Nonsense-mediated decay of RNA occurs frequently in carbamyl phosphate synthetase I deficiency.

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In this study using cells from 26 patients with CPSI deficiency, 21/52 alleles have proven to be infrequently found in the cDNA, suggesting RNA instability. In liver tissue from two patients, Northern blot proved CPSI-specific RNA degradation.
Mol Genet Metab. 2006 Sep-Oct;89(1-2):80-6. Epub 2006 Jun 5.

The frequent observation of evidence for nonsense-mediated decay in RNA from
patients with carbamyl phosphate synthetase I deficiency.

Eeds AM, Hall LD, Yadav M, Willis A, Summar S, Putnam A, Barr F, Summar ML.


For more information on urea cycle defects, please see chapter 85 of OMMBID.
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Philippe Campeau, MD
Resident in Medical Genetics at McGill University
OMMBID Blog Administrator
Chapter 85 : Urea Cycle Enzymes

Authors: Saul W. Brusilow, Arthur L. Horwich

The urea cycle, which consists of a series of five biochemical reactions, has two roles. In order to prevent the accumulation of toxic nitrogenous compounds, the urea cycle incorporates nitrogen not used for net biosynthetic purposes into urea, which serves as the waste nitrogen product in mammals. The urea cycle also contains several of the biochemical reactions required for the de novo synthesis of arginine.

Urea cycle disorders are characterized by the triad of hyperammonemia, encephalopathy, and respiratory alkalosis (the earliest objective evidence of encephalopathy). Five well-documented diseases (each with considerable genetic and phenotypic variability) have been described, each representing a defect in the biosynthesis of one of the normally expressed enzymes of the urea cycle. Four of these five diseases—deficiencies of carbamyl phosphate synthetase (CPS) (OMIM 237300), ornithine transcarbamylase (OTC) (OMIM 311250), argininosuccinic acid synthetase (AS) (OMIM 215700), and argininosuccinate lyase (AL) (OMIM 207900)—are characterized by signs and symptoms induced by the accumulation of precursors of urea, principally ammonium and glutamine. The most dramatic clinical presentation of these four diseases occurs in full-term infants with no obstetric risk factors who appear normal for 24 to 48 hours and then exhibit progressive lethargy, hypothermia, and apnea all related to very high plasma ammonium levels.

Milder forms of these diseases occur; they may present with signs of encephalopathy at any age from infancy to adulthood. The most common of these late-onset diseases occurs in female carriers of a mutation at the OTC locus of one of their X chromosomes. The late-onset cases present with respiratory alkalosis and episodic mental status changes progressing, if not emergently treated, to cerebral edema, brainstem compression, and death. The acute encephalopathy is characterized by brain edema and swollen astrocytes, the cause of which is attributed to intraglial accumulation of glutamine resulting in osmotic shifts of water into the cell. Axons, dendrites, synapses, and oligodendroglia are normal. A fifth disease, arginase deficiency (OMIM 107830), is characterized by a clinical picture consisting of progressive spastic quadriplegia and mental retardation; symptomatic hyperammonemia, which can be life-threatening, occurs neither as severely or as commonly as in the other four diseases. Apart from OTC deficiency, which is inherited as an X-linked disorder, the other four diseases are inherited as autosomal-recessive traits. Carrier status of OTC mutations in women is determined by pedigree analysis and molecular methods. For fetuses at risk, antenatal diagnosis is available by a number of methods, particular to each disease, including enzyme analysis of fibroblasts cultured from aminocytes, as well as molecular (DNA) methods.

Molecular genetic analysis of the urea cycle enzymes has addressed their structure and expression and has permitted DNA-based diagnosis of deficiency, in many cases by direct analysis of mutations. Using the cloned complementary DNA as probes, expression in liver of RNA for all the enzymes has been observed to be increased severalfold by starvation. RNA coding for the 160-kDa subunit of the CPS I homodimer is detected almost exclusively in the liver and translates a precursor protein representing the product of fusion of two ancestral prokaryotic subunits, joined with an N-terminal mitochondrial targeting sequence. Few mutations have been identified in this large coding sequence in affected pedigrees so far, but a restriction fragment-length polymorphism (RFLP) in the human CPS locus is useful in prenatal diagnosis of deficiency. OTC is also expressed principally in the liver, and its subunit is also translated as a precursor, comprising an N-terminal mitochondrial targeting sequence that functions via an α-helical structure and net positive charge, joined with a mature portion that resembles prokaryotic transcarbamylases. Mitochondrial import requires the action of a variety of components in the cytosol to maintain an import-competent conformation, in the outer mitochondrial membrane for recognition of the precursor, in both outer and inner membrane for protein translocation, and in the matrix for proteolytic processing and folding to the active conformation. Gene deletions have been observed in approximately 15 percent of affected males. More than 100 different single base substitutions have been identified, producing amino acid substitution in many cases, involving either of the two domains of the OTC subunit. In other cases, splicing is affected, either destabilizing the messenger RNA (mRNA) or frameshifting the subunit. Prenatal diagnosis can be offered to most women who are established as heterozygous carriers by pedigree analysis, allopurinol testing, or DNA analysis, using direct DNA analysis of fetal DNA where the mutation is known, or using RFLPs. Recombinant OTC retroviruses have transduced cultured hepatocytes of mice with inherited OTC deficiency, and recombinant OTC adenoviruses have been injected into newborn mutant animals with evidence of rescue of deficiency. These gene transfer experiments aim toward achieving stable long-term OTC expression. Argininosuccinate synthetase (AS) is programmed from a single locus, but a large number of homologous processed pseudogenes are localized throughout the genome. Expression of AS mRNA has been studied in cultured cells, where the level of mRNA is greatly increased in response to canavanine treatment and repressed by the presence of arginine. The AS coding sequence has been successfully transferred into both cultured cells and mouse bone marrow cells as an approach to AS deficiency of supplying enzyme activity outside the liver. Analysis of AS mutations reveals considerable heterogeneity in the position of mutation, with most composed of codon substitutions that produce unstable protein products. Where direct mutation analysis is not possible, a number of polymorphisms at the AS locus enable linkage study of affected pedigrees. Human AL is similar to avian δ-crystallins, in which a virtually identical protein is apparently used as a structural component. Analysis of AL mutants also reveals considerable heterogeneity. Arginase in human liver and red cells is a cytosolic enzyme distinct from a second mitochondrial-localized enzyme. Deficient patients have shown heterogeneity in the site of mutation. Two RFLPs at the locus have been identified.

Treatment requires restriction of dietary protein intake and activation of other pathways of waste nitrogen synthesis and excretion. For patients deficient in CPS, OTC, and AS, treatment with sodium phenylbutyrate activates the synthesis of phenylacetylglutamine, which has a dual effect. By providing a new vehicle for waste nitrogen excretion, which suppresses residual urea synthesis in the late-onset group, a reserve urea synthetic capacity is generated that may support nitrogen homeostasis when required. In patients deficient in AS and argininosuccinase, supplementation of the diet with arginine promotes the synthesis of citrulline in the former and argininosuccinate in the latter, both of which serve as waste nitrogen products.

Outcome of treatment of neonatal-onset disease has been disappointing. Even those neonates treated prospectively prior to the onset of hyperammonemia are at high risk for neurologic deficits. Parents should be realistically counseled as to the likely outcome if the infant is rescued. Treatment of late-onset disease appears to preserve the neurologic status found at the start of therapy.



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