Diagnosis of Aromatic L-Amino Acid Decarboxylase (AADC) Deficiency via Epilepsy Gene Panel Screening in a Patient with Atypical Presentation

We describe an atypical presentation of a girl with aromatic L-amino acid decarboxylase (AADC) deficiency identified via a genetic testing program for children with epilepsy. At 21 months of age, she presented with poor head control, diffuse hypotonia, poor fixation, developmental delay, and dysphagia. She was lost to follow-up, then presented back at 3 years of age with staring spells and brief episodes of upward eye deviation. The diagnosis of unprovoked epilepsy allowed her to be included in a genetic testing program, which identified two heterozygous variants in the dopa decarboxylase (DCC) gene. Based on the genetic testing, plasma AADC enzyme activity and plasma 3-O-methyldopa results, a diagnosis of AADC deficiency was made when she was 4 years and 2 months of age. This case report shows that AADC deficiency can be the underlying diagnosis in patients with suspected epilepsy.

Analytical Methods for Quantitative Plasma Carnitine Determination

Carnitine is an essential molecule for mitochondrial beta-oxidation of long-chain fatty acids and other cellular functions. Several rare, inherited disorders of carnitine metabolism occur in humans, and secondary carnitine deficiency is an important feature in a variety of clinical settings. Many of these conditions can be detected via quantitative analysis of free and esterified carnitine in plasma or urine, which thus offers an effective means for assessing the transport and initial processing of fatty acids. Here, we describe some of the methods most commonly employed for quantification of plasma carnitine and consider some of the advantages and disadvantages of these approaches. © 2019 by John Wiley & Sons, Inc.

Methods for Quantitative Creatinine Determination

Reliable measurement of creatinine is necessary to assess kidney function, and also to quantitate drug levels and diagnostic compounds in urine samples. The most commonly used methods are based on the Jaffe principal of alkaline creatinine-picric acid complex color formation. However, other compounds commonly found in serum and urine may interfere with Jaffe creatinine measurements. Therefore, many laboratories have made modifications to the basic method to remove or account for these interfering substances. This appendix will summarize the basic Jaffe method, as well as a modified, automated version. Also described is a high performance liquid chromatography (HPLC) method that separates creatinine from contaminants prior to direct quantification by UV absorption. Lastly, a liquid chromatography-tandem mass spectrometry (LC-MS/MS) method is described that uses stable isotope dilution to reliably quantify creatinine in any sample. This last approach has been recommended by experts in the field as a means to standardize all quantitative creatinine methods against an accepted reference. © 2017 by John Wiley & Sons, Inc.

An Overview of Biochemical Genetics

Biochemical genetics focuses on the pathophysiology, diagnosis, and treatment of inherited metabolic disorders. While individually rare, the combined incidence of these diseases makes them a significant source of morbidity and mortality, particularly among infants and young children, and new conditions continue to be identified. Inherited metabolic disorders may present as an acute, life-threatening illness or with more chronic, progressive symptoms. Population-scale newborn screening allows for early detection and treatment for >40 different metabolic disorders. This introductory unit is intended to provide an overview of the different clinical categories of metabolic disorders, including a description of modern diagnostic methods and treatment options.

Simultaneous quantification of F2-isoprostanes and prostaglandins in human urine by liquid chromatography tandem-mass spectrometry

A specific and sensitive LC-MS/MS method for analysis of F(2)-isoprostanes (F(2)-IsoPs) and prostaglandins (PGs) in urine was developed and validated to examine the levels of F(2)-IsoPs and prostaglandin F(2α) (PGF(2α)), in human urine in patients undergoing cardiac surgery. The rapid extraction for F(2)-IsoPs and PGs from urine was achieved using a polymeric weak anion solid phase extraction cartridge. The base-line separation of 8-iso-PGF(2α), 8-iso-15(R)-PGF(2α), PGF(2α), and 15(R)-PGF(2α) was carried out on a Hydro-RP column (250mm×2.0mm i.d., Phenomenex, CA) using a linear gradient of methanol:acetonitrile (1:1, v/v) in 0.1% formic acid at a flow rate of 0.2mL/min. The method was proved to be accurate and precise for simultaneous quantification of each analyte over a linear dynamic range of 0.05-50ng/mL with correlation coefficients greater than 0.99. The intra-day and inter-day assay precision at the lowest quality control (0.07ng/mL) level were less than 17%. The mean extraction recoveries of F(2)-IsoPs and PGs were in a range of 79-100%. In applications of this method to patients undergoing cardiac surgery, post-surgery urinary concentrations of 8-iso-PGF(2α) increased significantly in patients (n=14) who did not develop acute kidney (AKI) (pre-surgery 0.344±0.039 vs. post-surgery 0.682±0.094ng/mg creatinine, p<0.01), whereas there was no significant change in this isoprostane in the patients (n=4) who developed AKI (pre-surgery 0.298±0.062 vs. post-surgery 0.383±0.117ng/mg creatinine, NS). Therefore, the method is suitable for the analysis of individual F(2)-IsoPs and PGF(2α)'s in both clinical and research studies.

An overview of biochemical genetics

Biochemical genetics focuses on the pathophysiology, diagnosis, and treatment of inherited metabolic disorders. While individually rare, the combined incidence of these diseases is likely greater than 1:3000 live births. These conditions may present in the neonatal period as an acute, life-threatening illness, or may manifest later in childhood with symptoms of progressive neurodegeneration, skeletal abnormalities, and/or dysmorphia. The purpose of this introductory unit is to provide an overview of the different clinical categories of metabolic disorders, modern diagnostic methods, and treatment options.

An overview of biochemical genetics

Biochemical genetics is focused on the pathophysiology, diagnosis, and treatment of inborn errors of metabolism, which result in potentially toxic accumulation of substrate or secondary metabolites, and/or inhibition of reaction products. Early-onset metabolic disorders often present during infancy as acute, life-threatening illnesses; other forms of inborn errors appear later in childhood and are often characterized by progressive neurodegeneration. This unit provides an overview of modern biochemical genetic diagnostic methods used to evaluate a patient's metabolic status via measurement of reaction products or a specific enzyme activity. One such technique, tandem mass spectrometry (MS/MS), has revolutionized population-scale newborn screening for metabolic disorders by providing rapid, accurate, multianalyte quantification on small samples. The combination of expanded newborn screening and novel therapeutic approaches, such as enzyme-replacement therapy, offers significant improvement in the management of metabolic disorders.

Homozygous carnitine palmitoyltransferase 1b (muscle isoform) deficiency is lethal in the mouse

Carnitine palmitoyltransferase-1 (CPT-1) catalyzes the rate-limiting step of mitochondrial beta-oxidation of long chain fatty acids (LCFA), the most abundant fatty acids in mammalian membranes and in energy metabolism. Human deficiency of the muscle isoform CPT-1b is poorly understood. In the current study, embryos with a homozygous knockout of Cpt-1b were lost before embryonic day 9.5-11.5. Also, while there were normal percentages of CPT-1b+/- pups born from both male and female CPT-1b+/- mice crossed with wild-type mates, the number of CPT-1b+/- pups from CPT-1b+/- breeding pairs was under-represented (63% of the expected number). Northern blot analysis demonstrated approximately 50% Cpt-1b mRNA expression in brown adipose tissue (BAT), heart and skeletal muscles in the CPT-1b+/- male mice. Consistent with tissue-specific expression of Cpt-1b mRNA in muscle but not liver, CPT-1+/- mice had approximately 60% CPT-1 activity in skeletal muscle and no change in total liver CPT-1 activity. CPT-1b+/- mice had normal fasting blood glucose concentration. Consistent with expression of CPT-1b in BAT and muscle, approximately 7% CPT-1b+/- mice (n=30) developed fatal hypothermia following a 3h cold challenge, while none of the CPT-1b+/+ mice (n=30) did. With a prolonged cold challenge (6h), significantly more CPT-1b+/- mice developed fatal hypothermia (52% CPT-1b+/- mice vs. 21% CPT-1b+/+ mice), with increased frequency in females of both genotypes (67% female vs. 38% male CPT-1b+/- mice, and 33% female vs. 8% male CPT-1b+/+ mice). Therefore, lethality of homozygous CPT-1b deficiency in the mice is consistent with paucity of human cases.

The adenine nucleotide translocase type 1 (ANT1): a new factor in mitochondrial disease

Mitochondrial disorders of oxidative phosphorylation (OXPHOS) comprise a growing list of potentially lethal diseases caused by mutations in either mitochondrial (mtDNA) or nuclear DNA (nDNA). Two such conditions, autosomal dominant progressive external ophthalmoplegia (adPEO) and Senger's Syndrome, are associated with dysfunction of the heart and muscle-specific isoform of the adenine nucleotide translocase (ANT1), a nDNA gene product that facilitates transport of ATP and ADP across the inner mitochondrial membrane. AdPEO is a mtDNA deletion disorder broadly characterized by pathology involving the eyes, skeletal muscle, and central nervous system. In addition to ANT1, mutations in at least two other nuclear genes, twinkle and POLG, have been shown to cause mtDNA destabilization associated with adPEO. Senger's syndrome is an autosomal recessive condition characterized by congenital heart defects, abnormalities of skeletal muscle mitochondria, cataracts, and elevated circulatory levels of lactic acid. This syndrome is associated with severe depletion of ANT1, which may be the result of an as yet unidentified ANT1-specific transcriptional or translational processing error. ANT1 has also been associated with a third condition, autosomal dominant facioscapulohumeral muscular dystrophy (FSHD), an adult onset disorder characterized by variable muscle weakness in the face, feet, shoulders, and hips. FSHD patients possess specific DNA deletions on chromosome 4, which appear to cause derepression of several nearby genes, including ANT1. Early development of FSHD may involve mitochondrial dysfunction and increased oxidative stress, possibly associated with overexpression of ANT1.

Medium-chain acyl-CoA dehydrogenase deficiency in gene-targeted mice

Medium-chain acyl-CoA dehydrogenase (MCAD) deficiency is the most common inherited disorder of mitochondrial fatty acid β-oxidation in humans. To better understand the pathogenesis of this disease, we developed a mouse model for MCAD deficiency (MCAD^−/−) by gene targeting in embryonic stem (ES) cells. The MCAD^−/− mice developed an organic aciduria and fatty liver, and showed profound cold intolerance at 4 °C with prior fasting. The sporadic cardiac lesions seen in MCAD^−/− mice have not been reported in human MCAD patients. There was significant neonatal mortality of MCAD^−/− pups demonstrating similarities to patterns of clinical episodes and mortality in MCAD-deficient patients. The MCAD-deficient mouse reproduced important aspects of human MCAD deficiency and is a valuable model for further analysis of the roles of fatty acid oxidation and pathogenesis of human diseases involving fatty acid oxidation.

Medium-chain acyl-CoA dehydrogenase (MCAD) deficiency is one of the most common inherited disorders of metabolism. This defect in fatty acid oxidation can lead to severe and sometimes fatal disease, especially in young children because they are unable to tolerate a fasting episode. Metabolic complications include very low blood glucose concentrations and generation of toxic by-products. This disorder can result in sudden infant death. Using a process known as gene targeting in mouse embryonic stem cells, the authors have developed a mouse model with the same enzyme deficiency. This mouse model of MCAD deficiency develops many of the same disease characteristics found in affected children. The MCAD-deficient mouse model shows a high rate of newborn loss, intolerance to cold, and the characteristic biochemical changes in the blood, tissues, and urine that are very similar to those found in the human disease counterpart. The MCAD-deficient mouse model will allow researchers to better understand disease mechanisms so that new preventive measures or therapies can be developed.

Assays used in the analysis of Arl2 and its binding partners

Arl2 is a approximately 20 kDa GTPase in the ADP-ribosylation factor (Arf) family within the Ras superfamily with roles in microtubule dynamics that impact the cytoskeleton, cell division, and cytokinesis. Arl2 has been implicated as a regulator of the pathway responsible for formation of properly folded tubulin heterodimers and in adenine nucleotide transport in mitochondria. The identification and characterization of Arl2 binding partners and regulators of Arl2 activities are critical steps in the further dissection of these and likely other Arl2-dependent functions. This chapter describes methods for preparing recombinant Arl2, loading different radiolabeled guanine nucleotides onto the GTPase, identifying high-affinity Arl2 binding proteins, and assaying Arl2 GTPase activating proteins (GAPs). These methods may also prove useful for studies of other Arls or other GTPases.

Cytosolic Arl2 is complexed with cofactor D and protein phosphatase 2A

Arl2 is a member of the ADP-ribosylation factor family of 20-kDa GTPases that is highly conserved in eukaryotes. Recent results revealed that a portion of cellular Arl2 and its binding partner, BART, localize to mitochondria. Because approximately 90% of cellular Arl2 is cytosolic, we investigated properties of the soluble protein and found that it is stably bound in a complex that migrates in gel filtration medium with a predicted molecular mass of approximately 300 kDa. This complex was purified approximately 500-fold from the soluble fraction of bovine brain. Protein components were identified by mass spectroscopy and revealed the presence of four other proteins that include the tubulin folding cochaperone cofactor D and all three subunits of at least two protein phosphatase 2A (PP2A) protein phosphatase trimers. The presence of more than one PP2A B-type subunit and the low stoichiometry of Arl2 indicate that the purified preparation still contains a mixture of complexes that cannot currently be completely resolved. Thus, although all the soluble Arl2 in bovine brain is in high molecular mass complexes, only a portion of the total cellular cofactor D and PP2A are associated with the Arl2. We further show that the Arl2 in the complex cannot bind GTP and that complexed cofactor D does not efficiently participate in tubulin refolding reactions in a manner comparable with free cofactor D. Our data suggest functional roles for the cytosolic Arl2 complex in modulating tubulin and microtubule behavior as well as a possible role in apoptosis.

ARL2 and BART enter mitochondria and bind the adenine nucleotide transporter

The ADP-ribosylation factor-like 2 (ARL2) GTPase and its binding partner binder of ARL2 (BART) are ubiquitously expressed in rodent and human tissues and are most abundant in brain. Both ARL2 and BART are predominantly cytosolic, but a pool of each was found associated with mitochondria in a protease-resistant form. ARL2 was found to lack covalent N-myristoylation, present on all other members of the ARF family, thereby preserving the N-terminal amphipathic alpha-helix as a potential mitochondrial import sequence. An overlay assay was developed to identify binding partners for the BART.ARL2.GTP complex and revealed a specific interaction with a protein in bovine brain mitochondria. Purification and partial microsequencing identified the protein as an adenine nucleotide transporter (ANT). The overlay assay was performed on mitochondria isolated from five different tissues from either wild-type or transgenic mice deleted for ANT1. Results confirmed that ANT1 is the predominant binding partner for the BART.ARL2.GTP complex and that the structurally homologous ANT2 protein does not bind the complex. Cardiac and skeletal muscle mitochondria from ant1(-)/ant1(-) mice had increased levels of ARL2, relative to that seen in mitochondria from wild-type animals. We conclude that the amount of ARL2 in mitochondria is subject to regulation via an ANT1-sensitive pathway in muscle tissues.

ADP-ribosylation factors (ARFs) and ARF-like 1 (ARL1) have both specific and shared effectors: characterizing ARL1-binding proteins

Despite the 40-60% identity between ADP-ribosylation factors (ARFs) and ARF-like (ARL) proteins, distinct functional roles have been inferred from findings that ARLs lack the biochemical or genetic activities characteristic of ARFs. The potential for functional overlap between ARFs and ARLs was examined by comparing effects of expression on intact cells and the ability to bind effectors. Expression of [Q71L]ARL1 in mammalian cells led to altered Golgi structure similar to, but less dramatic than, that reported previously for [Q71L]ARF1. Two previously identified partners of ARFs, MKLP1 and Arfaptin2/POR1, also bind ARL1 but not ARL2 or ARL3. Two-hybrid screens of human cDNA libraries with dominant active mutants of human ARL1, ARL2, and ARL3 identified eight different but overlapping sets of binding partners. Specific interactions between ARL1 and two binding proteins, SCOCO and Golgin-245, are defined and characterized in more detail. Like ARFs and ARL1, the binding of SCOCO to Golgi membranes is rapidly reversed by brefeldin A, suggesting the presence of a brefeldin A-sensitive ARL1 exchange factor. These data reveal a complex network of interactions between GTPases in the ARF family and their effectors and reveal a potential for cross-talk not demonstrated previously.

The function of conserved amino acid residues adjacent to the effector domain in elongation factor G

Bacterial elongation factor G (EF-G) physically associates with translocation-competent ribosomes and facilitates transition to the subsequent codon through the coordinate binding and hydrolysis of GTP. In order to investigate the amino acid positions necessary for EF-G functions, a series of mutations were constructed in the EF-G structural gene (fusA) of Escherichia coli, specifically at positions flanking the effector domain. A mutated allele was isolated in which the wild-type sequence from codons 29 to 47 ("EFG2947") was replaced with a sequence encoding 28 amino acids from ribosomal protein S7. This mutated gene was unable to complement a fusAts strain when supplied in trans at the nonpermissive temperature. In vitro biochemical analysis demonstrated that nucleotide crosslinking was unaffected in EFG2947, while ribosome binding appeared to be completely abolished. A series of point mutations created within this region, encoding L30A, Y32A, H37A, and K38A were shown to give rise to fully functional proteins, suggesting that side chains of these individual residues are not essential for EF-G function. A sixth mutant, E41A, was found to inefficiently rescue growth in a fusAts background, and was also unable to bind ribosomes normally in vitro. In contrast E41Q could restore growth at the nonpermissive temperature. These results can be explained within the context of a three-dimensional model for the effector region of EF-G. This model indicates that the effector domain contains a negative potential field that may be important for ribosome binding.

The ARF-like 2 (ARL2)-binding protein, BART. Purification, cloning, and initial characterization

ARF-like proteins (ARLs) comprise a functionally distinct group of incompletely characterized members in the ARF family of RAS-related GTPases. We took advantage of the GTP binding characteristics of human ARL2 to develop a specific, high affinity binding assay that allowed the purification of a novel ARL2-binding protein. A 19-kDa protein (BART, Binder of Arl Two) was identified and purified from bovine brain homogenate. BART binding is specific to ARL2.GTP with high affinity but does not interact with ARL2.GDP or activated ARF or RHO proteins. Based on peptide sequences of purified bovine BART, the human cDNA sequence was determined. The 489-base pair BART open reading frame encodes a novel 163-amino acid protein with a predicted molecular mass of 18,822 Da. Recombinant BART was found to bind ARL2.GTP in a manner indistinguishable from native BART. Northern and Western analyses indicated BART is expressed in all tissues sampled. The lack of detectable membrane association of ARL2 or BART upon activation of ARL2 is suggestive of actions quite distinct from those of the ARFs. The lack of ARL2 GTPase-activating protein activity in BART led us to conclude that the specific interaction with ARL2.GTP is most consistent with BART being the first identified ARL2-specific effector.

Cross-species complementation of the indispensable Escherichia coli era gene highlights amino acid regions essential for activity

Era is an essential GTP binding protein in Escherichia coli. Two homologs of this protein, Sgp from Streptococcus mutans and Era from Coxiella burnetii, can substitute for the essential function of Era in E. coli. Site-specific and randomly generated Era mutants which may indicate regions of the protein that are of functional importance are described.

In vivo selection of conditional-lethal mutations in the gene encoding elongation factor G of Escherichia coli

The ribosome translocation step that occurs during protein synthesis is a highly conserved, essential activity of all cells. The precise movement of one codon that occurs following peptide bond formation is regulated by elongation factor G (EF-G) in eubacteria or elongation factor 2 (EF-2) in eukaryotes. To begin to understand molecular interactions that regulate this process, a genetic selection was developed with the aim of obtaining conditional-lethal alleles of the gene (fusA) that encodes EF-G in Escherichia coli. The genetic selection depends on the observation that resistant strains arose spontaneously in the presence of sublethal concentrations of the antibiotic kanamycin. Replica plating was performed to obtain mutant isolates from this collection that were restrictive for growth at 42 degrees C. Two tightly temperature-sensitive strains were characterized in detail and shown to harbor single-site missense mutations within fusA. The fusA100 mutant encoded a glycine-to-aspartic acid change at codon 502. The fusA101 allele encoded a glutamine-to-proline alteration at position 495. Induction kinetics of beta-galactosidase activity suggested that both mutations resulted in slower elongation rates in vivo. These missense mutations were very near a small group of conserved amino acid residues (positions 483 to 493) that occur in EF-G and EF-2 but not EF-Tu. It is concluded that these sequences encode a specific domain that is essential for efficient translocase function.

GTPase-dependent signaling in bacteria: characterization of a membrane-binding site for era in Escherichia coli

Era is an Escherichia coli GTPase that is essential for cell viability and is peripherally associated with the cytoplasmic membrane. Both immunoelectron microscopy and subcellular-fractionation experiments have shown that Era is present in cytoplasmic as well as membrane-associated pools. These data led to speculation that the mechanism of action of Era may require cycling between membrane and cytoplasmic sites. In order to investigate this possibility, an in vitro binding assay was developed to characterize the binding of Era to membrane fractions. Competition and saturation binding experiments suggest that a site that is specific for Era and capable of binding up to 5 ng of Era per microgram of membrane protein is present in membrane preparations. The binding curve is complex, indicating that multiple equilibria describe the interaction. The binding of Era to this putative receptor is dependent on guanine nucleotides; binding cannot be measured in the absence of nucleotide, and neither ATP nor UTP can substitute. Subfractionation of cell walls showed that the guanine nucleotide-dependent binding site was present in fractions enriched in cytoplasmic membrane. These data provide evidence that Era may be involved in a GTPase-receptor-coupled membrane-signaling pathway that is essential for growth in E. coli.