvested at
T = 0.5, 4 and 12 h. Uniformly labelled
13C
6-glucose (99%) was purchased from Cambridge Isotope Laboratories, Inc. (MA, USA). To quantify the intracellular
13C
3-serine and
13C
2-glycine, we adapted the LC-MS/MS method described by Prinsen et al (
2016).
Protein analysis
Protein concentrations were quantified using the 96-well microplate protocol of the colorimetric bicinchoninic acid (BCA) Pierce™ BCA Protein Assay Kit (Thermo Fisher Scientific Incorporated), in accordance with the manufacturer’s protocol, with BSA as standard.
Statistical analysis
Statistical significance was determined with unpaired two-tailed t-test, using GraphPad Prism 6 (version 6.0.2, GraphPad Software Inc.) software.