Urinary pyrimidine excretion in arginase deficiency

QuTIE: quantum optimization for target identification by enzymes

Summary

Target identification by enzymes (TIE) problem aims to identify the set of enzymes in a given metabolic network, such that their inhibition eliminates a given set of target compounds associated with a disease while incurring minimum damage to the rest of the compounds. This is a NP-hard problem, and thus optimal solutions using classical computers fail to scale to large metabolic networks. In this article, we develop the first quantum optimization solution, called QuTIE (quantum optimization for target identification by enzymes), to this NP-hard problem. We do that by developing an equivalent formulation of the TIE problem in quadratic unconstrained binary optimization form. We then map it to a logical graph, and embed the logical graph on a quantum hardware graph. Our experimental results on 27 metabolic networks from Escherichia coli, Homo sapiens, and Mus musculus show that QuTIE yields solutions that are optimal or almost optimal. Our experiments also demonstrate that QuTIE can successfully identify enzyme targets already verified in wet-lab experiments for 14 major disease classes.

Availability and implementation

Code and sample data are available at: https://github.com/ngominhhoang/Quantum-Target-Identification-by-Enzymes.

Untargeted metabolomic profiling reveals multiple pathway perturbations and new clinical biomarkers in urea cycle disorders

Purpose:

Untargeted metabolomic analysis is increasingly being used in the screening and management of individuals with inborn errors of metabolism (IEM). We aimed to test whether untargeted metabolomic analysis in plasma might be useful for monitoring the disease course and management of urea cycle disorders (UCDs).

Methods:

Untargeted mass spectrometry-based metabolomic analysis was used to generate z-scores for more than 900 metabolites in plasma from 48 individuals with various UCDs. Pathway analysis was used to identify common pathways that were perturbed in each UCD.

Results:

Our metabolomic analysis in plasma identified multiple potentially neurotoxic metabolites of arginine in arginase deficiency and, thus, may have utility in monitoring the efficacy of treatment in arginase deficiency. In addition, we were also able to detect multiple biochemical perturbations in all UCDs that likely reflect clinical management, including metabolite alterations secondary to dietary and medication management.

Conclusions:

In addition to utility in screening for IEM, our results suggest that untargeted metabolomic analysis in plasma may be beneficial for monitoring efficacy of clinical management and off-target effects of medications in UCDs and potentially other IEM.

Congenital Glaucoma Associated with An Arginase Deficit: A Case Report

PURPOSE

Argininemia is a rare congenital disease caused by deficiency. We present here a case in which argininemia and buphthalmos are associated.

CASE REPORT

This female patient, who died at eighteen, had intraocular pressure correlated with her blood levels or arginine. Hyperammoniemia causes a change in pH that could explain an increase in aqueous humor (from the ciliary body). Ammonium ions could also damage the matrix of the trabecular meshwork.

CONCLUSIONS

The association of argininemia and buphthalmos have never been described. This might be because of the different expressions of the disease, or because nobody has ever looked for ocular hypertension in these patients unless they had subjective symptoms.

Newborn screening for hyperargininemia due to arginase 1 deficiency

Hyperargininemia caused by Arginase 1 deficiency is a rare disorder of the urea cycle that can be diagnosed by elevation of arginine in newborn screening blood spots when analyzed by tandem mass spectrometry. Hyperargininemia is currently included as a secondary target on the U.S. Recommended Uniform Screening Panel, which directly influences state-based newborn screening. Because of the apparent low disease frequency and lack of case detection and treatment data, detailed attention has not been given to a model newborn screening algorithm including appropriate analytical cutoff values for disease indicators. In this paper we assess the frequency of hyperargininemia in the U.S. identified by newborn screening to date and document the current status and variability of hyperargininemia newborn screening across U.S. newborn screening programs. We also review other data that support improved screening efficacy by utilizing the arginine/ornithine ratio and other amino acid ratios as discriminators in the screening algorithm. Analysis of archived California screening data showed that an arginine cutoff of 50μM combined with an arginine/ornithine ratio of 1.4 would have resulted in a recall rate of 0.01%. Using an arginine cutoff of 60μM and an arginine/(phenylalanine x leucine) ratio of 1.4, reportedly used in one screening program, or the R4S Tool Runner, would have resulted in a recall rate of <0.005%. All 9 diagnosed patients would have been found for either protocol. Thus, use of appropriate ratios as part of the screening algorithm has the potential to increase both screening sensitivity and specificity. Improved newborn screening effectiveness should lead to better case detection and more rapid treatment to lower plasma arginine levels hence improving long term outcome of individuals with hyperargininemia.

Arginase I deficiency: severe infantile presentation with hyperammonemia: more common than reported?

Enzyme defects of the urea cycle typically present with significant hyperammonemia and its associated toxicity, in the first few months of life. However, arginase I (ARG1) deficiency, a rare autosomal recessive disorder, has classically been the exception. ARG1 deficiency usually presents later in life with spasticity, seizures, failure to thrive and developmental regression. Neonatal and early infantile presentation of ARG1 deficiency with severe hyperammonemia remains rare and only six such cases have been described. We report a severely affected infant with ARG1 deficiency who presented at 6 weeks of age with lethargy, poor feeding and severe encephalopathy caused by hyperammonemia. The clinical and biochemical features of the proband and six other previously reported cases with neonatal or infantile-onset presentation of ARG1 deficiency with hyperammonemia are reviewed. In addition, the clinical spectrum of seven previously unpublished patients with later onset ARG1 deficiency, who also experienced recurrent hyperammonemia, is presented. Several biochemical abnormalities have been postulated to play a role in the pathogenesis of the neurological changes in ARG1 deficiency including hyperargininemia, elevated guanidino compounds and elevated glutamine levels, as well as the hyperammonemia. The index case demonstrated many of these. The cases reviewed here suggest a genotype/phenotype correlation and advocate for the addition of arginine as a primary target in newborn screening programs.

Orotic acid excretion and arginine metabolism

The urinary excretion of orotic acid, an intermediate in the pyrimidine biosynthetic pathway, is markedly increased in many inborn errors of the urea cycle and in a number of other disorders involving arginine metabolism. Carbamoyl phosphate, which accumulates within hepatic mitochondria in patients with ornithine transcarbamoylase deficiency, can diffuse to the cytosol and enter the pyrimidine pathway, resulting in greatly increased orotic acid production and excretion. This orotic aciduria also occurs in inborn errors of the mitochondrial ornithine/citrulline transporter, arginase, argininosuccinate synthetase, and argininosuccinate lyase. Increased orotic acid excretion is also found in a number of hypoargininemic states, such as lysinuric protein intolerance. However, orotic aciduria should not be used uncritically as an index of arginine deficiency because it is found in patients with arginase deficiency who exhibit hyperargininemia. Increased orotic acid excretion can also arise as a result of impairments of pyrimidine synthesis, whether brought about by a genetic defect (e.g., in UMP synthase) or by drugs that inhibit the terminal part of the pathway (e.g., allopurinol or 6-azauridine). When used appropriately, measurement of urinary orotic acid is a valuable tool for the study of many derangements of arginine metabolism, including arginine depletion, and to assess the efficacy of therapies used to replete this amino acid.

Hyperargininemia due to liver arginase deficiency

The urea cycle is a series of six reactions necessary to rid the body of the nitrogen generated by the metabolism, primarily of amino acids, from the diet or released as the result of endogenous protein catabolism. Arginase is the sixth and final enzyme of this cycle. Arginase catalyzes the conversion of arginine to urea and ornithine, the latter recycled to continue the cycle. Hyperargininemia due to arginase deficiency is inherited in an autosomal recessive manner and gene for arginase, designated AI, has been cloned. Unlike the other urea cycle enzymes, a second gene encoding arginase, with similar structural properties and enzyme characteristics, exists and has been named Arginase II (AII). Comprehensive histories and physical examinations confirm a strikingly uniform clinical picture and one notably different from patients with other urea cycle disorders. This condition rarely presents in the neonatal period and first symptoms typically present in children between 2 and 4 years of age. First symptoms are often neurologically based. If untreated, symptoms are progressive with a gradual loss of developmental milestones. With adherence to a dietary and drug regimen, a favorable outcome can be expected, with cessation of further neurological deterioration and in some instances, of improvement. This article summarizes the clinical course of selected patients who represent the full spectrum of presentations of arginase deficiency. In addition to the clinical characterization of this disorder; the biochemical, enzymatic, and molecular evidence of disease is summarized. Treatment and prenatal diagnosis are also discussed.

Laboratory evaluation of urea cycle disorders

The urea cycle disorders (UCDs) represent a group of inherited metabolic diseases with hyperammonemia as the primary laboratory abnormality. Affected individuals may become comatose or die if not treated rapidly. Diagnosis of a UCD requires a high index of suspicion and judicious use of the laboratory. It is important to rule out other conditions causing hyperammonemia that may require different treatment. The astute clinician may suspect a specific UCD in the appropriate clinical setting, but only laboratory results can confirm a specific diagnosis. The importance of the laboratory in helping the clinician to differentiate among various causes of hyperammonemia, in confirming a specific UCD, in carrier testing, and in prenatal diagnostic testing is highlighted in this review.

The age dependency of the creatinine-related concentration of ribonucleosides in human urine

We investigated the urinary excretion of ribonucleosides and an unidentified substance in 345 healthy probands from the age of a few weeks to 40 years. The concentration of ribonucleosides, related to the corresponding concentration of creatinine, decreases until nearly 20 years and remains constant between 20 and 40 years. The polynomial functions describing this dependency are presented. The biological significance of our findings is briefly discussed.

Treatment of hyperargininaemia due to arginase deficiency with a chemically defined diet

A brother and sister aged 11 and 17 years have been reported previously to have hyperargininaemia and arginase deficiency: they were treated with a semi-synthetic diet consisting of fat, carbohydrate, minerals, vitamins and essential amino acids in amounts equivalent to 0.55-0.65 g protein kg-1 day-1 for 2 years. Plasma arginine levels fell from 0.50-0.90 mumol/1 to 0.13-0.30 mumol/1 (normal range 0.02-0.15). Increased concentrations of arginine in the cerebrospinal fluid (CSF) fell from 0.069-0.098 mumol/l to 0.040-0.056 mumol/l (normal mean +/- SD = 0.020 +/- 0.006). Dibasic aminoaciduria returned to normal within 1 week. Substitution of the keto-acid analogues of five essential amino acids in the formula lowered arginine concentrations further, but proved to be unpalatable. Urinary concentrations of orotic acid, uridine and uracil fell toward normal but remained increased, even when the plasma ammonia concentration was measured as normal. Both patients showed a stable clinical improvement.