Inborn errors in the vitamin B6 salvage enzymes associated with neonatal epileptic encephalopathy and other pathologies

Innovative Strategies in X-ray Crystallography for Exploring Structural Dynamics and Reaction Mechanisms in Metabolic Disorders

Enzymes are crucial in metabolic processes, and their dysfunction can lead to severe metabolic disorders. Structural biology, particularly X-ray crystallography, has advanced our understanding of these diseases by providing 3D structures of pathological enzymes. However, traditional X-ray crystallography faces limitations, such as difficulties in obtaining suitable protein crystals and studying protein dynamics. X-ray free-electron lasers (XFELs) have revolutionized this field with their bright and brief X-ray pulses, providing high-resolution structures of radiation-sensitive and hard-to-crystallize proteins. XFELs also enable the study of protein dynamics through room temperature structures and time-resolved serial femtosecond crystallography, offering comprehensive insights into the molecular mechanisms of metabolic diseases. Understanding these dynamics is vital for developing effective therapies. This review highlights the contributions of protein dynamics studies using XFELs and synchrotrons to metabolic disorder research and their application in designing better therapies. It also discusses G protein-coupled receptors (GPCRs), which, though not enzymes, play key roles in regulating physiological systems and are implicated in many metabolic disorders.

Efficacy of vitamins B1 and B6 as an adjunctive therapy to lithium in bipolar-I disorder: A double-blind, randomized, placebo-controlled, clinical trial

BACKGROUND

The use of adjunctive therapy for bipolar disorder is increasingly considered to increase the efficacy of standard treatments. In this randomized clinical trial, we evaluated the effect of vitamins B1 and B6 in separate treatment arms on mood symptoms, cognitive status, and sleep quality in hospitalized patients with bipolar disorder in manic episodes.

METHOD

In addition to receiving standard lithium treatment, participants (N = 66) were randomized to one of three conditions: 100 mg of vitamin B1, 40 mg of vitamin B6, or placebo. Outcomes were assessed one and 8 weeks of daily treatment, including the Young Mania Rating Scale (YMRS), Pittsburgh Sleep Quality Scale (PSQI), and Mini-Mental State Examination (MMSE). This study was performed between December 2020 and September 2021 based on the registration code number IRCT20200307046712N1.

RESULTS

Vitamin B6 had a significant effect (P value < 0.025 as significant) on mood improvement compared to placebo (F (1, 27.42) = 30.25, P < 0.001, r = 0.72), but vitamin B1 had no significant effect on mood improvement compared to Placebo (F (1/35.68) = 4.76, P = 0.036, r = 0.34). The contrasts between groups on PSQI showed a significant effect (P value < 0.025 as significant) of vitamin B6 over placebo for sleep status improvement (F (1/32.91) = 16.24, P < 0.001, r = 0.57) and also a significant effect of vitamin B1 over placebo (F (1/41.21) = 13.32, P < 0.001, r = 0.49).

CONCLUSIONS

The use of vitamin B6 as an adjunctive therapy to lithium can be associated with the improvement of mood symptoms in patients with bipolar disorder in the midst of a manic episode.

Vitamin B6: a scoping review for Nordic Nutrition Recommendations 2023

Pyridoxal 5´-phosphate (PLP) is the main form of vitamin B6 in animal tissue and functions as a coenzyme for more than 160 different enzymatic reactions in the metabolism of amino acids, carbohydrates, lipids, and neurotransmitters. Estimated dietary intake of vitamin B6 and plasma PLP values differ a lot between studies, something which may be due to variable use of supplements, variations in dietary assessment and analytical methods. These factors make it difficult to achieve precise data for setting a correct recommended intake of vitamin B6. In addition, a plasma PLP concentration of 30 nmol/L is considered to be sufficient and the current recommendations for vitamin B6 intake is based on this concept. However, the metabolic marker for vitamin B6 status, HK ratio (HKr), starts to increase already when plasma PLP falls below 100 nmol/L and increases more steeply below 50 nmol/L, indicating biochemical deficiency. Consequently, a plasma PLP concentration of 30 nmol/L, may be too low as a marker for an adequate vitamin B6 status.

Impact of lifestyle factors on dietary vitamin B6 intake and plasma pyridoxal 5'-phosphate level in UK adults: National Diet and Nutrition Survey Rolling Programme (NDNS) (2008-2017)

Reduction in dietary vitamin B6 intake is associated with an increased relative risk of diseases such as cancer, atherosclerosis and cognitive dysfunction. The current research has assessed vitamin B6 intakes and PLP concentrations as a marker of vitamin B6 status among the UK adult (≥ 19 years) population. This study was carried out using a cross-sectional analysis of the National Diet and Nutrition Survey Rolling Programme (NDNS) (2008-2017). The impacts of lifestyle factors, including type of diet, smoking, alcohol consumption, and commonly used medications grouped by therapeutic usage, were determined, and data were analysed using IBM SPSS®. Results are expressed as medians (25th-75th percentiles), with P values ≤ 0·05 considered statistically significant. Among UK adults, the median intakes of total population of dietary vitamin B6 met the reference nutrient intake and median plasma PLP concentrations were above the cut-off of vitamin B6 deficiency; however, we found an association between reduction in vitamin B6 intake and plasma PLP concentration and age group (P < 0·001). Smokers had significantly lower plasma PLP concentrations than non-smokers (P < 0·001). Moreover, regression analysis showed some commonly used medications were associated with plasma PLP levels reduction (P < 0·05). Taken together, we report on a tendency for dietary vitamin B6 intake and plasma PLP concentrations to decrease with age and lifestyle factors such as smoking and medication usage. This information could have important implications for smokers and in the elderly population using multiple medications (polypharmacy).

Scientific opinion on the tolerable upper intake level for vitamin B6

Following a request from the European Commission, the EFSA Panel on Nutrition, Novel Foods and Food Allergens (NDA) was asked to deliver a scientific opinion on the tolerable upper intake level (UL) for vitamin B6. Systematic reviews of the literature were conducted by a contractor. The relationship between excess vitamin B6 intakes and the development of peripheral neuropathy is well established and is the critical effect on which the UL is based. A lowest-observed-effect-level (LOAEL) could not be established based on human data. A reference point (RP) of 50 mg/day is identified by the Panel from a case-control study, supported by data from case reports and vigilance data. An uncertainty factor (UF) of 4 is applied to the RP to account for the inverse relationship between dose and time to onset of symptoms and the limited data available. The latter covers uncertainties as to the level of intake that would represent a LOAEL. This leads to a UL of 12.5 mg/day. From a subchronic study in Beagle dogs, a LOAEL of 50 mg/kg body weight (bw) per day can be identified. Using an UF of 300, and a default bw of 70 kg, a UL of 11.7 mg/day can be calculated. From the midpoint of the range of these two ULs and rounding down, a UL of 12 mg/day is established by the Panel for vitamin B6 for adults (including pregnant and lactating women). ULs for infants and children are derived from the UL for adults using allometric scaling: 2.2-2.5 mg/day (4-11 months), 3.2-4.5 mg/day (1-6 years), 6.1-10.7 mg/day (7-17 years). Based on available intake data, EU populations are unlikely to exceed ULs, except for regular users of food supplements containing high doses of vitamin B6.

Traditional and Innovative Anti-seizure Medications Targeting Key Physiopathological Mechanisms: Focus on Neurodevelopment and Neurodegeneration

Despite the wide range of compounds currently available to treat epilepsy, there is still no drug that directly tackles the physiopathological mechanisms underlying its development. Indeed, antiseizure medications attempt to prevent seizures but are inefficacious in counteracting or rescuing the physiopathological phenomena that underlie their onset and recurrence, and hence do not cure epilepsy. Classically, the altered excitation/inhibition balance is postulated as the mechanism underlying epileptogenesis and seizure generation. This oversimplification, however, does not account for deficits in homeostatic plasticity resulting from either insufficient or excessive compensatory mechanisms in response to a change in network activity. In this respect, both neurodevelopmental epilepsies and those associated with neurodegeneration may share common underlying mechanisms that still need to be fully elucidated. The understanding of these molecular mechanisms shed light on the identification of new classes of drugs able not only to suppress seizures, but also to present potential antiepileptogenic effects or "disease-modifying" properties.

Elucidating the Interaction between Pyridoxine 5'-Phosphate Oxidase and Dopa Decarboxylase: Activation of B6-Dependent Enzyme

Pyridoxal 5'-phosphate (PLP), the active form of vitamin B6, serves as a cofactor for scores of B6-dependent (PLP-dependent) enzymes involved in many cellular processes. One such B6 enzyme is dopa decarboxylase (DDC), which is required for the biosynthesis of key neurotransmitters, e.g., dopamine and serotonin. PLP-dependent enzymes are biosynthesized as apo-B6 enzymes and then converted to the catalytically active holo-B6 enzymes by Schiff base formation between the aldehyde of PLP and an active site lysine of the protein. In eukaryotes, PLP is made available to the B6 enzymes through the activity of the B6-salvage enzymes, pyridoxine 5'-phosphate oxidase (PNPO) and pyridoxal kinase (PLK). To minimize toxicity, the cell keeps the content of free PLP (unbound) very low through dephosphorylation and PLP feedback inhibition of PNPO and PLK. This has led to a proposed mechanism of complex formation between the B6-salvage enzymes and apo-B6 enzymes prior to the transfer of PLP, although such complexes are yet to be characterized at the atomic level, presumably due to their transient nature. A computational study, for the first time, was used to predict a likely PNPO and DDC complex, which suggested contact between the allosteric PLP tight-binding site on PNPO and the active site of DDC. Using isothermal calorimetry and/or surface plasmon resonance, we also show that PNPO binds both apoDDC and holoDDC with dissociation constants of 0.93 ± 0.07 μM and 2.59 ± 0.11 μM, respectively. Finally, in the presence of apoDDC, the tightly bound PLP on PNPO is transferred to apoDDC, resulting in the formation of about 35% holoDDC.

Benchmarking of univariate pleiotropy detection methods applied to epilepsy

Pleiotropy is a widespread phenomenon that may increase insight into the etiology of biological and disease traits. Since genome-wide association studies frequently provide information on a single trait only, only univariate pleiotropy detection methods are applicable, with yet unknown comparative performance. Here, we compared five such methods with respect to their ability to detect pleiotropy, including meta-analysis, ASSET, cFDR, CPBayes, and PLACO, by performing extended computer simulations that varied the underlying etiological model for pleiotropy for a pair of traits, including the number of causal variants, degree of traits' overlap, effect sizes as well as trait prevalence, and varying sample sizes. Our results indicate that ASSET provides the best trade-off between power and protection against false positives. We then applied ASSET to a previously published ILAE consortium dataset on complex epilepsies, comprising genetic generalized epilepsy and focal epilepsy cases and corresponding controls. We identified a novel candidate locus at 17q21.32 and confirmed locus 2q24.3, previously identified to act pleiotropically on both epilepsy subtypes by a mega-analysis. Functional annotation, tissue-specific expression and regulatory function analysis as well as Bayesian co-localization analysis corroborated this result, rendering 17q21.32 a worthwhile candidate for follow-up studies on pleiotropy in epilepsies. This article is protected by copyright. All rights reserved.

Drosophila carrying epilepsy-associated variants in the vitamin B6 metabolism gene PNPO display allele- and diet-dependent phenotypes

Both genetic and environmental factors contribute to epilepsy. Understanding their contributions and interactions helps disease management. However, it is often challenging to study gene–environment interaction in humans due to their heterogeneous genetic background and less controllable environmental factors. The fruit fly, Drosophila melanogaster, has been proven to be a powerful model to study human diseases, including epilepsy. We generated knock-in flies carrying different epilepsy-associated pyridox(am)ine 5^′-phosphate oxidase (PNPO) alleles and studied the developmental, behavioral, electrophysiological, and fitness effects of each mutant allele under different dietary conditions. We showed that phenotypes in knock-in flies are allele and diet dependent, providing clues for timely and specific diet interventions. Our results offer biological insights into mechanisms underlying phenotypic variations and specific therapeutic strategies.

Pyridox(am)ine 5^′-phosphate oxidase (PNPO) catalyzes the rate-limiting step in the synthesis of pyridoxal 5^′-phosphate (PLP), the active form of vitamin B6 required for the synthesis of neurotransmitters gamma-aminobutyric acid (GABA) and the monoamines. Pathogenic variants in PNPO have been increasingly identified in patients with neonatal epileptic encephalopathy and early-onset epilepsy. These patients often exhibit different types of seizures and variable comorbidities. Recently, the PNPO gene has also been implicated in epilepsy in adults. It is unclear how these phenotypic variations are linked to specific PNPO alleles and to what degree diet can modify their expression. Using CRISPR-Cas9, we generated four knock-in Drosophila alleles, h^WT, h^R116Q, h^D33V , and h^R95H, in which the endogenous Drosophila PNPO was replaced by wild-type human PNPO complementary DNA (cDNA) and three epilepsy-associated variants. We found that these knock-in flies exhibited a wide range of phenotypes, including developmental impairments, abnormal locomotor activities, spontaneous seizures, and shortened life span. These phenotypes are allele dependent, varying with the known biochemical severity of these mutations and our characterized molecular defects. We also showed that diet treatments further diversified the phenotypes among alleles, and PLP supplementation at larval and adult stages prevented developmental impairments and seizures in adult flies, respectively. Furthermore, we found that h^R95H had a significant dominant-negative effect, rendering heterozygous flies susceptible to seizures and premature death. Together, these results provide biological bases for the various phenotypes resulting from multifunction of PNPO, specific molecular and/or genetic properties of each PNPO variant, and differential allele–diet interactions.

Phosphorylated B6 vitamer deficiency in SALT OVERLY SENSITIVE 4 mutants compromises shoot and root development

Stunted growth in saline conditions is a signature phenotype of the Arabidopsis SALT OVERLY SENSITIVE mutants (sos1-5) affected in pathways regulating the salt stress response. One of the mutants isolated, sos4, encodes a kinase that phosphorylates pyridoxal (PL), a B6 vitamer, forming the important coenzyme pyridoxal 5'-phosphate (PLP). Here, we show that sos4-1 and more recently isolated alleles are deficient in phosphorylated B6 vitamers including PLP. This deficit is concomitant with a lowered PL level. Ionomic profiling of plants under standard laboratory conditions (without salt stress) reveals that sos4 mutants are perturbed in mineral nutrient homeostasis, with a hyperaccumulation of transition metal micronutrients particularly in the root, accounting for stress sensitivity. This is coincident with the accumulation of reactive oxygen species, as well as enhanced lignification and suberization of the endodermis, although the Casparian strip is intact and functional. Further, micrografting shows that SOS4 activity in the shoot is necessary for proper root development. Growth under very low light alleviates the impairments, including salt sensitivity, suggesting that SOS4 is important for developmental processes under moderate light intensities. Our study provides a basis for the integration of SOS4 derived B6 vitamers into plant health and fitness.