Improvement of lipid and lipoprotein profiles in children and adolescents with cystic fibrosis on CFTR modulator therapy

BACKGROUND

Association of a high-fat diet with increased risks of cardiovascular disease (CVD) and type 2 diabetes, has prompted evaluation of lipids in people with CF (pwCF). However, most evidence on dyslipidemia was published before CF transmembrane conductance regulator (CFTR) modulators became a standard of care. The main goal of this study was to investigate the effect of CFTR modulator therapies on lipid and lipoprotein profiles in children and adolescents with CF.

METHODS

Blood samples were collected from 153 pwCF (10.1 ± 4.7 years of age) and 60 age-matched controls. Most pwCF were pancreatic insufficient on pancreatic enzyme replacement therapy. By the end of the study, 65% of CF participants were on CFTR modulator therapy for >1 month. The results of traditional and advanced lipid testing in pwCF were correlated with clinical and dietary information.

RESULTS

Total cholesterol and low-density lipoprotein (LDL) cholesterol were significantly lower in pwCF compared to non-CF participants. Those not receiving CFTR modulators also had significantly lower high-density lipoprotein (HDL) cholesterol and HDL particle number than controls. Individuals with CF on modulator therapy had significantly higher concentrations of anti-atherogenic HDL cholesterol and HDL particles along with lower levels of atherogenic large very-low density lipoprotein (VLDL) particles, total and small LDL particles, and triglycerides compared to those without CFTR modulator therapy.

CONCLUSION

CFTR modulator therapy has a beneficial effect on dyslipidemia in CF. It remains to be seen if these positive changes translate into decreased CVD risk later in life given the increasing life expectancy in CF.

Evaluating the strength of evidence for genes implicated in peroxisomal disorders using the ClinGen clinical validity framework and providing updates to the peroxisomal disease nomenclature

Peroxisomal disorders are heterogeneous in nature, with phenotypic overlap that is indistinguishable without molecular testing. Newborn screening and gene sequencing for a panel of genes implicated in peroxisomal diseases are critical tools for the early and accurate detection of these disorders. It is therefore essential to evaluate the clinical validity of the genes included in sequencing panels for peroxisomal disorders. The Peroxisomal Gene Curation Expert Panel (GCEP) assessed genes frequently included on clinical peroxisomal testing panels using the Clinical Genome Resource (ClinGen) gene-disease validity curation framework and classified gene-disease relationships as Definitive, Strong, Moderate, Limited, Disputed, Refuted, or No Known Disease Relationship. Subsequent to gene curation, the GCEP made recommendations to update the disease nomenclature and ontology in the Monarch Disease Ontology (Mondo) database. Thirty-six genes were assessed for the strength of evidence supporting their role in peroxisomal disease, leading to 36 gene-disease relationships, after two genes were removed for their lack of a role in peroxisomal disease and two genes were curated for two different disease entities each. Of these, 23 were classified as Definitive (64%), one as Strong (3%), eight as Moderate (23%), two as Limited (5%), and two as No known disease relationship (5%). No contradictory evidence was found to classify any relationships as Disputed or Refuted. The gene-disease relationship curations are publicly available on the ClinGen website (https://clinicalgenome.org/affiliation/40049/). The changes to peroxisomal disease nomenclature are displayed on the Mondo website (http://purl.obolibrary.org/obo/MONDO_0019053). The Peroxisomal GCEP-curated gene-disease relationships will inform clinical and laboratory diagnostics and enhance molecular testing and reporting. As new data will emerge, the gene-disease classifications asserted by the Peroxisomal GCEP will be re-evaluated periodically.

Acylglycine Analysis by Ultra-Performance Liquid Chromatography-Tandem Mass Spectrometry (UPLC-MS/MS)

Quantitative analysis of urine acylglycines has shown to be a highly sensitive and specific method with proven clinical utility for the diagnosis of several inherited metabolic disorders including: medium chain acyl-CoA dehydrogenase deficiency, multiple acyl-CoA dehydrogenase deficiency, short chain acyl-CoA dehydrogenase deficiency, 3-methylcrotonyl-CoA carboxylase deficiency, 2-methylbutyryl-CoA dehydrogenase deficiency, isovaleric acidemia, propionic academia, and isobutyryl-CoA dehydrogenase deficiency. Here, a method that is currently performed using ultra-performance liquid chromatography/tandem mass spectrometry (UPLC-MS/MS) is described. © 2023 Wiley Periodicals LLC. Basic Protocol: Urinary acylglycine analysis by UPLC-MS/MS Support Protocol 1: Quality control preparation Support Protocol 2: Internal standard (ISTD) preparation Support Protocol 3: Standard (STD)/calibrator preparation.

Quantitative analysis of ethanolamine plasmalogen species in red blood cells using liquid chromatography tandem mass spectrometry for diagnosing peroxisome biogenesis disorders

Plasmalogens are glycerophospholipids characterized by a vinyl-ether bond with a fatty alcohol at the sn-1 position, a polyunsaturated fatty acid at the sn-2 position, and a polar head at the sn-3 position, commonly phosphoethanolamine. Plasmalogens play crucial roles in several cellular processes. Reduced levels have been associated with Alzheimer's and Parkinson's disease progression. Markedly reduced plasmalogens are a classic feature of peroxisome biogenesis disorders (PBD) because plasmalogen synthesis requires functional peroxisomes. Particularly, severe plasmalogen deficiency is the biochemical hallmark of rhizomelic chondrodysplasia punctata (RCDP). Traditionally, plasmalogens are evaluated in red blood cells (RBCs) by gas-chromatography/mass-spectrometry (GC-MS), which cannot distinguish individual species. We developed a liquid-chromatography/tandem mass-spectrometry (LC-MS/MS) method to quantify eighteen phosphoethanolamine plasmalogens in RBCs to diagnose PBD patients, especially RCDP. Validation results showed a specific, robust, and precise method with broad analytical range. Age-specific reference intervals were established; control medians were used to assess plasmalogen deficiency in patients' RBCs. Clinical utility was also confirmed in Pex7 deficient mouse models recapitulating severe and milder RCDP clinical phenotypes. To our knowledge, this is the first attempt to replace the GC-MS method in the clinical laboratory. In addition to diagnosing PBDs, structure-specific plasmalogen quantitation could help understand disease pathogenesis and monitor therapy.

Quantitation of Fatty Acids in Serum/Plasma and Red Blood Cells by Gas Chromatography-Negative Chemical Ionization-Mass Spectrometry

Quantitation of long-chain fatty acids in serum/plasma and red blood cells is a useful diagnostic tool in the evaluation of nutritional status and assessment of risk for essential fatty acid deficiency (EFAD). Serum/plasma has been the traditional sample type for this method, yet it requires prolonged fasting which is not compatible with some patient populations. More recently, red blood cells have become an important sample type due to less intraindividual variability and obviating the need for fasting. Here we present a method for the quantitation of 22 fatty acids in serum/plasma or red blood cells. Fatty acids are hydrolyzed and extracted from the biological matrix, followed by derivatization with pentafluorobenzyl bromide and subsequent analysis by gas chromatography-negative chemical ionization-mass spectrometry (GC-NCI-MS).

Persistent Nutritional Deficiency in Pancreatic-Insufficient Children and Adolescents with Cystic Fibrosis Despite Therapeutic Intervention

Background

Cystic fibrosis (CF) is caused by mutations in the gene encoding the CF Transmembrane Conductance Regulator (CFTR) protein, resulting in compromised pulmonary function, malabsorption, and pancreatic insufficiency. The sequelae of CF are heterogeneous, and contributing factors are multifactorial. Nutritional deficiencies, particularly in essential fatty acids (EFA) and vitamins, are known to alter the trajectory of CF unfavorably. The current treatment modalities focus on proactive management of the pulmonary, gastrointestinal, and pancreatic functions; however, information on the monitoring and treatment of nutritional deficiencies in CF patients is scant. The objective of our study was to evaluate the effects of pancreatic function and CFTR modulator therapy on pertinent nutritional deficiencies in children and adolescents diagnosed with CF.

Methods

The study was approved by our institutional IRB and included 77 non-fasted CF participants, 10.4 + 5.2 years of age (range: 4 months-18 years), and an equal ratio of both sexes. Participants were stratified as pancreatic sufficient (PS, n=6), and pancreatic insufficient with (PI, n=48) or without CFTR modulator treatment (PI-M, n=23). Twenty-two fatty acids were measured in plasma by GC-MS, including omega-6 linoleic acid (LA), and omega-3 α-linoleic acid (ALA). Medical records and 24-hour dietary recalls were reviewed to correlate biochemical and clinical findings. Vitamins A and E and zinc levels of the participants were also obtained. Data analyses were performed by one-way ANOVA and Tukey’s multiple comparisons using Prism software (LaJolla, CA).

Results

There were no significant differences in BMI and caloric intake among the groups. The concentrations of EFA, LA, and ALA were significantly higher in the PS group (3904±229 nmol/mL and 149±24 nmol/mL) compared to the PI (2387±89 nmol/mL and 53±4 nmol/mL, p<0.01) and PI-M (2335±159 nmol/mL and 58±7 nmol/mL, p<0.01) groups, respectively. Similarly, the biologically active omega-6 arachidonic acid and omega-3 docosahexaenoic acid were lower in the PI and PI-M groups compared to the PS group (p<0.05). Interestingly, EFA deficiency biomarkers, omega-9 mead acid, and the Triene:Tetraene ratio, were significantly higher in the PI group (17±2 nmol/mL and 0.033±0.003) vs PS group (13±3 nmol/mL and 0.019±0.002, p<0.05), respectively. Higher concentrations of vitamins A and E were observed in the PS group vs PI-M groups (p<0.05), and zinc concentrations were not different among the groups. There were no associations between the concentrations of EFA and BMI, age, total caloric intake, and % calories from fat in PS, PI, and PI-M patients.

Conclusion

While advances in CF therapeutics are remarkable, our data show the persistence of nutritional deficiencies in pancreatic insufficient CF patients regardless of CFTR modulator therapy and support the clinical utility of EFA and vitamins as potential adjuvant biomarkers to assess the severity and assist in the clinical monitoring of CF.

Quantitative analysis of urine acylglycines by ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS): Reference intervals and disease specific patterns in individuals with organic acidemias and fatty acid oxidation disorders

BACKGROUND

Acylglycine species accumulate in specific disorders of branched-chain amino acid metabolism and fatty acid β-oxidation. These species are excreted in urine and their analysis can facilitate diagnosis. Previous studies evaluated reference ranges and increases in metabolic patients, but these involved small numbers of individuals. We have conducted an analysis encompassing large numbers of individuals to better characterize the reference ranges of these analytes and additionally describe our findings from patients with confirmed metabolic disorders.

METHODS

We conducted a retrospective analysis of approximately 9 y of urine acylglycine data from our clinical laboratory. Acylglycines were extracted from urine, derivatized and analyzed using UPLC-MS/MS. Reference ranges were determined from the non-diseased population. Data from confirmed patients were used to document the range of increases observed in these conditions and to generate multiple of the median graphs.

RESULTS

In total, 6162 urine specimens from 5633 patients with and without metabolic disorders were analyzed. Magnitude and pattern of acylglycine elevations in patients with confirmed metabolic disorders were documented.

CONCLUSION

This manuscript extends our previously published method by providing the reference ranges and disease specific elevations and patterns of urine acylglycine species using the largest data set published to date.

Establishing age-stratified red blood cell fatty acid reference ranges using model-based clustering and iterative application of the harris-boyd method

BACKGROUND

The current assessment of nutritional status and diagnosis of essential fatty acids deficiency (EFAD) utilizes the analysis of long-chain fatty acids (LCFAs) in serum or plasma; however, these concentrations do not represent habitual LCFA intake. LCFAs in red blood cells (RBCs) are less prone to intra-individual variability and exclude the need for fasting, which is unrealistic in pediatric populations. Our study objective was to characterize the RBC LCFA profiles in pediatric and adult reference populations and establish age-specific reference intervals (RIs).

METHODS

Twenty-one LCFAs in RBCs were measured in 523 pediatric and adult controls by gas chromatography-mass spectrometry. Model-based clustering was used to identify possible age subgroups. After removing outliers by the Tukey method, initial age subgroups were then compared using the Harris-Boyd method in an iterative manner. RIs (95%), with confidence intervals (90%), in the final age groups were established using parametric or non-parametric statistics.

RESULTS

Our data showed heterogeneous changes in the concentrations of most LCFAs and the EFAD biomarkers (mead acid, Triene/Tetraene ratio) during infancy. Model-based clustering identified six initial age subgroups per fatty acid, on average. Our application of the iterative Harris-Boyd method decreased the average number of age groups to three per fatty acid, with 13 total unique age cut-offs. Finally, using these age groups, we established age-specific RIs for 21 fatty acids, six group totals, and the Triene/Tetraene ratio.

CONCLUSION

Our study revealed significant age-dependent changes in RBC fatty acid profiles warranting separate pediatric and adults RIs. Model-based clustering and the iterative application of the Harris-Boyd method were successfully used to establish RBC fatty acid RIs for an objective assessment of long-term nutritional status in pediatric and adult populations.

Effect of fasting status and other pre-analytical variables on quantitation of long-chain fatty acids in red blood cells

Long-chain fatty acids (LCFAs), including omega-3 and omega-6 fatty acids, play essential roles in health maintenance and outcomes. Insufficient intake or the inability to absorb LCFAs from the diet can cause a number of health problems. Evaluation of fatty acid profiles in plasma, serum or red blood cells (RBCs) is routinely used to monitor patients at risk of developing deficiency. Quantitation of LCFAs in RBCs offers advantages over serum/plasma due to low intra-individual variability. Fatty acid composition in RBCs also reflects long-term dietary intake, providing additional information about the patient's nutritional status. However, the literature does not currently address the impact of pre-analytical factors (conditions of RBC collection, sample handling and short-term storage) on LCFA measurements. This study evaluated the effect of several anticoagulants, interferents, different storage conditions and fasting status on quantitation of the twenty-one most abundant LCFAs in RBCs by gas chromatography negative chemical ionization-mass spectrometry (GCNCI-MS). LCFA results were assessed quantitatively (nmol/mL) or as a percent of total. Most common tube types (containing citrate, sodium heparin or EDTA) were all appropriate for blood collection. Whole blood and lysed RBCs were stable at least 24 h at room temperature and up to 7 days refrigerated. Lysed RBCs were also stable for up to three freeze/thaw cycles. The presence of icterus or lipemia did not affect results. LCFAs concentrations in RBCs did not change ~4 h after high-fat intake when the lipid concentration in circulation reaches a peak, while plasma levels of most fatty acids increased up to 40% in response. In summary, RBCs are a reliable sample type for LCFA quantitation in the clinical laboratory. In contrast to plasma or serum, RBCs isolated from non-fasting, hemolyzed or lipemic whole blood specimens are all acceptable for testing. Therefore, RBCs might be a preferable sample type for evaluation of nutritional status of young pediatric patients and in patients with conditions associated with hemolytic anemia or hyperlipidemia.

The nuclear magnetic resonance metabolic profile: Impact of fasting status

INTRODUCTION

Measurement of lipoprotein subclass concentration (-c), particle number (-p), and size (-s) by nuclear magnetic resonance (NMR) has gained traction in the clinical laboratory due to associations between smaller lipid particle sizes and atherogenic risk, especially for LDL-p. The standard protocols for lipoprotein measurements by NMR require fasting blood samples; however, patients may not fast properly before sample collection. The study objective was to evaluate the impact of fasting status on the NMR-based lipid profile and to identify key parameters differentiating between fasting and post-meal specimens.

METHODS

Forty-eight self-reported healthy male and female participants were recruited. Blood was collected after a 12 h fast and 4 h after a high fat meal. Samples were analyzed using the AXINON LipoFIT by NMR assay. The measurements included triglyceride, total cholesterol, IDL-c, and LDL, HDL, VLDL concentration, particle number, and size, as well as glucose, and four amino acids (alanine, valine, leucine and isoleucine).

RESULTS

As expected, triglycerides increased after the meal (58%, p < 0.0001). Significant changes were also observed for VLDL, LDL, and HDL parameters, and the branched chain amino acids. The ratio of Valine*VLDL-c/LDL-c or Isoleucine*VLDL-c/LDL-c provided equally effective differentiation of fasting and post-meal samples. The ratio cutoffs (79.1 and 23.6 when calculated using valine and isoleucine, respectively) had sensitivities of 86% and specificities of 93-95%.

CONCLUSIONS

The clinical impact on NMR results from post-meal samples warrants further evaluation. Algorithms to differentiate fasting and post-meal specimens may be useful in identifying suboptimal specimens.

Laboratory evaluation of homocysteine remethylation disorders and classic homocystinuria: Long-term follow-up using a cohort of 123 patients

The homocystinurias, caused by defects of remethylation and cystathionine-beta-synthase (CBS) deficiency, are characterized by elevated homocysteine and abnormal methionine levels. Various treatments, including injectable hydroxycobalamin and oral betaine, aim to reduce homocysteine toxicity and normalize methionine, but only limited biochemical data has been reported assessing biochemical response to treatment. We analyzed laboratory results in 812 plasma samples from 56 patients with remethylation disorders and 67 patients with CBS deficiency. Total plasma homocysteine (tHcys) decreased with therapy, but rarely normalized regardless of treatment, with highest levels seen in CBS (116 ± 79 μmol/L) and MTHFR (102 ± 56 μmol/L) deficiencies. In CBS deficiency, tHcys correlated positively with methionine (rs = 0.51, p < 0.0001) and inversely with cystine (rs = -0.57, p < 0.0001) consistent with a metabolic block downstream of homocysteine. In patients with remethylation disorders, methionine was mostly normal on therapy, and inversely correlated with tHcys (rs = -0.57, p < 0.0001) demonstrating effectiveness of hydroxycobalamin and/or betaine in stimulating tHcys remethylation. Betaine also significantly increased sarcosine from its pre-treatment level on average 19-fold in remethylation disorders and 3-fold in CBS deficiency, with sarcosine > 5 μmol/L being 97% sensitive and 95% specific for betaine therapy. These results show that existing therapies improve sulfur amino acid metabolism without completely normalizing it and that sarcosine can determine compliance to betaine supplementation.

Galactose-1-Phosphate Uridyltransferase Activities in Different Genotypes: A Retrospective Analysis of 927 Samples

Background

Classic galactosemia is an inherited disorder of galactose metabolism caused by the impaired activity of galactose-1-phosphate uridyltransferase (GALT). Untreated galactosemia is life-threatening; however, early dietary intervention prevents mortality and reduces morbidity associated with this disease. The diagnosis of galactosemia includes the measurement of GALT activity in red blood cells (RBC) and GALT gene analysis. In this study, we evaluate GALT activity in different genotypes using the results of combined biochemical and molecular testing in 927 samples.

Methods

GALT activity in RBC was measured by LC-MS/MS. The analysis of the GALT gene was performed by targeted gene analysis and/or full gene sequencing. Samples were assigned based on the presence of pathogenic (G) or Duarte 2 (D) variants, or their absence (Neg), to G/G, D/G, G/Neg, D/D, D/Neg, and Neg/Neg genotypes. Finite mixture models were applied to investigate distributions of GALT activities in these genotypes. The reference ranges were determined using the central 95% of values of GALT activities.

Results

The ranges of GALT activity in G/G, D/G, G/Neg, D/D, D/Neg, and Neg/Neg genotypes are 0.0 to 0.7 μmol·h−1 gHb−1, 3.1 to 7.8 μmol·h−1 gHb−1, 6.5 to 16.2 μmol·h−1 gHb−1, 6.4 to 16.5 μmol·h−1 gHb−1, 12.0 to 24.0 μmol·h−1 gHb−1, and 19.4 to 33.4 μmol·h−1 gHb−1, respectively.

Conclusions

The GALT activity ranges established in this study are in agreement with the expected impact of the genotype on the enzymatic activity. Molecular findings should be interpreted in view of biochemical results to confirm genotype–phenotype correlation.

Quantitative Analysis of Lactate and Other Organic Acids in Plasma: Preanalytical Challenges

Background and Objectives

We developed a gas chromatography–mass spectrometry (GC-MS) method for the analysis of organic acids (OAs) in plasma using liquid-liquid extraction with acidified methanol. This method allows for the simultaneous analysis of several metabolites associated with energy metabolism, including lactic and pyruvic acids. Here, we evaluated the effect of different preanalytical variables (anticoagulants, delayed plasma separation, fasting vs nonfasting status) on plasma organic acid quantitation.

Methods

Nine organic acids (lactic, pyruvic, 3-hydroxybutyric, acetoacetic, 2-ketoisovaleric, 2-keto-3-methylvaleric, 2-ketoisocaproic, succinic, and glutaric) were extracted by deproteinizing with acidified methanol, oximated to preserve ketoacids, converted to volatile trimethylsilyl derivatives, and detected by GC-MS. Compound identification was obtained by retention time and fragmentation spectra using Agilent MassHunter software. We performed several comparison studies using blood collected from self-reported healthy participants (24-60 years of age; 14 females, 13 males). The effect of fasting/nonfasting status was evaluated in 14 participants by comparing samples collected after overnight fasting and 4 hours after meal. Paired t test was used for the statistical analysis of results.

Results

When compared to the preferred sample type, sodium heparin (green top) plasma EDTA plasma (purple top, n = 9) and serum (red top or serum separator tube; n = 5) displayed an unacceptable variability for several analytes. The biggest differences were observed for lactic and pyruvic acids. Lactic acid was significantly lower in EDTA plasma (9%-35% decrease; P = .0001), but higher in serum (4%-63% increase; P = .014), while pyruvic acid was significantly higher in EDTA plasma (4%-145% increase; P = .0002). The measurements of lactic and pyruvic acids were also affected by delayed separation of plasma in samples kept at room temperature. We observed a marked increase in lactate and decrease in pyruvate levels (+42% and –43% mean change, respectively) in plasma separated from whole blood after 2 hours of collection compared to samples processed within 30 minutes. Plasma separated 1 hour postcollection was acceptable. Overnight fasting (12-14 hours) did not have a significant impact on ketones (3-hydroxybutyric and acetoacetic acids) or branched-chain ketoacids (2-keto-3-methylvaleric, 2-ketoisocaproic, 2-ketoisovaleric acids). In contrast, fasting samples displayed higher lactic acid concentrations compared to nonfasting samples (24% increase on average, P = .0072), although in most fasting samples (13 out of 14), lactate concentrations were still within established normal range (600-2,600 µmol/L).

Conclusions

We identified several preanalytical factors influencing plasma organic acid quantitation, particularly lactic and pyruvic acids. Since those are critical analytes, suggestive of primary or secondary metabolic acidosis, appropriate steps should be taken to ensure sample quality during collection and processing.

Nuclear Magnetic Resonance (NMR)–Based Serum Metabolic Profiles: Impact of Fasting Status

Introduction

Measurement of lipoprotein subclass concentration (-c), particle number (-p), and size (-s) by nuclear magnetic resonance (NMR) has gained traction recently in the clinical laboratory due to associations between smaller lipid particle sizes and atherogenic risk, especially for LDL-p. Since patients may not comply with the clinician’s recommendation of fasting before sample collection, our objective was to evaluate the impact of fasting status on NMR-based lipid and amino acid determinations.

Methods

Fifty self-reported healthy participants were recruited using an internal review board-approved protocol: males (n = 25; 41.3 ± 10.5 years; BMI 27.7 ± 4.6 kg/m2) and females (n = 25; 35.6 ± 9.1 years; BMI 25.3 ± 5.4 kg/m2). Blood was collected after overnight fast and 4 hours after a high-fat meal. Samples were analyzed using the AXINON lipoFIT by NMR assay (Numares) with an Avance III NMR spectrometer and Ascend 600 MHz magnet (Bruker). This assay included measurements of triglycerides, total cholesterol, IDL-c, and LDL, HDL, VLDL concentrations; particle numbers; and sizes. Additionally, NMR-based glucose, alanine, valine, leucine, and isoleucine concentrations were acquired. Conventional lipid parameters were obtained using cobas 8000 chemistry system (Roche). Fasting and postprandial results were compared for significant differences.

Results

As expected, mean triglycerides increased after the meal (53%, P < .0001). Increases were also observed for VLDL-c (22%, P < .0001) and large VLDL-p (56%, P < .0001), as well as LDL-s, HDL-s, and VLDL-s (all <3.5%, P < .005). In contrast, LDL-p, small LDL-p, large LDL-p, HDL-p, small HDL-p, glucose, total cholesterol, and LDL, HDL, and IDL cholesterols demonstrated at most an 11% decrease (all P < .002). Valine, leucine, and isoleucine also increased after the meal (31%-46%, P < .0001 for all). Differences in individual lipids or amino acids were not sufficient to distinguish between fasting vs postprandial states, although incorporation of valine into a ratio with VLDL-c and LDL cholesterol (Valine*VLDL-c/LDL cholesterol) provided adequate differentiation (ROC analysis: AUC 0.91 [SD 0.03, P < .0001]). A cutoff of 75 for the ratio had a sensitivity of 88.9% (95% CI, 76.0%-96.3%) and specificity of 85.4% (95% CI, 72.2%-93.9%). Interference with NMR results occurred for three participants’ postprandial samples. These individuals had significantly higher fasting triglycerides, LDL-p, small LDL-p, large VLDL-p, VLDL-s, VLDL-c, IDL-c and lower LDL-s, and HDL-s compared to other participants.

Conclusions

The clinical impact on results from postprandial samples warrants further evaluation prior to accepting nonfasting samples for NMR analysis. Considering a subpar compliance with fasting, algorithms to differentiate fasting and postprandial specimens may be useful in identifying suboptimal specimens.

The Effects of a Single Oral Dose of Pyridoxine on Alpha-Aminoadipic Semialdehyde, Piperideine-6-Carboxylate, Pipecolic Acid, and Alpha-Aminoadipic Acid Levels in Pyridoxine-Dependent Epilepsy

Purpose: To evaluate the effects of a single oral dose of pyridoxine on lysine metabolites including α-aminoadipic semialdehyde (a-AASA), piperideine-6-carboxylate (P6C), the sum of AASA and P6C (AASA-P6C), pipecolic acid (PA), and α-aminoadipic acid (α-AAA) in PDE patients. Methods: The lysine metabolites of 15 patients with molecularly confirmed PDE were detected before and 4 h after taking a single oral dose of pyridoxine, respectively, using liquid chromatography-mass spectrometry (LC-MS/MS) method. Five types of samples were freshly prepared, including plasma, serum, dried blood spots (DBS), urine, and dried urine spots (DUS). Results: All the patients had been treated with long-term oral pyridoxine for several months to years, with doses of 30-360 mg/d. The concentrations of a-AASA, P6C, AASA-P6C, PA, and a-AAA before and after taking a single oral dose of pyridoxine for the same analyte detected in the same type of sample varied among patients. The mean concentrations increased in almost all the metabolites after taking an oral dose of pyridoxine, with or without statistical significance. Whereas, the metabolites concentrations might increase or decrease among different patients, or in different samples of the same patient, without a regular tendency. There was no statistical correlation between the concentrations before and after taking pyridoxine in the same type of sample for most metabolites. Conclusions: No obvious relationship between the metabolite levels or concentration differences and the age, pyridoxine dose (a single oral dose and long-term maintenance dose), duration of treatment, or neurodevelopmental phenotype was found at present study. The large individual differences among patients, probably affected by various genotypes, leading to quite different effects of pyridoxine on the change degree of metabolites concentrations. Our study suggested that long-term pyridoxine treatment could control seizures rather than getting toxic lysine metabolites such as a-AASA and P6C back to normal. In the future, more therapies should be focused to alleviate the metabolites accumulation and further improve the prognosis of PDE.

Effect of genotype on galactose-1-phosphate in classic galactosemia patients

Impaired activity of galactose-1-phosphate uridyltransferase (GALT) causes classic galactosemia (OMIM 230400), characterized by the accumulation of galactose-1-phosphate (GAL1P) in patients' red blood cells (RBCs). Our recent study demonstrated a correlation between RBC GAL1P and long-term outcomes in galactosemia patients. Here, we analyze biochemical and molecular results in 77 classic galactosemia patients to evaluate the association between GALT genotypes and GAL1P concentration in RBCs. Experimental data from model organisms were also included to assess the correlation between GAL1P and predicted residual activity of each genotype. Although all individuals in this study showed markedly reduced RBC GALT activity, we observed significant differences in RBC GAL1P concentrations among galactosemia genotypes. While levels of GAL1P on treatment did not correlate with RBC GALT activities (p = 0.166), there was a negative nonlinear correlation between mean GAL1P concentrations and predicted residual enzyme activity of genotype (p = 0.004). These studies suggest that GAL1P levels in RBCs on treatment likely reflect the overall functional impairment of GALT in patients with galactosemia.

Intra-individual variability of long-chain fatty acids (C12-C24) in plasma and red blood cells

Long-chain fatty acids (LCFA) play key roles in mammalian cells as sources of energy, structural components and signaling molecules. Given their importance in numerous physiological processes, the roles of LCFAs in health and disease have been extensively investigated. In the majority of studies, correlations are established using a single measurement in plasma or red blood cells (RBCs). Although a few studies have reported on reproducibility of individual fatty acid measurements, the comprehensive analysis of intra-individual LCFA variability has not been performed. Therefore, our goal was to determine intra-individual variability for the 22 most abundant LCFAs in both plasma and RBC samples collected from healthy individuals on a regular diet after overnight fasting. The measurements of LCFAs in RBCs were consistent throughout the course of study reflecting long-term nutritional status. In contrast, the results in plasma showed considerable LCFA intra-individual variability, even between fatty acids of the same type. Plasma intra-individual variability for omega-3 alpha-linolenic and eicosapentaenoic acids in some participants were >40% whereas the variability of docosahexaenoic acid was consistently <12.8%. Omega-6 linoleic and arachidonic acids also showed low variability in plasma. The results suggest that some LCFAs have less variability and would be more reliable as biomarkers. Reliability of biomarkers can have a profound impact on the research outcomes. Intra-individual variability of LCFAs should be taken into consideration in designing, conducting and interpreting results of clinical studies.

Biochemical changes and clinical outcomes in 34 patients with classic galactosemia

Impaired activity of galactose-1-phosphate uridyltransferase (GALT) causes galactosemia, an autosomal recessive disorder of galactose metabolism. Early initiation of a galactose-restricted diet can prevent or resolve neonatal complications. Despite therapy, patients often experience long-term complications including speech impairment, learning disabilities, and premature ovarian insufficiency in females. This study evaluates clinical outcomes in 34 galactosemia patients with markedly reduced GALT activity and compares outcomes between patients with different levels of mean galactose-1-phosphate in red blood cells (GAL1P) using logistic regression: group 1 (n = 13) GAL1P ≤1.7 mg/dL vs. group 2 (n = 21) GAL1P ≥ 2 mg/dL. Acute symptoms at birth were comparable between groups (p = 0.30) with approximately 50% of patients presenting with jaundice, liver failure, and failure-to-thrive. However, group 2 patients had significantly higher prevalence of negative long-term outcomes compared to group 1 patients (p = 0.01). Only one of 11 patients >3 yo in group 1 developed neurological and severe behavioral problems of unclear etiology. In contrast, 17 of 20 patients >3 yo in group 2 presented with one or more long-term complications associated with galactosemia. The majority of females ≥15 yo in this group also had impaired ovarian function with markedly reduced levels of anti-Müllerian hormone. These findings suggest that galactosemia patients with higher GAL1P levels are more likely to have negative long-term outcome. Therefore, evaluation of GAL1P levels on a galactose-restricted diet might be helpful in providing a prognosis for galactosemia patients with rare or novel genotypes whose clinical presentations are not well known.

Mild orotic aciduria in UMPS heterozygotes: a metabolic finding without clinical consequences

BACKGROUND

Elevated urinary excretion of orotic acid is associated with treatable disorders of the urea cycle and pyrimidine metabolism. Establishing the correct and timely diagnosis in a patient with orotic aciduria is key to effective treatment. Uridine monophosphate synthase is involved in de novo pyrimidine synthesis. Uridine monophosphate synthase deficiency (or hereditary orotic aciduria), due to biallelic mutations in UMPS, is a rare condition presenting with megaloblastic anemia in the first months of life. If not treated with the pyrimidine precursor uridine, neutropenia, failure to thrive, growth retardation, developmental delay, and intellectual disability may ensue.

METHODS AND RESULTS

We identified mild and isolated orotic aciduria in 11 unrelated individuals with diverse clinical signs and symptoms, the most common denominator being intellectual disability/developmental delay. Of note, none had blood count abnormalities, relevant hyperammonemia or altered plasma amino acid profile. All individuals were found to have heterozygous alterations in UMPS. Four of these variants were predicted to be null alleles with complete loss of function. The remaining variants were missense changes and predicted to be damaging to the normal encoded protein. Interestingly, family screening revealed heterozygous UMPS variants in combination with mild orotic aciduria in 19 clinically asymptomatic family members.

CONCLUSIONS

We therefore conclude that heterozygous UMPS-mutations can lead to mild and isolated orotic aciduria without clinical consequence. Partial UMPS-deficiency should be included in the differential diagnosis of mild orotic aciduria. The discovery of heterozygotes manifesting clinical symptoms such as hypotonia and developmental delay are likely due to ascertainment bias.

Effect of dietary lysine restriction and arginine supplementation in two patients with pyridoxine-dependent epilepsy

Pyridoxine-Dependent Epilepsy (PDE) is a recessive disorder caused by deficiency of α-aminoadipic semialdehyde dehydrogenase in the catabolic pathway of lysine. It is characterized by intractable seizures controlled by the administration of pharmacological doses of vitamin B6. Despite seizure control with pyridoxine, intellectual disability and developmental delays are still observed in some patients with PDE, likely due to the accumulation of toxic intermediates in the lysine catabolic pathway: alpha-aminoadipic semialdehyde (AASA), delta-1-piperideine-6-carboxylate (P6C), and pipecolic acid. Here we evaluate biochemical and clinical parameters in two PDE patients treated with a lysine-restricted diet and arginine supplementation (100-150mg/kg), aimed at reducing the levels of PDE biomarkers. Lysine restriction resulted in decreased accumulation of PDE biomarkers and improved development. Plasma lysine but not plasma arginine, directly correlated with plasma levels of AASA-P6C (p<0.001, r(2)=0.640) and pipecolic acid (p<0.01, r(2)=0.484). In addition, plasma threonine strongly correlated with the levels of AASA-P6C (p<0.0001, r(2)=0.732) and pipecolic acid (p<0.005, r(2)=0.527), suggesting extreme sensitivity of threonine catabolism to pyridoxine availability. Our results further support the use of dietary therapies in combination with pyridoxine for the treatment of PDE.

Diagnosis, Treatment, and Clinical Outcome of Patients with Mitochondrial Trifunctional Protein/Long-Chain 3-Hydroxy Acyl-CoA Dehydrogenase Deficiency

Deficiency of the mitochondrial trifunctional protein (TFP) and long-chain 3-Hydroxy Acyl-CoA dehydrogenase (LCHAD) impairs long-chain fatty acid oxidation and presents with hypoglycemia, cardiac, liver, eye, and muscle involvement. Without treatment, both conditions can be life-threatening. These diseases are identified by newborn screening (NBS), but the impact of early treatment on long-term clinical outcome is unknown. Moreover, there is lack of consensus on treatment, particularly on the use of carnitine supplementation. Here, we report clinical and biochemical data in five patients with TFP/LCHAD deficiency, three of whom were diagnosed by newborn screening. All patients had signs and symptoms related to their metabolic disorder, including hypoglycemia, elevated creatine kinase (CK), and rhabdomyolysis, and experienced episodes of metabolic decompensation triggered by illness. Treatment was started shortly after diagnosis in all patients and consisted of a diet low in long-chain fats supplemented with medium chain triglycerides (MCT), essential fatty acids, and low-dose carnitine (25 mg/kg/day). Patients had growth restriction early in life that resolved after 2 years of age. All patients but the youngest (2 years old) developed pigmentary retinopathy. Long-chain hydroxylated acylcarnitines did not change significantly with age, but increased during acute illnesses. Free carnitine levels were maintained within the normal range and did not correlate with long-chain hydroxylated acylcarnitines. These results show that patients with LCHAD deficiency can have normal growth and development with appropriate treatment. Low-dose carnitine supplements prevented carnitine deficiency and did not result in increased long-chain hydroxylated acylcarnitines or any specific toxicity.

A novel method for simultaneous quantification of alpha-aminoadipic semialdehyde/piperideine-6-carboxylate and pipecolic acid in plasma and urine

OBJECTIVES

Elevated levels of pipecolic acid (PA), α-aminoadipic semialdehyde (AASA) and its cyclic form Δ1-piperideine-6-carboxylate (P6C) are characteristic of pyridoxine dependent epilepsy (PDE), a rare disorder of inborn error of metabolism. Recent studies showed the effectiveness of dietary therapy in PDE patients and emphasized the importance of the assessment of these metabolites for monitoring treatment efficacy. The objective of this study was to develop a robust and sensitive method for simultaneous quantification of AASA-P6C and PA in plasma and urine.

DESIGN AND METHODS

Plasma and urine samples were derivatized with 3N HCl in n-butanol (v/v) and injected onto ACQUITY BEH-C18 column. A gradient of water/methanol containing 0.1% formic acid was used for the chromatographic separation of AASA, P6C and PA. The analytes' concentrations were calculated using their calibration curves and the sum of AASA and P6C (AASA-P6C) was calculated. To evaluate the clinical utility of this test, samples from unaffected controls and patients with confirmed PDE were analyzed.

RESULTS

The performance characteristics of the assay as well as sample stability and interferences were determined. The intra- and inter- assay CVs were ≤2.9% and ≤10.9% for AASA-P6C, and ≤3.3% and ≤12.6% for PA, respectively. Reference ranges for AASA-P6C and PA in plasma and urine were established. Comparison of values obtained from unaffected controls and PDE patients showed high clinical sensitivity and specificity of the assay.

CONCLUSIONS

This novel method for the simultaneous quantification of AASA-P6C and PA in plasma and urine can be used in a clinical laboratory setting for the diagnosis and monitoring of patients with PDE.

Feasibility of newborn screening for guanidinoacetate methyltransferase (GAMT) deficiency

Guanidinoacetate methyltransferase (GAMT) deficiency causes brain creatine deficiency characterized by developmental delays, speech delay, seizures and autism-like behavior. Identification and therapy at birth because of a positive family history has prevented intellectual disability and seizures in all cases reported. The objective of this study was to develop a method to identify patients with GAMT deficiency from newborn screening blood spots. Creatine and guanidinoacetate were extracted from 10,000 deidentified blood spots using the same protocol routinely used for newborn screening and quantified by stable isotope dilution using deuterated creatine and guanidinoacetate as internal standards. Residual dried blood spots from three infants with GAMT deficiency were used to evaluate the sensitivity of the method. A second tier test using UPLC-MS/MS was performed to analyze samples with a concentration of guanidinoacetate >2.44 μmol/L (99.5th centile of the normal population). Fifty four blood spots required second tier testing in addition to seven blood spots from three patients with GAMT deficiency retrospectively analyzed. With second tier testing, only the samples from GAMT deficiency patients had elevated concentration of guanidinoacetate. Our results show that GAMT deficiency can be identified in newborns using routine extraction methods. The cost of this additional screening is minimal, as it does not require additional instrumentation, procedure, or sample collection. The use of a second tier test can reduce the false positive rate to a minimum. Summary Brain creatine deficiency syndromes cause mental retardation that can be prevented if therapy is initiated early in life. This manuscript reports that infants with GAMT deficiency (one of the brain creatine deficiency syndromes) can be identified from elevated guanidinoacetate in newborn blood spots with virtually absent false-positive results using a second tier test.

The polycomb complex protein mes-2/E(z) promotes the transition from developmental plasticity to differentiation in C. elegans embryos

We have used expression profiling and in vivo imaging to characterize Caenorhabditis elegans embryos as they transit from a developmentally plastic state to the onset of differentiation. Normally, this transition is accompanied by activation of developmental regulators and differentiation genes, downregulation of early-expressed genes, and large-scale reorganization of chromatin. We find that loss of plasticity and differentiation onset depends on the Polycomb complex protein mes-2/E(Z). mes-2 mutants display prolonged developmental plasticity in response to heterologous developmental regulators. Early-expressed genes remain active, differentiation genes fail to reach wild-type levels, and chromatin retains a decompacted morphology in mes-2 mutants. By contrast, loss of the developmental regulators pha-4/FoxA or end-1/GATA does not prolong plasticity. This study establishes a model by which to analyze developmental plasticity within an intact embryo. mes-2 orchestrates large-scale changes in chromatin organization and gene expression to promote the timely loss of developmental plasticity. Our findings indicate that loss of plasticity can be uncoupled from cell fate specification.

Actin recovery and bud emergence in osmotically stressed cells requires the conserved actin interacting mitogen-activated protein kinase kinase kinase Ssk2p/MTK1 and the scaffold protein Spa2p

Osmotic stress causes actin cytoskeleton disassembly, a cell cycle arrest, and activation of the high osmolarity growth mitogen-activated protein kinase pathway. A previous study showed that Ssk2p, a mitogen-activated protein kinase kinase kinase of the high osmolarity growth pathway, promotes actin cytoskeleton recovery to the neck of late cell cycle, osmotically stressed yeast cells. Data presented herein examined the role of Ssk2p in actin recovery early in the cell cycle. We found that actin recovery at all stages of the cell cycle is not controlled by Ssk1p, the known activator of Ssk2p, but required a polarized distribution of Ssk2p as well as its actin-interacting and kinase activity. Stress-induced localization of Ssk2p to the neck required the septin Shs1p, whereas localization to the bud cortex depended on the polarity scaffold protein Spa2p. spa2delta cells, like ssk2delta cells, were defective for actin recovery from osmotic stress. These spa2delta defects could be suppressed by overexpression of catalytically active Ssk2p. Furthermore, Spa2p could be precipitated by GST-Ssk2p from extracts of osmotically stressed cells. The Ssk2p mediated actin recovery pathway seems to be conserved; MTK1, a human mitogen-activated protein kinase kinase kinase of the p38 stress response pathway and Ssk2p homolog, was also able to localize at polarized growth sites, form a complex with actin and Spa2p, and complement actin recovery defects in osmotically stressed ssk2delta and spa2delta yeast cells. We hypothesize that osmotic stress-induced actin disassembly leads to the formation of an Ssk2p-actin complex and the polarized localization of Ssk2p. Polarized Ssk2p associates with the scaffold protein Spa2p in the bud and Shs1p in the neck, allowing Ssk2p to regulate substrates involved in polarized actin assembly.

The MEK kinase Ssk2p promotes actin cytoskeleton recovery after osmotic stress

Saccharomyces cerevisiae adapts to osmotic stress through the activation of a conserved high-osmolarity growth (HOG) mitogen-activated protein (MAP) kinase pathway. Transmission through the HOG pathway is very well understood, yet other aspects of the cellular response to osmotic stress remain poorly understood, most notably regulation of actin organization. The actin cytoskeleton rapidly disassembles in response to osmotic insult and is induced to reassemble only after osmotic balance with the environment is reestablished. Here, we show that one of three MEK kinases of the HOG pathway, Ssk2p, is specialized to facilitate actin cytoskeleton reassembly after osmotic stress. Within minutes of cells' experiencing osmotic stress or catastrophic disassembly of the actin cytoskeleton through latrunculin A treatment, Ssk2p concentrates in the neck of budding yeast cells and concurrently forms a 1:1 complex with actin. These observations suggest that Ssk2p has a novel, previously undescribed function in sensing damage to the actin cytoskeleton. We also describe a second function for Ssk2p in facilitating reassembly of a polarized actin cytoskeleton at the end of the cell cycle, a prerequisite for efficient cell cycle completion. Loss of Ssk2p, its kinase activity, or its ability to localize and interact with actin led to delays in actin recovery and a resulting delay in cell cycle completion. These unique capabilities of Ssk2p are activated by a novel mechanism that does not involve known components of the HOG pathway.