51
|
Bliziotis NG, Kluijtmans LAJ, Tinnevelt GH, Reel P, Reel S, Langton K, Robledo M, Pamporaki C, Pecori A, Van Kralingen J, Tetti M, Engelke UFH, Erlic Z, Engel J, Deutschbein T, Nölting S, Prejbisz A, Richter S, Adamski J, Januszewicz A, Ceccato F, Scaroni C, Dennedy MC, Williams TA, Lenzini L, Gimenez-Roqueplo AP, Davies E, Fassnacht M, Remde H, Eisenhofer G, Beuschlein F, Kroiss M, Jefferson E, Zennaro MC, Wevers RA, Jansen JJ, Deinum J, Timmers HJLM. Preanalytical Pitfalls in Untargeted Plasma Nuclear Magnetic Resonance Metabolomics of Endocrine Hypertension. Metabolites 2022; 12:679. [PMID: 35893246 PMCID: PMC9394285 DOI: 10.3390/metabo12080679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/17/2022] [Accepted: 07/11/2022] [Indexed: 11/24/2022] Open
Abstract
Despite considerable morbidity and mortality, numerous cases of endocrine hypertension (EHT) forms, including primary aldosteronism (PA), pheochromocytoma and functional paraganglioma (PPGL), and Cushing's syndrome (CS), remain undetected. We aimed to establish signatures for the different forms of EHT, investigate potentially confounding effects and establish unbiased disease biomarkers. Plasma samples were obtained from 13 biobanks across seven countries and analyzed using untargeted NMR metabolomics. We compared unstratified samples of 106 PHT patients to 231 EHT patients, including 104 PA, 94 PPGL and 33 CS patients. Spectra were subjected to a multivariate statistical comparison of PHT to EHT forms and the associated signatures were obtained. Three approaches were applied to investigate and correct confounding effects. Though we found signatures that could separate PHT from EHT forms, there were also key similarities with the signatures of sample center of origin and sample age. The study design restricted the applicability of the corrections employed. With the samples that were available, no biomarkers for PHT vs. EHT could be identified. The complexity of the confounding effects, evidenced by their robustness to correction approaches, highlighted the need for a consensus on how to deal with variabilities probably attributed to preanalytical factors in retrospective, multicenter metabolomics studies.
Collapse
Affiliation(s)
- Nikolaos G. Bliziotis
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands;
| | - Leo A. J. Kluijtmans
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands;
| | - Gerjen H. Tinnevelt
- Department of Analytical Chemistry, Institute for Molecules and Materials, Radboud University, 6500 HB Nijmegen, The Netherlands; (G.H.T.); (J.J.J.)
| | - Parminder Reel
- Division of Population Health and Genomics, School of Medicine, University of Dundee, Dundee DD2 4BF, UK; (P.R.); (S.R.); (E.J.)
| | - Smarti Reel
- Division of Population Health and Genomics, School of Medicine, University of Dundee, Dundee DD2 4BF, UK; (P.R.); (S.R.); (E.J.)
| | - Katharina Langton
- Department of Medicine III, University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany; (K.L.); (C.P.); (G.E.)
| | - Mercedes Robledo
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre (CNIO), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28029 Madrid, Spain;
| | - Christina Pamporaki
- Department of Medicine III, University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany; (K.L.); (C.P.); (G.E.)
| | - Alessio Pecori
- Division of Internal Medicine and Hypertension Unit, Department of Medical Sciences, University of Torino, 10124 Torino, Italy; (A.P.); (M.T.); (T.A.W.)
| | - Josie Van Kralingen
- British Heart Foundation Glasgow Cardiovascular Research Centre (BHF GCRC), Institute of Cardiovascular & Medical Sciences (ICAMS), University of Glasgow, Glasgow G12 8TA, UK; (J.V.K.); (E.D.)
| | - Martina Tetti
- Division of Internal Medicine and Hypertension Unit, Department of Medical Sciences, University of Torino, 10124 Torino, Italy; (A.P.); (M.T.); (T.A.W.)
| | - Udo F. H. Engelke
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands;
| | - Zoran Erlic
- Department of Endocrinology, Diabetology and Clinical Nutrition, University Hospital Zurich (USZ), University of Zurich (UZH), 8006 Zurich, Switzerland; (Z.E.); (F.B.)
| | - Jasper Engel
- Biometris, Wageningen University & Research, 6708 PB Wageningen, The Netherlands;
| | - Timo Deutschbein
- Department of Internal Medicine I, Division of Endocrinology and Diabetes, University Hospital, University of Würzburg, 97080 Würzburg, Germany; (T.D.); (M.F.); (H.R.); (M.K.)
- Medicover Oldenburg MVZ, 26122 Oldenburg, Germany
| | - Svenja Nölting
- Department of Medicine IV, University Hospital, LMU Munich, 80336 Munich, Germany;
| | - Aleksander Prejbisz
- Department of Hypertension, Institute of Cardiology, 04-628 Warsaw, Poland; (A.P.); (A.J.)
| | - Susan Richter
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Carl Gustav Carus at the Technische Universität Dresden, 01307 Dresden, Germany;
| | - Jerzy Adamski
- Research Unit Molecular Endocrinology and Metabolism, Genome Analysis Center, Helmholtz Center München, German Research Center for Environmental Health, 85764 Neuherberg, Germany;
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
- Institute of Experimental Genetics, Technical University München, 85350 Freising-Weihenstephan, Germany
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 119077 Singapore, Singapore
| | - Andrzej Januszewicz
- Department of Hypertension, Institute of Cardiology, 04-628 Warsaw, Poland; (A.P.); (A.J.)
| | - Filippo Ceccato
- Endocrinology Unit, Department of Medicine DIMED, University-Hospital of Padova, 35128 Padova, Italy; (F.C.); (C.S.)
| | - Carla Scaroni
- Endocrinology Unit, Department of Medicine DIMED, University-Hospital of Padova, 35128 Padova, Italy; (F.C.); (C.S.)
| | - Michael C. Dennedy
- The Discipline of Pharmacology and Therapeutics, School of Medicine, National University of Ireland, H91 CF50 Galway, Ireland;
| | - Tracy A. Williams
- Division of Internal Medicine and Hypertension Unit, Department of Medical Sciences, University of Torino, 10124 Torino, Italy; (A.P.); (M.T.); (T.A.W.)
| | - Livia Lenzini
- Department of Medicine-DIMED, Emergency and Hypertension Unit, University of Padova, University Hospital, 35126 Padova, Italy;
| | - Anne-Paule Gimenez-Roqueplo
- INSERM, PARCC, Université de Paris, 75015 Paris, France; (A.-P.G.-R.); (M.-C.Z.)
- Service de Genétique, Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, 75015 Paris, France
| | - Eleanor Davies
- British Heart Foundation Glasgow Cardiovascular Research Centre (BHF GCRC), Institute of Cardiovascular & Medical Sciences (ICAMS), University of Glasgow, Glasgow G12 8TA, UK; (J.V.K.); (E.D.)
| | - Martin Fassnacht
- Department of Internal Medicine I, Division of Endocrinology and Diabetes, University Hospital, University of Würzburg, 97080 Würzburg, Germany; (T.D.); (M.F.); (H.R.); (M.K.)
- Core Unit Clinical Mass Spectrometry, University Hospital Würzburg, 97080 Würzburg, Germany
- Comprehensive Cancer Center Mainfranken, Würzburg University, 97070 Würzburg, Germany
| | - Hanna Remde
- Department of Internal Medicine I, Division of Endocrinology and Diabetes, University Hospital, University of Würzburg, 97080 Würzburg, Germany; (T.D.); (M.F.); (H.R.); (M.K.)
| | - Graeme Eisenhofer
- Department of Medicine III, University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany; (K.L.); (C.P.); (G.E.)
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Carl Gustav Carus at the Technische Universität Dresden, 01307 Dresden, Germany;
| | - Felix Beuschlein
- Department of Endocrinology, Diabetology and Clinical Nutrition, University Hospital Zurich (USZ), University of Zurich (UZH), 8006 Zurich, Switzerland; (Z.E.); (F.B.)
- Department of Medicine IV, University Hospital, LMU Munich, 80336 Munich, Germany;
| | - Matthias Kroiss
- Department of Internal Medicine I, Division of Endocrinology and Diabetes, University Hospital, University of Würzburg, 97080 Würzburg, Germany; (T.D.); (M.F.); (H.R.); (M.K.)
- Department of Medicine IV, University Hospital, LMU Munich, 80336 Munich, Germany;
- Core Unit Clinical Mass Spectrometry, University Hospital Würzburg, 97080 Würzburg, Germany
- Comprehensive Cancer Center Mainfranken, Würzburg University, 97070 Würzburg, Germany
| | - Emily Jefferson
- Division of Population Health and Genomics, School of Medicine, University of Dundee, Dundee DD2 4BF, UK; (P.R.); (S.R.); (E.J.)
- Institute of Health & Wellbeing, Glasgow University, Glasgow G12 8RZ, UK
| | - Maria-Christina Zennaro
- INSERM, PARCC, Université de Paris, 75015 Paris, France; (A.-P.G.-R.); (M.-C.Z.)
- Service de Genétique, Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, 75015 Paris, France
| | - Ron A. Wevers
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands;
| | - Jeroen J. Jansen
- Department of Analytical Chemistry, Institute for Molecules and Materials, Radboud University, 6500 HB Nijmegen, The Netherlands; (G.H.T.); (J.J.J.)
| | - Jaap Deinum
- Department of Internal Medicine, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands;
| | - Henri J. L. M. Timmers
- Department of Internal Medicine, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands;
| |
Collapse
|
52
|
Wortmann SB, Oud MM, Alders M, Coene KLM, van der Crabben SN, Feichtinger RG, Garanto A, Hoischen A, Langeveld M, Lefeber D, Mayr JA, Ockeloen CW, Prokisch H, Rodenburg R, Waterham HR, Wevers RA, van de Warrenburg BPC, Willemsen MAAP, Wolf NI, Vissers LELM, van Karnebeek CDM. How to proceed after "negative" exome: A review on genetic diagnostics, limitations, challenges, and emerging new multiomics techniques. J Inherit Metab Dis 2022; 45:663-681. [PMID: 35506430 PMCID: PMC9539960 DOI: 10.1002/jimd.12507] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 11/28/2022]
Abstract
Exome sequencing (ES) in the clinical setting of inborn metabolic diseases (IMDs) has created tremendous improvement in achieving an accurate and timely molecular diagnosis for a greater number of patients, but it still leaves the majority of patients without a diagnosis. In parallel, (personalized) treatment strategies are increasingly available, but this requires the availability of a molecular diagnosis. IMDs comprise an expanding field with the ongoing identification of novel disease genes and the recognition of multiple inheritance patterns, mosaicism, variable penetrance, and expressivity for known disease genes. The analysis of trio ES is preferred over singleton ES as information on the allelic origin (paternal, maternal, "de novo") reduces the number of variants that require interpretation. All ES data and interpretation strategies should be exploited including CNV and mitochondrial DNA analysis. The constant advancements in available techniques and knowledge necessitate the close exchange of clinicians and molecular geneticists about genotypes and phenotypes, as well as knowledge of the challenges and pitfalls of ES to initiate proper further diagnostic steps. Functional analyses (transcriptomics, proteomics, and metabolomics) can be applied to characterize and validate the impact of identified variants, or to guide the genomic search for a diagnosis in unsolved cases. Future diagnostic techniques (genome sequencing [GS], optical genome mapping, long-read sequencing, and epigenetic profiling) will further enhance the diagnostic yield. We provide an overview of the challenges and limitations inherent to ES followed by an outline of solutions and a clinical checklist, focused on establishing a diagnosis to eventually achieve (personalized) treatment.
Collapse
Affiliation(s)
- Saskia B. Wortmann
- Radboud Center for Mitochondrial and Metabolic Medicine, Department of PediatricsAmalia Children's Hospital, Radboud University Medical CenterNijmegenThe Netherlands
- University Children's Hospital, Paracelsus Medical UniversitySalzburgAustria
| | - Machteld M. Oud
- United for Metabolic DiseasesAmsterdamThe Netherlands
- Department of Human GeneticsDonders Institute for Brain, Cognition and Behaviour, Radboud University Medical CenterNijmegenThe Netherlands
| | - Mariëlle Alders
- Department of Human GeneticsAmsterdam UMC, University of Amsterdam, Amsterdam Reproduction and Development Research InstituteAmsterdamThe Netherlands
| | - Karlien L. M. Coene
- United for Metabolic DiseasesAmsterdamThe Netherlands
- Translational Metabolic Laboratory, Department of Laboratory MedicineRadboud University Medical CenterNijmegenThe Netherlands
| | - Saskia N. van der Crabben
- Department of Human GeneticsAmsterdam University Medical Centers, University of AmsterdamAmsterdamThe Netherlands
| | - René G. Feichtinger
- University Children's Hospital, Paracelsus Medical UniversitySalzburgAustria
| | - Alejandro Garanto
- Radboud Center for Mitochondrial and Metabolic Medicine, Department of PediatricsAmalia Children's Hospital, Radboud University Medical CenterNijmegenThe Netherlands
- Department of PediatricsAmalia Children's Hospital, Radboud Institute for Molecular LifesciencesNijmegenThe Netherlands
- Department of Human GeneticsRadboud Institute for Molecular LifesciencesNijmegenThe Netherlands
| | - Alex Hoischen
- Department of Human Genetics, Department of Internal Medicine and Radboud Center for Infectious DiseasesRadboud Institute of Medical Life Sciences, Radboud University Medical CenterNijmegenthe Netherlands
| | - Mirjam Langeveld
- Department of Endocrinology and MetabolismAmsterdam University Medical Centers, location AMC, University of AmsterdamAmsterdamThe Netherlands
| | - Dirk Lefeber
- United for Metabolic DiseasesAmsterdamThe Netherlands
- Translational Metabolic Laboratory, Department of Laboratory MedicineRadboud University Medical CenterNijmegenThe Netherlands
- Department of Neurology, Donders Institute for BrainCognition and Behaviour, Radboud University Medical CenterNijmegenThe Netherlands
| | - Johannes A. Mayr
- University Children's Hospital, Paracelsus Medical UniversitySalzburgAustria
| | - Charlotte W. Ockeloen
- Department of Human GeneticsRadboud Institute for Molecular LifesciencesNijmegenThe Netherlands
| | - Holger Prokisch
- School of MedicineInstitute of Human Genetics, Technical University Munich and Institute of NeurogenomicsNeuherbergGermany
| | - Richard Rodenburg
- Radboud Center for Mitochondrial and Metabolic MedicineTranslational Metabolic Laboratory, Department of Pediatrics, Radboud University Medical CenterNijmegenThe Netherlands
| | - Hans R. Waterham
- United for Metabolic DiseasesAmsterdamThe Netherlands
- Laboratory Genetic Metabolic Diseases, Department of Clinical ChemistryAmsterdam University Medical Centers, location AMC, University of AmsterdamAmsterdamThe Netherlands
| | - Ron A. Wevers
- United for Metabolic DiseasesAmsterdamThe Netherlands
- Translational Metabolic Laboratory, Department of Laboratory MedicineRadboud University Medical CenterNijmegenThe Netherlands
| | - Bart P. C. van de Warrenburg
- Department of Neurology, Donders Institute for BrainCognition and Behaviour, Radboud University Medical CenterNijmegenThe Netherlands
| | - Michel A. A. P. Willemsen
- Departments of Pediatric Neurology and PediatricsAmalia Children's Hospital, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical CenterNijmegenThe Netherlands
| | - Nicole I. Wolf
- Amsterdam Leukodystrophy Center, Department of Child NeurologyEmma Children's Hospital, Amsterdam University Medical Centers, Vrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Lisenka E. L. M. Vissers
- Department of Human GeneticsDonders Institute for Brain, Cognition and Behaviour, Radboud University Medical CenterNijmegenThe Netherlands
| | - Clara D. M. van Karnebeek
- Radboud Center for Mitochondrial and Metabolic Medicine, Department of PediatricsAmalia Children's Hospital, Radboud University Medical CenterNijmegenThe Netherlands
- United for Metabolic DiseasesAmsterdamThe Netherlands
- Department of Human GeneticsAmsterdam UMC, University of Amsterdam, Amsterdam Reproduction and Development Research InstituteAmsterdamThe Netherlands
- Department of Pediatrics, Emma Center for Personalized MedicineAmsterdam University Medical Centers, Amsterdam, Amsterdam Genetics Endocrinology Metabolism Research Institute, University of AmsterdamAmsterdamThe Netherlands
| |
Collapse
|
53
|
2022 Overview of Metabolic Epilepsies. Genes (Basel) 2022; 13:genes13030508. [PMID: 35328062 PMCID: PMC8952328 DOI: 10.3390/genes13030508] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 03/09/2022] [Accepted: 03/10/2022] [Indexed: 12/04/2022] Open
Abstract
Understanding the genetic architecture of metabolic epilepsies is of paramount importance, both to current clinical practice and for the identification of further research directions. The main goals of our study were to identify the scope of metabolic epilepsies and to investigate their clinical presentation, diagnostic approaches and treatments. The International Classification of Inherited Metabolic Disorders and IEMbase were used as a basis for the identification and classification of metabolic epilepsies. Six hundred metabolic epilepsies have been identified, accounting for as much as 37% of all currently described inherited metabolic diseases (IMD). Epilepsy is a particularly common symptom in disorders of energy metabolism, congenital disorders of glycosylation, neurotransmitter disorders, disorders of the synaptic vesicle cycle and some other IMDs. Seizures in metabolic epilepsies may present variably, and most of these disorders are complex and multisystem. Abnormalities in routine laboratory tests and/or metabolic testing may be identified in 70% of all metabolic epilepsies, but in many cases they are non-specific. In total, 111 metabolic epilepsies (18% of all) have specific treatments that may significantly change health outcomes if diagnosed in time. Although metabolic epilepsies comprise an important and significant group of disorders, their real scope and frequency may have been underestimated.
Collapse
|
54
|
Methods to Improve Molecular Diagnosis in Genomic Cold Cases in Pediatric Neurology. Genes (Basel) 2022; 13:genes13020333. [PMID: 35205378 PMCID: PMC8871714 DOI: 10.3390/genes13020333] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/06/2022] [Accepted: 02/07/2022] [Indexed: 02/04/2023] Open
Abstract
During the last decade, genetic testing has emerged as an important etiological diagnostic tool for Mendelian diseases, including pediatric neurological conditions. A genetic diagnosis has a considerable impact on disease management and treatment; however, many cases remain undiagnosed after applying standard diagnostic sequencing techniques. This review discusses various methods to improve the molecular diagnostic rates in these genomic cold cases. We discuss extended analysis methods to consider, non-Mendelian inheritance models, mosaicism, dual/multiple diagnoses, periodic re-analysis, artificial intelligence tools, and deep phenotyping, in addition to integrating various omics methods to improve variant prioritization. Last, novel genomic technologies, including long-read sequencing, artificial long-read sequencing, and optical genome mapping are discussed. In conclusion, a more comprehensive molecular analysis and a timely re-analysis of unsolved cases are imperative to improve diagnostic rates. In addition, our current understanding of the human genome is still limited due to restrictions in technologies. Novel technologies are now available that improve upon some of these limitations and can capture all human genomic variation more accurately. Last, we recommend a more routine implementation of high molecular weight DNA extraction methods that is coherent with the ability to use and/or optimally benefit from these novel genomic methods.
Collapse
|
55
|
Lorentzen J, Born AP, Svane C, Forman C, Laursen B, Langkilde AR, Uldall P, Hoei‐Hansen CE. Using both electromyography and movement disorder assessment improved the classification of children with dyskinetic cerebral palsy. Acta Paediatr 2022; 111:323-335. [PMID: 34655503 DOI: 10.1111/apa.16152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 10/06/2021] [Accepted: 10/12/2021] [Indexed: 11/29/2022]
Abstract
AIM Children with dyskinetic cerebral palsy (CP) are often severely affected and effective treatment is difficult, due to different underlying disease mechanisms. Comprehensive systematic movement disorder evaluations were carried out on patients with this disorder. METHODS Patients born from 1995 to 2007 were identified from the Danish Cerebral Palsy Register and referrals to the neuropaediatric centre, Rigshospitalet, Copenhagen. They were classified by gross motor function, manual functional ability, communication ability, dystonia and spasticity. Electromyography was carried out on the upper and lower limbs. Magnetic resonance imaging scans were revised, and aetiological searches for underlying genetic disorders were performed. RESULTS We investigated 25 patients with dyskinetic CP at a mean age of 11.7 years. Dystonia, spasticity and rigidity were found in the upper limbs of 21, four and six children, respectively, and in the lower limbs of 18, 18 and three children. The mean total Burke-Fahn-Marsden score for dystonia was 45.02, and the mean Disability Impairment Scale level was 38% for dystonia and 13% for choreoathetosis. Sustained electromyography activity was observed in 20/25 children. Stretching increased electromyography activity more in children with spasticity. There were 10 re-classifications. CONCLUSION The children had heterogenic characteristics, and 40% were reclassified after systematic movement disorder evaluation.
Collapse
Affiliation(s)
- Jakob Lorentzen
- Department of Neuroscience Copenhagen University Copenhagen Denmark
| | - Alfred P. Born
- Department of Paediatrics Copenhagen University HospitalRigshospitalet Copenhagen Denmark
| | - Christian Svane
- Department of Neuroscience Copenhagen University Copenhagen Denmark
| | - Christian Forman
- Department of Neuroscience Copenhagen University Copenhagen Denmark
| | - Bjarne Laursen
- National Institute of Public Health University of Southern Denmark Copenhagen Denmark
| | - Annika R. Langkilde
- Department of Radiology Copenhagen University HospitalRigshospitalet Copenhagen Denmark
| | - Peter Uldall
- Department of Paediatrics Copenhagen University HospitalRigshospitalet Copenhagen Denmark
| | - Christina E. Hoei‐Hansen
- Department of Paediatrics Copenhagen University HospitalRigshospitalet Copenhagen Denmark
- Department of Clinical Medicine University of Copenhagen Copenhagen Denmark
| |
Collapse
|
56
|
OUP accepted manuscript. Clin Chem 2022; 68:732-735. [DOI: 10.1093/clinchem/hvab276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 12/02/2021] [Indexed: 11/13/2022]
|
57
|
Bliziotis NG, Kluijtmans LAJ, Soto S, Tinnevelt GH, Langton K, Robledo M, Pamporaki C, Engelke UFH, Erlic Z, Engel J, Deutschbein T, Nölting S, Prejbisz A, Richter S, Prehn C, Adamski J, Januszewicz A, Reincke M, Fassnacht M, Eisenhofer G, Beuschlein F, Kroiss M, Wevers RA, Jansen JJ, Deinum J, Timmers HJLM. Pre- versus post-operative untargeted plasma nuclear magnetic resonance spectroscopy metabolomics of pheochromocytoma and paraganglioma. Endocrine 2022; 75:254-265. [PMID: 34536194 PMCID: PMC8763816 DOI: 10.1007/s12020-021-02858-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/24/2021] [Indexed: 11/25/2022]
Abstract
PURPOSE Pheochromocytomas and Paragangliomas (PPGL) result in chronic catecholamine excess and serious health complications. A recent study obtained a metabolic signature in plasma from PPGL patients; however, its targeted nature may have generated an incomplete picture and a broader approach could provide additional insights. We aimed to characterize the plasma metabolome of PPGL patients before and after surgery, using an untargeted approach, and to broaden the scope of the investigated metabolic impact of these tumors. DESIGN A cohort of 36 PPGL patients was investigated. Blood plasma samples were collected before and after surgical tumor removal, in association with clinical and tumor characteristics. METHODS Plasma samples were analyzed using untargeted nuclear magnetic resonance (NMR) spectroscopy metabolomics. The data were evaluated using a combination of uni- and multi-variate statistical methods. RESULTS Before surgery, patients with a nonadrenergic tumor could be distinguished from those with an adrenergic tumor based on their metabolic profiles. Tyrosine levels were significantly higher in patients with high compared to those with low BMI. Comparing subgroups of pre-operative samples with their post-operative counterparts, we found a metabolic signature that included ketone bodies, glucose, organic acids, methanol, dimethyl sulfone and amino acids. Three signals with unclear identities were found to be affected. CONCLUSIONS Our study suggests that the pathways of glucose and ketone body homeostasis are affected in PPGL patients. BMI-related metabolite levels were also found to be altered, potentially linking muscle atrophy to PPGL. At baseline, patient metabolomes could be discriminated based on their catecholamine phenotype.
Collapse
Affiliation(s)
- Nikolaos G Bliziotis
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, the Netherlands.
| | - Leo A J Kluijtmans
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Sebastian Soto
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Gerjen H Tinnevelt
- Department of Analytical Chemistry, Institute for Molecules and Materials, Radboud University, Nijmegen, the Netherlands
| | - Katharina Langton
- Department of Medicine III, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Mercedes Robledo
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Christina Pamporaki
- Department of Medicine III, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Udo F H Engelke
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Zoran Erlic
- Klinik für Endokrinologie, Diabetologie und Klinische Ernährung, Universitätsspital Zürich, Zürich, Switzerland
| | - Jasper Engel
- Biometris, Wageningen UR, Wageningen, The Netherlands
| | - Timo Deutschbein
- Schwerpunkt Endokrinologie/Diabetologie, Medizinische Klinik und Poliklinik I, Universitätsklinikum Würzburg, Zürich, Germany
- Medicover Oldenburg MVZ, Oldenburg, Germany
| | - Svenja Nölting
- Medizinische Klinik und Poliklinik IV, Klinikum der Universität, Ludwig-Maximilians-Universität, München, Munich, Germany
| | | | - Susan Richter
- Institut für Klinische Chemie und Labormedizin, Universitätsklinikum Carl Gustav Carus, Dresden, Germany
| | - Cornelia Prehn
- Helmholtz Zentrum München, Research Unit Molecular Endocrinology and Metabolism, Neuherberg, Germany
| | - Jerzy Adamski
- Helmholtz Zentrum München, Research Unit Molecular Endocrinology and Metabolism, Neuherberg, Germany
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | | | - Martin Reincke
- Medizinische Klinik und Poliklinik IV, Klinikum der Universität, Ludwig-Maximilians-Universität, München, Munich, Germany
| | - Martin Fassnacht
- Schwerpunkt Endokrinologie/Diabetologie, Medizinische Klinik und Poliklinik I, Universitätsklinikum Würzburg, Zürich, Germany
- Core Unit Clinical Mass Spectrometry, University Hospital Würzburg, Würzburg, Germany
- Comprehensive Cancer Center Mainfranken, Universität Würzburg, Würzburg, Germany
| | - Graeme Eisenhofer
- Department of Medicine III, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Institut für Klinische Chemie und Labormedizin, Universitätsklinikum Carl Gustav Carus, Dresden, Germany
| | - Felix Beuschlein
- Klinik für Endokrinologie, Diabetologie und Klinische Ernährung, Universitätsspital Zürich, Zürich, Switzerland
- Medizinische Klinik und Poliklinik IV, Klinikum der Universität, Ludwig-Maximilians-Universität, München, Munich, Germany
| | - Matthias Kroiss
- Schwerpunkt Endokrinologie/Diabetologie, Medizinische Klinik und Poliklinik I, Universitätsklinikum Würzburg, Zürich, Germany
- Medizinische Klinik und Poliklinik IV, Klinikum der Universität, Ludwig-Maximilians-Universität, München, Munich, Germany
- Core Unit Clinical Mass Spectrometry, University Hospital Würzburg, Würzburg, Germany
- Comprehensive Cancer Center Mainfranken, Universität Würzburg, Würzburg, Germany
| | - Ron A Wevers
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Jeroen J Jansen
- Department of Analytical Chemistry, Institute for Molecules and Materials, Radboud University, Nijmegen, the Netherlands
| | - Jaap Deinum
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Henri J L M Timmers
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands.
| |
Collapse
|
58
|
Mukherjee S, Ray SK. Inborn Errors of Metabolism Screening in Neonates: Current Perspective with Diagnosis and Therapy. Curr Pediatr Rev 2022; 18:274-285. [PMID: 35379134 DOI: 10.2174/1573396318666220404194452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 01/24/2022] [Accepted: 02/14/2022] [Indexed: 11/22/2022]
Abstract
Inborn errors of metabolism (IEMs) are rare hereditary or acquired disorders resulting from an enzymatic deformity in biochemical and metabolic pathways influencing proteins, fats, carbohydrate metabolism, or hampered some organelle function. Even though individual IEMs are uncommon, together, they represent a diverse class of genetic diseases, with new issues and disease mechanisms being portrayed consistently. IEM includes the extraordinary multifaceted nature of the fundamental pathophysiology, biochemical diagnosis, molecular level investigation, and complex therapeutic choices. However, due to the molecular, biochemical, and clinical heterogeneity of IEM, screening alone will not detect and diagnose all illnesses included in newborn screening programs. Early diagnosis prevents the emergence of severe clinical symptoms in the majority of IEM cases, lowering morbidity and death. The appearance of IEM disease can vary from neonates to adult people, with the more serious conditions showing up in juvenile stages along with significant morbidity as well as mortality. Advances in understanding the physiological, biochemical, and molecular etiologies of numerous IEMs by means of modalities, for instance, the latest molecular-genetic technologies, genome engineering knowledge, entire exome sequencing, and metabolomics, have prompted remarkable advancement in detection and treatment in modern times. In this review, we analyze the biochemical basis of IEMs, clinical manifestations, the present status of screening, ongoing advances, and efficiency of diagnosis in treatment for IEMs, along with prospects for further exploration as well as innovation.
Collapse
Affiliation(s)
- Sukhes Mukherjee
- Department of Biochemistry, All India Institute of Medical Sciences, Bhopal, Madhya Pradesh-462020, India
| | - Suman Kumar Ray
- Independent Researcher, Bhopal, Madhya Pradesh-462020, India
| |
Collapse
|
59
|
van Outersterp R, Engelke UF, Merx J, Berden G, Paul M, Thomulka T, Berkessel A, Huigen MC, Kluijtmans LA, Mecinović J, Rutjes FP, van Karnebeek CD, Wevers RA, Boltje TJ, Coene KL, Martens J, Oomens J. Metabolite Identification Using Infrared Ion Spectroscopy─Novel Biomarkers for Pyridoxine-Dependent Epilepsy. Anal Chem 2021; 93:15340-15348. [PMID: 34756024 PMCID: PMC8613736 DOI: 10.1021/acs.analchem.1c02896] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 10/25/2021] [Indexed: 11/30/2022]
Abstract
Untargeted liquid chromatography-mass spectrometry (LC-MS)-based metabolomics strategies are being increasingly applied in metabolite screening for a wide variety of medical conditions. The long-standing "grand challenge" in the utilization of this approach is metabolite identification─confidently determining the chemical structures of m/z-detected unknowns. Here, we use a novel workflow based on the detection of molecular features of interest by high-throughput untargeted LC-MS analysis of patient body fluids combined with targeted molecular identification of those features using infrared ion spectroscopy (IRIS), effectively providing diagnostic IR fingerprints for mass-isolated targets. A significant advantage of this approach is that in silico-predicted IR spectra of candidate chemical structures can be used to suggest the molecular structure of unknown features, thus mitigating the need for the synthesis of a broad range of physical reference standards. Pyridoxine-dependent epilepsy (PDE-ALDH7A1) is an inborn error of lysine metabolism, resulting from a mutation in the ALDH7A1 gene that leads to an accumulation of toxic levels of α-aminoadipic semialdehyde (α-AASA), piperideine-6-carboxylate (P6C), and pipecolic acid in body fluids. While α-AASA and P6C are known biomarkers for PDE in urine, their instability makes them poor candidates for diagnostic analysis from blood, which would be required for application in newborn screening protocols. Here, we use combined untargeted metabolomics-IRIS to identify several new biomarkers for PDE-ALDH7A1 that can be used for diagnostic analysis in urine, plasma, and cerebrospinal fluids and that are compatible with analysis in dried blood spots for newborn screening. The identification of these novel metabolites has directly provided novel insights into the pathophysiology of PDE-ALDH7A1.
Collapse
Affiliation(s)
- Rianne
E. van Outersterp
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Udo F.H. Engelke
- Department
of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Jona Merx
- Institute
for Molecules and Materials, Synthetic Organic Chemistry, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Giel Berden
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Mathias Paul
- Department
of Chemistry, University of Cologne, Greinstrasse 4, 50939 Cologne, Germany
| | - Thomas Thomulka
- Department
of Chemistry, University of Cologne, Greinstrasse 4, 50939 Cologne, Germany
| | - Albrecht Berkessel
- Department
of Chemistry, University of Cologne, Greinstrasse 4, 50939 Cologne, Germany
| | - Marleen C.D.G. Huigen
- Department
of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Leo A.J. Kluijtmans
- Department
of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Jasmin Mecinović
- University
of Southern Denmark, Department of Physics,
Chemistry and Pharmacy, Campusvej 55, 5230 Odense, Denmark
| | - Floris P.J.T. Rutjes
- Institute
for Molecules and Materials, Synthetic Organic Chemistry, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Clara D.M. van Karnebeek
- Department
of Pediatrics-Metabolic Diseases, Radboud Center for Mitochondrial
Medicine, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Ron A. Wevers
- Department
of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Thomas J. Boltje
- Institute
for Molecules and Materials, Synthetic Organic Chemistry, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Karlien L.M. Coene
- Department
of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Jonathan Martens
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Jos Oomens
- Institute
for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
- van’t
Hoff Institute for Molecular Sciences, University
of Amsterdam, Science
Park 908, 1098XH Amsterdam, The Netherlands
| |
Collapse
|
60
|
|
61
|
Dijkstra AM, van Vliet N, van Vliet D, Romani C, Huijbregts SCJ, van der Goot E, Hovens IB, van der Zee EA, Kema IP, Heiner-Fokkema MR, van Spronsen FJ. Correlations of blood and brain biochemistry in phenylketonuria: Results from the Pah-enu2 PKU mouse. Mol Genet Metab 2021; 134:250-256. [PMID: 34656426 DOI: 10.1016/j.ymgme.2021.09.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 09/12/2021] [Accepted: 09/18/2021] [Indexed: 11/30/2022]
Abstract
BACKGROUND In phenylketonuria (PKU), treatment monitoring is based on frequent blood phenylalanine (Phe) measurements, as this is the predictor of neurocognitive and behavioural outcome by reflecting brain Phe concentrations and brain biochemical changes. Despite clinical studies describing the relevance of blood Phe to outcome in PKU patients, blood Phe does not explain the variance in neurocognitive and behavioural outcome completely. METHODS In a PKU mouse model we investigated 1) the relationship between plasma Phe and brain biochemistry (Brain Phe and monoaminergic neurotransmitter concentrations), and 2) whether blood non-Phe Large Neutral Amino Acids (LNAA) would be of additional value to blood Phe concentrations to explain brain biochemistry. To this purpose, we assessed blood amino acid concentrations and brain Phe as well as monoaminergic neurotransmitter levels in in 114 Pah-Enu2 mice on both B6 and BTBR backgrounds using (multiple) linear regression analyses. RESULTS Plasma Phe concentrations were strongly correlated to brain Phe concentrations, significantly negatively correlated to brain serotonin and norepinephrine concentrations and only weakly correlated to brain dopamine concentrations. From all blood markers, Phe showed the strongest correlation to brain biochemistry in PKU mice. Including non-Phe LNAA concentrations to the multiple regression model, in addition to plasma Phe, did not help explain brain biochemistry. CONCLUSION This study showed that blood Phe is still the best amino acid predictor of brain biochemistry in PKU. Nevertheless, neurocognitive and behavioural outcome cannot fully be explained by blood or brain Phe concentrations, necessitating a search for other additional parameters. TAKE-HOME MESSAGE Blood Phe is still the best amino acid predictor of brain biochemistry in PKU. Nevertheless, neurocognitive and behavioural outcome cannot fully be explained by blood or brain Phe concentrations, necessitating a search for other additional parameters.
Collapse
Affiliation(s)
- Allysa M Dijkstra
- University of Groningen, University Medical Center Groningen, Beatrix Children's Hospital, Groningen, the Netherlands
| | - Ninke van Vliet
- University of Groningen, University Medical Center Groningen, Beatrix Children's Hospital, Groningen, the Netherlands
| | - Danique van Vliet
- University of Groningen, University Medical Center Groningen, Beatrix Children's Hospital, Groningen, the Netherlands
| | - Cristina Romani
- School of Life and Health Sciences, Aston University, Birmingham, UK
| | - Stephan C J Huijbregts
- Department of Clinical Child and Adolescent Studies-Neurodevelopmental Disorders, Faculty of Social Sciences, Leiden University, Leiden, the Netherlands
| | - Els van der Goot
- University of Groningen, Groningen Institute for Evolutionary Life Sciences (GELIFES), Department of Molecular Neurobiology, Groningen, the Netherlands
| | - Iris B Hovens
- University of Groningen, Groningen Institute for Evolutionary Life Sciences (GELIFES), Department of Molecular Neurobiology, Groningen, the Netherlands
| | - Eddy A van der Zee
- University of Groningen, Groningen Institute for Evolutionary Life Sciences (GELIFES), Department of Molecular Neurobiology, Groningen, the Netherlands
| | - Ido P Kema
- University of Groningen, University Medical Center Groningen, Department of laboratory Medicine, Groningen, the Netherlands
| | - M Rebecca Heiner-Fokkema
- University of Groningen, University Medical Center Groningen, Department of laboratory Medicine, Groningen, the Netherlands
| | - Francjan J van Spronsen
- University of Groningen, University Medical Center Groningen, Beatrix Children's Hospital, Groningen, the Netherlands.
| |
Collapse
|
62
|
Odom JD, Sutton VR. Metabolomics in Clinical Practice: Improving Diagnosis and Informing Management. Clin Chem 2021; 67:1606-1617. [PMID: 34633032 DOI: 10.1093/clinchem/hvab184] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 08/17/2021] [Indexed: 11/14/2022]
Abstract
BACKGROUND Metabolomics is the study of small molecules to simultaneously identify multiple low molecular weight molecules in a system. Broadly speaking, metabolomics can be subdivided into targeted and untargeted types of analysis, each type having advantages and drawbacks. Targeted metabolomics can quantify analytes but only looks for known or expected analytes related to particular disease(s), whereas untargeted metabolomics is typically nonquantitative but can detect thousands of analytes from an agnostic or nonhypothesis driven perspective, allowing for novel discoveries. CONTENT One application of metabolomics is the study of inborn errors of metabolism (IEM). The biochemical hallmark of IEMs is decreased concentrations of analytes distal to the enzymatic defect and buildup of analytes proximal to the defect. Metabolomics can detect these changes with one test and is effective in screening for and diagnosis of IEMs. Metabolomics has also been used to study many nonmetabolic diseases such as autism spectrum disorder, various cancers, and multiple congenital anomalies syndromes. Metabolomics has led to the discovery of many novel biomarkers of disease. Recent publications demonstrate how metabolomics can be useful clinically in the diagnosis and management of patients, as well as for research and clinical discovery. SUMMARY Metabolomics has proved to be a useful tool clinically for screening and diagnostic purposes and from a research perspective for the detection of novel biomarkers. In the future, metabolomics will likely become a routine part of the evaluation for many diseases as either a supplementary test or it may simply replace historical analyses that require several individual tests and sample types.
Collapse
Affiliation(s)
- John D Odom
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - V Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX.,Baylor Genetics Laboratory, Houston, TX
| |
Collapse
|
63
|
Liu H, Zhu J, Li Q, Wang D, Wan K, Yuan Z, Zhang J, Zou L, He X, Miao J. Untargeted metabolomic analysis of urine samples for diagnosis of inherited metabolic disorders. Funct Integr Genomics 2021; 21:645-653. [PMID: 34585279 DOI: 10.1007/s10142-021-00804-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 08/07/2021] [Accepted: 08/27/2021] [Indexed: 11/30/2022]
Abstract
Metabolomics has become an important tool for clinical research, especially for analyzing inherited metabolic disorders (IMDs). The purpose of this study was to explore the performance of metabolomics in diagnosing IMDs using an untargeted metabolomic approach. A total of 40 urine samples were collected: 20 samples from healthy children and 20 from pediatric patients, of whom 13 had confirmed IMDs and seven had suspected IMDs. Samples were analyzed by Orbitrap mass spectrometry in positive and negative mode alternately, coupled with ultra-high liquid chromatography. Raw data were processed using Compound Discovery 2.0 ™ and then exported for partial least squares discriminant analysis (PLS-DA) by SIMCA-P 14.1. After comparing with m/zCloud and chemSpider libraries, compounds with similarity above 80% were selected and normalized for subsequent relative quantification analysis. The uncommon compounds discovered were analyzed based on the Kyoto Encyclopedia of Genes and Genomes to explore their possible metabolic pathways. All IMDs patients were successfully distinguished from controls in the PLS-DA. Untargeted metabolomics revealed a broader metabolic spectrum in patients than what is observed using routine chromatographic methods for detecting IMDs. Higher levels of certain compounds were found in all 13 confirmed IMD patients and 5 of 7 suspected IMD patients. Several potential novel markers emerged after relative quantification. Untargeted metabolomics may be able to diagnose IMDs from urine and may deepen insights into the disease by revealing changes in various compounds such as amino acids, acylcarnitines, organic acids, and nucleosides. Such analyses may identify biomarkers to improve the study and treatment of IMDs.
Collapse
Affiliation(s)
- Hao Liu
- Newborn Screening Center, Chongqing Health Center for Women and Children, Longshan Road 120th, Yubei District, Chongqing, 401147, People's Republic of China.,Center for Clinical Molecular Medicine, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Zhongshan Road 2nd, Yuzhong District, Chongqing, 400014, People's Republic of China
| | - Jiang Zhu
- Chongqing Key Laboratory of Child Nutrition and Health, Children's Hospital of Chongqing Medical University, Chongqing, 400014, People's Republic of China
| | - Qiu Li
- Chongqing Key Laboratory of Child Nutrition and Health, Children's Hospital of Chongqing Medical University, Chongqing, 400014, People's Republic of China
| | - Dongjuan Wang
- Center for Clinical Molecular Medicine, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Zhongshan Road 2nd, Yuzhong District, Chongqing, 400014, People's Republic of China
| | - Kexing Wan
- Center for Clinical Molecular Medicine, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Zhongshan Road 2nd, Yuzhong District, Chongqing, 400014, People's Republic of China
| | - Zhaojian Yuan
- Center for Clinical Molecular Medicine, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Zhongshan Road 2nd, Yuzhong District, Chongqing, 400014, People's Republic of China
| | - Juan Zhang
- Center for Clinical Molecular Medicine, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Zhongshan Road 2nd, Yuzhong District, Chongqing, 400014, People's Republic of China
| | - Lin Zou
- Center for Clinical Molecular Medicine, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Zhongshan Road 2nd, Yuzhong District, Chongqing, 400014, People's Republic of China
| | - Xiaoyan He
- Center for Clinical Molecular Medicine, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Zhongshan Road 2nd, Yuzhong District, Chongqing, 400014, People's Republic of China.
| | - Jingkun Miao
- Newborn Screening Center, Chongqing Health Center for Women and Children, Longshan Road 120th, Yubei District, Chongqing, 401147, People's Republic of China.
| |
Collapse
|
64
|
Mak J, Cowan TM. Detecting lysosomal storage disorders by glycomic profiling using liquid chromatography mass spectrometry. Mol Genet Metab 2021; 134:43-52. [PMID: 34474962 PMCID: PMC9069563 DOI: 10.1016/j.ymgme.2021.08.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 08/14/2021] [Accepted: 08/15/2021] [Indexed: 01/15/2023]
Abstract
BACKGROUND Urine and plasma biomarker testing for lysosomal storage disorders by liquid chromatography mass spectrometry (LC-MS) currently requires multiple analytical methods to detect the abnormal accumulation of oligosaccharides, mucopolysaccharides, and glycolipids. To improve clinical testing efficiency, we developed a single LC-MS method to simultaneously identify disorders of oligosaccharide, mucopolysaccharide, and glycolipid metabolism with minimal sample preparation. METHODS We created a single chromatographic method for separating free glycans and glycolipids in their native form, using an amide column and high pH conditions. We used this glycomic profiling method both in untargeted analyses of patient and control urines using LC ion-mobility high-resolution MS (biomarker discovery), and targeted analyses of urine, serum, and dried blood spot samples by LC-MS/MS (clinical validation). RESULTS Untargeted glycomic profiling revealed twenty biomarkers that could identify and subtype mucopolysaccharidoses. We incorporated these with known oligosaccharide and glycolipid biomarkers into a rapid test that identifies at least 27 lysosomal storage disorders, including oligosaccharidoses, mucopolysaccharidoses, sphingolipidoses, glycogen storage disorders, and congenital disorders of glycosylation and de-glycosylation. In a validation set containing 115 urine samples from patients with lysosomal storage disorders, all were unambiguously distinguished from normal controls, with correct disease subtyping for 88% (101/115) of cases. Glucosylsphingosine was reliably elevated in dried blood spots from Gaucher disease patients with baseline resolution from galactosylsphingosine. CONCLUSION Glycomic profiling by liquid chromatography mass spectrometry identifies a range of lysosomal storage disorders. This test can be used in clinical evaluations to rapidly focus a diagnosis, as well as to clarify or support additional gene sequencing and enzyme studies.
Collapse
Affiliation(s)
- Justin Mak
- Clinical Biochemical Genetics Laboratory, Stanford Health Care, United States of America.
| | - Tina M Cowan
- Clinical Biochemical Genetics Laboratory, Stanford Health Care, United States of America; Department of Pathology, Stanford University Medical Center, United States of America
| |
Collapse
|
65
|
Steinbusch LK, Wang P, Waterval HW, Stassen FA, Coene KL, Engelke UF, Habets DD, Bierau J, Körver‐Keularts IM. Targeted urine metabolomics with a graphical reporting tool for rapid diagnosis of inborn errors of metabolism. J Inherit Metab Dis 2021; 44:1113-1123. [PMID: 33843072 PMCID: PMC8518793 DOI: 10.1002/jimd.12385] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 04/02/2021] [Accepted: 04/09/2021] [Indexed: 12/16/2022]
Abstract
The current diagnostic work-up of inborn errors of metabolism (IEM) is rapidly moving toward integrative analytical approaches. We aimed to develop an innovative, targeted urine metabolomics (TUM) screening procedure to accelerate the diagnosis of patients with IEM. Urinary samples, spiked with three stable isotope-labeled internal standards, were analyzed for 258 diagnostic metabolites with an ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UHPLC-QTOF-MS) configuration run in positive and negative ESI modes. The software automatically annotated peaks, corrected for peak overloading, and reported peak quality and shifting. Robustness and reproducibility were satisfactory for most metabolites. Z-scores were calculated against four age-group-matched control cohorts. Disease phenotypes were scored based on database metabolite matching. Graphical reports comprised a needle plot, annotating abnormal metabolites, and a heatmap showing the prioritized disease phenotypes. In the clinical validation, we analyzed samples of 289 patients covering 78 OMIM phenotypes from 12 of the 15 society for the study of inborn errors of metabolism (SSIEM) disease groups. The disease groups include disorders in the metabolism of amino acids, fatty acids, ketones, purines and pyrimidines, carbohydrates, porphyrias, neurotransmitters, vitamins, cofactors, and creatine. The reporting tool easily and correctly diagnosed most samples. Even subtle aberrant metabolite patterns as seen in mild multiple acyl-CoA dehydrogenase deficiency (GAII) and maple syrup urine disease (MSUD) were correctly called without difficulty. Others, like creatine transporter deficiency, are illustrative of IEM that remain difficult to diagnose. We present TUM as a powerful diagnostic screening tool that merges most urinary diagnostic assays expediting the diagnostics for patients suspected of an IEM.
Collapse
Affiliation(s)
- Laura K.M. Steinbusch
- Department of Clinical GeneticsMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Ping Wang
- Department of Clinical GeneticsMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Huub W.A.H. Waterval
- Department of Clinical GeneticsMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Fons A.P.M. Stassen
- Department of Clinical GeneticsMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Karlien L.M. Coene
- Translational Metabolic Laboratory, Department of Laboratory MedicineRadboud University Medical CentreNijmegenThe Netherlands
| | - Udo F.H. Engelke
- Translational Metabolic Laboratory, Department of Laboratory MedicineRadboud University Medical CentreNijmegenThe Netherlands
| | - Daphna D.J. Habets
- Department of Clinical GeneticsMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Jörgen Bierau
- Department of Clinical GeneticsMaastricht University Medical CenterMaastrichtThe Netherlands
| | | |
Collapse
|
66
|
Metabolomics-Based Screening of Inborn Errors of Metabolism: Enhancing Clinical Application with a Robust Computational Pipeline. Metabolites 2021; 11:metabo11090568. [PMID: 34564390 PMCID: PMC8470724 DOI: 10.3390/metabo11090568] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 11/17/2022] Open
Abstract
Inborn errors of metabolism (IEM) are inherited conditions caused by genetic defects in enzymes or cofactors. These defects result in a specific metabolic fingerprint in patient body fluids, showing accumulation of substrate or lack of an end-product of the defective enzymatic step. Untargeted metabolomics has evolved as a high throughput methodology offering a comprehensive readout of this metabolic fingerprint. This makes it a promising tool for diagnostic screening of IEM patients. However, the size and complexity of metabolomics data have posed a challenge in translating this avalanche of information into knowledge, particularly for clinical application. We have previously established next-generation metabolic screening (NGMS) as a metabolomics-based diagnostic tool for analyzing plasma of individual IEM-suspected patients. To fully exploit the clinical potential of NGMS, we present a computational pipeline to streamline the analysis of untargeted metabolomics data. This pipeline allows for time-efficient and reproducible data analysis, compatible with ISO:15189 accredited clinical diagnostics. The pipeline implements a combination of tools embedded in a workflow environment for large-scale clinical metabolomics data analysis. The accompanying graphical user interface aids end-users from a diagnostic laboratory for efficient data interpretation and reporting. We also demonstrate the application of this pipeline with a case study and discuss future prospects.
Collapse
|
67
|
Urine Phenylacetylglutamine Determination in Patients with Hyperphenylalaninemia. J Clin Med 2021; 10:jcm10163674. [PMID: 34441968 PMCID: PMC8396897 DOI: 10.3390/jcm10163674] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/10/2021] [Accepted: 08/16/2021] [Indexed: 12/11/2022] Open
Abstract
Phenylketonuria (PKU), an autosomal-recessive inborn error of phenylalanine (Phe) metabolism is the most prevalent disorder of amino acid metabolism. Currently, clinical follow-up relies on frequent monitoring of Phe levels in blood. We hypothesize that the urine level of phenylacetylglutamine (PAG), a phenyl-group marker, could be used as a non-invasive biomarker. In this cross-sectional study, a validated liquid chromatography coupled to tandem mass spectrometry (LC-MS) method was used for urinary PAG quantification in 35 participants with hyperphenylalaninemia (HPA) and 33 age- and sex-matched healthy controls. We have found that (a) PKU patients present higher urine PAG levels than healthy control subjects, and that (b) there is a significant correlation between urine PAG and circulating Phe levels in patients with HPA. In addition, we show a significant strong correlation between Phe levels from venous blood samples and from capillary finger-prick dried blood spot (DBS) samples collected at the same time in patients with HPA. Further research in order to assess the potential role of urine PAG as a non-invasive biomarker in PKU is warranted.
Collapse
|
68
|
Engelke UF, van Outersterp RE, Merx J, van Geenen FA, van Rooij A, Berden G, Huigen MC, Kluijtmans LA, Peters TM, Al-Shekaili HH, Leavitt BR, de Vrieze E, Broekman S, van Wijk E, Tseng LA, Kulkarni P, Rutjes FP, Mecinović J, Struys EA, Jansen LA, Gospe SM, Mercimek-Andrews S, Hyland K, Willemsen MA, Bok LA, van Karnebeek CD, Wevers RA, Boltje TJ, Oomens J, Martens J, Coene KL. Untargeted metabolomics and infrared ion spectroscopy identify biomarkers for pyridoxine-dependent epilepsy. J Clin Invest 2021; 131:e148272. [PMID: 34138754 DOI: 10.1172/jci148272] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 06/16/2021] [Indexed: 12/30/2022] Open
Abstract
BackgroundPyridoxine-dependent epilepsy (PDE-ALDH7A1) is an inborn error of lysine catabolism that presents with refractory epilepsy in newborns. Biallelic ALDH7A1 variants lead to deficiency of α-aminoadipic semialdehyde dehydrogenase/antiquitin, resulting in accumulation of piperideine-6-carboxylate (P6C), and secondary deficiency of the important cofactor pyridoxal-5'-phosphate (PLP, active vitamin B6) through its complexation with P6C. Vitamin B6 supplementation resolves epilepsy in patients, but intellectual disability may still develop. Early diagnosis and treatment, preferably based on newborn screening, could optimize long-term clinical outcome. However, no suitable PDE-ALDH7A1 newborn screening biomarkers are currently available.MethodsWe combined the innovative analytical methods untargeted metabolomics and infrared ion spectroscopy to discover and identify biomarkers in plasma that would allow for PDE-ALDH7A1 diagnosis in newborn screening.ResultsWe identified 2S,6S-/2S,6R-oxopropylpiperidine-2-carboxylic acid (2-OPP) as a PDE-ALDH7A1 biomarker, and confirmed 6-oxopiperidine-2-carboxylic acid (6-oxoPIP) as a biomarker. The suitability of 2-OPP as a potential PDE-ALDH7A1 newborn screening biomarker in dried bloodspots was shown. Additionally, we found that 2-OPP accumulates in brain tissue of patients and Aldh7a1-knockout mice, and induced epilepsy-like behavior in a zebrafish model system.ConclusionThis study has opened the way to newborn screening for PDE-ALDH7A1. We speculate that 2-OPP may contribute to ongoing neurotoxicity, also in treated PDE-ALDH7A1 patients. As 2-OPP formation appears to increase upon ketosis, we emphasize the importance of avoiding catabolism in PDE-ALDH7A1 patients.FundingSociety for Inborn Errors of Metabolism for Netherlands and Belgium (ESN), United for Metabolic Diseases (UMD), Stofwisselkracht, Radboud University, Canadian Institutes of Health Research, Dutch Research Council (NWO), and the European Research Council (ERC).
Collapse
Affiliation(s)
- Udo Fh Engelke
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | | | - Jona Merx
- Institute for Molecules and Materials, Synthetic Organic Chemistry, Radboud University, Nijmegen, Netherlands
| | | | - Arno van Rooij
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | - Giel Berden
- Institute for Molecules and Materials, FELIX Laboratory and
| | - Marleen Cdg Huigen
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | - Leo Aj Kluijtmans
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | - Tessa Ma Peters
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, Netherlands.,Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, Netherlands
| | - Hilal H Al-Shekaili
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia Vancouver, British Columbia, Canada
| | - Blair R Leavitt
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia Vancouver, British Columbia, Canada
| | - Erik de Vrieze
- Department of Otorhinolaryngology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, Netherlands
| | - Sanne Broekman
- Department of Otorhinolaryngology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, Netherlands
| | - Erwin van Wijk
- Department of Otorhinolaryngology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, Netherlands
| | - Laura A Tseng
- Department of Pediatrics, Emma Children's Hospital, Amsterdam University Medical Centers, Amsterdam, Netherlands
| | - Purva Kulkarni
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | - Floris Pjt Rutjes
- Institute for Molecules and Materials, Synthetic Organic Chemistry, Radboud University, Nijmegen, Netherlands
| | - Jasmin Mecinović
- Institute for Molecules and Materials, Synthetic Organic Chemistry, Radboud University, Nijmegen, Netherlands.,Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Eduard A Struys
- Department of Clinical Chemistry, Amsterdam University Medical Centers, location VU Medical Centre, Amsterdam, Netherlands
| | - Laura A Jansen
- Division of Pediatric Neurology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Sidney M Gospe
- Departments of Neurology and Pediatrics, University of Washington, Seattle, Washington, USA.,Department of Pediatrics, Duke University, Durham, North Carolina, USA
| | - Saadet Mercimek-Andrews
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada.,Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - Keith Hyland
- Medical Neurogenetics Laboratories, Atlanta, Georgia, USA
| | - Michèl Aap Willemsen
- Department of Pediatric Neurology, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Levinus A Bok
- Department of Pediatrics, Máxima Medical Centre, Veldhoven, Netherlands
| | - Clara Dm van Karnebeek
- Department of Pediatrics, Emma Children's Hospital, Amsterdam University Medical Centers, Amsterdam, Netherlands.,Department of Pediatrics-Metabolic Diseases, Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, Netherlands.,United for Metabolic Diseases (UMD), Netherlands
| | - Ron A Wevers
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | - Thomas J Boltje
- Institute for Molecules and Materials, Synthetic Organic Chemistry, Radboud University, Nijmegen, Netherlands
| | - Jos Oomens
- Institute for Molecules and Materials, FELIX Laboratory and.,Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, Netherlands
| | | | - Karlien Lm Coene
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| |
Collapse
|
69
|
Classical Xanthinuria in Nine Israeli Families and Two Isolated Cases from Germany: Molecular, Biochemical and Population Genetics Aspects. Biomedicines 2021; 9:biomedicines9070788. [PMID: 34356852 PMCID: PMC8301430 DOI: 10.3390/biomedicines9070788] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/23/2021] [Accepted: 07/01/2021] [Indexed: 11/17/2022] Open
Abstract
Classical xanthinuria is a rare autosomal recessive metabolic disorder caused by variants in the XDH (type I) or MOCOS (type II) genes. Thirteen Israeli kindred (five Jewish and eight Arab) and two isolated cases from Germany were studied between the years 1997 and 2013. Four and a branch of a fifth of these families were previously described. Here, we reported the demographic, clinical, molecular and biochemical characterizations of the remaining cases. Seven out of 20 affected individuals (35%) presented with xanthinuria-related symptoms of varied severity. Among the 10 distinct variants identified, six were novel: c.449G>T (p.(Cys150Phe)), c.1434G>A (p.(Trp478*)), c.1871C>G (p.(Ser624*)) and c.913del (p.(Leu305fs*1)) in the XDH gene and c.1046C>T (p.(Thr349Ileu)) and c.1771C>T (p.(Pro591Ser)) in the MOCOS gene. Heterologous protein expression studies revealed that the p.Cys150Phe variant within the Fe/S-I cluster-binding site impairs XDH biogenesis, the p.Thr349Ileu variant in the NifS-like domain of MOCOS affects protein stability and cysteine desulfurase activity, while the p.Pro591Ser and a previously described p.Arg776Cys variant in the C-terminal domain affect Molybdenum cofactor binding. Based on the results of haplotype analyses and historical genealogy findings, the potential dispersion of the identified variants is discussed. As far as we are aware, this is the largest cohort of xanthinuria cases described so far, substantially expanding the repertoire of pathogenic variants, characterizing structurally and functionally essential amino acid residues in the XDH and MOCOS proteins and addressing the population genetic aspects of classical xanthinuria.
Collapse
|
70
|
Liu N, Xiao J, Gijavanekar C, Pappan KL, Glinton KE, Shayota BJ, Kennedy AD, Sun Q, Sutton VR, Elsea SH. Comparison of Untargeted Metabolomic Profiling vs Traditional Metabolic Screening to Identify Inborn Errors of Metabolism. JAMA Netw Open 2021; 4:e2114155. [PMID: 34251446 PMCID: PMC8276086 DOI: 10.1001/jamanetworkopen.2021.14155] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
IMPORTANCE Recent advances in newborn screening (NBS) have improved the diagnosis of inborn errors of metabolism (IEMs); however, many potentially treatable IEMs are not included on NBS panels, nor are they covered in standard, first-line biochemical testing. OBJECTIVE To examine the utility of untargeted metabolomics as a primary screening tool for IEMs by comparing the diagnostic rate of clinical metabolomics with the recommended traditional metabolic screening approach. DESIGN, SETTING, AND PARTICIPANTS This cross-sectional study compares data from 4464 clinical samples received from 1483 unrelated families referred for trio testing of plasma amino acids, plasma acylcarnitine profiling, and urine organic acids (June 2014 to October 2018) and 2000 consecutive plasma samples from 1807 unrelated families (July 2014 to February 2019) received for clinical metabolomic screening at a College of American Pathologists and Clinical Laboratory Improvement Amendments-certified biochemical genetics laboratory. Data analysis was performed from September 2019 to August 2020. EXPOSURES Metabolic and molecular tests performed at a genetic testing reference laboratory in the US and available clinical information for each patient were assessed to determine diagnostic rate. MAIN OUTCOMES AND MEASURES The diagnostic rate of traditional metabolic screening compared with clinical metabolomic profiling was assessed in the context of expanded NBS. RESULTS Of 1483 cases screened by the traditional approach, 912 patients (61.5%) were male and 1465 (98.8%) were pediatric (mean [SD] age, 4.1 [6.0] years; range, 0-65 years). A total of 19 families were identified with IEMs, resulting in a 1.3% diagnostic rate. A total of 14 IEMs were detected, including 3 conditions not included in the Recommended Uniform Screening Panel for NBS. Of the 1807 unrelated families undergoing plasma metabolomic profiling, 1059 patients (58.6%) were male, and 1665 (92.1%) were pediatric (mean [SD] age, 8.1 [10.4] years; range, 0-80 years). Screening identified 128 unique cases with IEMs, giving an overall diagnostic rate of 7.1%. In total, 70 different metabolic conditions were identified, including 49 conditions not presently included on the Recommended Uniform Screening Panel for NBS. CONCLUSIONS AND RELEVANCE These findings suggest that untargeted metabolomics provided a 6-fold higher diagnostic yield compared with the conventional screening approach and identified a broader spectrum of IEMs. Notably, with the expansion of NBS programs, traditional metabolic testing approaches identify few disorders beyond those covered on the NBS. These data support the capability of clinical untargeted metabolomics in screening for IEMs and suggest that broader screening approaches should be considered in the initial evaluation for metabolic disorders.
Collapse
Affiliation(s)
- Ning Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics, Houston, Texas
| | - Jing Xiao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | | | - Kirk L Pappan
- Metabolon, Inc, Durham, North Carolina
- Now with Owlstone Medical, Inc, Research Triangle Park, North Carolina
| | - Kevin E Glinton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Brian J Shayota
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Now with Division of Medical Genetics, Department of Pediatrics, University of Utah, Salt Lake City
| | | | - Qin Sun
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics, Houston, Texas
| | - V Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics, Houston, Texas
| | - Sarah H Elsea
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics, Houston, Texas
| |
Collapse
|
71
|
Metabolomics: A Scoping Review of Its Role as a Tool for Disease Biomarker Discovery in Selected Non-Communicable Diseases. Metabolites 2021; 11:metabo11070418. [PMID: 34201929 PMCID: PMC8305588 DOI: 10.3390/metabo11070418] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/21/2021] [Accepted: 06/23/2021] [Indexed: 12/29/2022] Open
Abstract
Metabolomics is a branch of ‘omics’ sciences that utilises a couple of analytical tools for the identification of small molecules (metabolites) in a given sample. The overarching goal of metabolomics is to assess these metabolites quantitatively and qualitatively for their diagnostic, therapeutic, and prognostic potentials. Its use in various aspects of life has been documented. We have also published, howbeit in animal models, a few papers where metabolomic approaches were used in the study of metabolic disorders, such as metabolic syndrome, diabetes, and obesity. As the goal of every research is to benefit humankind, the purpose of this review is to provide insights into the applicability of metabolomics in medicine vis-à-vis its role in biomarker discovery for disease diagnosis and management. Here, important biomarkers with proven diagnostic and therapeutic relevance in the management of disease conditions, such as Alzheimer’s disease, dementia, Parkinson’s disease, inborn errors of metabolism (IEM), diabetic retinopathy, and cardiovascular disease, are noted. The paper also discusses a few reasons why most metabolomics-based laboratory discoveries are not readily translated to the clinic and how these could be addressed going forward.
Collapse
|
72
|
den Hollander B, Rasing A, Post MA, Klein WM, Oud MM, Brands MM, de Boer L, Engelke UFH, van Essen P, Fuchs SA, Haaxma CA, Jensson BO, Kluijtmans LAJ, Lengyel A, Lichtenbelt KD, Østergaard E, Peters G, Salvarinova R, Simon MEH, Stefansson K, Thorarensen Ó, Ulmen U, Coene KLM, Willemsen MA, Lefeber DJ, van Karnebeek CDM. NANS-CDG: Delineation of the Genetic, Biochemical, and Clinical Spectrum. Front Neurol 2021; 12:668640. [PMID: 34163424 PMCID: PMC8215539 DOI: 10.3389/fneur.2021.668640] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 04/09/2021] [Indexed: 12/18/2022] Open
Abstract
Background: NANS-CDG is a recently described congenital disorder of glycosylation caused by biallelic genetic variants in NANS, encoding an essential enzyme in de novo sialic acid synthesis. Sialic acid at the end of glycoconjugates plays a key role in biological processes such as brain and skeletal development. Here, we present an observational cohort study to delineate the genetic, biochemical, and clinical phenotype and assess possible correlations. Methods: Medical and laboratory records were reviewed with retrospective extraction and analysis of genetic, biochemical, and clinical data (2016–2020). Results: Nine NANS-CDG patients (nine families, six countries) referred to the Radboudumc CDG Center of Expertise were included. Phenotyping confirmed the hallmark features including intellectual developmental disorder (IDD) (n = 9/9; 100%), facial dysmorphisms (n = 9/9; 100%), neurologic impairment (n = 9/9; 100%), short stature (n = 8/9; 89%), skeletal dysplasia (n = 8/9; 89%), and short limbs (n = 8/9; 89%). Newly identified features include ophthalmological abnormalities (n = 6/9; 67%), an abnormal septum pellucidum (n = 6/9; 67%), (progressive) cerebral atrophy and ventricular dilatation (n = 5/9; 56%), gastrointestinal dysfunction (n = 5/9; 56%), thrombocytopenia (n = 5/9; 56%), and hypo–low-density lipoprotein cholesterol (n = 4/9; 44%). Biochemically, elevated urinary excretion of N-acetylmannosamine (ManNAc) is pathognomonic, the concentrations of which show a significant correlation with clinical severity. Genotypically, eight novel NANS variants were identified. Three severely affected patients harbored identical compound heterozygous pathogenic variants, one of whom was initiated on experimental prenatal and postnatal treatment with oral sialic acid. This patient showed markedly better psychomotor development than the other two genotypically identical males. Conclusions: ManNAc screening should be considered in all patients with IDD, short stature with short limbs, facial dysmorphisms, neurologic impairment, and an abnormal septum pellucidum +/– congenital and neurodegenerative lesions on brain imaging, to establish a precise diagnosis and contribute to prognostication. Personalized management includes accurate genetic counseling and access to proper supports and tailored care for gastrointestinal symptoms, thrombocytopenia, and epilepsy, as well as rehabilitation services for cognitive and physical impairments. Motivated by the short-term positive effects of experimental treatment with oral sialic, we have initiated this intervention with protocolized follow-up of neurologic, systemic, and growth outcomes in four patients. Research is ongoing to unravel pathophysiology and identify novel therapeutic targets.
Collapse
Affiliation(s)
- Bibiche den Hollander
- Department of Pediatric Metabolic Diseases, Emma Children's Hospital, Amsterdam University Medical Center, Amsterdam, Netherlands.,Department of Pediatric Metabolic Diseases, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, Netherlands.,United for Metabolic Diseases, Amsterdam, Netherlands
| | - Anne Rasing
- Department of Pediatric Metabolic Diseases, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, Netherlands
| | - Merel A Post
- United for Metabolic Diseases, Amsterdam, Netherlands.,Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, Netherlands.,Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | - Willemijn M Klein
- Department of Radiology and Nuclear Medicine and Anatomy, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Machteld M Oud
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, Netherlands
| | - Marion M Brands
- Department of Pediatric Metabolic Diseases, Emma Children's Hospital, Amsterdam University Medical Center, Amsterdam, Netherlands.,United for Metabolic Diseases, Amsterdam, Netherlands
| | - Lonneke de Boer
- Department of Pediatric Metabolic Diseases, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, Netherlands
| | - Udo F H Engelke
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | - Peter van Essen
- Radboudumc Technology Center Clinical Studies, Radboud University Medical Center, Nijmegen, Netherlands
| | - Sabine A Fuchs
- United for Metabolic Diseases, Amsterdam, Netherlands.,Department of Pediatric Metabolic Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, Netherlands
| | - Charlotte A Haaxma
- Department of Pediatric Neurology, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, Netherlands
| | | | - Leo A J Kluijtmans
- United for Metabolic Diseases, Amsterdam, Netherlands.,Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | - Anna Lengyel
- 2nd Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | | | - Elsebet Østergaard
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Gera Peters
- Department of Rehabilitation Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | - Ramona Salvarinova
- Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada.,BC Children's Hospital Research Institute, The University of British Columbia, Vancouver, BC, Canada
| | - Marleen E H Simon
- Department of Genetics, University Medical Center Utrecht, Utrecht, Netherlands
| | - Kari Stefansson
- Decode Genetics/Amgen, Inc., Reykjavik, Iceland.,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Ólafur Thorarensen
- Department of Pediatrics, Children's Medical Center, Landspitali-The National University Hospital of Iceland, Reykjavík, Iceland
| | - Ulrike Ulmen
- Department of Pediatrics, Sana Klinikum Lichtenberg, Berlin, Germany
| | - Karlien L M Coene
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | - Michèl A Willemsen
- United for Metabolic Diseases, Amsterdam, Netherlands.,Department of Pediatric Neurology, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, Netherlands
| | - Dirk J Lefeber
- United for Metabolic Diseases, Amsterdam, Netherlands.,Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, Netherlands.,Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | - Clara D M van Karnebeek
- Department of Pediatric Metabolic Diseases, Emma Children's Hospital, Amsterdam University Medical Center, Amsterdam, Netherlands.,Department of Pediatric Metabolic Diseases, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, Netherlands.,United for Metabolic Diseases, Amsterdam, Netherlands.,Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada.,BC Children's Hospital Research Institute, The University of British Columbia, Vancouver, BC, Canada
| |
Collapse
|
73
|
Sung J, Wang L, Long D, Yang C, Merlin D. PepT1-knockout mice harbor a protective metabolome beneficial for intestinal wound healing. Am J Physiol Gastrointest Liver Physiol 2021; 320:G888-G896. [PMID: 33759563 PMCID: PMC8202197 DOI: 10.1152/ajpgi.00299.2020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Genetic knockout (KO) of peptide transporter-1 (PepT1) protein is known to provide resistance to acute colitis and colitis-associated cancer (CAC) in mouse models. However, it was unclear which molecule(s) or pathway(s) formed the basis for these protective effects. Recently, we demonstrated that the PepT1-/- microbiota is sufficient to protect against colitis and CAC. Given that PepT1 KO alters the gut microbiome and thereby changes the intestinal metabolites that are ultimately reflected in the feces, we investigated the fecal metabolites of our PepT1 KO mice. Using a liquid chromatography-mass spectrometry (LC-MS)-based untargeted-metabolomics technique, we found that the fecal metabolites were significantly different between the KO and normal wild-type (WT) mice. Among the altered fecal metabolites, tuberonic acid (TA) was sevenfold higher in KO mouse feces than in WT mouse feces. Accordingly, we studied whether the increased TA could direct an anti-inflammatory effect. Using in vitro models, we discovered that TA not only prevented lipopolysaccharide (LPS)-induced inflammation in macrophages but also improved the epithelial cell healing processes. Our results suggest that TA, and possibly other fecal metabolites, play a crucial role in the pathway(s) associated with the anticolitis effects of PepT1 KO.NEW & NOTEWORTHY Fecal metabolites were significantly different between the KO and normal wild-type (WT) mice. One fecal metabolite, tuberonic acid (TA), was sevenfold higher in KO mouse feces than in WT mouse feces. TA prevented lipopolysaccharide (LPS)-induced inflammation in macrophages and improved the epithelial cell healing process.
Collapse
Affiliation(s)
- Junsik Sung
- 1Institute for Biomedical Sciences, Digestive Diseases Research Group, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia
| | - Lixin Wang
- 1Institute for Biomedical Sciences, Digestive Diseases Research Group, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia,2Atlanta Veterans Affairs Medical Center, Decatur, Georgia
| | - Dingpei Long
- 1Institute for Biomedical Sciences, Digestive Diseases Research Group, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia
| | - Chunhua Yang
- 1Institute for Biomedical Sciences, Digestive Diseases Research Group, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia
| | - Didier Merlin
- 1Institute for Biomedical Sciences, Digestive Diseases Research Group, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia,2Atlanta Veterans Affairs Medical Center, Decatur, Georgia
| |
Collapse
|
74
|
Berling É, Laforêt P, Wahbi K, Labrune P, Petit F, Ronzitti G, O'Brien A. Narrative review of glycogen storage disorder type III with a focus on neuromuscular, cardiac and therapeutic aspects. J Inherit Metab Dis 2021; 44:521-533. [PMID: 33368379 DOI: 10.1002/jimd.12355] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/19/2020] [Accepted: 12/22/2020] [Indexed: 12/26/2022]
Abstract
Glycogen storage disorder type III (GSDIII) is a rare inborn error of metabolism due to loss of glycogen debranching enzyme activity, causing inability to fully mobilize glycogen stores and its consequent accumulation in various tissues, notably liver, cardiac and skeletal muscle. In the pediatric population, it classically presents as hepatomegaly with or without ketotic hypoglycemia and failure to thrive. In the adult population, it should also be considered in the differential diagnosis of left ventricular hypertrophy or hypertrophic cardiomyopathy, myopathy, exercise intolerance, as well as liver cirrhosis or fibrosis with subsequent liver failure. In this review article, we first present an overview of the biochemical and clinical aspects of GSDIII. We then focus on the recent findings regarding cardiac and neuromuscular impairment associated with the disease. We review new insights into the pathophysiology and clinical picture of this disorder, including symptomatology, imaging and electrophysiology. Finally, we discuss current and upcoming treatment strategies such as gene therapy aimed at the replacement of the malfunctioning enzyme to provide a stable and long-term therapeutic option for this debilitating disease.
Collapse
Affiliation(s)
- Édouard Berling
- Généthon, Evry, France
- Université Paris-Saclay, Univ Evry, INSERM, Généthon, Integrare Research Unit UMR_S951, Evry, France
| | - Pascal Laforêt
- APHP, Department of Neurology, Raymond Poincaré Hospital, Centre de Référence de Pathologie Neuromusculaire Nord-Est-Ile-de-France, Garches, France
- INSERM U 1179, Université Versailles Saint Quentin en Yvelines, Paris-Saclay, France
| | - Karim Wahbi
- APHP, Cochin Hospital, Cardiology Department, FILNEMUS, Paris-Descartes, Sorbonne Paris Cité University, Paris, France
- Sorbonne Paris Cité, Université Paris Descartes, Paris, France
- INSERM Unit 970, Paris Cardiovascular Research Centre (PARCC), Paris, France
| | - Philippe Labrune
- APHP, Université Paris-Saclay, Hôpital Antoine Béclère, Centre de Référence Maladies Héréditaires du Métabolisme Hépatique, Service de Pédiatrie, 92141 Clamart cedex, France
- INSERM U1195, Université Paris-Saclay, Le Kremlin Bicêtre, France
| | - François Petit
- Department of Genetics, APHP, Université Paris Saclay, Hôpital Antoine Béclère, Clamart, France
| | - Giuseppe Ronzitti
- Généthon, Evry, France
- Université Paris-Saclay, Univ Evry, INSERM, Généthon, Integrare Research Unit UMR_S951, Evry, France
| | - Alan O'Brien
- Généthon, Evry, France
- Service de Médecine Génique, Département de Médecine, Centre Hospitalier de l'Université de Montréal (CHUM), Montréal, Quebec, Canada
| |
Collapse
|
75
|
Hoytema van Konijnenburg EMM, Wortmann SB, Koelewijn MJ, Tseng LA, Houben R, Stöckler-Ipsiroglu S, Ferreira CR, van Karnebeek CDM. Treatable inherited metabolic disorders causing intellectual disability: 2021 review and digital app. Orphanet J Rare Dis 2021; 16:170. [PMID: 33845862 PMCID: PMC8042729 DOI: 10.1186/s13023-021-01727-2] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 02/03/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The Treatable ID App was created in 2012 as digital tool to improve early recognition and intervention for treatable inherited metabolic disorders (IMDs) presenting with global developmental delay and intellectual disability (collectively 'treatable IDs'). Our aim is to update the 2012 review on treatable IDs and App to capture the advances made in the identification of new IMDs along with increased pathophysiological insights catalyzing therapeutic development and implementation. METHODS Two independent reviewers queried PubMed, OMIM and Orphanet databases to reassess all previously included disorders and therapies and to identify all reports on Treatable IDs published between 2012 and 2021. These were included if listed in the International Classification of IMDs (ICIMD) and presenting with ID as a major feature, and if published evidence for a therapeutic intervention improving ID primary and/or secondary outcomes is available. Data on clinical symptoms, diagnostic testing, treatment strategies, effects on outcomes, and evidence levels were extracted and evaluated by the reviewers and external experts. The generated knowledge was translated into a diagnostic algorithm and updated version of the App with novel features. RESULTS Our review identified 116 treatable IDs (139 genes), of which 44 newly identified, belonging to 17 ICIMD categories. The most frequent therapeutic interventions were nutritional, pharmacological and vitamin and trace element supplementation. Evidence level varied from 1 to 3 (trials, cohort studies, case-control studies) for 19% and 4-5 (case-report, expert opinion) for 81% of treatments. Reported effects included improvement of clinical deterioration in 62%, neurological manifestations in 47% and development in 37%. CONCLUSION The number of treatable IDs identified by our literature review increased by more than one-third in eight years. Although there has been much attention to gene-based and enzyme replacement therapy, the majority of effective treatments are nutritional, which are relatively affordable, widely available and (often) surprisingly effective. We present a diagnostic algorithm (adjustable to local resources and expertise) and the updated App to facilitate a swift and accurate workup, prioritizing treatable IDs. Our digital tool is freely available as Native and Web App (www.treatable-id.org) with several novel features. Our Treatable ID endeavor contributes to the Treatabolome and International Rare Diseases Research Consortium goals, enabling clinicians to deliver rapid evidence-based interventions to our rare disease patients.
Collapse
Affiliation(s)
| | - Saskia B Wortmann
- Department of Pediatrics, Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
- University Children's Hospital, Paracelsus Medical University, Salzburg, Austria
- On Behalf of United for Metabolic Diseases, Amsterdam, The Netherlands
| | - Marina J Koelewijn
- Department of Pediatrics, Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Laura A Tseng
- Department of Pediatrics, Amsterdam UMC, Amsterdam, The Netherlands
- On Behalf of United for Metabolic Diseases, Amsterdam, The Netherlands
| | | | - Sylvia Stöckler-Ipsiroglu
- Division of Biochemical Diseases, Department of Pediatrics, BC Children's Hospital, Vancouver, BC, V6H 3V4, Canada
| | - Carlos R Ferreira
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Clara D M van Karnebeek
- Department of Pediatrics, Amsterdam UMC, Amsterdam, The Netherlands.
- Department of Pediatrics, Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, The Netherlands.
- On Behalf of United for Metabolic Diseases, Amsterdam, The Netherlands.
- Department of Pediatrics - Metabolic Diseases, Amalia Children's Hospital, Geert Grooteplein 10, Radboud University Medical Center, 6525 GA, Nijmegen, The Netherlands.
| |
Collapse
|
76
|
Alston CL, Stenton SL, Hudson G, Prokisch H, Taylor RW. The genetics of mitochondrial disease: dissecting mitochondrial pathology using multi-omic pipelines. J Pathol 2021; 254:430-442. [PMID: 33586140 PMCID: PMC8600955 DOI: 10.1002/path.5641] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/07/2021] [Accepted: 02/09/2021] [Indexed: 12/12/2022]
Abstract
Mitochondria play essential roles in numerous metabolic pathways including the synthesis of adenosine triphosphate through oxidative phosphorylation. Clinically, mitochondrial diseases occur when there is mitochondrial dysfunction – manifesting at any age and affecting any organ system; tissues with high energy requirements, such as muscle and the brain, are often affected. The clinical heterogeneity is parallel to the degree of genetic heterogeneity associated with mitochondrial dysfunction. Around 10% of human genes are predicted to have a mitochondrial function, and defects in over 300 genes are reported to cause mitochondrial disease. Some involve the mitochondrial genome (mtDNA), but the vast majority occur within the nuclear genome. Except for a few specific genetic defects, there remains no cure for mitochondrial diseases, which means that a genetic diagnosis is imperative for genetic counselling and the provision of reproductive options for at‐risk families. Next‐generation sequencing strategies, particularly exome and whole‐genome sequencing, have revolutionised mitochondrial diagnostics such that the traditional muscle biopsy has largely been replaced with a minimally‐invasive blood sample for an unbiased approach to genetic diagnosis. Where these genomic approaches have not identified a causative defect, or where there is insufficient support for pathogenicity, additional functional investigations are required. The application of supplementary ‘omics’ technologies, including transcriptomics, proteomics, and metabolomics, has the potential to greatly improve diagnostic strategies. This review aims to demonstrate that whilst a molecular diagnosis can be achieved for many cases through next‐generation sequencing of blood DNA, the use of patient tissues and an integrated, multidisciplinary multi‐omics approach is pivotal for the diagnosis of more challenging cases. Moreover, the analysis of clinically relevant tissues from affected individuals remains crucial for understanding the molecular mechanisms underlying mitochondrial pathology. © 2021 The Authors. The Journal of Pathology published by John Wiley & Sons, Ltd. on behalf of The Pathological Society of Great Britain and Ireland.
Collapse
Affiliation(s)
- Charlotte L Alston
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.,NHS Highly Specialised Services for Rare Mitochondrial Disorders, Royal Victoria Infirmary, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Sarah L Stenton
- Institute of Human Genetics, Technische Universität München, München, Germany.,Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Gavin Hudson
- Wellcome Centre for Mitochondrial Research, Bioscience Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Holger Prokisch
- Institute of Human Genetics, Technische Universität München, München, Germany.,Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.,NHS Highly Specialised Services for Rare Mitochondrial Disorders, Royal Victoria Infirmary, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| |
Collapse
|
77
|
Gusic M, Prokisch H. Genetic basis of mitochondrial diseases. FEBS Lett 2021; 595:1132-1158. [PMID: 33655490 DOI: 10.1002/1873-3468.14068] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/17/2021] [Accepted: 02/18/2021] [Indexed: 12/13/2022]
Abstract
Mitochondrial disorders are monogenic disorders characterized by a defect in oxidative phosphorylation and caused by pathogenic variants in one of over 340 different genes. The implementation of whole-exome sequencing has led to a revolution in their diagnosis, duplicated the number of associated disease genes, and significantly increased the diagnosed fraction. However, the genetic etiology of a substantial fraction of patients exhibiting mitochondrial disorders remains unknown, highlighting limitations in variant detection and interpretation, which calls for improved computational and DNA sequencing methods, as well as the addition of OMICS tools. More intriguingly, this also suggests that some pathogenic variants lie outside of the protein-coding genes and that the mechanisms beyond the Mendelian inheritance and the mtDNA are of relevance. This review covers the current status of the genetic basis of mitochondrial diseases, discusses current challenges and perspectives, and explores the contribution of factors beyond the protein-coding regions and monogenic inheritance in the expansion of the genetic spectrum of disease.
Collapse
Affiliation(s)
- Mirjana Gusic
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Human Genetics, Technical University of Munich, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Germany
| | - Holger Prokisch
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Human Genetics, Technical University of Munich, Germany
| |
Collapse
|
78
|
Amadori rearrangement products as potential biomarkers for inborn errors of amino-acid metabolism. Commun Biol 2021; 4:367. [PMID: 33742102 PMCID: PMC7979741 DOI: 10.1038/s42003-021-01909-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 02/23/2021] [Indexed: 01/18/2023] Open
Abstract
The identification of disease biomarkers plays a crucial role in developing diagnostic strategies for inborn errors of metabolism and understanding their pathophysiology. A primary metabolite that accumulates in the inborn error phenylketonuria is phenylalanine, however its levels do not always directly correlate with clinical outcomes. Here we combine infrared ion spectroscopy and NMR spectroscopy to identify the Phe-glucose Amadori rearrangement product as a biomarker for phenylketonuria. Additionally, we find analogous amino acid-glucose metabolites formed in the body fluids of patients accumulating methionine, lysine, proline and citrulline. Amadori rearrangement products are well-known intermediates in the formation of advanced glycation end-products and have been associated with the pathophysiology of diabetes mellitus and ageing, but are now shown to also form under conditions of aminoacidemia. They represent a general class of metabolites for inborn errors of amino acid metabolism that show potential as biomarkers and may provide further insight in disease pathophysiology.
Collapse
|
79
|
Opladen T, Gleich F, Kozich V, Scarpa M, Martinelli D, Schaefer F, Jeltsch K, Juliá-Palacios N, García-Cazorla Á, Dionisi-Vici C, Kölker S. U-IMD: the first Unified European registry for inherited metabolic diseases. Orphanet J Rare Dis 2021; 16:95. [PMID: 33602304 PMCID: PMC7893973 DOI: 10.1186/s13023-021-01726-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 02/03/2021] [Indexed: 11/21/2022] Open
Abstract
Background Following the broad application of new analytical methods, more and more pathophysiological processes in previously unknown diseases have been elucidated. The spectrum of clinical presentation of rare inherited metabolic diseases (IMDs) is broad and ranges from single organ involvement to multisystemic diseases. With the aim of overcoming the limited knowledge about the natural course, current diagnostic and therapeutic approaches, the project has established the first unified patient registry for IMDs that fully meets the requirements of the European Infrastructure for Rare Diseases (ERDRI). Results In collaboration with the European Reference Network for Rare Hereditary Metabolic Disorders (MetabERN), the Unified European registry for Inherited Metabolic Diseases (U-IMD) was established to collect patient data as an observational, non-interventional natural history study. Following the recommendations of the ERDRI the U-IMD registry uses common data elements to define the IMDs, report the clinical phenotype, describe the biochemical markers and to capture the drug treatment. Until today, more than 1100 IMD patients have been registered. Conclusion The U-IMD registry is the first observational, non-interventional patient registry that encompasses all known IMDs. Full semantic interoperability for other registries has been achieved, as demonstrated by the use of a minimum common core data set for equivalent description of metabolic patients in U-IMD and in the patient registry of the European Rare Kidney Disease Reference Network (ERKNet). In conclusion, the U-IMD registry will contribute to a better understanding of the long-term course of IMDs and improved patients care by understanding the natural disease course and by enabling an optimization of diagnostic and therapeutic strategies.
Collapse
Affiliation(s)
- Thomas Opladen
- Division of Neuropediatrics and Metabolic Medicine, Department of General Pediatrics, Centre for Child and Adolescent Medicine, Im Neuenheimer Feld 430, 69120, Heidelberg, Germany.
| | - Florian Gleich
- Division of Neuropediatrics and Metabolic Medicine, Department of General Pediatrics, Centre for Child and Adolescent Medicine, Im Neuenheimer Feld 430, 69120, Heidelberg, Germany
| | - Viktor Kozich
- Department of Pediatrics and Inherited Metabolic Disorders, Charles University - First Faculty of Medicine and General University Hospital, Prague, Czech Republic
| | - Maurizio Scarpa
- Regional Coordinating Center for Rare Diseases, Udine University Hospital, Udine, Italy
| | - Diego Martinelli
- U.O.C. di Patologia Metabolica, Dipartimento di Medicina Pediatrica, IRCCS Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Franz Schaefer
- Division of Pediatric Nephrology, Department of General Pediatrics, Centre for Child and Adolescent Medicine, Heidelberg, Germany
| | - Kathrin Jeltsch
- Division of Neuropediatrics and Metabolic Medicine, Department of General Pediatrics, Centre for Child and Adolescent Medicine, Im Neuenheimer Feld 430, 69120, Heidelberg, Germany
| | - Natalia Juliá-Palacios
- Inborn Errors of Metabolism Unit, Neurology Department, Institut de Recerca Sant Joan de Déu, and CIBERER-ISCIII, Barcelona, Spain
| | - Ángels García-Cazorla
- Inborn Errors of Metabolism Unit, Neurology Department, Institut de Recerca Sant Joan de Déu, and CIBERER-ISCIII, Barcelona, Spain
| | - Carlo Dionisi-Vici
- U.O.C. di Patologia Metabolica, Dipartimento di Medicina Pediatrica, IRCCS Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Stefan Kölker
- Division of Neuropediatrics and Metabolic Medicine, Department of General Pediatrics, Centre for Child and Adolescent Medicine, Im Neuenheimer Feld 430, 69120, Heidelberg, Germany
| |
Collapse
|
80
|
Martins Conde P, Pfau T, Pires Pacheco M, Sauter T. A dynamic multi-tissue model to study human metabolism. NPJ Syst Biol Appl 2021; 7:5. [PMID: 33483512 PMCID: PMC7822846 DOI: 10.1038/s41540-020-00159-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 10/19/2020] [Indexed: 11/08/2022] Open
Abstract
Metabolic modeling enables the study of human metabolism in healthy and in diseased conditions, e.g., the prediction of new drug targets and biomarkers for metabolic diseases. To accurately describe blood and urine metabolite dynamics, the integration of multiple metabolically active tissues is necessary. We developed a dynamic multi-tissue model, which recapitulates key properties of human metabolism at the molecular and physiological level based on the integration of transcriptomics data. It enables the simulation of the dynamics of intra-cellular and extra-cellular metabolites at the genome scale. The predictive capacity of the model is shown through the accurate simulation of different healthy conditions (i.e., during fasting, while consuming meals or during exercise), and the prediction of biomarkers for a set of Inborn Errors of Metabolism with a precision of 83%. This novel approach is useful to prioritize new biomarkers for many metabolic diseases, as well as for the integration of various types of personal omics data, towards the personalized analysis of blood and urine metabolites.
Collapse
Affiliation(s)
- Patricia Martins Conde
- Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Megeno S.A., Esch-sur-Alzette, Luxembourg
| | - Thomas Pfau
- Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Maria Pires Pacheco
- Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Thomas Sauter
- Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
| |
Collapse
|
81
|
Messa GM, Napolitano F, Elsea SH, di Bernardo D, Gao X. A Siamese neural network model for the prioritization of metabolic disorders by integrating real and simulated data. Bioinformatics 2020; 36:i787-i794. [PMID: 33381827 DOI: 10.1093/bioinformatics/btaa841] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Untargeted metabolomic approaches hold a great promise as a diagnostic tool for inborn errors of metabolisms (IEMs) in the near future. However, the complexity of the involved data makes its application difficult and time consuming. Computational approaches, such as metabolic network simulations and machine learning, could significantly help to exploit metabolomic data to aid the diagnostic process. While the former suffers from limited predictive accuracy, the latter is normally able to generalize only to IEMs for which sufficient data are available. Here, we propose a hybrid approach that exploits the best of both worlds by building a mapping between simulated and real metabolic data through a novel method based on Siamese neural networks (SNN). RESULTS The proposed SNN model is able to perform disease prioritization for the metabolic profiles of IEM patients even for diseases that it was not trained to identify. To the best of our knowledge, this has not been attempted before. The developed model is able to significantly outperform a baseline model that relies on metabolic simulations only. The prioritization performances demonstrate the feasibility of the method, suggesting that the integration of metabolic models and data could significantly aid the IEM diagnosis process in the near future. AVAILABILITY AND IMPLEMENTATION Metabolic datasets used in this study are publicly available from the cited sources. The original data produced in this study, including the trained models and the simulated metabolic profiles, are also publicly available (Messa et al., 2020).
Collapse
Affiliation(s)
- Gian Marco Messa
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Francesco Napolitano
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Sarah H Elsea
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Diego di Bernardo
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli 80078, Italy.,Department of Chemical, Materials and Industrial Production Engineering, University of Naples Federico II, 80125 Naples, Italy
| | - Xin Gao
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| |
Collapse
|
82
|
Bongaerts M, Bonte R, Demirdas S, Jacobs EH, Oussoren E, van der Ploeg AT, Wagenmakers MAEM, Hofstra RMW, Blom HJ, Reinders MJT, Ruijter GJG. Using Out-of-Batch Reference Populations to Improve Untargeted Metabolomics for Screening Inborn Errors of Metabolism. Metabolites 2020; 11:metabo11010008. [PMID: 33375624 PMCID: PMC7824495 DOI: 10.3390/metabo11010008] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/14/2020] [Accepted: 12/18/2020] [Indexed: 01/15/2023] Open
Abstract
Untargeted metabolomics is an emerging technology in the laboratory diagnosis of inborn errors of metabolism (IEM). Analysis of a large number of reference samples is crucial for correcting variations in metabolite concentrations that result from factors, such as diet, age, and gender in order to judge whether metabolite levels are abnormal. However, a large number of reference samples requires the use of out-of-batch samples, which is hampered by the semi-quantitative nature of untargeted metabolomics data, i.e., technical variations between batches. Methods to merge and accurately normalize data from multiple batches are urgently needed. Based on six metrics, we compared the existing normalization methods on their ability to reduce the batch effects from nine independently processed batches. Many of those showed marginal performances, which motivated us to develop Metchalizer, a normalization method that uses 10 stable isotope-labeled internal standards and a mixed effect model. In addition, we propose a regression model with age and sex as covariates fitted on reference samples that were obtained from all nine batches. Metchalizer applied on log-transformed data showed the most promising performance on batch effect removal, as well as in the detection of 195 known biomarkers across 49 IEM patient samples and performed at least similar to an approach utilizing 15 within-batch reference samples. Furthermore, our regression model indicates that 6.5-37% of the considered features showed significant age-dependent variations. Our comprehensive comparison of normalization methods showed that our Log-Metchalizer approach enables the use out-of-batch reference samples to establish clinically-relevant reference values for metabolite concentrations. These findings open the possibilities to use large scale out-of-batch reference samples in a clinical setting, increasing the throughput and detection accuracy.
Collapse
Affiliation(s)
- Michiel Bongaerts
- Department of Clinical Genetics, Erasmus Medical Centre, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands; (R.B.); (S.D.); (E.H.J.); (R.M.W.H.); (H.J.B.)
- Correspondence: (M.B.); (G.J.G.R.)
| | - Ramon Bonte
- Department of Clinical Genetics, Erasmus Medical Centre, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands; (R.B.); (S.D.); (E.H.J.); (R.M.W.H.); (H.J.B.)
| | - Serwet Demirdas
- Department of Clinical Genetics, Erasmus Medical Centre, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands; (R.B.); (S.D.); (E.H.J.); (R.M.W.H.); (H.J.B.)
| | - Edwin H. Jacobs
- Department of Clinical Genetics, Erasmus Medical Centre, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands; (R.B.); (S.D.); (E.H.J.); (R.M.W.H.); (H.J.B.)
| | - Esmee Oussoren
- Department of Pediatrics, Center for Lysosomal and Metabolic Diseases, Erasmus Medical Centre, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands; (E.O.); (A.T.v.d.P.)
| | - Ans T. van der Ploeg
- Department of Pediatrics, Center for Lysosomal and Metabolic Diseases, Erasmus Medical Centre, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands; (E.O.); (A.T.v.d.P.)
| | - Margreet A. E. M. Wagenmakers
- Department of Internal Medicine, Center for Lysosomal and Metabolic Diseases, Erasmus Medical Centre, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands;
| | - Robert M. W. Hofstra
- Department of Clinical Genetics, Erasmus Medical Centre, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands; (R.B.); (S.D.); (E.H.J.); (R.M.W.H.); (H.J.B.)
| | - Henk J. Blom
- Department of Clinical Genetics, Erasmus Medical Centre, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands; (R.B.); (S.D.); (E.H.J.); (R.M.W.H.); (H.J.B.)
| | - Marcel J. T. Reinders
- Faculty of Electrical Engineering, Mathematics and Computer Science, TU Delft, Van Mourik Broekmanweg 6, 2628 XE Delft, The Netherlands;
| | - George J. G. Ruijter
- Department of Clinical Genetics, Erasmus Medical Centre, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands; (R.B.); (S.D.); (E.H.J.); (R.M.W.H.); (H.J.B.)
- Correspondence: (M.B.); (G.J.G.R.)
| |
Collapse
|
83
|
Sánchez Pintos P, Cocho de Juan JÁ, Bóveda Fontán MD, Castiñeiras Ramos DE, Colón Mejeras C, Iglesias Rodríguez AJ, de Castro López MJ, Alonso Fernández JR, Fraga Bermúdez JM, Couce Pico ML. [Evaluation and perspective of 20 years of neonatal screening in Galicia. Program results.]. Rev Esp Salud Publica 2020; 94:e202012161. [PMID: 33323918 PMCID: PMC11582800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 10/14/2020] [Indexed: 06/12/2023] Open
Abstract
Galician newborn screening program for early detection of endocrine and metabolic diseases began in 1978 and was a pioneer in expanded newborn screening in Spain with the incorporation of mass spectrometry in July 2000. As a primary objective, 28 diseases are screened, including those recommended SNS except sickle cell anemia which is in the inclusion phase. In its 20-year history, 404,616 newborns (nb) have been analyzed, identifying 547 cases affected by the diseases included, with a global incidence of 1: 739 newborns and 1: 1.237 of the screened inborn errors of metabolism (IEM) (1:1.580 nb if excluding benign hyperphenylalaninemia-HPA), with an average participation of 99.35%, progressively higher during the analyzed period. Among the pathologies screened, congenital hypothyroidism (1:2.211 nb), cystinuria (1:4.129 nb) and HPA (1:5.699 nb), followed by phenylketonuria and cystic fibrosis (1:10,936 nb) stand out for their incidence. Sixty-six cases of false positives were identified (seventeen of them in relation to maternal pathology) and five false negatives, being the overall PPV and NPV of the program respectively of 89.2% and 99.99%, with a sensitivity of 99.09% and a specificity of 99.98%. The mortality rate of diagnosed CME patients is 1.52%, with eleven cases presenting symptoms prior to the screening result (2%). The intelligence quotient of IEM patients at risk of neurological involvement is normal in more than 95% of cases.
Collapse
Affiliation(s)
- Paula Sánchez Pintos
- Unidad de Diagnóstico y Tratamiento de Enfermedades Metabólicas Congénitas. Servicio de Neonatología. Hospital Clínico Universitario. Santiago de Compostela. España
| | - José Ángel Cocho de Juan
- Unidad de Diagnóstico y Tratamiento de Enfermedades Metabólicas Congénitas. Servicio de Neonatología. Hospital Clínico Universitario. Santiago de Compostela. España
| | - M Dolores Bóveda Fontán
- Unidad de Diagnóstico y Tratamiento de Enfermedades Metabólicas Congénitas. Servicio de Neonatología. Hospital Clínico Universitario. Santiago de Compostela. España
| | - Daisy E Castiñeiras Ramos
- Unidad de Diagnóstico y Tratamiento de Enfermedades Metabólicas Congénitas. Servicio de Neonatología. Hospital Clínico Universitario. Santiago de Compostela. España
| | - Cristóbal Colón Mejeras
- Unidad de Diagnóstico y Tratamiento de Enfermedades Metabólicas Congénitas. Servicio de Neonatología. Hospital Clínico Universitario. Santiago de Compostela. España
| | - Agustin Javier Iglesias Rodríguez
- Unidad de Diagnóstico y Tratamiento de Enfermedades Metabólicas Congénitas. Servicio de Neonatología. Hospital Clínico Universitario. Santiago de Compostela. España
| | - María José de Castro López
- Unidad de Diagnóstico y Tratamiento de Enfermedades Metabólicas Congénitas. Servicio de Neonatología. Hospital Clínico Universitario. Santiago de Compostela. España
| | - José Ramón Alonso Fernández
- Unidad de Diagnóstico y Tratamiento de Enfermedades Metabólicas Congénitas. Servicio de Neonatología. Hospital Clínico Universitario. Santiago de Compostela. España
| | - José María Fraga Bermúdez
- Unidad de Diagnóstico y Tratamiento de Enfermedades Metabólicas Congénitas. Servicio de Neonatología. Hospital Clínico Universitario. Santiago de Compostela. España
| | - María Luz Couce Pico
- Unidad de Diagnóstico y Tratamiento de Enfermedades Metabólicas Congénitas. Servicio de Neonatología. Hospital Clínico Universitario. Santiago de Compostela. España
| |
Collapse
|
84
|
Borodina I, Kenny LC, McCarthy CM, Paramasivan K, Pretorius E, Roberts TJ, van der Hoek SA, Kell DB. The biology of ergothioneine, an antioxidant nutraceutical. Nutr Res Rev 2020; 33:190-217. [PMID: 32051057 PMCID: PMC7653990 DOI: 10.1017/s0954422419000301] [Citation(s) in RCA: 107] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 11/20/2019] [Accepted: 11/25/2019] [Indexed: 02/07/2023]
Abstract
Ergothioneine (ERG) is an unusual thio-histidine betaine amino acid that has potent antioxidant activities. It is synthesised by a variety of microbes, especially fungi (including in mushroom fruiting bodies) and actinobacteria, but is not synthesised by plants and animals who acquire it via the soil and their diet, respectively. Animals have evolved a highly selective transporter for it, known as solute carrier family 22, member 4 (SLC22A4) in humans, signifying its importance, and ERG may even have the status of a vitamin. ERG accumulates differentially in various tissues, according to their expression of SLC22A4, favouring those such as erythrocytes that may be subject to oxidative stress. Mushroom or ERG consumption seems to provide significant prevention against oxidative stress in a large variety of systems. ERG seems to have strong cytoprotective status, and its concentration is lowered in a number of chronic inflammatory diseases. It has been passed as safe by regulatory agencies, and may have value as a nutraceutical and antioxidant more generally.
Collapse
Affiliation(s)
- Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Building 220, Chemitorvet 200, Technical University of Denmark, 2800Kongens Lyngby, Denmark
| | - Louise C. Kenny
- Department of Women’s and Children’s Health, Institute of Translational Medicine, University of Liverpool, Crown Street, LiverpoolL8 7SS, UK
| | - Cathal M. McCarthy
- Irish Centre for Fetal and Neonatal Translational Research (INFANT), Cork University Maternity Hospital, Cork, Republic of Ireland
- Department of Pharmacology and Therapeutics, Western Gateway Building, University College Cork, Cork, Republic of Ireland
| | - Kalaivani Paramasivan
- The Novo Nordisk Foundation Center for Biosustainability, Building 220, Chemitorvet 200, Technical University of Denmark, 2800Kongens Lyngby, Denmark
| | - Etheresia Pretorius
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch, Private Bag X1 Matieland, 7602, South Africa
| | - Timothy J. Roberts
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch, Private Bag X1 Matieland, 7602, South Africa
- Department of Biochemistry, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Crown Street, LiverpoolL69 7ZB, UK
| | - Steven A. van der Hoek
- The Novo Nordisk Foundation Center for Biosustainability, Building 220, Chemitorvet 200, Technical University of Denmark, 2800Kongens Lyngby, Denmark
| | - Douglas B. Kell
- The Novo Nordisk Foundation Center for Biosustainability, Building 220, Chemitorvet 200, Technical University of Denmark, 2800Kongens Lyngby, Denmark
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch, Private Bag X1 Matieland, 7602, South Africa
- Department of Biochemistry, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Crown Street, LiverpoolL69 7ZB, UK
| |
Collapse
|
85
|
Tinnevelt GH, Engelke UF, Wevers RA, Veenhuis S, Willemsen MA, Coene KL, Kulkarni P, Jansen JJ. Variable Selection in Untargeted Metabolomics and the Danger of Sparsity. Metabolites 2020; 10:metabo10110470. [PMID: 33213095 PMCID: PMC7698561 DOI: 10.3390/metabo10110470] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/05/2020] [Accepted: 11/10/2020] [Indexed: 12/27/2022] Open
Abstract
The goal of metabolomics is to measure as many metabolites as possible in order to capture biomarkers that may indicate disease mechanisms. Variable selection in chemometric methods can be divided into the following two groups: (1) sparse methods that find the minimal set of variables to discriminate between groups and (2) methods that find all variables important for discrimination. Such important variables can be summarized into metabolic pathways using pathway analysis tools like Mummichog. As a test case, we studied the metabolic effects of treatment with nicotinamide riboside, a form of vitamin B3, in a cohort of patients with ataxia–telangiectasia. Vitamin B3 is an important co-factor for many enzymatic reactions in the human body. Thus, the variable selection method was expected to find vitamin B3 metabolites and also other secondary metabolic changes during treatment. However, sparse methods did not select any vitamin B3 metabolites despite the fact that these metabolites showed a large difference when comparing intensity before and during treatment. Univariate analysis or significance multivariate correlation (sMC) in combination with pathway analysis using Mummichog were able to select vitamin B3 metabolites. Moreover, sMC analysis found additional metabolites. Therefore, in our comparative study, sMC displayed the best performance for selection of relevant variables.
Collapse
Affiliation(s)
- Gerjen H. Tinnevelt
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands;
- Correspondence: or
| | - Udo F.H. Engelke
- Translational Metabolic Laboratory (TML), Department of Laboratory Medicine, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (U.F.H.E.); (R.A.W.); (K.L.M.C.); (P.K.)
| | - Ron A. Wevers
- Translational Metabolic Laboratory (TML), Department of Laboratory Medicine, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (U.F.H.E.); (R.A.W.); (K.L.M.C.); (P.K.)
| | - Stefanie Veenhuis
- Department of Pediatric Neurology, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands; (S.V.); (M.A.W.)
| | - Michel A. Willemsen
- Department of Pediatric Neurology, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands; (S.V.); (M.A.W.)
| | - Karlien L.M. Coene
- Translational Metabolic Laboratory (TML), Department of Laboratory Medicine, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (U.F.H.E.); (R.A.W.); (K.L.M.C.); (P.K.)
| | - Purva Kulkarni
- Translational Metabolic Laboratory (TML), Department of Laboratory Medicine, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (U.F.H.E.); (R.A.W.); (K.L.M.C.); (P.K.)
| | - Jeroen J. Jansen
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands;
| |
Collapse
|
86
|
Ortigoza-Escobar JD. A Proposed Diagnostic Algorithm for Inborn Errors of Metabolism Presenting With Movements Disorders. Front Neurol 2020; 11:582160. [PMID: 33281718 PMCID: PMC7691570 DOI: 10.3389/fneur.2020.582160] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 09/30/2020] [Indexed: 12/13/2022] Open
Abstract
Inherited metabolic diseases or inborn errors of metabolism frequently manifest with both hyperkinetic (dystonia, chorea, myoclonus, ataxia, tremor, etc.) and hypokinetic (rigid-akinetic syndrome) movement disorders. The diagnosis of these diseases is in many cases difficult, because the same movement disorder can be caused by several diseases. Through a literature review, two hundred and thirty one inborn errors of metabolism presenting with movement disorders have been identified. Fifty-one percent of these diseases exhibits two or more movement disorders, of which ataxia and dystonia are the most frequent. Taking into account the wide range of these disorders, a methodical evaluation system needs to be stablished. This work proposes a six-step diagnostic algorithm for the identification of inborn errors of metabolism presenting with movement disorders comprising red flags, characterization of the movement disorders phenotype (type of movement disorder, age and nature of onset, distribution and temporal pattern) and other neurological and non-neurological signs, minimal biochemical investigation to diagnose treatable diseases, radiological patterns, genetic testing and ultimately, symptomatic, and disease-specific treatment. As a strong action, it is emphasized not to miss any treatable inborn error of metabolism through the algorithm.
Collapse
Affiliation(s)
- Juan Darío Ortigoza-Escobar
- Movement Disorders Unit, Institut de Recerca Sant Joan de Déu, CIBERER-ISCIII and European Reference Network for Rare Neurological Diseases (ERN-RND), Barcelona, Spain
| |
Collapse
|
87
|
Wang XN, Liu JQ, Shi ZQ, Sun FY, Liu LF, Xin GZ. Orthogonal label and label-free dual pretreatment for targeted profiling of neurotransmitters in enteric nervous system. Anal Chim Acta 2020; 1139:68-78. [PMID: 33190711 DOI: 10.1016/j.aca.2020.09.031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 09/14/2020] [Indexed: 01/23/2023]
Abstract
Neurotransmitter (NT) abnormalities in the enteric nervous system have been reported as crucial roles to regulate the intestinal inflammation and gut immune homeostasis. Capturing quantitative changes at the NT metabolome provides an opportunity to develop an understanding of neuroimmune-mediated inflammation. Given the wide diversity of chemical characterizations in the NTs, only partial coverage of the NT metabolome can be simultaneously quantified in a single-run analysis. Herein, we summarized the distribution of functional groups of compound entries in the NT metabolome. Based on this information, an orthogonal dansyl-labeling and label-free dual pretreatment approach was separately designed to target phenol and amine NTs and tertiary amine and choline NTs. By combining the dansyl-labeled and unlabeled NTs within a single vial, a comprehensive and practical approach was optimized for quantifying high coverage of NT metabolome in a single-run analysis on the reversed-phase C18 column. Method validation indicated good linearity with correlation coefficients (R2) > 0.99, intra- and interday accuracy with relative error < ±20%, and precision with relative standard deviations of ≤15%. With this method, we could simultaneously monitor the alterations of cholines, amines, amino acids, tryptophan and phenylalanine biological pathways in dextran sulphate sodium-induced colitis mice. The measured levels of NT metabolome ranged from 0.0007 to 3.540 μg/mg in intestinal contents and 0.013-154.54 μg/mL in serum samples. The NT metabolism was disrupted by colitis, characterized by the changed NT levels in serum and excessive amino acid NTs accumulation in the intestinal contents. We envisage that the orthogonal approach is of great significance for the comprehensive determination of targeted metabolomics. NTs have the potential to be biomarkers for clinical metabolomics.
Collapse
Affiliation(s)
- Xin-Nan Wang
- State Key Laboratory of Natural Medicines, Department of Chinese Medicines Analysis, School of Traditional Chinese Pharmacy, China Pharmaceutical University, No. 24 Tongjia Lane, Nanjing, China
| | - Jian-Qun Liu
- Key Laboratory of Modern Preparation of TCM, Ministry of Education, Jiangxi University of Traditional Chinese Medicine, No. 818 Xingwan Road, Nanchang, 330004, Jiangxi Province, China
| | - Zi-Qi Shi
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210028, Jiangsu, China
| | - Fang-Yuan Sun
- State Key Laboratory of Natural Medicines, Department of Chinese Medicines Analysis, School of Traditional Chinese Pharmacy, China Pharmaceutical University, No. 24 Tongjia Lane, Nanjing, China
| | - Li-Fang Liu
- State Key Laboratory of Natural Medicines, Department of Chinese Medicines Analysis, School of Traditional Chinese Pharmacy, China Pharmaceutical University, No. 24 Tongjia Lane, Nanjing, China.
| | - Gui-Zhong Xin
- State Key Laboratory of Natural Medicines, Department of Chinese Medicines Analysis, School of Traditional Chinese Pharmacy, China Pharmaceutical University, No. 24 Tongjia Lane, Nanjing, China.
| |
Collapse
|
88
|
Peters TMA, Engelke UFH, de Boer S, van der Heeft E, Pritsch C, Kulkarni P, Wevers RA, Willemsen MAAP, Verbeek MM, Coene KLM. Confirmation of neurometabolic diagnoses using age-dependent cerebrospinal fluid metabolomic profiles. J Inherit Metab Dis 2020; 43:1112-1120. [PMID: 32406085 PMCID: PMC7540372 DOI: 10.1002/jimd.12253] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 04/30/2020] [Accepted: 05/11/2020] [Indexed: 11/24/2022]
Abstract
Timely diagnosis is essential for patients with neurometabolic disorders to enable targeted treatment. Next-Generation Metabolic Screening (NGMS) allows for simultaneous screening of multiple diseases and yields a holistic view of disturbed metabolic pathways. We applied this technique to define a cerebrospinal fluid (CSF) reference metabolome and validated our approach with patients with known neurometabolic disorders. Samples were measured using ultra-high-performance liquid chromatography-quadrupole time-of-flight mass spectrometry followed by (un)targeted analysis. For the reference metabolome, CSF samples from patients with normal general chemistry results and no neurometabolic diagnosis were selected and grouped based on sex and age (0-2/2-5/5-10/10-15 years). We checked the levels of known biomarkers in CSF from seven patients with five different neurometabolic disorders to confirm the suitability of our method for diagnosis. Untargeted analysis of 87 control CSF samples yielded 8036 features for semiquantitative analysis. No sex differences were found, but 1782 features (22%) were different between age groups (q < 0.05). We identified 206 diagnostic metabolites in targeted analysis. In a subset of 20 high-intensity metabolites and 10 biomarkers, 17 (57%) were age-dependent. For each neurometabolic patient, ≥1 specific biomarker(s) could be identified in CSF, thus confirming the diagnosis. In two cases, age-matching was essential for correct interpretation of the metabolomic profile. In conclusion, NGMS in CSF is a powerful tool in defining a diagnosis for neurometabolic disorders. Using our database with many (age-dependent) features in CSF, our untargeted approach will facilitate biomarker discovery and further understanding of mechanisms of neurometabolic disorders.
Collapse
Affiliation(s)
- Tessa M. A. Peters
- Department of Laboratory Medicine, Translational Metabolic Laboratory (TML)Radboud University Medical CenterNijmegenThe Netherlands
- Department of Neurology, Donders Institute for Brain, Cognition and BehaviorRadboud University Medical CenterNijmegenThe Netherlands
| | - Udo F. H. Engelke
- Department of Laboratory Medicine, Translational Metabolic Laboratory (TML)Radboud University Medical CenterNijmegenThe Netherlands
| | - Siebolt de Boer
- Department of Laboratory Medicine, Translational Metabolic Laboratory (TML)Radboud University Medical CenterNijmegenThe Netherlands
| | - Ed van der Heeft
- Department of Laboratory Medicine, Translational Metabolic Laboratory (TML)Radboud University Medical CenterNijmegenThe Netherlands
| | - Cynthia Pritsch
- Department of Pediatric NeurologyDonders Institute for Brain, Cognition and Behavior, Radboud University Medical CenterNijmegenThe Netherlands
| | - Purva Kulkarni
- Department of Laboratory Medicine, Translational Metabolic Laboratory (TML)Radboud University Medical CenterNijmegenThe Netherlands
| | - Ron A. Wevers
- Department of Laboratory Medicine, Translational Metabolic Laboratory (TML)Radboud University Medical CenterNijmegenThe Netherlands
| | - Michèl A. A. P. Willemsen
- Department of Pediatric NeurologyDonders Institute for Brain, Cognition and Behavior, Radboud University Medical CenterNijmegenThe Netherlands
| | - Marcel M. Verbeek
- Department of Laboratory Medicine, Translational Metabolic Laboratory (TML)Radboud University Medical CenterNijmegenThe Netherlands
- Department of Neurology, Donders Institute for Brain, Cognition and BehaviorRadboud University Medical CenterNijmegenThe Netherlands
| | - Karlien L. M. Coene
- Department of Laboratory Medicine, Translational Metabolic Laboratory (TML)Radboud University Medical CenterNijmegenThe Netherlands
| |
Collapse
|
89
|
Husain RA, Grimmel M, Wagner M, Hennings JC, Marx C, Feichtinger RG, Saadi A, Rostásy K, Radelfahr F, Bevot A, Döbler-Neumann M, Hartmann H, Colleaux L, Cordts I, Kobeleva X, Darvish H, Bakhtiari S, Kruer MC, Besse A, Ng ACH, Chiang D, Bolduc F, Tafakhori A, Mane S, Ghasemi Firouzabadi S, Huebner AK, Buchert R, Beck-Woedl S, Müller AJ, Laugwitz L, Nägele T, Wang ZQ, Strom TM, Sturm M, Meitinger T, Klockgether T, Riess O, Klopstock T, Brandl U, Hübner CA, Deschauer M, Mayr JA, Bonnen PE, Krägeloh-Mann I, Wortmann SB, Haack TB. Bi-allelic HPDL Variants Cause a Neurodegenerative Disease Ranging from Neonatal Encephalopathy to Adolescent-Onset Spastic Paraplegia. Am J Hum Genet 2020; 107:364-373. [PMID: 32707086 DOI: 10.1016/j.ajhg.2020.06.015] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 06/22/2020] [Indexed: 11/28/2022] Open
Abstract
We report bi-allelic pathogenic HPDL variants as a cause of a progressive, pediatric-onset spastic movement disorder with variable clinical presentation. The single-exon gene HPDL encodes a protein of unknown function with sequence similarity to 4-hydroxyphenylpyruvate dioxygenase. Exome sequencing studies in 13 families revealed bi-allelic HPDL variants in each of the 17 individuals affected with this clinically heterogeneous autosomal-recessive neurological disorder. HPDL levels were significantly reduced in fibroblast cell lines derived from more severely affected individuals, indicating the identified HPDL variants resulted in the loss of HPDL protein. Clinical presentation ranged from severe, neonatal-onset neurodevelopmental delay with neuroimaging findings resembling mitochondrial encephalopathy to milder manifestation of adolescent-onset, isolated hereditary spastic paraplegia. All affected individuals developed spasticity predominantly of the lower limbs over the course of the disease. We demonstrated through bioinformatic and cellular studies that HPDL has a mitochondrial localization signal and consequently localizes to mitochondria suggesting a putative role in mitochondrial metabolism. Taken together, these genetic, bioinformatic, and functional studies demonstrate HPDL is a mitochondrial protein, the loss of which causes a clinically variable form of pediatric-onset spastic movement disorder.
Collapse
Affiliation(s)
- Ralf A Husain
- Department of Neuropediatrics, Jena University Hospital, 07747 Jena, Germany
| | - Mona Grimmel
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, 72076 Tübingen, Germany
| | - Matias Wagner
- Institute of Human Genetics, Technical University of Munich (TUM), School of Medicine, 81675 Munich, Germany; Institute of Human Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Neurogenomics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | | | - Christian Marx
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - René G Feichtinger
- University Children's Hospital, Salzburger Landeskliniken (SALK) and Paracelsus Medical University (PMU), 5020 Salzburg, Austria
| | - Abdelkrim Saadi
- Department of Neurology, Ben Aknoun Hospital, Benyoucef Benkhedda University, 16028 Algiers, Algeria
| | - Kevin Rostásy
- Department of Pediatric Neurology, Children's Hospital Datteln, Witten/Herdecke University, 45711 Datteln, Germany
| | - Florentine Radelfahr
- Department of Neurology, Friedrich-Baur-Institute, Ludwig-Maximilians-University, 80336 Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), 81377 Munich, Germany
| | - Andrea Bevot
- Department of Pediatric Neurology and Developmental Medicine, University Children's Hospital, 72072 Tübingen, Germany
| | - Marion Döbler-Neumann
- Department of Pediatric Neurology and Developmental Medicine, University Children's Hospital, 72072 Tübingen, Germany
| | - Hans Hartmann
- Clinic for Pediatric Kidney-, Liver- and Metabolic Diseases, Hannover Medical School, 30625 Hannover, Germany
| | - Laurence Colleaux
- INSERM UMR1163, Developmental Brain Disorders Laboratory, Imagine Institute, Paris-Descartes University, Paris, France
| | - Isabell Cordts
- Department of Neurology, Technische Universität München, School of Medicine, 81675 Munich, Germany
| | - Xenia Kobeleva
- Department of Neurology, University of Bonn, 53127 Bonn, Germany
| | - Hossein Darvish
- Cancer Research Center and Department of Medical Genetics, School of Medicine, Semnan University of Medical Sciences, Semnan, Iran
| | - Somayeh Bakhtiari
- Barrow Neurological Institute, Phoenix Children's Hospital & University of Arizona College of Medicine, Phoenix, AZ 85004, USA
| | - Michael C Kruer
- Barrow Neurological Institute, Phoenix Children's Hospital & University of Arizona College of Medicine, Phoenix, AZ 85004, USA
| | - Arnaud Besse
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Andy Cheuk-Him Ng
- Division of Pediatric Neurology, Department of Pediatrics, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Diana Chiang
- Division of Pediatric Neurology, Department of Pediatrics, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Francois Bolduc
- Division of Pediatric Neurology, Department of Pediatrics, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Abbas Tafakhori
- Iranian Center of Neurological Research, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Shrikant Mane
- Yale Center for Genome Analysis, Yale University School of Medicine, West Haven, CT 06516, USA
| | | | - Antje K Huebner
- Institute of Human Genetics, Jena University Hospital, 07747 Jena, Germany
| | - Rebecca Buchert
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, 72076 Tübingen, Germany
| | - Stefanie Beck-Woedl
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, 72076 Tübingen, Germany
| | - Amelie J Müller
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, 72076 Tübingen, Germany
| | - Lucia Laugwitz
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, 72076 Tübingen, Germany; Department of Pediatric Neurology and Developmental Medicine, University Children's Hospital, 72072 Tübingen, Germany
| | - Thomas Nägele
- Department of Neuroradiology, University Hospital Tuebingen, 72072 Tübingen, Germany
| | - Zhao-Qi Wang
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), 07745 Jena, Germany; Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Tim M Strom
- Institute of Human Genetics, Technical University of Munich (TUM), School of Medicine, 81675 Munich, Germany; Institute of Human Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Marc Sturm
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, 72076 Tübingen, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Technical University of Munich (TUM), School of Medicine, 81675 Munich, Germany; Institute of Human Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Munich Cluster for Systems Neurology (SyNergy), 81377 Munich, Germany
| | - Thomas Klockgether
- Department of Neurology, University of Bonn, 53127 Bonn, Germany; German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, 72076 Tübingen, Germany; Centre for Rare Diseases, University of Tuebingen, 72076 Tübingen, Germany
| | - Thomas Klopstock
- Department of Neurology, Friedrich-Baur-Institute, Ludwig-Maximilians-University, 80336 Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), 81377 Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), 81377 Munich, Germany
| | - Ulrich Brandl
- Department of Neuropediatrics, Jena University Hospital, 07747 Jena, Germany
| | - Christian A Hübner
- Institute of Human Genetics, Jena University Hospital, 07747 Jena, Germany
| | - Marcus Deschauer
- Department of Neurology, Technische Universität München, School of Medicine, 81675 Munich, Germany
| | - Johannes A Mayr
- University Children's Hospital, Salzburger Landeskliniken (SALK) and Paracelsus Medical University (PMU), 5020 Salzburg, Austria
| | - Penelope E Bonnen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ingeborg Krägeloh-Mann
- Department of Pediatric Neurology and Developmental Medicine, University Children's Hospital, 72072 Tübingen, Germany
| | - Saskia B Wortmann
- Institute of Human Genetics, Technical University of Munich (TUM), School of Medicine, 81675 Munich, Germany; Institute of Human Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany; University Children's Hospital, Salzburger Landeskliniken (SALK) and Paracelsus Medical University (PMU), 5020 Salzburg, Austria; Radboud Center for Mitochondrial Medicine, Department of Pediatrics, Amalia Children's Hospital, Radboudumc, 6525 GA Nijmegen, the Netherlands
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, 72076 Tübingen, Germany; Centre for Rare Diseases, University of Tuebingen, 72076 Tübingen, Germany.
| |
Collapse
|
90
|
Precision Medicine for Lysosomal Disorders. Biomolecules 2020; 10:biom10081110. [PMID: 32722587 PMCID: PMC7463721 DOI: 10.3390/biom10081110] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/21/2020] [Accepted: 07/23/2020] [Indexed: 12/16/2022] Open
Abstract
Precision medicine (PM) is an emerging approach for disease treatment and prevention that accounts for the individual variability in the genes, environment, and lifestyle of each person. Lysosomal diseases (LDs) are a group of genetic metabolic disorders that include approximately 70 monogenic conditions caused by a defect in lysosomal function. LDs may result from primary lysosomal enzyme deficiencies or impairments in membrane-associated proteins, lysosomal enzyme activators, or modifiers that affect lysosomal function. LDs are heterogeneous disorders, and the phenotype of the affected individual depends on the type of substrate and where it accumulates, which may be impacted by the type of genetic change and residual enzymatic activity. LDs are individually rare, with a combined incidence of approximately 1:4000 individuals. Specific therapies are already available for several LDs, and many more are in development. Early identification may enable disease course prediction and a specific intervention, which is very important for clinical outcome. Driven by advances in omics technology, PM aims to provide the most appropriate management for each patient based on the disease susceptibility or treatment response predictions for specific subgroups. In this review, we focused on the emerging diagnostic technologies that may help to optimize the management of each LD patient and the therapeutic options available, as well as in clinical developments that enable customized approaches to be selected for each subject, according to the principles of PM.
Collapse
|
91
|
Graham Linck EJ, Richmond PA, Tarailo-Graovac M, Engelke U, Kluijtmans LAJ, Coene KLM, Wevers RA, Wasserman W, van Karnebeek CDM, Mostafavi S. metPropagate: network-guided propagation of metabolomic information for prioritization of metabolic disease genes. NPJ Genom Med 2020; 5:25. [PMID: 32637154 PMCID: PMC7331614 DOI: 10.1038/s41525-020-0132-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Accepted: 05/05/2020] [Indexed: 12/18/2022] Open
Abstract
Many inborn errors of metabolism (IEMs) are amenable to treatment, therefore early diagnosis is imperative. Whole-exome sequencing (WES) variant prioritization coupled with phenotype-guided clinical and bioinformatics expertise is typically used to identify disease-causing variants; however, it can be challenging to identify the causal candidate gene when a large number of rare and potentially pathogenic variants are detected. Here, we present a network-based approach, metPropagate, that uses untargeted metabolomics (UM) data from a single patient and a group of controls to prioritize candidate genes in patients with suspected IEMs. We validate metPropagate on 107 patients with IEMs diagnosed in Miller et al. (2015) and 11 patients with both CNS and metabolic abnormalities. The metPropagate method ranks candidate genes by label propagation, a graph-smoothing algorithm that considers each gene's metabolic perturbation in addition to the network of interactions between neighbors. metPropagate was able to prioritize at least one causative gene in the top 20th percentile of candidate genes for 92% of patients with known IEMs. Applied to patients with suspected neurometabolic disease, metPropagate placed at least one causative gene in the top 20th percentile in 9/11 patients, and ranked the causative gene more highly than Exomiser's phenotype-based ranking in 6/11 patients. Interestingly, ranking by a weighted combination of metPropagate and Exomiser scores resulted in improved prioritization. The results of this study indicate that network-based analysis of UM data can provide an additional mode of evidence to prioritize causal genes in patients with suspected IEMs.
Collapse
Affiliation(s)
- Emma J. Graham Linck
- BC Children’s Hospital Research Institute, Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, Canada
| | - Phillip A. Richmond
- BC Children’s Hospital Research Institute, Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, Canada
| | - Maja Tarailo-Graovac
- Departments of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
- Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, Canada
| | - Udo Engelke
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Leo A. J. Kluijtmans
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Karlien L. M. Coene
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ron A. Wevers
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Wyeth Wasserman
- BC Children’s Hospital Research Institute, Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Clara D. M. van Karnebeek
- Department of Pediatrics, BC Children’s Hospital Research Institute, Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, Canada
- Department of Pediatrics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Sara Mostafavi
- BC Children’s Hospital Research Institute, Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
- Department of Statistics, University of British Columbia, Vancouver, Canada
| |
Collapse
|
92
|
Almontashiri NAM, Zha L, Young K, Law T, Kellogg MD, Bodamer OA, Peake RWA. Clinical Validation of Targeted and Untargeted Metabolomics Testing for Genetic Disorders: A 3 Year Comparative Study. Sci Rep 2020; 10:9382. [PMID: 32523032 PMCID: PMC7287104 DOI: 10.1038/s41598-020-66401-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 05/19/2020] [Indexed: 02/04/2023] Open
Abstract
Global untargeted metabolomics (GUM) has entered clinical diagnostics for genetic disorders. We compared the clinical utility of GUM with traditional targeted metabolomics (TM) as a screening tool in patients with established genetic disorders and determined the scope of GUM as a discovery tool in patients with no diagnosis under investigation. We compared TM and GUM data in 226 patients. The first cohort (n = 87) included patients with confirmed inborn errors of metabolism (IEM) and genetic syndromes; the second cohort (n = 139) included patients without diagnosis who were undergoing evaluation for a genetic disorder. In patients with known disorders (n = 87), GUM performed with a sensitivity of 86% (95% CI: 78–91) compared with TM for the detection of 51 diagnostic metabolites. The diagnostic yield of GUM in patients under evaluation with no established diagnosis (n = 139) was 0.7%. GUM successfully detected the majority of diagnostic compounds associated with known IEMs. The diagnostic yield of both targeted and untargeted metabolomics studies is low when assessing patients with non-specific, neurological phenotypes. GUM shows promise as a validation tool for variants of unknown significance in candidate genes in patients with non-specific phenotypes.
Collapse
Affiliation(s)
- Naif A M Almontashiri
- Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Faculty of Applied Medical Sciences and the Center for Genetics and Inherited Disorders, Taibah University, Almadinah Almunwarah, Saudi Arabia
| | - Li Zha
- Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Kim Young
- Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Terence Law
- Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Mark D Kellogg
- Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Olaf A Bodamer
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Broad Institute of Harvard University and MIT, Cambridge, Massachusetts, USA
| | - Roy W A Peake
- Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.
| |
Collapse
|
93
|
Stenton SL, Prokisch H. Genetics of mitochondrial diseases: Identifying mutations to help diagnosis. EBioMedicine 2020; 56:102784. [PMID: 32454403 PMCID: PMC7248429 DOI: 10.1016/j.ebiom.2020.102784] [Citation(s) in RCA: 131] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/21/2020] [Accepted: 04/22/2020] [Indexed: 12/15/2022] Open
Abstract
Mitochondrial diseases are amongst the most genetically and phenotypically diverse groups of inherited diseases. The vast phenotypic overlap with other disease entities together with the absence of reliable biomarkers act as driving forces for the integration of unbiased methodologies early in the diagnostic algorithm, such as whole exome sequencing (WES) and whole genome sequencing (WGS). Such approaches are used in variant discovery and in combination with high-throughput functional assays such as transcriptomics in simultaneous variant discovery and validation. By capturing all genes, they not only increase the diagnostic rate in heterogenous mitochondrial disease patients, but accelerate novel disease gene discovery, and are valuable in side-stepping the risk of overlooking unexpected or even treatable genetic disease diagnoses.
Collapse
Affiliation(s)
- Sarah L Stenton
- Institut für Humangenetik, Klinikum rechts der Isar, Technische Universität München, Trogerstraße 32, 81675 München, Germany; Institute of Neurogenomics, Helmholtz Zentrum München, Ingolstaedter Landstraße 1, D-85764 Neuherberg, Germany
| | - Holger Prokisch
- Institut für Humangenetik, Klinikum rechts der Isar, Technische Universität München, Trogerstraße 32, 81675 München, Germany; Institute of Neurogenomics, Helmholtz Zentrum München, Ingolstaedter Landstraße 1, D-85764 Neuherberg, Germany.
| |
Collapse
|
94
|
Kerkhofs MHPM, Haijes HA, Willemsen AM, van Gassen KLI, van der Ham M, Gerrits J, de Sain-van der Velden MGM, Prinsen HCMT, van Deutekom HWM, van Hasselt PM, Verhoeven-Duif NM, Jans JJM. Cross-Omics: Integrating Genomics with Metabolomics in Clinical Diagnostics. Metabolites 2020; 10:metabo10050206. [PMID: 32443577 PMCID: PMC7281020 DOI: 10.3390/metabo10050206] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/03/2020] [Accepted: 05/15/2020] [Indexed: 11/16/2022] Open
Abstract
Next-generation sequencing and next-generation metabolic screening are, independently, increasingly applied in clinical diagnostics of inborn errors of metabolism (IEM). Integrated into a single bioinformatic method, these two –omics technologies can potentially further improve the diagnostic yield for IEM. Here, we present cross-omics: a method that uses untargeted metabolomics results of patient’s dried blood spots (DBSs), indicated by Z-scores and mapped onto human metabolic pathways, to prioritize potentially affected genes. We demonstrate the optimization of three parameters: (1) maximum distance to the primary reaction of the affected protein, (2) an extension stringency threshold reflecting in how many reactions a metabolite can participate, to be able to extend the metabolite set associated with a certain gene, and (3) a biochemical stringency threshold reflecting paired Z-score thresholds for untargeted metabolomics results. Patients with known IEMs were included. We performed untargeted metabolomics on 168 DBSs of 97 patients with 46 different disease-causing genes, and we simulated their whole-exome sequencing results in silico. We showed that for accurate prioritization of disease-causing genes in IEM, it is essential to take into account not only the primary reaction of the affected protein but a larger network of potentially affected metabolites, multiple steps away from the primary reaction.
Collapse
Affiliation(s)
- Marten H. P. M. Kerkhofs
- Section Metabolic Diagnostics, Department of Genetics, University Medical Centre Utrecht, Utrecht University, Lundlaan 6, 3584 EA Utrecht, The Netherlands; (M.H.P.M.K.); (H.A.H.); (A.M.W.); (M.v.d.H.); (J.G.); (M.G.M.d.S.-v.d.V.); (H.C.M.T.P.); (N.M.V.-D.)
| | - Hanneke A. Haijes
- Section Metabolic Diagnostics, Department of Genetics, University Medical Centre Utrecht, Utrecht University, Lundlaan 6, 3584 EA Utrecht, The Netherlands; (M.H.P.M.K.); (H.A.H.); (A.M.W.); (M.v.d.H.); (J.G.); (M.G.M.d.S.-v.d.V.); (H.C.M.T.P.); (N.M.V.-D.)
- Section Metabolic Diseases, Department of Child Health, Wilhelmina Children’s Hospital, University Medical Centre Utrecht, Utrecht University, Lundlaan 6, 3584 EA Utrecht, The Netherlands;
| | - A. Marcel Willemsen
- Section Metabolic Diagnostics, Department of Genetics, University Medical Centre Utrecht, Utrecht University, Lundlaan 6, 3584 EA Utrecht, The Netherlands; (M.H.P.M.K.); (H.A.H.); (A.M.W.); (M.v.d.H.); (J.G.); (M.G.M.d.S.-v.d.V.); (H.C.M.T.P.); (N.M.V.-D.)
| | - Koen L. I. van Gassen
- Section Genomic Diagnostics, Department of Genetics, University Medical Centre Utrecht, Utrecht University, Lundlaan 6, 3584 EA Utrecht, The Netherlands; (K.L.I.v.G.); (H.W.M.v.D.)
| | - Maria van der Ham
- Section Metabolic Diagnostics, Department of Genetics, University Medical Centre Utrecht, Utrecht University, Lundlaan 6, 3584 EA Utrecht, The Netherlands; (M.H.P.M.K.); (H.A.H.); (A.M.W.); (M.v.d.H.); (J.G.); (M.G.M.d.S.-v.d.V.); (H.C.M.T.P.); (N.M.V.-D.)
| | - Johan Gerrits
- Section Metabolic Diagnostics, Department of Genetics, University Medical Centre Utrecht, Utrecht University, Lundlaan 6, 3584 EA Utrecht, The Netherlands; (M.H.P.M.K.); (H.A.H.); (A.M.W.); (M.v.d.H.); (J.G.); (M.G.M.d.S.-v.d.V.); (H.C.M.T.P.); (N.M.V.-D.)
| | - Monique G. M. de Sain-van der Velden
- Section Metabolic Diagnostics, Department of Genetics, University Medical Centre Utrecht, Utrecht University, Lundlaan 6, 3584 EA Utrecht, The Netherlands; (M.H.P.M.K.); (H.A.H.); (A.M.W.); (M.v.d.H.); (J.G.); (M.G.M.d.S.-v.d.V.); (H.C.M.T.P.); (N.M.V.-D.)
| | - Hubertus C. M. T. Prinsen
- Section Metabolic Diagnostics, Department of Genetics, University Medical Centre Utrecht, Utrecht University, Lundlaan 6, 3584 EA Utrecht, The Netherlands; (M.H.P.M.K.); (H.A.H.); (A.M.W.); (M.v.d.H.); (J.G.); (M.G.M.d.S.-v.d.V.); (H.C.M.T.P.); (N.M.V.-D.)
| | - Hanneke W. M. van Deutekom
- Section Genomic Diagnostics, Department of Genetics, University Medical Centre Utrecht, Utrecht University, Lundlaan 6, 3584 EA Utrecht, The Netherlands; (K.L.I.v.G.); (H.W.M.v.D.)
| | - Peter M. van Hasselt
- Section Metabolic Diseases, Department of Child Health, Wilhelmina Children’s Hospital, University Medical Centre Utrecht, Utrecht University, Lundlaan 6, 3584 EA Utrecht, The Netherlands;
| | - Nanda M. Verhoeven-Duif
- Section Metabolic Diagnostics, Department of Genetics, University Medical Centre Utrecht, Utrecht University, Lundlaan 6, 3584 EA Utrecht, The Netherlands; (M.H.P.M.K.); (H.A.H.); (A.M.W.); (M.v.d.H.); (J.G.); (M.G.M.d.S.-v.d.V.); (H.C.M.T.P.); (N.M.V.-D.)
| | - Judith J. M. Jans
- Section Metabolic Diagnostics, Department of Genetics, University Medical Centre Utrecht, Utrecht University, Lundlaan 6, 3584 EA Utrecht, The Netherlands; (M.H.P.M.K.); (H.A.H.); (A.M.W.); (M.v.d.H.); (J.G.); (M.G.M.d.S.-v.d.V.); (H.C.M.T.P.); (N.M.V.-D.)
- Correspondence:
| |
Collapse
|
95
|
Metabolic profiling by reversed-phase/ion-exchange mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2020; 1143:122072. [PMID: 32220802 DOI: 10.1016/j.jchromb.2020.122072] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 03/06/2020] [Accepted: 03/15/2020] [Indexed: 01/22/2023]
Abstract
Metabolic profiling is commonly achieved by mass spectrometry (MS) following reversed-phase (RP) and hydrophilic interaction chromatography (HILIC) either performed independently, leading to overlapping datasets, or in a coupled configuration, requiring multiple liquid chromatography (LC) systems. To overcome these limitations, we developed a single, 20-minute chromatographic method using an in-line RP-ion-exchange (IEX) column arrangement and a single LC system. This configuration separates clinically significant polar and non-polar compounds without derivatization or ion-pairing reagents, allowing ionization in both polarities. An in-house library was created with 397 authentic standards, including acylcarnitines, amino acids, bile acids, nucleosides, organic acids, steroid hormones, and vitamins. Analysis of pooled plasma and urine samples revealed 5445 and 4111 ion features, leading to 88 and 82 confirmed metabolite identifications, respectively. Metabolites were detected at clinically relevant concentrations with good precision, and good chromatographic separation was demonstrated for clinically significant isomers including methylmalonic acid and succinic acid, as well as alloisoleucine and isoleucine/leucine. Evaluation of the samples by unsupervised principal component analysis showed excellent analytical quality.
Collapse
|
96
|
Knottnerus SJG, Pras-Raves ML, van der Ham M, Ferdinandusse S, Houtkooper RH, Schielen PCJI, Visser G, Wijburg FA, de Sain-van der Velden MGM. Prediction of VLCAD deficiency phenotype by a metabolic fingerprint in newborn screening bloodspots. Biochim Biophys Acta Mol Basis Dis 2020; 1866:165725. [PMID: 32061778 DOI: 10.1016/j.bbadis.2020.165725] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 01/20/2020] [Accepted: 02/10/2020] [Indexed: 02/09/2023]
Abstract
PURPOSE Newborns who test positive for very long-chain acyl-CoA dehydrogenase deficiency (VLCADD) in newborn screening may have a severe phenotype with early onset of life-threatening symptoms but may also have an attenuated phenotype and never become symptomatic. The objective of this study is to investigate whether metabolomic profiles in dried bloodspots (DBS) of newborns allow early phenotypic prediction, permitting tailored treatment and follow-up. METHODS A metabolic fingerprint was generated by direct infusion high resolution mass spectrometry in DBS of VLCADD patients (n = 15) and matched controls. Multivariate analysis of the metabolomic profiles was applied to differentiate subgroups. RESULTS Concentration of six acylcarnitine species differed significantly between patients and controls. The concentration of C18:2- and C20:0-carnitine, 13,14-dihydroretinol and deoxycytidine monophosphate allowed separation between mild and severe patients. Two patients who could not be prognosticated on early clinical symptoms, were correctly fitted for severity in the score plot based on the untargeted metabolomics. CONCLUSION Distinctive metabolomic profiles in DBS of newborns with VLCADD may allow phenotypic prognostication. The full potential of this approach as well as the underlying biochemical mechanisms need further investigation.
Collapse
Affiliation(s)
- Suzan J G Knottnerus
- Section Metabolic Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Lundlaan 6, 3584 EA, Utrecht, The Netherlands; Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam Cardiovascular Sciences, Amsterdam Gastroenterology and Metabolism, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Mia L Pras-Raves
- Section Metabolic Diagnostics, Department of Genetics, University Medical Center Utrecht, Utrecht University, Lundlaan 6, 3584 EA Utrecht, The Netherlands; Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam Cardiovascular Sciences, Amsterdam Gastroenterology and Metabolism, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Maria van der Ham
- Section Metabolic Diagnostics, Department of Genetics, University Medical Center Utrecht, Utrecht University, Lundlaan 6, 3584 EA Utrecht, The Netherlands
| | - Sacha Ferdinandusse
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam Cardiovascular Sciences, Amsterdam Gastroenterology and Metabolism, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Riekelt H Houtkooper
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam Cardiovascular Sciences, Amsterdam Gastroenterology and Metabolism, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Peter C J I Schielen
- Reference Laboratory for Neonatal Screening, Center for Health Protection, National Institute for Public Health and Environment (RIVM), The Netherlands
| | - Gepke Visser
- Section Metabolic Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Lundlaan 6, 3584 EA, Utrecht, The Netherlands
| | - Frits A Wijburg
- Section Metabolic Diseases, Emma's Children's Hospital, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Monique G M de Sain-van der Velden
- Section Metabolic Diagnostics, Department of Genetics, University Medical Center Utrecht, Utrecht University, Lundlaan 6, 3584 EA Utrecht, The Netherlands.
| |
Collapse
|
97
|
Mordaunt D, Cox D, Fuller M. Metabolomics to Improve the Diagnostic Efficiency of Inborn Errors of Metabolism. Int J Mol Sci 2020; 21:ijms21041195. [PMID: 32054038 PMCID: PMC7072749 DOI: 10.3390/ijms21041195] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 02/08/2020] [Accepted: 02/09/2020] [Indexed: 12/21/2022] Open
Abstract
Early diagnosis of inborn errors of metabolism (IEM)—a large group of congenital disorders—is critical, given that many respond well to targeted therapy. Newborn screening programs successfully capture a proportion of patients enabling early recognition and prompt initiation of therapy. For others, the heterogeneity in clinical presentation often confuses diagnosis with more common conditions. In the absence of family history and following clinical suspicion, the laboratory diagnosis typically begins with broad screening tests to circumscribe specialised metabolite and/or enzyme assays to identify the specific IEM. Confirmation of the biochemical diagnosis is usually achieved by identifying pathogenic genetic variants that will also enable cascade testing for family members. Unsurprisingly, this diagnostic trajectory is too often a protracted and lengthy process resulting in delays in diagnosis and, importantly, therapeutic intervention for these rare conditions is also postponed. Implementation of mass spectrometry technologies coupled with the expanding field of metabolomics is changing the landscape of diagnosing IEM as numerous metabolites, as well as enzymes, can now be measured collectively on a single mass spectrometry-based platform. As the biochemical consequences of impaired metabolism continue to be elucidated, the measurement of secondary metabolites common across groups of IEM will facilitate algorithms to further increase the efficiency of diagnosis.
Collapse
Affiliation(s)
- Dylan Mordaunt
- Genetics and Molecular Pathology, SA Pathology at Women’s and Children’s Hospital, 72 King William Road, North Adelaide, SA 5006, Australia; (D.M.); (D.C.)
- School of Medicine, University of Adelaide, Adelaide, SA 5000, Australia
| | - David Cox
- Genetics and Molecular Pathology, SA Pathology at Women’s and Children’s Hospital, 72 King William Road, North Adelaide, SA 5006, Australia; (D.M.); (D.C.)
| | - Maria Fuller
- Genetics and Molecular Pathology, SA Pathology at Women’s and Children’s Hospital, 72 King William Road, North Adelaide, SA 5006, Australia; (D.M.); (D.C.)
- School of Medicine, University of Adelaide, Adelaide, SA 5000, Australia
- Correspondence: ; Tel.: +61-8-8161-6741
| |
Collapse
|
98
|
Haijes HA, van der Ham M, Prinsen HC, Broeks MH, van Hasselt PM, de Sain-van der Velden MG, Verhoeven-Duif NM, Jans JJ. Untargeted Metabolomics for Metabolic Diagnostic Screening with Automated Data Interpretation Using a Knowledge-Based Algorithm. Int J Mol Sci 2020; 21:ijms21030979. [PMID: 32024143 PMCID: PMC7037085 DOI: 10.3390/ijms21030979] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 01/26/2020] [Accepted: 01/29/2020] [Indexed: 11/16/2022] Open
Abstract
Untargeted metabolomics may become a standard approach to address diagnostic requests, but, at present, data interpretation is very labor-intensive. To facilitate its implementation in metabolic diagnostic screening, we developed a method for automated data interpretation that preselects the most likely inborn errors of metabolism (IEM). The input parameters of the knowledge-based algorithm were (1) weight scores assigned to 268 unique metabolites for 119 different IEM based on literature and expert opinion, and (2) metabolite Z-scores and ranks based on direct-infusion high resolution mass spectrometry. The output was a ranked list of differential diagnoses (DD) per sample. The algorithm was first optimized using a training set of 110 dried blood spots (DBS) comprising 23 different IEM and 86 plasma samples comprising 21 different IEM. Further optimization was performed using a set of 96 DBS consisting of 53 different IEM. The diagnostic value was validated in a set of 115 plasma samples, which included 58 different IEM and resulted in the correct diagnosis being included in the DD of 72% of the samples, comprising 44 different IEM. The median length of the DD was 10 IEM, and the correct diagnosis ranked first in 37% of the samples. Here, we demonstrate the accuracy of the diagnostic algorithm in preselecting the most likely IEM, based on the untargeted metabolomics of a single sample. We show, as a proof of principle, that automated data interpretation has the potential to facilitate the implementation of untargeted metabolomics for metabolic diagnostic screening, and we provide suggestions for further optimization of the algorithm to improve diagnostic accuracy.
Collapse
Affiliation(s)
- Hanneke A. Haijes
- Section Metabolic Diagnostics, Department of Genetics, University Medical Centre Utrecht, Utrecht University, Lundlaan 6, 3584 EA Utrecht, The Netherlands
- Section Metabolic Diagnostics, Department of Child Health, Wilhelmina Children’s Hospital, University Medical Centre Utrecht, Utrecht University, Lundlaan 6, 3584 EA Utrecht, The Netherlands
- Correspondence: (H.A.H.); (J.J.M.J.)
| | - Maria van der Ham
- Section Metabolic Diagnostics, Department of Genetics, University Medical Centre Utrecht, Utrecht University, Lundlaan 6, 3584 EA Utrecht, The Netherlands
| | - Hubertus C.M.T. Prinsen
- Section Metabolic Diagnostics, Department of Genetics, University Medical Centre Utrecht, Utrecht University, Lundlaan 6, 3584 EA Utrecht, The Netherlands
| | - Melissa H. Broeks
- Section Metabolic Diagnostics, Department of Genetics, University Medical Centre Utrecht, Utrecht University, Lundlaan 6, 3584 EA Utrecht, The Netherlands
| | - Peter M. van Hasselt
- Section Metabolic Diagnostics, Department of Child Health, Wilhelmina Children’s Hospital, University Medical Centre Utrecht, Utrecht University, Lundlaan 6, 3584 EA Utrecht, The Netherlands
| | - Monique G.M. de Sain-van der Velden
- Section Metabolic Diagnostics, Department of Genetics, University Medical Centre Utrecht, Utrecht University, Lundlaan 6, 3584 EA Utrecht, The Netherlands
| | - Nanda M. Verhoeven-Duif
- Section Metabolic Diagnostics, Department of Genetics, University Medical Centre Utrecht, Utrecht University, Lundlaan 6, 3584 EA Utrecht, The Netherlands
| | - Judith J.M. Jans
- Section Metabolic Diagnostics, Department of Genetics, University Medical Centre Utrecht, Utrecht University, Lundlaan 6, 3584 EA Utrecht, The Netherlands
- Correspondence: (H.A.H.); (J.J.M.J.)
| |
Collapse
|
99
|
Stenton SL, Kremer LS, Kopajtich R, Ludwig C, Prokisch H. The diagnosis of inborn errors of metabolism by an integrative "multi-omics" approach: A perspective encompassing genomics, transcriptomics, and proteomics. J Inherit Metab Dis 2020; 43:25-35. [PMID: 31119744 DOI: 10.1002/jimd.12130] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 05/21/2019] [Accepted: 05/21/2019] [Indexed: 12/12/2022]
Abstract
Given the rapidly decreasing cost and increasing speed and accessibility of massively parallel technologies, the integration of comprehensive genomic, transcriptomic, and proteomic data into a "multi-omics" diagnostic pipeline is within reach. Even though genomic analysis has the capability to reveal all possible perturbations in our genetic code, analysis typically reaches a diagnosis in just 35% of cases, with a diagnostic gap arising due to limitations in prioritization and interpretation of detected variants. Here we review the utility of complementing genetic data with transcriptomic data and give a perspective for the introduction of proteomics into the diagnostic pipeline. Together these methodologies enable comprehensive capture of the functional consequence of variants, unobtainable by the analysis of each methodology in isolation. This facilitates functional annotation and reprioritization of candidate genes and variants-a promising approach to shed light on the underlying molecular cause of a patient's disease, increasing diagnostic rate, and allowing actionability in clinical practice.
Collapse
Affiliation(s)
- Sarah L Stenton
- Institute of Human Genetics, Technische Universität München, München, Germany
- Institute of Human Genetics, Helmholtz Zentrum München, München, Germany
| | - Laura S Kremer
- Institute of Human Genetics, Technische Universität München, München, Germany
- Institute of Human Genetics, Helmholtz Zentrum München, München, Germany
| | - Robert Kopajtich
- Institute of Human Genetics, Technische Universität München, München, Germany
- Institute of Human Genetics, Helmholtz Zentrum München, München, Germany
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technische Universität München, München, Germany
| | - Holger Prokisch
- Institute of Human Genetics, Technische Universität München, München, Germany
- Institute of Human Genetics, Helmholtz Zentrum München, München, Germany
| |
Collapse
|
100
|
Verhoeven A, Giera M, Mayboroda OA. Scientific workflow managers in metabolomics: an overview. Analyst 2020; 145:3801-3808. [DOI: 10.1039/d0an00272k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Metabolomics workflows for data processing reproducibility and accelerated clinical deployment.
Collapse
Affiliation(s)
- Aswin Verhoeven
- Center for Proteomics and Metabolomics
- Leiden University Medical Center
- Leiden
- The Netherlands
| | - Martin Giera
- Center for Proteomics and Metabolomics
- Leiden University Medical Center
- Leiden
- The Netherlands
| | - Oleg A. Mayboroda
- Center for Proteomics and Metabolomics
- Leiden University Medical Center
- Leiden
- The Netherlands
| |
Collapse
|