Predicting metabolic biomarkers of human inborn errors of metabolism

Early diagnosis of inborn errors of metabolism is commonly performed through biofluid metabolomics, which detects specific metabolic biomarkers whose concentration is altered due to genomic mutations. The identification of new biomarkers is of major importance to biomedical research and is usually performed through data mining of metabolomic data. After the recent publication of the genome‐scale network model of human metabolism, we present a novel computational approach for systematically predicting metabolic biomarkers in stochiometric metabolic models. Applying the method to predict biomarkers for disruptions of red‐blood cell metabolism demonstrates a marked correlation with altered metabolic concentrations inferred through kinetic model simulations. Applying the method to the genome‐scale human model reveals a set of 233 metabolites whose concentration is predicted to be either elevated or reduced as a result of 176 possible dysfunctional enzymes. The method's predictions are shown to significantly correlate with known disease biomarkers and to predict many novel potential biomarkers. Using this method to prioritize metabolite measurement experiments to identify new biomarkers can provide an order of a 10‐fold increase in biomarker detection performance.     

Antenatal diagnosis of inborn errors of metabolism: Tissue culture aspects

Summary The cells from 62 amniotic fluids have been cultured to the stage at which biochemical studies could have been undertaken. Although all cultures showed initial signs of cellular proliferation in only 90% of these were sufficient cells obtained for biochemical assay. If a time limit of 6 weeks was to be imposed, only 58% of the cultures could have been regarded as successful. The problems involved in culturing amniotic fluid cells for the antenatal diagnosis of inborn errors of metabolism are discussed.

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Zusammenfassung Von 62 Amnionflüssigkeits-Proben wurden die Zellen bis zu einem Stadium kultiviert, in dem biochemische Untersuchungen möglich wurden. Obwohl alle Kulturen anfänglich Zeichen einer Zellproliferation zeigten, wurden nur in 90% genügend Zellen für biochemische Untersuchungen gewonnen. Unter Annahme einer Zeitbegrenzung von 6 Wochen konnten sogar nur 58% aller Kulturen als erfolgreich betrachtet werden. Die Probleme bei der Kultivierung von Amnionzellen für die pränatale Diagnose angeborener Stoffwechselstörungen werden diskutiert.

     

Screening mutant mice for inborn errors of metabolism

We described our methods of screening mice for inborn errors of metabolism including metabolic storage diseases, disorders of amino acid metabolism, and organic acidemias. Our screening program consisted of histopathology, quantitative serum amino acid analysis, and urinary organic acid analysis. In this preliminary study, we tested mice representing 28 different mutations whose clinical signs suggested a possible metabolic disorder. We documented the normal values for mouse serum amino acids and urinary organic acids. No mutant tested had relevant or consistent biochemical abnormalities as determined by our screening tests. Some mutants showed histopathology as described previously. However, we were unable to confirm the histopathology described originally for the shambling mutant.     

Stable isotopes in the management and diagnosis of inborn errors of metabolism

Stable isotope techniques offer advantages over older methods in safety, sensitivity, specificity, and reduction in number of subjects required for analytic determinations in some types of studies in "inborn errors of metabolism." In addition to their use as internal standards for gas chromatography - mass spectrometry, quantitation of plasma substrates, and their urinary metabolites, stable isotopes have been successfully employed in studies of metabolite identification, enzyme activity, nutrient turnover and requirements, and diagnosis of inborn errors of metabolism.     

Radiological innovations in the screening and diagnosis of the inborn errors of metabolism

New metabolic diseases are regularly identified by a genetic or biochemical approach. Indeed, the metabolic diseases result from an enzymatic block with accumulation of a metabolite upstream to the block and deficit of a metabolite downstream. The characterization of these abnormal metabolites by MRI spectroscopy permitted to identify the deficient enzyme in two new groups of diseases, creatine deficiencies and polyol anomalies. Creatine deficiency is implicated in unspecific mental retardation. A low peak of creatine at MRI spectroscopy is evocating of creatine deficiency which is treatable by creatine administration. Deficiency of synthesis of polyols, metabolites on the pentose pathway, represent new described metabolic diseases with variable symptoms including a neurological distress, liver disease, splenomegaly, cutis laxa and renal insufficiency. The deficit of ribose-5-phosphate isomerase, one of the enzymes whose diagnosis is evoked in front of the accumulation of ribitol, arabitol and xylitol leads to a leucodystrophy in adults. This new deficit was highlighted by the identification of an abnormal peak in cerebral MRI-spectroscopy corresponding to the abnormal accumulation of polyols in brain. Congenital hyperinsulinism (HI) is characterized by profound hypoglycaemia related to inappropriate insulin secretion. Focal and diffuse forms of hyperinsulinism share a similar clinical presentation but their treatment is dramatically different. Until recently, preoperative differential diagnosis was based on pancreatic venous sampling, an invasive and technically demanding technique. Positron emission tomography (PET) after injection of [18F]Fluoro-L-DOPA has been evaluated for the preoperative differentiation between focal and diffuse HI, by imaging uptake of radiotracer and the conversion of [18F]Fluoro-L-DOPA into dopamine by DOPA decarboxylase. PET with [18F]Fluoro-L-DOPA has been validated as a reliable test to differentiate diffuse and focal HI and is now a major differential diagnosis tool in infantile hyperinsulinemic hypoglycaemia.     

Prenatal diagnosis of inborn errors of metabolism. Present status and new approaches

The evolution of the techniques aiming at the prenatal diagnosis of inborn metabolic disorders has closely reflected the progress in the knowledge of their underlying molecular defects. Initially, abnormal metabolites have been looked for in amniotic fluid. Recently, improved techniques of detection have permitted fast and reliable prenatal diagnoses through biochemical studies of cell-free amniotic fluid. Presently, the most widely used approach is the search for the defective gene product in cultured amniotic cells obtained through amniocentesis. Because of its relative safety, this procedure should be recommended, provided three prerequisites are met: a most accurate diagnosis of the index patient, the knowledge of the defective enzyme and its expression in cultured cells. For a correct interpretation of the results, cell culture parameters as well as specific activities of the mutant enzyme in the index case and the parental cells must be taken into account. Fetal blood sampling is a valuable alternative for some of the genetic disorders that cannot be detected in cultured amniocytes. The recently developed technique of chorion biopsy enables now to sample fetal cells during the first trimester of gestation. Meanwhile, the progress in DNA technology has uncovered exciting perspectives for the prenatal diagnosis of monogenic disorders at the gene level. Restriction endonuclease mapping has enabled to diagnose prenatally some forms of haemoglobinopathies, first through the polymorphism of sequences adjacent to the beta-globin gene, and now for the sickle-cell disease, by direct identification of the mutation.     

Current strategies for the treatment of inborn errors of metabolism

Inborn errors of metabolism (IEMs) are a large group of inherited disorders characterized by disruption of metabolic pathways due to deficient enzymes, cofactors, or transporters. The rapid advances in the understanding of the molecular pathophysiology of many IEMs, have led to significant progress in the development of many new treatments. The institution and continued expansion of newborn screening provide the opportunity for early treatment, leading to reduced morbidity and mortality. This review provides an overview of the diverse therapeutic approaches and recent advances in the treatment of IEMs that focus on the basic principles of reducing substrate accumulation, replacing or enhancing absent or reduced enzyme or cofactor, and supplementing product deficiency. In addition, the challenges and obstacles of current treatment modalities and future treatment perspectives are reviewed and discussed.     

Experience with bone marrow transplantation for inborn errors of metabolism

Westminster experience had by 1973 evolved the concept of displacement bone marrow transplantation and extended the donors from matched siblings to other family and unrelated donors. The principles of its use to install donor bone marrow as a component factory for the life of the recipient, together with the importance of immunoprophylaxis are detailed. Satisfying correction has been achieved for 48 previously fatal genetic diseases, partial correction for another 5 with failure for 3 diseases. Displacement bone marrow transplantation is not a panacea, but could be applied to about 7% of known inborn errors, devising in vitro tests which can predict in vivo donor effects, especially since some 80% of our patients are not found in known families and could not have been prevented.     

A compendium of inborn errors of metabolism mapped onto the human metabolic network

Inborn errors of metabolism (IEMs) are hereditary metabolic defects, which are encountered in almost all major metabolic pathways occurring in man. Many IEMs are screened for in neonates through metabolomic analysis of dried blood spot samples. To enable the mapping of these metabolomic data onto the published human metabolic reconstruction, we added missing reactions and pathways involved in acylcarnitine (AC) and fatty acid oxidation (FAO) metabolism. Using literary data, we reconstructed an AC/FAO module consisting of 352 reactions and 139 metabolites. When this module was combined with the human metabolic reconstruction, the synthesis of 39 acylcarnitines and 22 amino acids, which are routinely measured, was captured and 235 distinct IEMs could be mapped. We collected phenotypic and clinical features for each IEM enabling comprehensive classification. We found that carbohydrate, amino acid, and lipid metabolism were most affected by the IEMs, while the brain was the most commonly affected organ. Furthermore, we analyzed the IEMs in the context of metabolic network topology to gain insight into common features between metabolically connected IEMs. While many known examples were identified, we discovered some surprising IEM pairs that shared reactions as well as clinical features but not necessarily causal genes. Moreover, we could also re-confirm that acetyl-CoA acts as a central metabolite. This network based analysis leads to further insight of hot spots in human metabolism with respect to IEMs. The presented comprehensive knowledge base of IEMs will provide a valuable tool in studying metabolic changes involved in inherited metabolic diseases.     

A fungal perspective on human inborn errors of metabolism: alkaptonuria and beyond

Crucial for the establishment and development of biochemical genetics as a self-standing discipline was Beadle and Tatum's choice of Neurospora crassa as experimental organism some 60 years ago. Although Garrod's insights on biochemical genetics and his astonishingly modern concepts of biochemical individuality and susceptibility to disease had been ignored by their contemporaries, Beadle acknowledged on several occasions how close Garrod had come to the "one-gene-one-enzyme" hypothesis. In an unexpected turn of events, several genes involved in human inborn errors of metabolism, including the gene for Garrod's favorite disease, alkaptonuria, have been characterized by exploitation of the experimental advantages of another mold, Aspergillus nidulans, which shares with N. crassa the experimental advantages that prompted pioneers of biochemical genetics to use them: rapid growth, facile genetic manipulation, and an environment (the composition of the growth medium) that can be manipulated à la carte.