Evaluation of comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry for the diagnosis of inherited metabolic disorders using an automated data processing strategy

Variant analysis of HPD genes from two families showing elevated tyrosine upon newborn screening by tandem mass spectrometry (MS/MS)

Background Alterations in the structure and activity of 4-hydroxyphenylpyruvate dioxygenase (HPD) are causally related to two different metabolic disorders: recessively inherited tyrosinemia type III and dominantly inherited hawkinsinuria. The aim of this study was to provide a new perspective for the clinical understanding of the pathogenesis of tyrosinemia type III or hawkinsinuria. Case presentation A full-term newborn baby born after a safe pregnancy and childbirth with a birth weight of 3200 g and another full-term baby born after a safe pregnancy and childbirth with a birth weight of 2800 g are reported and analysed. DNA extraction, next-generation sequencing, bioinformatics analysis, Sanger sequencing and biochemical analysis were performed. One patient with a heterozygous HPD gene (NM_002150.2) c.460G > A mutation and one patient with a heterozygous HPD gene (NM_002150.2) c.248delG mutation showing elevated tyrosine levels upon newborn screening by tandem mass spectrometry (MS/MS) are reported. Conclusions The HPD gene may not be a strictly autosomal recessive pathogenic gene, which provides a new perspective for the clinical understanding of the pathogenesis of tyrosinemia type III or hawkinsinuria.

Spectrum of mutations underlying Propionic acidemia and further insight into a genotype-phenotype correlation for the common mutation in Saudi Arabia

Propionic acidemia (PA) is an autosomal recessive metabolic disorder. PA is characterized by deficiency of the mitochondrial enzyme propionyl CoA carboxylase (PCC) that results in the accumulation of propionic acid. Alpha and beta subunits of the PCC enzyme are encoded by the PCCA and PCCB genes, respectively. Pathogenic variants in PCCA or PCCB disrupt the function of the PCC enzyme preventing the proper breakdown of certain amino acids and metabolites. To determine the frequency of pathogenic variants in PA in our population, 84 Saudi Arabian patients affected with PA were sequenced for both the PCCA and PCCB genes. We found that variants in PCCA accounted for 81% of our cohort (68 patients), while variants in PCCB only accounted for 19% (16 patients). In total, sixteen different sequence variants were detected in the study, where 7 were found in PCCA and 9 in PCCB. The pathogenic variant (c.425G > A; p.Gly142Asp) in PCCA is the most common cause of PA in our cohort and was found in 59 families (70.2%), followed by the frameshift variant (c.990dupT; p.E331Xfs*1) in PCCB that was found in 7 families (8.3%). The p.Gly142Asp missense variant is likely to be a founder pathogenic variant in patients of Saudi Arabian tribal origin and is associated with a severe phenotype. All variants were inherited in a homozygous state except for one family who was compound heterozygous. A total of 11 novel pathogenic variants were detected in this study thereby increasing the known spectrum of pathogenic variants in the PCCA and PCCB genes.

Mass spectrometric based approaches in urine metabolomics and biomarker discovery

Urine metabolomics has recently emerged as a prominent field for the discovery of non-invasive biomarkers that can detect subtle metabolic discrepancies in response to a specific disease or therapeutic intervention. Urine, compared to other biofluids, is characterized by its ease of collection, richness in metabolites and its ability to reflect imbalances of all biochemical pathways within the body. Following urine collection for metabolomic analysis, samples must be immediately frozen to quench any biogenic and/or non-biogenic chemical reactions. According to the aim of the experiment; sample preparation can vary from simple procedures such as filtration to more specific extraction protocols such as liquid-liquid extraction. Due to the lack of comprehensive studies on urine metabolome stability, higher storage temperatures (i.e. 4°C) and repetitive freeze-thaw cycles should be avoided. To date, among all analytical techniques, mass spectrometry (MS) provides the best sensitivity, selectivity and identification capabilities to analyze the majority of the metabolite composition in the urine. Combined with the qualitative and quantitative capabilities of MS, and due to the continuous improvements in its related technologies (i.e. ultra high-performance liquid chromatography [UPLC] and hydrophilic interaction liquid chromatography [HILIC]), liquid chromatography (LC)-MS is unequivocally the most utilized and the most informative analytical tool employed in urine metabolomics. Furthermore, differential isotope tagging techniques has provided a solution to ion suppression from urine matrix thus allowing for quantitative analysis. In addition to LC-MS, other MS-based technologies have been utilized in urine metabolomics. These include direct injection (infusion)-MS, capillary electrophoresis-MS and gas chromatography-MS. In this article, the current progresses of different MS-based techniques in exploring the urine metabolome as well as the recent findings in providing potentially diagnostic urinary biomarkers are discussed. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 36:115-134, 2017.

Mass Spectrometry-Based Metabolomic and Proteomic Strategies in Organic Acidemias

Organic acidemias (OAs) are inherited metabolic disorders caused by deficiency of enzymatic activities in the catabolism of amino acids, carbohydrates, or lipids. These disorders result in the accumulation of mono-, di-, or tricarboxylic acids, generally referred to as organic acids. The OA outcomes can involve different organs and/or systems. Some OA disorders are easily managed if promptly diagnosed and treated, whereas, in others cases, such as propionate metabolism-related OAs (propionic acidemia, PA; methylmalonic acidemia, MMA), neither diet, vitamin therapy, nor liver transplantation appears to prevent multiorgan impairment. Here, we review the recent developments in dissecting molecular bases of OAs by using integration of mass spectrometry- (MS-) based metabolomic and proteomic strategies. MS-based techniques have facilitated the rapid and economical evaluation of a broad spectrum of metabolites in various body fluids, also collected in small samples, like dried blood spots. This approach has enabled the timely diagnosis of OAs, thereby facilitating early therapeutic intervention. Besides providing an overview of MS-based approaches most frequently used to study the molecular mechanisms underlying OA pathophysiology, we discuss the principal challenges of metabolomic and proteomic applications to OAs.

Hawkinsinuria in two unrelated Greek newborns: identification of a novel variant, biochemical findings and treatment

BACKGROUND

Hawkinsinuria is a rare inborn error of tyrosine metabolism.

OBJECTIVES

To study novel hawkinsinuria cases by monitoring their biochemical profile and conducting a mutation analysis.

SUBJECTS AND METHODS

Among 92,519 newborns that underwent expanded newborn screening, two unrelated cases with high tyrosine blood levels were further investigated by chromatographic techniques and via genetic testing for 4-hydroxyphenylpyruvate dioxygenase (HPD) gene.

RESULTS

Elevated levels were monitored for blood/plasma tyrosine and for the specific diagnostic markers in urine. The two newborns were put on a special low tyrosine diet. Till completion of the 1st year of their life, liver function tests and brain MRI were normal. The mutation A33T was identified in both cases, while one neonate carried an additional novel mutation of HPD gene (V212M).

CONCLUSIONS

Two mutations of HPD gene, A33T, which are associated with hawkinsinuria and a novel one (V212M) were detected for the 1st time in Greek newborns.

Advances in the metabolic profiling of acidic compounds in children's urines achieved by comprehensive two-dimensional gas chromatography

The main objective of this work was to evaluate a comprehensive two-dimensional gas chromatographic (GCxGC) coupled to quadrupole mass spectrometry (qMS) method in the field of biomarker candidates' discovery. To this purpose we developed a GCxGC-qMS method suitable for the separation of organic acids and other classes of compounds with silylable polar hydrogen such as sugars, amino-acids, and vitamins. As compared to those obtained by a widely used 1D-GC method, the urinary chromatographic profiles performed by the proposed 2D-GC method exhibit higher resolution and sensitivity, leading to the detection of up to 92 additional compounds in some urine samples including some well-known biomarkers. In order to validate the proposed method we focused on three metabolites of interest with various functional groups and polarities including CH3-malonic acid (MMA: biomarker of methylmalonic acidemia), 3-hydroxy-3-methyl-glutaric acid (3-OHMGA: biomarker of 3-hydroxy-3-methylglutaric acidemia), and phenylpiruvic acid (PhPA: marker of phenylketonuria). While these three metabolites can be considered as representative of organic acids classically determined by 1D-GC, they cannot be representative of new detected metabolites. Thus, we also focused on quinolic acid (QUIN), taken as an example of biomarker not detected at basal levels with the classical 1D GC-qMS method. In order to obtain sufficient recoveries for all tested compounds, we developed a sample preparation protocol including a step of urea removal followed by two extraction steps using two solvents of different polarity and selectivity. Recoveries with the proposed method reached more than 80% for all targeted compounds and the linearity was satisfactory up to 50μmol/L. The CVs of the within-run and within-laboratory precisions were less than 8% for all tested compounds. The limits of quantification (LOQs) were 0.6μmol/L for MMA, 0.4μmol/L for 3-OHMGA, 0.7μmol/L for PhPA, and 1μmol/L for QUIN. The LOQs of these metabolites obtained by a classical GC-MS method under the same chromatographic conditions were 5μmol/L for MMA, 4μmol/L for 3-OHMGA, 6μmol/L for PhPA while QUIN was below the limit of detection. As compared to 1D-GC, these results highlight the enhanced detectability of urine metabolites by the 2D-GC technique. Our results also show that for each new detected compound it is necessary to develop and validate an appropriate sample preparation procedure.

Propionic acidemia in the Arab World

The autosomal recessive disease propionic acidemia (PA) is an inborn error of metabolism with highly variable clinical manifestations, caused by a deficiency of propionyl-CoA carboxylase (PCC) enzyme, due to mutations in either PCCA or PCCB genes, which encode the alpha and beta subunits of the PCC enzyme, respectively. The classical clinical presentation consists of poor feeding, vomiting, metabolic acidosis, hyperammonemia, lethargy, neurological problems, and developmental delay. PA seems to be a prevalent disease in the Arab World. Arab patients with PA seem to have the same classical clinical picture for PA with distinctive associated complications and other diseases. Most of the mutations found in Arab patients seem to be specific to the Arab population, and not observed in other ethnic groups. In this review, I will discuss in details the clinical and molecular profile of Arab patients with PA.

Multidimensional gas chromatography methods for bioanalytical research

Multidimensional gas chromatography (MDGC) methods are high-resolution volatile chemical separation techniques, and comprise classical heart-cutting MDGC and its more recent incarnation, comprehensive 2D GC. Although available for a long period, MDGC approaches are still not widely practiced in the field of bioanalysis, possibly reflecting the general preference for regular GC versus MDGC approaches. With the recent introduction of ‘-omic’ techniques that emphasize global nontargeted profiling of metabolites within living systems, it is evident that MDGC is gaining momentum as a separation tool, since it offers very high resolution. By untangling metabolites within highly complex biological matrices, and expanding the metabolic coverage, MDGC plays a frontline role in ‘-omics’ based studies. This review highlights state-of-the-art MDGC approaches, and summarizes the recent developments in bioanalytics.

Exploring the human urine metabolomic potentialities by comprehensive two-dimensional gas chromatography coupled to time of flight mass spectrometry

Metabolomics represents an emerging issue that can aid in the diagnosis and/or prognosis of different diseases. Metabolomic study of urine is particularly interesting as it can be on the base of the developing of new faster and non-invasive methodologies. In response to this actual trend, comprehensive two-dimensional gas chromatography-time of flight mass spectrometry (GC×GC-ToFMS) combined with headspace solid phase microextraction (HS-SPME) is applied, for the first time to our knowledge, to the untargeted and comprehensive study of the volatile composition of human urine. From a total of ca. 700 compounds detected per sample, 294 were tentatively identified and distributed over the chemical families of hydrocarbons, amines, amides, esters, ketones, aldehydes, alcohols, carboxylic acids, ethers, nitriles, halides, sulfides, thiols, terpenoids, and heterocyclic compounds. To our knowledge, this is the most complete information available so far about whole human urine volatile composition, which represents a valuable data for future advanced studies in the clinical field based on urine fingerprinting. Relevant SPME and GC×GC parameters were considered. Complex sample characterization of human urine is significantly simplified due to the structured GC×GC chromatogram that produces distinct spaces for metabolite chemical families. Furthermore, the potential of this methodology in health related applications was explored by comparing the urinary volatile profiles between smoker (high-risk population for lung cancer) vs. non-smoker adults, focusing on metabolites related to oxidative stress (aliphatic alkanes and aldehydes). In spite of the small sample numbers considered, the results suggest that the urinary volatile profiles may be useful for differentiating subjects with different physiological conditions, thus making it worth to further explore its diagnostic potential.