Urinary organic acids in peroxisomal disorders: a simple screening method

A homozygous Gly470Ala variant in PEX6 causes severe Zellweger spectrum disorder

Zellweger spectrum disorder (ZSD) is a group of autosomal recessive disorders caused by biallelic pathogenic variants in any one of the 13 PEX genes essential for peroxisomal biogenesis. We report a cohort of nine infants who presented at birth with severe neonatal features suggestive of ZSD and found to be homozygous for a variant in PEX6 (NM_000287.4:c.1409G > C[p.Gly470Ala]). All were of Mixtec ancestry and identified by the California Newborn Screening (NBS) Program to have elevated C26:0-lysophosphatidylcholine but no reportable variants in ABCD1. The clinical and biochemical features of this cohort are described within. Gly470Ala may represent a founder variant in the Mixtec population of Central California. ZSD should be considered in patients who present at birth with severe hypotonia and enlarged fontanelles, especially in the setting of an abnormal NBS, Mixtec ancestry, or family history of infant death. There is a need to further characterize the natural history of ZSD, the Gly470Ala variant, and expand upon possible genotype-phenotype correlations.

Determination of up to twenty carboxylic acid containing compounds in clinically relevant matrices by o-benzylhydroxylamine derivatization and liquid chromatography-tandem mass spectrometry

Carboxylic acid containing compounds (R-COOH) are involved in a large number of biological processes and they are relevant for several pathological processes such as neurodegeneration or cancer. Comprehensive methodologies for the quantitative determination of R-COOH in biological samples are required. In this study we have developed a LC-MS/MS method for the quantification of 20 endogenous R-COOH belonging to different pathways such as kynurenine metabolism, serotoninergic pathway, glycolysis, tricarboxylic acid cycle, dopaminergic pathway, short chain fatty acids and glycine metabolism. The approach included derivatization with o-benzylhydroxylamine (reaction time 1 h), liquid-liquid extraction with ethyl acetate and LC-MS/MS detection (run time 10 min). The method was optimized and validated in 5 different matrices (urine, plasma, saliva, brain and liver) following two different approaches: (i) using surrogate matrices and (ii) using actual human samples by standard additions. A suitable linearity was obtained in the endogenous range of the analytes. Adequate intra and inter-assay accuracies (80-120%) and intra- and inter-assay precisions (<20%) were achieved for almost all analytes in all studied matrices. The method was applied in several scenarios to confirm (i) human urinary changes produced in glycolysis after exercise, (ii) metabolic changes produced in rat brain and plasma by methamphetamine administration and (iii) metabolic alterations in human plasma caused by vitamin B6 deficiency. Additionally, the application of the method allowed for establishing previously unreported alterations in R-COOH metabolites under these conditions. Due to the comprehensive analyte and matrix coverage and the wide applicability of the developed methodology, it can be considered as a suitable tool for the study of R-COOH status in health and disease by targeted metabolomics.

Dysmorphic features in a newborn with neurological, liver and kidney involvement by defective peroxisomal biogenesis. Case report

Introduction: Inborn errors of metabolism have significant morbidity and mortality rates in the neonatal period. One of these disorders is defective peroxisomal biogenesis, which causes complex and severe clinical pictures because peroxisomes are present in all nucleated cells of mammals.Case presentation: This is the case of a newborn with dysmorphic features who had seizures at birth and presented with neurological, liver, kidney and heart involvement during her 20 days of life. Necropsy confirmed liver and kidney involvement, which, together with family history of death of a sibling and a cousin, led to suspect a peroxisomal disease that was confirmed by the biochemical alterations observed.Discussion: Dysmorphism and seizures at birth may be an expression of a metabolic disease. The findings of the physical examination and the demonstration of liver, kidney and heart involvement are consistent with the initial description of Zellweger syndrome; the biochemical alterations are conclusive.Conclusions: It is necessary to define if dysmorphism is an isolated finding or if there is involvement of other organ(s) or system(s) to establish a suitable diagnosis of peroxisome biogenesis. Inborn errors of metabolism should be included in the diagnosis of dysmorphic newborns when several organs are involved, since their identification enables genetic counseling.

Clinical, biochemical and metabolic characterisation of a mild form of human short-chain enoyl-CoA hydratase deficiency: significance of increased N-acetyl-S-(2-carboxypropyl)cysteine excretion

BACKGROUND

Short-chain enoyl-CoA hydratase-ECHS1-catalyses many metabolic pathways, including mitochondrial short-chain fatty acid β-oxidation and branched-chain amino acid catabolic pathways; however, the metabolic products essential for the diagnosis of ECHS1 deficiency have not yet been determined. The objective of this report is to characterise ECHS1 and a mild form of its deficiency biochemically, and to determine the candidate metabolic product that can be efficiently used for neonatal diagnosis.

METHODS

We conducted a detailed clinical, molecular genetics, biochemical and metabolic analysis of sibling patients with ECHS1 deficiency. Moreover, we purified human ECHS1, and determined the substrate specificity of ECHS1 for five substrates via different metabolic pathways.

RESULTS

Human ECHS1 catalyses the hydration of five substrates via different metabolic pathways, with the highest specificity for crotonyl-CoA and the lowest specificity for tiglyl-CoA. The patients had relatively high (∼7%) residual ECHS1 enzyme activity for crotonyl-CoA and methacrylyl-CoA caused by the compound heterozygous mutations (c.176A>G, (p.N59S) and c.413C>T, (p.A138V)) with normal mitochondrial complex I-IV activities. Affected patients excrete large amounts of N-acetyl-S-(2-carboxypropyl)cysteine, a metabolite of methacrylyl-CoA.

CONCLUSIONS

Laboratory data and clinical features demonstrated that the patients have a mild form of ECHS1 deficiency harbouring defective valine catabolic and β-oxidation pathways. N-Acetyl-S-(2-carboxypropyl) cysteine level was markedly high in the urine of the patients, and therefore, N-acetyl-S-(2-carboxypropyl)cysteine was regarded as a candidate metabolite for the diagnosis of ECHS1 deficiency. This metabolite is not part of current routine metabolic screening protocols, and its inclusion, therefore, holds immense potential in accurate diagnosis.

Zellweger syndrome and associated brain malformations: report of a novel Peroxin1 (PEX1) mutation in a Native American infant

Zellweger syndrome (cerebrohepatorenal syndrome) is very rare and is the most severe form of peroxisomal biogenesis disorders. These can be caused by mutations in any of the currently known Peroxin genes and typically present in the neonatal period with multiorgan involvement. Patients usually do not survive beyond 1 year of age. This article reports a case of Zellweger syndrome in a male Native American infant confirmed by clinical findings, imaging studies, and biochemical analysis. Genetic studies show a novel mutation (c.3030G>T, p. Glutamine1010Histidine) altering the last nucleotide of exon 19 in the Peroxin1 (PEX1) gene.

Bezafibrate can be a new treatment option for mitochondrial fatty acid oxidation disorders: evaluation by in vitro probe acylcarnitine assay

BACKGROUND

The number of patients with mitochondrial fatty acid oxidation (FAO) disorders is recently becoming larger with the spread of newborn mass screening. Despite the advances in metabolic and molecular characterization of FAO disorders, the therapeutic studies are still limited. It was reported recently that bezafibrate (BEZ), an agonist of peroxisome proliferating activator receptor (PPAR), can restore FAO activity in cells from carnitine palmitoyltransferase-2 (CPT2) and very-long-chain acyl-CoA dehydrogenase (VLCAD) deficiencies as well as clinical symptoms in the adult patients.

METHODS

In this study, the therapeutic effect of BEZ was determined by in vitro probe acylcarnitine (IVP) assay using cultured fibroblasts and tandem mass spectrometry on various FAO disorders. The clinical trial of BEZ treatment for a boy with the intermediate form of glutaric acidemia type 2 (GA2) was also performed.

RESULTS

The effect of BEZ was proven in cells from various FAO disorders including GA2, deficiencies of VLCAD, medium-chain acyl-CoA dehydrogenase, CPT2, carnitine acylcarnitine translocase and trifunctional protein, by the IVP assay. The aberrantly elevated long- or medium-chain acylcarnitines that are characteristic for each FAO disorder were clearly corrected by the presence of BEZ (0.4 mmol/L) in culture medium. Moreover, daily administration of BEZ in a 2-year-old boy with GA2 dramatically improved his motor and cognitive skills, accompanied by sustained reduction of C4, C8, C10 and C12 acylcarnitines in blood, and normalized the urinary organic acid profile. No major adverse effects have been observed.

CONCLUSION

These results indicate that BEZ could be a new treatment option for FAO disorders.

Data processing in metabolic fingerprinting by CE-UV: Application to urine samples from autistic children

Metabolic fingerprinting of biofluids such as urine can be used to detect and analyse differences between individuals. However, before pattern recognition methods can be utilised for classification, preprocessing techniques for the denoising, baseline removal, normalisation and alignment of electropherograms must be applied. Here a MEKC method using diode array detection has been used for high-resolution separation of both charged and neutral metabolites. Novel and generic algorithms have been developed for use prior to multivariate data analysis. Alignment is achieved by combining the use of reference peaks with a method that uses information from multiple wavelengths to align electropherograms to a reference signal. This metabolic fingerprinting approach by MEKC has been applied for the first time to urine samples from autistic and control children in a nontargeted and unbiased search for markers for autism. Although no biomarkers for autism could be determined using MEKC data here, the general approach presented could also be applied to the processing of other data collected by CE with UV-Vis detection.

Development and validation of a liquid chromatographic method for the determination of hydroxymethylfurfural and alpha-ketoglutaric acid in human plasma

Hydroxymethylfurfural (HMF) and alpha-ketoglutaric acid (KG) have been recently investigated as potential cancer cell damaging agents. We herein report for the first time a validated quantitative assay for their simultaneous determination in human plasma which is amenable to be applied in the future screening of the target compounds in human probands in order to properly design a targeted chemotherapeutic regimen for certain types of malignant tumors. A simple liquid chromatographic method in conjunction to derivatization after a two-step optimized solid phase clean-up procedure is described. The method is based on the reaction of HMF and KG with 2-nitrophenylhydrazine or 2,4-dinitrophenylhydrazine in an aqueous environment. Reaction conditions were studied with respect to pH, reagent volume, reaction temperature and time. Exact testing of such parameters beside careful selection of the mobile phase composition rendered feasible the quantification of the chemically significantly differing analytes along a single chromatographic run. The formed derivatives could be separated isocratically by reversed-phase LC on a C(8)-column. Detection in the UV and in the visible range is possible. Results showed good recovery and reproducibility with detection limits (S/N=3) down to 2 picomoles analyte on column. Resolution of the syn and anti geometric isomers of the HMF and KG derivatives is possible. The isomeric ratio in relation to the reaction pH is discussed.

Systems Toxicology: Integrated Genomic, Proteomic and Metabonomic Analysis of Methapyrilene Induced Hepatotoxicity in the Rat

Administration of high doses of the histamine antagonist methapyrilene to rats causes periportal liver necrosis. The mechanism of toxicity is ill-defined and here we have utilized an integrated systems approach to understanding the toxic mechanisms by combining proteomics, metabonomics by 1H NMR spectroscopy and genomics by microarray gene expression profiling. Male rats were dosed with methapyrilene for 3 days at 150 mg/kg/day, which was sufficient to induce liver necrosis, or a subtoxic dose of 50 mg/kg/day. Urine was collected over 24 h each day, while blood and liver tissues were obtained at 2 h after the final dose. The resulting data further define the changes that occur in signal transduction and metabolic pathways during methapyrilene hepatotoxicity, revealing modification of expression levels of genes and proteins associated with oxidative stress and a change in energy usage that is reflected in both gene/protein expression patterns and metabolites. The difficulties of combining and interpreting multiomic data are considered.

Probing lipid-protein interactions using lipid microarrays

Lipids are central to the regulation and control of several cellular functions. They form many of the important structural features of cells, and are critical members of cellular signal transduction pathways. Cellular dysfunction is often caused by errors in lipid signaling; therefore, the proteins that interact with, synthesize or metabolize the lipids are potential therapeutic targets. Characterizing the contingent of cellular lipids and their abundance and how this is associated with disease will facilitate understanding how to intervene to correct diseases caused by dysfunctional lipid signaling. Since lipid-signaling networks involve several classes of proteins it is essential to determine the identity and role of these proteins in order to understand the networks. These proteins may be receptors, effectors, transporters or enzymes. We present tools, specifically, a lipid microarray platform, to uncover lipid-binding effector proteins that function in lipid signaling pathways. Lipid microarrays will allow researchers to obtain a comparable fingerprint of the proteins from a cell or tissue that bind to lipids, and also enable the identification of functionally important lipid-binding proteins. By applying a systematic approach to the quantification of lipid-protein interactions, lipid microarrays will provide an integrated knowledge base for the human lipidome. These tools have the potential to identify and validate targets to improve personalized medicine and health.

Metabolic evaluation of the sick neonate

Inherited metabolic diseases are rare causes of neonatal morbidity, but they are associated with significant recurrence risks for the parents. Prompt identification and treatment of an infant with an inherited metabolic disease can minimize morbidity, mortality, and lifelong developmental problems. Diagnosis often requires specialized laboratory testing, but common laboratory tests can help identify those infants needing further evaluation. This paper reviews the laboratory abnormalities which can be found in various inherited metabolic diseases and can guide selection of specialized metabolic testing. Consultation with a metabolic specialist is essential for timely diagnosis and treatment to ensure the best possible outcome.

Micellar electrokinetic chromatographic and capillary zone electrophoretic methods for screening urinary biomarkers of human disorders: a critical review of the state-of-the-art

Human urine plays a central role in clinical diagnostic being one of the most-frequently used body fluid for detection of biological markers. Samples from patients with different diseases display patterns of biomarkers that differ significantly from those obtained from healthy subjects. The availability of fast, reproducible, and easy-to-apply analytical techniques that would allow identification of a large number of these analytes is thus highly desiderable since they may provide detailed information about the progression of a pathological process. From among the variety of methods so far applied for the determination of urinary metabolites, capillary electrophoresis, both in the capillary zone electrophoresis (CZE) and micellar electrokinetic chromatography (MEKC) modes, represents a robust and reliable analytical tool widely used in this area. The aim of the present article is to focus the interest of the reader on recent applications of MEKC and CZE in the field of urinary biomarkers and to discuss advantages and/or limitations of each mode.

Clinical onset and prognosis of Asian children with organic acidemias, as detected by analysis of urinary organic acids using GC/MS, instead of mass screening

Organic acidemias (OAs) have been detected worldwide in symptomatic patients using gas chromatography mass spectrometry. We diagnosed 188 Asian cases of OAs by analysis of urinary organic acids and investigated their clinical onset and outcome. Methylmalonic acidemia (MMA) was most common (74 cases), followed by propionic acidemia (23 cases), ornitine transcarbamylase deficiency (22 cases), and multiple carboxylase deficiency (15 cases). For these 188 patients, onset was most frequent in the neonatal period or early infancy. Approximately 30% of the patients had a family history of similar symptoms or diseases. Although the outcome of OA patients varied, patients with early onset generally had poor outcomes despite early detection. Of the 45 MMA patients whose clinical data were available, 25 were clinically vitamin B12-responsive, while the remaining 20 were non-responsive. A favorable outcome was obtained in 7 of the 25 B12-responsive patients, and in only 3 of the 20 B12-nonresponsive patients. It was suggested that even in B12-responsive MMA cases, earlier detection and B12 therapy were needed to improve the prognosis. We concluded that detection of such patients at the presymptomatic stages using newborn mass screening is essential for prognosis improvement with OAs.

Comprehensive analysis of metabolites in Corynebacterium glutamicum by gas chromatography/mass spectrometry

An analytical method based on gas chromatography/mass spectrometry was developed for metabolome investigation ofCorynebacterium glutamicum. For the first time a fast method for metabolic screening that can be automated is described for this organism. More than 1000 compounds could be detected per experiment, ca. 330 of those showed a peak area significantly above background. Out of these 164 compounds were identified so far, representing derivatives of 121 different metabolites, which were quantified in one sample. In spite of the different chemical nature of metabolites and high matrix content, a measurement reproducibility in the range of 6% error was achieved. The application of this method for the analysis of the adaptation ofC. glutamicumto different growth conditions is demonstrated.

Micellar electrokinetic capillary chromatography and data alignment analysis: a new tool in urine profiling

The complex nature of biofluids demands efficient, sensitive and high-resolution analytical methodologies to examine how the 'metabolic fingerprint' changes during disease. This paper describes how sulphated beta-cyclodextrin-modified micellar electrokinetic capillary chromatography (SbetaCD-MECC) has been combined with data alignment analysis and may prove a useful new tool in urine profiling, allowing for separation of over 80 urinary analytes in under 25 min. The optimised and validated SbetaCD-MECC methodology combined with data alignment analysis provides rapid identification of 'mismatches' between urine profiles which are not easily detected with the naked eye as well as a 'similarity score' which indicates the total sum of differences between one profile and another. The combination of SbetaCD-MECC with data alignment software should prove a useful alternative tool in metabonomic studies for rapid comparison of urine profiles.

PEROXISOMEBIOGENESISDISORDERS

The peroxisome biogenesis disorders (PBDs) comprise 12 autosomal recessive complementation groups (CGs). The multisystem clinical phenotype varies widely in severity and results from disturbances in both development and metabolic homeostasis. Progress over the last several years has lead to identification of the genes responsible for all of these disorders and to a much improved understanding of the biogenesis and function of the peroxisome. Increasing availability of mouse models for these disorders offers hope for a better understanding of their pathophysiology and for development of therapies that might especially benefit patients at the milder end of the clinical phenotype.

Simultaneous enantioselective analysis of chiral urinary metabolites in patients with Zellweger syndrome

Enantio-MDGC-MS analysis with heptakis-(2,3-di-O-methyl-6-O-tert.-butyl-dimethylsilyl)-beta-cyclodextrin as the chiral main column is a powerful tool for the separation of chiral compounds. This paper reports on the simultaneous stereodifferentiation of 2-hydroxyisocaproic acid (HICA), 3-methyladipic acid (3-MA), 2-hydroxyglutaric acid (2-HG), 3-(4-hydroxyphenyl)-lactic acid (HPLA), 2-hydroxysebacic acid (2-HS) and 3-hydroxysebacic acid (3-HS) in a single chromatographic run. These chiral urinary metabolites are useful in the diagnosis of peroxisomal diseases such as Zellweger syndrome (ZS). In this investigation, urine samples from nine patients with ZS were analysed in order to reveal the enantiomeric ratio of these chiral metabolites. The stereodifferentiation of the analysed chiral compounds may provide important information on their biochemical origin.

Stereoselective analysis of 2-hydroxysebacic acid in urine of patients with Zellweger syndrome and of premature infants fed with medium-chain triglycerides

The chiral metabolite 2-hydroxysebacic acid (2-HS) is considered to be an important diagnostic marker for peroxisomal disorders. The pathway of formation of 2-HS, excreted in increased amounts in patients with peroxisomal diseases, is not absolutely clear. Moreover, there is no information about the enantiomeric distribution of 2-HS in human urine. Here, we describe the stereodifferentiation of 2-HS in urine samples of nine patients with Zellweger syndrome (ZS), and for the first time in urine samples of premature infants fed a medium-chain triglyceride (MCT)-containing diet. Using enantioselective multidimensional gas chromatography-mass spectrometry, an increased excretion of 2R-HS was observed in all investigated ZS patients. 2-HS was also present in urine samples of premature infants fed MCT. Analogously to the ZS patients, a dominant 2R-HS excretion in the urine samples of the premature infants was identified. The formation of 2-HS is expected to result from the same or similar pathways as described for ZS patients. Additionally, we determined the absolute configuration of urinary 3-hydroxysebacic acid (3-HS) in the cases investigated. The enantioselective analysis provides further information for the diagnosis and treatment of patients with impaired peroxisomal fatty acid oxidation. Further insight into the metabolic origin and the biochemical pathway leading to these urinary metabolites is provided.

Toward the implementation of metabolomic assessments of human health and nutrition

Metabolomics is emerging as an exciting post-genomic science with applications that span the scope of biotechnology and medicine. Although metabolomics is still in its infancy, it has already been used to identify the function of genes, describe the effects of toxicological, pharmaceutical, nutritional and environmental interventions, and to build integrated databases of metabolite concentrations across human and research animal populations. Metabolomics provides nutrition with an invaluable tool for determining the distributions of metabolite concentrations in humans, the relationship of these metabolite concentrations to disease, and the extent to which nutrition can modulate metabolite concentrations.

Contiguous deletion of the X-linked adrenoleukodystrophy gene (ABCD1) and DXS1357E: a novel neonatal phenotype similar to peroxisomal biogenesis disorders

X-linked adrenoleukodystrophy (X-ALD) results from mutations in ABCD1. ABCD1 resides on Xq28 and encodes an integral peroxisomal membrane protein (ALD protein [ALDP]) that is of unknown function and that belongs to the ATP-binding cassette-transporter superfamily. Individuals with ABCD1 mutations accumulate very-long-chain fatty acids (VLCFA) (carbon length >22). Childhood cerebral X-ALD is the most devastating form of the disease. These children have the earliest onset (age 7.2 +/- 1.7 years) among the clinical phenotypes for ABCD1 mutations, but onset does not occur at <3 years of age. Individuals with either peroxisomal biogenesis disorders (PBD) or single-enzyme deficiencies (SED) in the peroxisomal beta-oxidation pathway--disorders such as acyl CoA oxidase deficiency and bifunctional protein deficiency--also accumulate VLCFA, but they present during the neonatal period. Until now, it has been possible to distinguish unequivocally between individuals with these autosomal recessively inherited syndromes and individuals with ABCD1 mutations, on the basis of the clinical presentation and measurement of other biochemical markers. We have identified three newborn boys who had clinical symptoms and initial biochemical results consistent with PBD or SED. In further study, however, we showed that they lacked ALDP, and we identified deletions that extended into the promoter region of ABCD1 and the neighboring gene, DXS1357E. Mutations in DXS1357E and the ABCD1 promoter region have not been described previously. We propose that the term "contiguous ABCD1 DXS1357E deletion syndrome" (CADDS) be used to identify this new contiguous-gene syndrome. The three patients with CADDS who are described here have important implications for genetic counseling, because individuals with CADDS may previously have been misdiagnosed as having an autosomal recessive PBD or SED