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Wurth R, Turgeon C, Stander Z, Oglesbee D. An evaluation of untargeted metabolomics methods to characterize inborn errors of metabolism. Mol Genet Metab 2024; 141:108115. [PMID: 38181458 PMCID: PMC10843816 DOI: 10.1016/j.ymgme.2023.108115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/19/2023] [Accepted: 12/12/2023] [Indexed: 01/07/2024]
Abstract
Inborn errors of metabolism (IEMs) encompass a diverse group of disorders that can be difficult to classify due to heterogenous clinical, molecular, and biochemical manifestations. Untargeted metabolomics platforms have become a popular approach to analyze IEM patient samples because of their ability to detect many metabolites at once, accelerating discovery of novel biomarkers, and metabolic mechanisms of disease. However, there are concerns about the reproducibility of untargeted metabolomics research due to the absence of uniform reporting practices, data analyses, and experimental design guidelines. Therefore, we critically evaluated published untargeted metabolomic platforms used to characterize IEMs to summarize the strengths and areas for improvement of this technology as it progresses towards the clinical laboratory. A total of 96 distinct IEMs were collectively evaluated by the included studies. However, most of these IEMs were evaluated by a single untargeted metabolomic method, in a single study, with a limited cohort size (55/96, 57%). The goals of the included studies generally fell into two, often overlapping, categories: detecting known biomarkers from many biochemically distinct IEMs using a single platform, and detecting novel metabolites or metabolic pathways. There was notable diversity in the design of the untargeted metabolomic platforms. Importantly, the majority of studies reported adherence to quality metrics, including the use of quality control samples and internal standards in their experiments, as well as confirmation of at least some of their feature annotations with commercial reference standards. Future applications of untargeted metabolomics platforms to the study of IEMs should move beyond single-subject analyses, and evaluate reproducibility using a prospective, or validation cohort.
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Affiliation(s)
- Rachel Wurth
- Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, 200 1(st) St SW, Rochester, MN 55905, USA
| | - Coleman Turgeon
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 1st St SW, Rochester, MN 55905, USA
| | - Zinandré Stander
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 1st St SW, Rochester, MN 55905, USA
| | - Devin Oglesbee
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 1st St SW, Rochester, MN 55905, USA.
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Willems AP, van der Ham M, Schiebergen-Bronkhorst BGM, van Aalderen M, de Barse MMJ, De Gruyter FE, van Hoek IN, Pras-Raves ML, de Sain-van der Velden MGM, Prinsen HCMT, Verhoeven-Duif NM, Jans JJM. A one-year pilot study comparing direct-infusion high resolution mass spectrometry based untargeted metabolomics to targeted diagnostic screening for inherited metabolic diseases. Front Mol Biosci 2023; 10:1283083. [PMID: 38028537 PMCID: PMC10657655 DOI: 10.3389/fmolb.2023.1283083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023] Open
Abstract
Background: Early diagnosis of inherited metabolic diseases (IMDs) is important because treatment may lead to reduced mortality and improved prognosis. Due to their diversity, it is a challenge to diagnose IMDs in time, effecting an emerging need for a comprehensive test to acquire an overview of metabolite status. Untargeted metabolomics has proven its clinical potential in diagnosing IMDs, but is not yet widely used in genetic metabolic laboratories. Methods: We assessed the potential role of plasma untargeted metabolomics in a clinical diagnostic setting by using direct infusion high resolution mass spectrometry (DI-HRMS) in parallel with traditional targeted metabolite assays. We compared quantitative data and qualitative performance of targeted versus untargeted metabolomics in patients suspected of an IMD (n = 793 samples) referred to our laboratory for 1 year. To compare results of both approaches, the untargeted data was limited to polar metabolites that were analyzed in targeted plasma assays. These include amino acid, (acyl)carnitine and creatine metabolites and are suitable for diagnosing IMDs across many of the disease groups described in the international classification of inherited metabolic disorders (ICIMD). Results: For the majority of metabolites, the concentrations as measured in targeted assays correlated strongly with the semi quantitative Z-scores determined with DI-HRMS. For 64/793 patients, targeted assays showed an abnormal metabolite profile possibly indicative of an IMD. In 55 of these patients, similar aberrations were found with DI-HRMS. The remaining 9 patients showed only marginally increased or decreased metabolite concentrations that, in retrospect, were most likely to be clinically irrelevant. Illustrating its potential, DI-HRMS detected additional patients with aberrant metabolites that were indicative of an IMD not detected by targeted plasma analysis, such as purine and pyrimidine disorders and a carnitine synthesis disorder. Conclusion: This one-year pilot study showed that DI-HRMS untargeted metabolomics can be used as a first-tier approach replacing targeted assays of amino acid, acylcarnitine and creatine metabolites with ample opportunities to expand. Using DI-HRMS untargeted metabolomics as a first-tier will open up possibilities to look for new biomarkers.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Judith J. M. Jans
- Section Metabolic Diagnostics, Department of Genetics, University Medical Center Utrecht, Utrecht, Netherlands
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Edridge A, Namazzi R, Tebulo A, Mfizi A, Deijs M, Koekkoek S, de Wever B, van der Ende A, Umiwana J, de Jong MD, Jans J, Verhoeven-Duif N, Titulaer M, van Karnebeek C, Seydel K, Taylor T, Asiimwe-Kateera B, van der Hoek L, Kabayiza JC, Mallewa M, Idro R, Boele van Hensbroek M, van Woensel JBM. Viral, Bacterial, Metabolic, and Autoimmune Causes of Severe Acute Encephalopathy in Sub-Saharan Africa: A Multicenter Cohort Study. J Pediatr 2023; 258:113360. [PMID: 36828342 DOI: 10.1016/j.jpeds.2023.02.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 02/11/2023] [Accepted: 02/19/2023] [Indexed: 02/24/2023]
Abstract
OBJECTIVES To assess whether viral, bacterial, metabolic, and autoimmune diseases are missed by conventional diagnostics among children with severe acute encephalopathy in sub-Saharan Africa. STUDY DESIGN One hundred thirty-four children (6 months to 18 years) presenting with nontraumatic coma or convulsive status epilepticus to 1 of 4 medical referral centers in Uganda, Malawi, and Rwanda were enrolled between 2015 and 2016. Locally available diagnostic tests could be supplemented in 117 patients by viral, bacterial, and 16s quantitative polymerase chain reaction testing, metagenomics, untargeted metabolomics, and autoimmune immunohistochemistry screening. RESULTS Fourteen (12%) cases of viral encephalopathies, 8 (7%) cases of bacterial central nervous system (CNS) infections, and 4 (4%) cases of inherited metabolic disorders (IMDs) were newly identified by additional diagnostic testing as the most likely cause of encephalopathy. No confirmed cases of autoimmune encephalitis were found. Patients for whom additional diagnostic testing aided causal evaluation (aOR 3.59, 90% CI 1.57-8.36), patients with a viral CNS infection (aOR 7.91, 90% CI 2.49-30.07), and patients with an IMD (aOR 9.10, 90% CI 1.37-110.45) were at increased risk for poor outcome of disease. CONCLUSIONS Viral and bacterial CNS infections and IMDs are prevalent causes of severe acute encephalopathy in children in Uganda, Malawi, and Rwanda that are missed by conventional diagnostics and are associated with poor outcome of disease. Improved diagnostic capacity may increase diagnostic yield and might improve outcome of disease.
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Affiliation(s)
- Arthur Edridge
- Amsterdam Centre for Global Child Health, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands; Department of Medical Microbiology & Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.
| | - Ruth Namazzi
- Department of Paediatrics, Makerere University, Kampala, Uganda
| | - Andrew Tebulo
- Blantyre Malaria Project, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Anan Mfizi
- Department of Paediatrics, University Teaching Hospital of Kigali, Kigali, Rwanda
| | - Martin Deijs
- Department of Medical Microbiology & Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Sylvie Koekkoek
- Department of Medical Microbiology & Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Bob de Wever
- Department of Medical Microbiology & Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Arie van der Ende
- Department of Medical Microbiology & Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Jeanine Umiwana
- Department of Paediatrics, University Teaching Hospital of Kigali, Kigali, Rwanda
| | - Menno D de Jong
- Department of Medical Microbiology & Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Judith Jans
- Laboratory of Metabolic Diseases, UMC Utrecht, Utrecht, The Netherlands
| | | | | | - Clara van Karnebeek
- Departments of Pediatrics and Human Genetics, Emma Center for Personalized Medicine, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Karl Seydel
- Blantyre Malaria Project, Kamuzu University of Health Sciences, Blantyre, Malawi; Department of Osteopathic Medical Specialties, College of Osteopathic Medicine, Michigan State University, East Lansing, MI
| | - Terrie Taylor
- Blantyre Malaria Project, Kamuzu University of Health Sciences, Blantyre, Malawi; Department of Osteopathic Medical Specialties, College of Osteopathic Medicine, Michigan State University, East Lansing, MI
| | | | - Lia van der Hoek
- Department of Medical Microbiology & Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Jean-Claude Kabayiza
- Department of Paediatrics, University Teaching Hospital of Kigali, Kigali, Rwanda
| | - Macpherson Mallewa
- Blantyre Malaria Project, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Richard Idro
- Department of Paediatrics, Makerere University, Kampala, Uganda
| | - Michael Boele van Hensbroek
- Amsterdam Centre for Global Child Health, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Job B M van Woensel
- Amsterdam Centre for Global Child Health, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands; Paediatric Intensive Care Unit, Emma Children's Hospital, Amsterdam UMC, Amsterdam, The Netherlands
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Sun X, Jia Z, Zhang Y, Zhao X, Zhao C, Lu X, Xu G. A Strategy for Uncovering the Serum Metabolome by Direct-Infusion High-Resolution Mass Spectrometry. Metabolites 2023; 13:metabo13030460. [PMID: 36984900 PMCID: PMC10057860 DOI: 10.3390/metabo13030460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 03/18/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
Direct infusion nanoelectrospray high-resolution mass spectrometry (DI-nESI-HRMS) is a promising tool for high-throughput metabolomics analysis. However, metabolite assignment is limited by the inadequate mass accuracy and chemical space of the metabolome database. Here, a serum metabolome characterization method was proposed to make full use of the potential of DI-nESI-HRMS. Different from the widely used database search approach, unambiguous formula assignments were achieved by a reaction network combined with mass accuracy and isotopic patterns filter. To provide enough initial known nodes, an initial network was directly constructed by known metabolite formulas. Then experimental formula candidates were screened by the predefined reaction with the network. The effects of sources and scales of networks on assignment performance were investigated. Further, a scoring rule for filtering unambiguous formula candidates was proposed. The developed approach was validated by a pooled serum sample spiked with reference standards. The coverage and accuracy rates for the spiked standards were 98.9% and 93.6%, respectively. A total of 1958 monoisotopic features were assigned with unique formula candidates for the pooled serum, which is twice more than the database search. Finally, a case study of serum metabolomics in diabetes was carried out using the developed method.
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Affiliation(s)
- Xiaoshan Sun
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, China
| | - Zhen Jia
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, China
- Department of Cell Biology, College of Life Sciences, China Medical University, Shenyang 110122, China
| | - Yuqing Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, China
- Zhang Dayu School of Chemistry, Dalian University of Technology, Dalian 116024, China
| | - Xinjie Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, China
| | - Chunxia Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, China
| | - Xin Lu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, China
| | - Guowang Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, China
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Cossu M, Pintus R, Zaffanello M, Mussap M, Serra F, Marcialis MA, Fanos V. Metabolomic Studies in Inborn Errors of Metabolism: Last Years and Future Perspectives. Metabolites 2023; 13:metabo13030447. [PMID: 36984887 PMCID: PMC10058105 DOI: 10.3390/metabo13030447] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/14/2023] [Accepted: 03/15/2023] [Indexed: 03/30/2023] Open
Abstract
The inborn errors of metabolism (IEMs or Inherited Metabolic Disorders) are a heterogeneous group of diseases caused by a deficit of some specific metabolic pathways. IEMs may present with multiple overlapping symptoms, sometimes difficult delayed diagnosis and postponed therapies. Additionally, many IEMs are not covered in newborn screening and the diagnostic profiling in the metabolic laboratory is indispensable to reach a correct diagnosis. In recent years, Metabolomics helped to obtain a better understanding of pathogenesis and pathophysiology of IEMs, by validating diagnostic biomarkers, discovering new specific metabolic patterns and new IEMs itself. The expansion of Metabolomics in clinical biochemistry and laboratory medicine has brought these approaches in clinical practice as part of newborn screenings, as an exam for differential diagnosis between IEMs, and evaluation of metabolites in follow up as markers of severity or therapies efficacy. Lastly, several research groups are trying to profile metabolomics data in platforms to have a holistic vision of the metabolic, proteomic and genomic pathways of every single patient. In 2018 this team has made a review of literature to understand the value of Metabolomics in IEMs. Our review offers an update on use and perspectives of metabolomics in IEMs, with an overview of the studies available from 2018 to 2022.
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Affiliation(s)
- Marcello Cossu
- School of Pediatrics, University of Cagliari, 09042 Monserrato, Italy
| | - Roberta Pintus
- Department of Surgical Science, University of Cagliari, 09042 Monserrato, Italy
| | - Marco Zaffanello
- Department of Surgical Science, Dentistry, Gynecology and Pediatrics, University of Verona, 37100 Verona, Italy
| | - Michele Mussap
- Laboratory Medicine, Department of Surgical Sciences, University of Cagliari, 09042 Monserrato, Italy
| | - Fabiola Serra
- School of Pediatrics, University of Cagliari, 09042 Monserrato, Italy
| | | | - Vassilios Fanos
- Neonatal Intensive Care Unit, Department of Surgery, University of Cagliari, 09042 Monserrato, Italy
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Tobin NH, Murphy A, Li F, Brummel SS, Taha TE, Saidi F, Owor M, Violari A, Moodley D, Chi B, Goodman KD, Koos B, Aldrovandi GM. Comparison of dried blood spot and plasma sampling for untargeted metabolomics. Metabolomics 2021; 17:62. [PMID: 34164733 PMCID: PMC8340475 DOI: 10.1007/s11306-021-01813-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 06/11/2021] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Untargeted metabolomics holds significant promise for biomarker detection and development. In resource-limited settings, a dried blood spot (DBS)-based platform would offer significant advantages over plasma-based approaches that require a cold supply chain. OBJECTIVES The primary goal of this study was to compare the ability of DBS- and plasma-based assays to characterize maternal metabolites. Utility of the two assays was also assessed in the context of a case-control predictive model in pregnant women living with HIV. METHODS Untargeted metabolomics was performed on archived paired maternal plasma and DBS from n = 79 women enrolled in a large clinical trial. RESULTS A total of 984 named biochemicals were detected across both plasma and DBS samples, of which 627 (63.7%), 260 (26.4%), and 97 (9.9%) were detected in both plasma and DBS, plasma alone, and DBS alone, respectively. Variation attributable to study individual (R2 = 0.54, p < 0.001) exceeded that of the sample type (R2 = 0.21, p < 0.001), suggesting that both plasma and DBS were capable of differentiating individual metabolomic profiles. Log-transformed metabolite abundances were strongly correlated (mean Spearman rho = 0.51) but showed low agreement (mean intraclass correlation of 0.15). However, following standardization, DBS and plasma metabolite profiles were strongly concordant (mean intraclass correlation of 0.52). Random forests classification models for cases versus controls identified distinct feature sets with comparable performance in plasma and DBS (86.5% versus 91.2% mean accuracy, respectively). CONCLUSION Maternal plasma and DBS samples yield distinct metabolite profiles highly predictive of the individual subject. In our case study, classification models showed similar performance albeit with distinct feature sets. Appropriate normalization and standardization methods are critical to leverage data from both sample types. Ultimately, the choice of sample type will likely depend on the compounds of interest as well as logistical demands.
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Affiliation(s)
- Nicole H Tobin
- Division of Infectious Diseases, Department of Pediatrics, David Geffen School of Medicine at the University of California, Los Angeles, California, USA
| | - Aisling Murphy
- Department of Obstetrics and Gynecology, David Geffen School of Medicine at the University of California, Los Angeles, California, USA
| | - Fan Li
- Division of Infectious Diseases, Department of Pediatrics, David Geffen School of Medicine at the University of California, Los Angeles, California, USA
| | - Sean S Brummel
- Center for Biostatistics in AIDS Research, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Taha E Taha
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Friday Saidi
- UNC Project-Malawi, Kamuzu Central Hospital, Lilongwe, Malawi
| | - Maxie Owor
- MU-JHU Research Collaboration (MUJHU CARE LTD) CRS, Kampala, Uganda
| | - Avy Violari
- Perinatal HIV Research Unit, Chris Hani Baragwanath Hospital, Soweto, South Africa
| | - Dhayendre Moodley
- Centre for AIDS Research in South Africa, Durban, South Africa
- Department of Obstetrics and Gynecology, School of Clinical Medicine, University of KwaZulu Natal, Durban, South Africa
| | - Benjamin Chi
- Department of Obstetrics and Gynecology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Brian Koos
- Department of Obstetrics and Gynecology, David Geffen School of Medicine at the University of California, Los Angeles, California, USA
| | - Grace M Aldrovandi
- Division of Infectious Diseases, Department of Pediatrics, David Geffen School of Medicine at the University of California, Los Angeles, California, USA.
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Pautova AK, Khesina ZB, Litvinova TN, Revelsky AI, Beloborodova NV. Metabolic profiling of aromatic compounds in cerebrospinal fluid of neurosurgical patients using microextraction by packed sorbent and liquid-liquid extraction with gas chromatography-mass spectrometry analysis. Biomed Chromatogr 2020; 35:e4969. [PMID: 32845527 DOI: 10.1002/bmc.4969] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 08/17/2020] [Accepted: 08/21/2020] [Indexed: 12/16/2022]
Abstract
A new approach to the quantitative analysis of aromatic metabolites in cerebrospinal fluid samples of neurosurgical patients based on microextraction by packed sorbent coupled with derivatization and GC-MS was developed. Analytical characteristics such as recoveries (40-90%), limit of detection (0.1-0.3 μm) and limit of quantitation (0.4-0.7 μm) values, accuracy (<±20%), precision (<20%) and linear correlations (R2 ≥ 0.99) over a 0.4-10 μm range of concentrations demonstrated that microextraction by packed sorbent provides results for the quantitative analysis of target compounds comparable with those for liquid-liquid extraction. Similar results were achieved using 40 μl of sample for microextraction by packed sorbent instead of 200 μl for liquid-liquid extraction. Benzoic, 3-phenylpropionic, 3-phenyllactic, 4-hydroxybenzoic, 2-(4-hydroxyphenyl)acetic, homovanillic and 3-(4-hydroxyphenyl)lactic acids were found in cerebrospinal fluid samples (n = 138) of neurosurgical patients in lower concentrations than in serum samples (n = 110) of critically ill patients. Analysis of the cerebrospinal fluid and serum samples taken at the same time from neurosurgical patients (n = 5) revealed similar results for patients without infection and multidirectional results for patients with central nervous system infection. Our preliminary results demonstrate the necessity of further evaluating the aromatic compound profile in cerebrospinal fluid for its subsequent verification for potential diagnostic markers.
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Affiliation(s)
- Alisa K Pautova
- Laboratory of Human Metabolism in Critical States, Negovsky Research Institute of General Reanimatology, Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, Moscow, Russia
| | - Zoya B Khesina
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow, Russia
| | - Tatiana N Litvinova
- Laboratory of Human Metabolism in Critical States, Negovsky Research Institute of General Reanimatology, Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, Moscow, Russia
| | - Alexander I Revelsky
- Laboratory of Mass Spectrometry, Chemistry Department, Lomonosov Moscow State University, Moscow, Russia
| | - Natalia V Beloborodova
- Laboratory of Human Metabolism in Critical States, Negovsky Research Institute of General Reanimatology, Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, Moscow, Russia
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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: 10] [Impact Index Per Article: 2.5] [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.
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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
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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.
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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:
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10
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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.
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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.)
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11
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Haijes HA, Willemse EAJ, Gerrits J, van der Flier WM, Teunissen CE, Verhoeven-Duif NM, Jans JJM. Assessing the Pre-Analytical Stability of Small-Molecule Metabolites in Cerebrospinal Fluid Using Direct-Infusion Metabolomics. Metabolites 2019; 9:metabo9100236. [PMID: 31635433 PMCID: PMC6835587 DOI: 10.3390/metabo9100236] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 10/08/2019] [Accepted: 10/17/2019] [Indexed: 01/17/2023] Open
Abstract
Metabolomics studies aiming to find biomarkers frequently make use of historical or multicenter cohorts. These samples often have different pre-analytical conditions that potentially affect metabolite concentrations. We studied the effect of different storage conditions on the stability of small-molecule metabolites in cerebrospinal fluid to aid a reliable interpretation of metabolomics data. Three cerebrospinal fluid pools were prepared from surplus samples from the Amsterdam Dementia Cohort biobank. Aliquoted pools were exposed to different storage conditions to assess the temperature and freeze/thaw stability before final storage at −80 °C: storage up to four months at −20 °C and up to one week at either 5–8 °C or 18–22 °C and exposure to up to seven freeze/thaw cycles. Direct-infusion high-resolution mass spectrometry was performed, resulting in the identification of 1852 m/z peaks. To test the storage stability, principal component analyses, repeated measures analysis of variance, Kruskal–Wallis tests, and fold change analyses were performed, all demonstrating that small-molecule metabolites in the cerebrospinal fluid (CSF) are relatively unaffected by 1–3 freeze/thaw cycles, by storage at −20 °C up to two months, by storage at 5–8 °C for up to 72 h, or by storage at 18–22 °C for up to 8 h. This suggests that these differences do not affect the interpretation of potential small-molecule biomarkers in multicenter or historical cohorts and implies that these cohorts are suitable for biomarker studies.
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Affiliation(s)
- Hanneke A Haijes
- Section Metabolic Diagnostics, Department of Genetics, University Medical Center Utrecht, Utrecht University, Lundlaan 6, 3584 EA Utrecht, The Netherlands.
- Section Metabolic Diseases, Department of Child Health, University Medical Center Utrecht, Utrecht University, Lundlaan 6, 3584 EA Utrecht, The Netherlands.
| | - Eline A J Willemse
- Neurochemistry Laboratory and Biobank, Department of Clinical Chemistry, Amsterdam Neuroscience, Amsterdam University Medical Center, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands.
| | - Johan Gerrits
- Section Metabolic Diagnostics, Department of Genetics, University Medical Center Utrecht, Utrecht University, Lundlaan 6, 3584 EA Utrecht, The Netherlands.
| | - Wiesje M van der Flier
- Alzheimer Center and Department of Neurology, Amsterdam Neuroscience, Amsterdam University Medical Center, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands.
- Department of Epidemiology and Biostatistics, Amsterdam University Medical Center, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands.
| | - Charlotte E Teunissen
- Neurochemistry Laboratory and Biobank, Department of Clinical Chemistry, Amsterdam Neuroscience, Amsterdam University Medical Center, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands.
| | - Nanda M Verhoeven-Duif
- Section Metabolic Diagnostics, Department of Genetics, University Medical Center Utrecht, Utrecht University, Lundlaan 6, 3584 EA Utrecht, The Netherlands.
| | - Judith J M Jans
- Section Metabolic Diagnostics, Department of Genetics, University Medical Center Utrecht, Utrecht University, Lundlaan 6, 3584 EA Utrecht, The Netherlands.
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