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Grooms AJ, Burris BJ, Badu-Tawiah AK. Mass spectrometry for metabolomics analysis: Applications in neonatal and cancer screening. MASS SPECTROMETRY REVIEWS 2024; 43:683-712. [PMID: 36524560 PMCID: PMC10272294 DOI: 10.1002/mas.21826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 11/18/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
Chemical analysis by analytical instrumentation has played a major role in disease diagnosis, which is a necessary step for disease treatment. While the treatment process often targets specific organs or compounds, the diagnostic step can occur through various means, including physical or chemical examination. Chemically, the genome may be evaluated to give information about potential genetic outcomes, the transcriptome to provide information about expression actively occurring, the proteome to offer insight on functions causing metabolite expression, or the metabolome to provide a picture of both past and ongoing physiological function in the body. Mass spectrometry (MS) has been elevated among other analytical instrumentation because it can be used to evaluate all four biological machineries of the body. In addition, MS provides enhanced sensitivity, selectivity, versatility, and speed for rapid turnaround time, qualities that are important for instance in clinical procedures involving the diagnosis of a pediatric patient in intensive care or a cancer patient undergoing surgery. In this review, we provide a summary of the use of MS to evaluate biomarkers for newborn screening and cancer diagnosis. As many reviews have recently appeared focusing on MS methods and instrumentation for metabolite analysis, we sought to describe the biological basis for many metabolomic and additional omics biomarkers used in newborn screening and how tandem MS methods have recently been applied, in comparison to traditional methods. Similar comparison is done for cancer screening, with emphasis on emerging MS approaches that allow biological fluids, tissues, and breath to be analyzed for the presence of diagnostic metabolites yielding insight for treatment options based on the understanding of prior and current physiological functions of the body.
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Affiliation(s)
- Alexander J Grooms
- Department of Chemistry and Biochemistry, The Ohio State University, Ohio, Columbus, USA
| | - Benjamin J Burris
- Department of Chemistry and Biochemistry, The Ohio State University, Ohio, Columbus, USA
| | - Abraham K Badu-Tawiah
- Department of Chemistry and Biochemistry, The Ohio State University, Ohio, Columbus, USA
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2
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Georgiou T, Petrou PP, Malekkou A, Ioannou I, Gavatha M, Skordis N, Nicolaidou P, Savvidou I, Athanasiou E, Ourani S, Papamichael E, Vogazianos M, Dionysiou M, Mavrikiou G, Grafakou O, Tanteles GA, Anastasiadou V, Drousiotou A. Inherited metabolic disorders in Cyprus. Mol Genet Metab Rep 2024; 39:101083. [PMID: 38694234 PMCID: PMC11061750 DOI: 10.1016/j.ymgmr.2024.101083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 05/04/2024] Open
Abstract
Selective screening for inherited metabolic disorders (IMD) began in Cyprus in 1990. Over the last thirty-three years 7388 patients were investigated for IMD and 200 diagnoses were made (diagnostic yield 2.7%). The existence of a single laboratory of Biochemical Genetics for the whole island facilitated the creation of a national registry for IMD. The minimal prevalence of IMD in Cyprus is 53.3 cases per 100,000 live births. The most common group are disorders of amino acid metabolism (41.0%), followed by disorders of carbohydrate metabolism (16.5%), disorders of complex molecule degradation (16.5%), mitochondrial disorders (10.5%) and disorders of vitamin and co-factor metabolism (5.5%). Hyperphenylalaninaemia is the most common IMD (14.0%) followed by galactosaemia (7.0%), glutaric aciduria type I (5.5%) and MSUD (4.0%). Some disorders were found to have a relatively high incidence in specific communities, for example Sandhoff disease among the Cypriot Maronites and GM1 gangliosidosis in one particular area of the island. Other disorders were found to have a relatively higher overall incidence, compared to other Caucasian populations, for example galactosaemia, glutaric aciduria type I and MSUD, while fatty acid oxidation defects, Gaucher disease and classic PKU were found to have a relatively lower incidence. Molecular characterization of selected disorders revealed many novel genetic variants, specific to the Cypriot population.
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Affiliation(s)
- Theodoros Georgiou
- Biochemical Genetics Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Petros P. Petrou
- Biochemical Genetics Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Anna Malekkou
- Biochemical Genetics Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Ioannis Ioannou
- Paediatric Neurology Clinic, Archbishop Makarios III Hospital, Nicosia, Cyprus
| | - Marina Gavatha
- Paediatric Neurology Clinic, Archbishop Makarios III Hospital, Nicosia, Cyprus
| | - Nicos Skordis
- School of Medicine, University of Nicosia, Nicosia, Cyprus
| | - Paola Nicolaidou
- Basic and Clinical Sciences Department, University of Nicosia Medical School, Nicosia, Cyprus
| | - Irini Savvidou
- Clinical Genetics Department, Archbishop Makarios III Hospital, Nicosia, Cyprus
| | - Emilia Athanasiou
- Clinical Genetics Department, Archbishop Makarios III Hospital, Nicosia, Cyprus
| | - Sofia Ourani
- Clinical Genetics Department, Archbishop Makarios III Hospital, Nicosia, Cyprus
| | - Elena Papamichael
- Neonatal Intensive Care Unit, Archbishop Makarios III Hospital, Nicosia, Cyprus
| | - Marios Vogazianos
- Centre for Preventive Paediatrics “Americos Argyriou”, Limassol, Cyprus
| | - Maria Dionysiou
- Biochemical Genetics Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Gabriella Mavrikiou
- Biochemical Genetics Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Olga Grafakou
- Clinical Genetics Department, Archbishop Makarios III Hospital, Nicosia, Cyprus
- Inborn Errors of Metabolism Clinic, Archbishop Makarios III Hospital, Nicosia, Cyprus
| | - George A. Tanteles
- Basic and Clinical Sciences Department, University of Nicosia Medical School, Nicosia, Cyprus
- Clinical Genetics and Genomics Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | | | - Anthi Drousiotou
- Biochemical Genetics Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
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3
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Rodríguez-Pombo L, de Castro-López MJ, Sánchez-Pintos P, Giraldez-Montero JM, Januskaite P, Duran-Piñeiro G, Dolores Bóveda M, Alvarez-Lorenzo C, Basit AW, Goyanes A, Couce ML. Paediatric clinical study of 3D printed personalised medicines for rare metabolic disorders. Int J Pharm 2024; 657:124140. [PMID: 38643809 DOI: 10.1016/j.ijpharm.2024.124140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/17/2024] [Accepted: 04/18/2024] [Indexed: 04/23/2024]
Abstract
Rare diseases are infrequent, but together they affect up to 6-10 % of the world's population, mainly children. Patients require precise doses and strict adherence to avoid metabolic or cardiac failure in some cases, which cannot be addressed in a reliable way using pharmaceutical compounding. 3D printing (3DP) is a disruptive technology that allows the real-time personalization of the dose and the modulation of the dosage form to adapt the medicine to the therapeutic needs of each patient. 3D printed chewable medicines containing amino acids (citrulline, isoleucine, valine, and isoleucine and valine combinations) were prepared in a hospital setting, and the efficacy and acceptability were evaluated in comparison to conventional compounded medicines in six children. The inclusion of new flavours (lemon, vanilla and peach) to obtain more information on patient preferences and the implementation of a mobile app to obtain patient feedback in real-time was also used. The 3D printed medicines controlled amino acid levels within target levels as well as the conventional medicines. The deviation of citrulline levels was narrower and closer within the target concentration with the chewable formulations. According to participants' responses, the chewable formulations were well accepted and can improve adherence and quality of life. For the first time, 3DP enabled two actives to be combined in the same formulation, reducing the number of administrations. This study demonstrated the benefits of preparing 3D printed personalized treatments for children diagnosed with rare metabolic disorders using a novel technology in real clinical practice.
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Affiliation(s)
- Lucía Rodríguez-Pombo
- Departamento de Farmacología, Farmacia y Tecnología Farmacéutica, I+D Farma (GI-1645), Facultad de Farmacia, Materials Institute iMATUS and Health Research Institute of Santiago de Compostela (IDIS), Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - María José de Castro-López
- Servicio de Neonatología, Unidad de Diagnóstico y Tratamiento de Enfermedades Metabólicas Congénitas, Health Research Institute of Santiago de Compostela (IDIS), Hospital Clínico Universitario de Santiago de Compostela, Universidad de Santiago de Compostela, IDIS, RICORS, CIBERER, MetabERN, Spain
| | - Paula Sánchez-Pintos
- Servicio de Neonatología, Unidad de Diagnóstico y Tratamiento de Enfermedades Metabólicas Congénitas, Health Research Institute of Santiago de Compostela (IDIS), Hospital Clínico Universitario de Santiago de Compostela, Universidad de Santiago de Compostela, IDIS, RICORS, CIBERER, MetabERN, Spain
| | - Jose Maria Giraldez-Montero
- Pharmacy Department, Xerencia de Xestión Integrada de Santiago de Compostela, SERGAS, Travesía Choupana s/n, Santiago de Compostela 15706, Spain
| | - Patricija Januskaite
- Department of Pharmaceutics, UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Goretti Duran-Piñeiro
- Pharmacy Department, Xerencia de Xestión Integrada de Santiago de Compostela, SERGAS, Travesía Choupana s/n, Santiago de Compostela 15706, Spain
| | - M Dolores Bóveda
- Servicio de Neonatología, Unidad de Diagnóstico y Tratamiento de Enfermedades Metabólicas Congénitas, Health Research Institute of Santiago de Compostela (IDIS), Hospital Clínico Universitario de Santiago de Compostela, Universidad de Santiago de Compostela, IDIS, RICORS, CIBERER, MetabERN, Spain
| | - Carmen Alvarez-Lorenzo
- Departamento de Farmacología, Farmacia y Tecnología Farmacéutica, I+D Farma (GI-1645), Facultad de Farmacia, Materials Institute iMATUS and Health Research Institute of Santiago de Compostela (IDIS), Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Abdul W Basit
- Department of Pharmaceutics, UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK; FABRX Ltd., Henwood House, Henwood, Ashford, Kent TN24 8DH, UK; FABRX Artificial Intelligence, Carretera de Escairón, 14, Currelos (O Saviñao), CP 27543, Spain
| | - Alvaro Goyanes
- Departamento de Farmacología, Farmacia y Tecnología Farmacéutica, I+D Farma (GI-1645), Facultad de Farmacia, Materials Institute iMATUS and Health Research Institute of Santiago de Compostela (IDIS), Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain; Department of Pharmaceutics, UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK; FABRX Ltd., Henwood House, Henwood, Ashford, Kent TN24 8DH, UK; FABRX Artificial Intelligence, Carretera de Escairón, 14, Currelos (O Saviñao), CP 27543, Spain.
| | - Maria L Couce
- Servicio de Neonatología, Unidad de Diagnóstico y Tratamiento de Enfermedades Metabólicas Congénitas, Health Research Institute of Santiago de Compostela (IDIS), Hospital Clínico Universitario de Santiago de Compostela, Universidad de Santiago de Compostela, IDIS, RICORS, CIBERER, MetabERN, Spain.
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Couce ML, Bóveda MD, Castiñeiras DE, Vázquez-Mosquera ME, Barbosa-Gouveia S, De Castro MJ, Iglesias-Rodríguez AJ, Colón C, Cocho JA, Sánchez P. A newborn Screening Programme for Inborn errors of metabolism in Galicia: 22 years of evaluation and follow-up. Orphanet J Rare Dis 2024; 19:202. [PMID: 38760795 PMCID: PMC11102203 DOI: 10.1186/s13023-024-03204-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 05/05/2024] [Indexed: 05/19/2024] Open
Abstract
BACKGROUND There is a notable lack of harmonisation in newborn screening (NBS) programmes worldwide. The Galician programme for early detection of inborn errors of metabolism (IEM) was one of the first NBS programmes in Europe to incorporate mass spectrometry (July 2000). This programme currently screens for 26 IEMs in dried blood and urine samples collected 24-72 h after birth. RESULTS In its 22-year history, this programme has analysed samples from 440,723 neonates and identified 326 cases of IEM with a prevalence of 1:1351. The most prevalent IEMs were hyperphenylalaninaemia (n = 118), followed by medium chain acyl-CoA dehydrogenase deficiency (MCADD, n = 26), galactosaemia (n = 20), and cystinurias (n = 43). Sixty-one false positives and 18 conditions related to maternal pathologies were detected. Urine samples have been identified as a useful secondary sample to reduce the rate of false positives and identify new defects. There were 5 false negatives. The overall positive value was 84.23%. The fatality rate over a median of 12.1 years of follow-up was 2.76%. The intelligence quotient of patients was normal in 95.7% of cases, and school performance was largely optimal, with pedagogic special needs assistance required in < 10% of cases. Clinical onset of disease preceded diagnosis in 4% of cases. The age at which first NBS report is performed was reduced by 4 days since 2021. CONCLUSIONS This study highlights the benefits of collecting urine samples, reduce NBS reporting time and expanding the number of IEMs included in NBS programmes.
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Affiliation(s)
- María L Couce
- Diagnosis and Treatment of Congenital Metabolic Diseases, University Clinical Hospital of Santiago de Compostela, A Coruña, Spain.
- Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela University, CIBERER, RICORS, MetabERN, A Coruña, Spain.
| | - María-Dolores Bóveda
- Diagnosis and Treatment of Congenital Metabolic Diseases, University Clinical Hospital of Santiago de Compostela, A Coruña, Spain
- Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela University, CIBERER, RICORS, MetabERN, A Coruña, Spain
| | - Daisy E Castiñeiras
- Diagnosis and Treatment of Congenital Metabolic Diseases, University Clinical Hospital of Santiago de Compostela, A Coruña, Spain
- Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela University, CIBERER, RICORS, MetabERN, A Coruña, Spain
| | - María-Eugenia Vázquez-Mosquera
- Diagnosis and Treatment of Congenital Metabolic Diseases, University Clinical Hospital of Santiago de Compostela, A Coruña, Spain
- Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela University, CIBERER, RICORS, MetabERN, A Coruña, Spain
| | - Sofía Barbosa-Gouveia
- Diagnosis and Treatment of Congenital Metabolic Diseases, University Clinical Hospital of Santiago de Compostela, A Coruña, Spain
- Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela University, CIBERER, RICORS, MetabERN, A Coruña, Spain
| | - María-José De Castro
- Diagnosis and Treatment of Congenital Metabolic Diseases, University Clinical Hospital of Santiago de Compostela, A Coruña, Spain
- Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela University, CIBERER, RICORS, MetabERN, A Coruña, Spain
| | - Agustin J Iglesias-Rodríguez
- Diagnosis and Treatment of Congenital Metabolic Diseases, University Clinical Hospital of Santiago de Compostela, A Coruña, Spain
- Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela University, CIBERER, RICORS, MetabERN, A Coruña, Spain
| | - Cristóbal Colón
- Diagnosis and Treatment of Congenital Metabolic Diseases, University Clinical Hospital of Santiago de Compostela, A Coruña, Spain
- Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela University, CIBERER, RICORS, MetabERN, A Coruña, Spain
| | - José A Cocho
- Diagnosis and Treatment of Congenital Metabolic Diseases, University Clinical Hospital of Santiago de Compostela, A Coruña, Spain
- Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela University, CIBERER, RICORS, MetabERN, A Coruña, Spain
| | - Paula Sánchez
- Diagnosis and Treatment of Congenital Metabolic Diseases, University Clinical Hospital of Santiago de Compostela, A Coruña, Spain
- Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela University, CIBERER, RICORS, MetabERN, A Coruña, Spain
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Calame DG, Emrick LT. Functional genomics and small molecules in mitochondrial neurodevelopmental disorders. Neurotherapeutics 2024; 21:e00316. [PMID: 38244259 PMCID: PMC10903096 DOI: 10.1016/j.neurot.2024.e00316] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 12/16/2023] [Accepted: 01/02/2024] [Indexed: 01/22/2024] Open
Abstract
Mitochondria are critical for brain development and homeostasis. Therefore, pathogenic variation in the mitochondrial or nuclear genome which disrupts mitochondrial function frequently results in developmental disorders and neurodegeneration at the organismal level. Large-scale application of genome-wide technologies to individuals with mitochondrial diseases has dramatically accelerated identification of mitochondrial disease-gene associations in humans. Multi-omic and high-throughput studies involving transcriptomics, proteomics, metabolomics, and saturation genome editing are providing deeper insights into the functional consequence of mitochondrial genomic variation. Integration of deep phenotypic and genomic data through allelic series continues to uncover novel mitochondrial functions and permit mitochondrial gene function dissection on an unprecedented scale. Finally, mitochondrial disease-gene associations illuminate disease mechanisms and thereby direct therapeutic strategies involving small molecules and RNA-DNA therapeutics. This review summarizes progress in functional genomics and small molecule therapeutics in mitochondrial neurodevelopmental disorders.
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Affiliation(s)
- Daniel G Calame
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| | - Lisa T Emrick
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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Astarita G, Kelly RS, Lasky-Su J. Metabolomics and lipidomics strategies in modern drug discovery and development. Drug Discov Today 2023; 28:103751. [PMID: 37640150 PMCID: PMC10543515 DOI: 10.1016/j.drudis.2023.103751] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/09/2023] [Accepted: 08/21/2023] [Indexed: 08/31/2023]
Abstract
Metabolomics and lipidomics have an increasingly pivotal role in drug discovery and development. In the context of drug discovery, monitoring changes in the levels or composition of metabolites and lipids relative to genetic variations yields functional insights, bolstering human genetics and (meta)genomic methodologies. This approach also sheds light on potential novel targets for therapeutic intervention. In the context of drug development, metabolite and lipid biomarkers contribute to enhanced success rates, promising a transformative impact on precision medicine. In this review, we deviate from analytical chemist-focused perspectives, offering an overview tailored to drug discovery. We provide introductory insight into state-of-the-art mass spectrometry (MS)-based metabolomics and lipidomics techniques utilized in drug discovery and development, drawing from the collective expertise of our research teams. We comprehensively outline the application of metabolomics and lipidomics in advancing drug discovery and development, spanning fundamental research, target identification, mechanisms of action, and the exploration of biomarkers.
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Affiliation(s)
- Giuseppe Astarita
- Georgetown University, Washington, DC, USA; Arkuda Therapeutics, Watertown, MA, USA.
| | - Rachel S Kelly
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
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Smirnov D, Konstantinovskiy N, Prokisch H. Integrative omics approaches to advance rare disease diagnostics. J Inherit Metab Dis 2023; 46:824-838. [PMID: 37553850 DOI: 10.1002/jimd.12663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/10/2023]
Abstract
Over the past decade high-throughput DNA sequencing approaches, namely whole exome and whole genome sequencing became a standard procedure in Mendelian disease diagnostics. Implementation of these technologies greatly facilitated diagnostics and shifted the analysis paradigm from variant identification to prioritisation and evaluation. The diagnostic rates vary widely depending on the cohort size, heterogeneity and disease and range from around 30% to 50% leaving the majority of patients undiagnosed. Advances in omics technologies and computational analysis provide an opportunity to increase these unfavourable rates by providing evidence for disease-causing variant validation and prioritisation. This review aims to provide an overview of the current application of several omics technologies including RNA-sequencing, proteomics, metabolomics and DNA-methylation profiling for diagnostics of rare genetic diseases in general and inborn errors of metabolism in particular.
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Affiliation(s)
- Dmitrii Smirnov
- School of Medicine, Institute of Human Genetics, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Computational Health Center, Helmholtz Munich, Neuherberg, Germany
| | - Nikita Konstantinovskiy
- School of Medicine, Institute of Human Genetics, Technical University of Munich, Munich, Germany
| | - Holger Prokisch
- School of Medicine, Institute of Human Genetics, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Computational Health Center, Helmholtz Munich, Neuherberg, Germany
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8
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Cannet C, Bayat A, Frauendienst-Egger G, Freisinger P, Spraul M, Himmelreich N, Kockaya M, Ahring K, Godejohann M, MacDonald A, Trefz F. Phenylketonuria (PKU) Urinary Metabolomic Phenotype Is Defined by Genotype and Metabolite Imbalance: Results in 51 Early Treated Patients Using Ex Vivo 1H-NMR Analysis. Molecules 2023; 28:4916. [PMID: 37446577 DOI: 10.3390/molecules28134916] [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: 04/24/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 07/15/2023] Open
Abstract
Phenylketonuria (PKU) is a rare metabolic disorder caused by mutations in the phenylalanine hydroxylase gene. Depending on the severity of the genetic mutation, medical treatment, and patient dietary management, elevated phenylalanine (Phe) may occur in blood and brain tissues. Research has recently shown that high Phe not only impacts the central nervous system, but also other organ systems (e.g., heart and microbiome). This study used ex vivo proton nuclear magnetic resonance (1H-NMR) analysis of urine samples from PKU patients (mean 14.9 ± 9.2 years, n = 51) to identify the impact of elevated blood Phe and PKU treatment on metabolic profiles. Our results found that 24 out of 98 urinary metabolites showed a significant difference (p < 0.05) for PKU patients compared to age-matched healthy controls (n = 51) based on an analysis of urinary metabolome. These altered urinary metabolites were related to Phe metabolism, dysbiosis, creatine synthesis or intake, the tricarboxylic acid (TCA) cycle, end products of nicotinamide-adenine dinucleotide degradation, and metabolites associated with a low Phe diet. There was an excellent correlation between the metabolome and genotype of PKU patients and healthy controls of 96.7% in a confusion matrix model. Metabolomic investigations may contribute to a better understanding of PKU pathophysiology.
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Affiliation(s)
| | - Allan Bayat
- Kennedy Centre, Center for PKU, 2600 Glostrup, Denmark
| | | | - Peter Freisinger
- Department of Pediatrics, School of Medicine, University of Tübingen, 72074 Tübingen, Germany
| | | | | | - Musa Kockaya
- Private Pediatric Practice, 68307 Mannheim, Germany
| | | | | | - Anita MacDonald
- Dietetic Department, Birmingham Children's Hospital, Birmingham B4 6NH, UK
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9
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Dai HD, Qiu F, Jackson K, Fruttiger M, Rizzo WB. Untargeted Metabolomic Analysis of Sjögren-Larsson Syndrome Reveals a Distinctive Pattern of Multiple Disrupted Biochemical Pathways. Metabolites 2023; 13:682. [PMID: 37367841 DOI: 10.3390/metabo13060682] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/13/2023] [Accepted: 05/16/2023] [Indexed: 06/28/2023] Open
Abstract
Sjögren-Larsson syndrome (SLS) is a rare inherited neurocutaneous disease characterized by ichthyosis, spastic diplegia or tetraplegia, intellectual disability and a distinctive retinopathy. SLS is caused by bi-allelic mutations in ALDH3A2, which codes for fatty aldehyde dehydrogenase (FALDH) and results in abnormal lipid metabolism. The biochemical abnormalities in SLS are not completely known, and the pathogenic mechanisms leading to symptoms are still unclear. To search for pathways that are perturbed in SLS, we performed untargeted metabolomic screening in 20 SLS subjects along with age- and sex-matched controls. Of 823 identified metabolites in plasma, 121 (14.7%) quantitatively differed in the overall SLS cohort from controls; 77 metabolites were decreased and 44 increased. Pathway analysis pointed to disrupted metabolism of sphingolipids, sterols, bile acids, glycogen, purines and certain amino acids such as tryptophan, aspartate and phenylalanine. Random forest analysis identified a unique metabolomic profile that had a predictive accuracy of 100% for discriminating SLS from controls. These results provide new insight into the abnormal biochemical pathways that likely contribute to disease in SLS and may constitute a biomarker panel for diagnosis and future therapeutic studies.
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Affiliation(s)
- Hongying Daisy Dai
- Department of Biostatistics, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Fang Qiu
- Department of Biostatistics, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | | | - Marcus Fruttiger
- UCL Institute of Ophthalmology, University College London, London EC1V 9EL, UK
| | - William B Rizzo
- Department of Pediatrics and Child Health Research Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Children's Hospital & Medical Center, Omaha, NE 68114, USA
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10
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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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11
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Chantada-Vázquez MDP, Bravo SB, Barbosa-Gouveia S, Alvarez JV, Couce ML. Proteomics in Inherited Metabolic Disorders. Int J Mol Sci 2022; 23:ijms232314744. [PMID: 36499071 PMCID: PMC9740208 DOI: 10.3390/ijms232314744] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/17/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022] Open
Abstract
Inherited metabolic disorders (IMD) are rare medical conditions caused by genetic defects that interfere with the body's metabolism. The clinical phenotype is highly variable and can present at any age, although it more often manifests in childhood. The number of treatable IMDs has increased in recent years, making early diagnosis and a better understanding of the natural history of the disease more important than ever. In this review, we discuss the main challenges faced in applying proteomics to the study of IMDs, and the key advances achieved in this field using tandem mass spectrometry (MS/MS). This technology enables the analysis of large numbers of proteins in different body fluids (serum, plasma, urine, saliva, tears) with a single analysis of each sample, and can even be applied to dried samples. MS/MS has thus emerged as the tool of choice for proteome characterization and has provided new insights into many diseases and biological systems. In the last 10 years, sequential window acquisition of all theoretical fragmentation spectra mass spectrometry (SWATH-MS) has emerged as an accurate, high-resolution technique for the identification and quantification of proteins differentially expressed between healthy controls and IMD patients. Proteomics is a particularly promising approach to help obtain more information on rare genetic diseases, including identification of biomarkers to aid early diagnosis and better understanding of the underlying pathophysiology to guide the development of new therapies. Here, we summarize new and emerging proteomic technologies and discuss current uses and limitations of this approach to identify and quantify proteins. Moreover, we describe the use of proteomics to identify the mechanisms regulating complex IMD phenotypes; an area of research essential to better understand these rare disorders and many other human diseases.
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Affiliation(s)
- Maria del Pilar Chantada-Vázquez
- Proteomic Platform, Health Research Institute of Santiago de Compostela (IDIS), Hospital Clínico Universitario de Santiago de Compostela, 15706 Santiago de Compostela, Spain
| | - Susana B. Bravo
- Proteomic Platform, Health Research Institute of Santiago de Compostela (IDIS), Hospital Clínico Universitario de Santiago de Compostela, 15706 Santiago de Compostela, Spain
| | - Sofía Barbosa-Gouveia
- Department of Forensic Sciences, Pathology, Gynecology and Obstetrics, Pediatrics, Neonatology Service, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Health Research Institute of Santiago de Compostela (IDIS), CIBERER, MetabERN, 15706 Santiago de Compostela, Spain
| | - José V. Alvarez
- Department of Forensic Sciences, Pathology, Gynecology and Obstetrics, Pediatrics, Neonatology Service, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Health Research Institute of Santiago de Compostela (IDIS), CIBERER, MetabERN, 15706 Santiago de Compostela, Spain
| | - María L. Couce
- Department of Forensic Sciences, Pathology, Gynecology and Obstetrics, Pediatrics, Neonatology Service, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Health Research Institute of Santiago de Compostela (IDIS), CIBERER, MetabERN, 15706 Santiago de Compostela, Spain
- Correspondence: ; Tel.: +349-81-951-100
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12
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Yu M, Xu J, Song X, Du J. Cost-effectiveness analysis of newborn screening by tandem mass spectrometry in Shenzhen, China: value and affordability of new screening technology. BMC Health Serv Res 2022; 22:1039. [PMID: 35971172 PMCID: PMC9376130 DOI: 10.1186/s12913-022-08394-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 07/27/2022] [Indexed: 11/16/2022] Open
Abstract
Background Newborn screening (NBS) can prevent inborn errors of metabolism (IEMs), which may cause long-term disability and even death in newborns. However, in China, tandem mass spectrometry (MS/MS) screening has just started. This study aimed to assess the cost-effectiveness of NBS using MS/MS in Shenzhen under the nationally recommended program, as well as evaluate the value and affordability of introducing this new screening technology. Methods A Markov model was built to estimate the cost and quality-adjusted life-years (QALYs) of different screening programs. We compared PKU screening using traditional immunofluorescence (IF) with the other 11 IEMs not screened and all 12 IEMs screened using MS/MS, and the programs detecting different numbers of IEMs chosen from the national recommended program were also compared. A sensitivity analysis and budget impact analysis (BIA) were performed. Results The incremental cost-effectiveness ratio (ICER) of detecting all 12 IEMs in the national program is 277,823 RMB per QALY, below three times per capita GDP in Shenzhen. MS/MS screening in Shenzhen can be cost-effective only if at least three diseases (PKU, PCD and MMA) are covered and when the screening program covers five diseases (PKU, PCD, MMA, MSUD, IVA), the ICER closely approaches its critical threshold. The BIA indicated the implementation cost of the national program to be around 490 million RMB over 10 years and showed no difference in budget between programs detecting different numbers of IEMs. Conclusions We conclude that the newborn screening using MS/MS in Shenzhen is cost-effective, and the budget affordable for the Shenzhen government. Two concepts for selecting the IEMs to be detected are also presented. One is to choose the most cost-effective screening programs detecting highest number of IEMs to achieve a minimal ICER. The other considers the curability and affordability of the disease as the basis of healthcare decisions to screen suitable IEMs, achieving an ICER under the threshold and close to the minimum value. Supplementary Information The online version contains supplementary material available at 10.1186/s12913-022-08394-4.
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Affiliation(s)
- Mingren Yu
- School of Medicine and Health Management, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, China
| | - Juan Xu
- School of Medicine and Health Management, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, China. .,Hubei Provincial Research Center for Health Technology Assessment, Wuhan, China.
| | - Xiaohong Song
- Department of Family Development and Maternal and Child Health, Shenzhen Municipal Health Commission, Shenzhen, China
| | - Jiayue Du
- Department of Science and Education, the Fourth Affiliated Hospital of School of Medicine, Zhejiang University, Zhejiang, China
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13
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Ford L, Mitchell M, Wulff J, Evans A, Kennedy A, Elsea S, Wittmann B, Toal D. Clinical metabolomics for inborn errors of metabolism. Adv Clin Chem 2022; 107:79-138. [PMID: 35337606 DOI: 10.1016/bs.acc.2021.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Metabolism is a highly regulated process that provides nutrients to cells and essential building blocks for the synthesis of protein, DNA and other macromolecules. In healthy biological systems, metabolism maintains a steady state in which the concentrations of metabolites are relatively constant yet are subject to metabolic demands and environmental stimuli. Rare genetic disorders, such as inborn errors of metabolism (IEM), cause defects in regulatory enzymes or proteins leading to metabolic pathway disruption and metabolite accumulation or deficiency. Traditionally, the laboratory diagnosis of IEMs has been limited to analytical methods that target specific metabolites such as amino acids and acyl carnitines. This approach is effective as a screening method for the most common IEM disorders but lacks the comprehensive coverage of metabolites that is necessary to identify rare disorders that present with nonspecific clinical symptoms. Fortunately, advancements in technology and data analytics has introduced a new field of study called metabolomics which has allowed scientists to perform comprehensive metabolite profiling of biological systems to provide insight into mechanism of action and gene function. Since metabolomics seeks to measure all small molecule metabolites in a biological specimen, it provides an innovative approach to evaluating disease in patients with rare genetic disorders. In this review we provide insight into the appropriate application of metabolomics in clinical settings. We discuss the advantages and limitations of the method and provide details related to the technology, data analytics and statistical modeling required for metabolomic profiling of patients with IEMs.
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Affiliation(s)
- Lisa Ford
- Metabolon, Inc., Morrisville, NC, United States
| | | | - Jacob Wulff
- Metabolon, Inc., Morrisville, NC, United States
| | - Annie Evans
- Metabolon, Inc., Morrisville, NC, United States
| | | | - Sarah Elsea
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | | | - Douglas Toal
- Metabolon, Inc., Morrisville, NC, United States.
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14
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Gonzalez-Covarrubias V, Martínez-Martínez E, del Bosque-Plata L. The Potential of Metabolomics in Biomedical Applications. Metabolites 2022; 12:metabo12020194. [PMID: 35208267 PMCID: PMC8880031 DOI: 10.3390/metabo12020194] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/28/2022] [Accepted: 01/30/2022] [Indexed: 12/12/2022] Open
Abstract
The metabolome offers a dynamic, comprehensive, and precise picture of the phenotype. Current high-throughput technologies have allowed the discovery of relevant metabolites that characterize a wide variety of human phenotypes with respect to health, disease, drug monitoring, and even aging. Metabolomics, parallel to genomics, has led to the discovery of biomarkers and has aided in the understanding of a diversity of molecular mechanisms, highlighting its application in precision medicine. This review focuses on the metabolomics that can be applied to improve human health, as well as its trends and impacts in metabolic and neurodegenerative diseases, cancer, longevity, the exposome, liquid biopsy development, and pharmacometabolomics. The identification of distinct metabolomic profiles will help in the discovery and improvement of clinical strategies to treat human disease. In the years to come, metabolomics will become a tool routinely applied to diagnose and monitor health and disease, aging, or drug development. Biomedical applications of metabolomics can already be foreseen to monitor the progression of metabolic diseases, such as obesity and diabetes, using branched-chain amino acids, acylcarnitines, certain phospholipids, and genomics; these can assess disease severity and predict a potential treatment. Future endeavors should focus on determining the applicability and clinical utility of metabolomic-derived markers and their appropriate implementation in large-scale clinical settings.
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Affiliation(s)
| | - Eduardo Martínez-Martínez
- Laboratory of Cell Communication and Extracellular Vesicles, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico;
| | - Laura del Bosque-Plata
- Laboratory of Nutrigenetics and Nutrigenomics, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico
- Correspondence: ; Tel.: +52-55-53-50-1974
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15
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Anklam E, Bahl MI, Ball R, Beger RD, Cohen J, Fitzpatrick S, Girard P, Halamoda-Kenzaoui B, Hinton D, Hirose A, Hoeveler A, Honma M, Hugas M, Ishida S, Kass GEN, Kojima H, Krefting I, Liachenko S, Liu Y, Masters S, Marx U, McCarthy T, Mercer T, Patri A, Pelaez C, Pirmohamed M, Platz S, Ribeiro AJS, Rodricks JV, Rusyn I, Salek RM, Schoonjans R, Silva P, Svendsen CN, Sumner S, Sung K, Tagle D, Tong L, Tong W, van den Eijnden-van-Raaij J, Vary N, Wang T, Waterton J, Wang M, Wen H, Wishart D, Yuan Y, Slikker Jr. W. Emerging technologies and their impact on regulatory science. Exp Biol Med (Maywood) 2022; 247:1-75. [PMID: 34783606 PMCID: PMC8749227 DOI: 10.1177/15353702211052280] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
There is an evolution and increasing need for the utilization of emerging cellular, molecular and in silico technologies and novel approaches for safety assessment of food, drugs, and personal care products. Convergence of these emerging technologies is also enabling rapid advances and approaches that may impact regulatory decisions and approvals. Although the development of emerging technologies may allow rapid advances in regulatory decision making, there is concern that these new technologies have not been thoroughly evaluated to determine if they are ready for regulatory application, singularly or in combinations. The magnitude of these combined technical advances may outpace the ability to assess fit for purpose and to allow routine application of these new methods for regulatory purposes. There is a need to develop strategies to evaluate the new technologies to determine which ones are ready for regulatory use. The opportunity to apply these potentially faster, more accurate, and cost-effective approaches remains an important goal to facilitate their incorporation into regulatory use. However, without a clear strategy to evaluate emerging technologies rapidly and appropriately, the value of these efforts may go unrecognized or may take longer. It is important for the regulatory science field to keep up with the research in these technically advanced areas and to understand the science behind these new approaches. The regulatory field must understand the critical quality attributes of these novel approaches and learn from each other's experience so that workforces can be trained to prepare for emerging global regulatory challenges. Moreover, it is essential that the regulatory community must work with the technology developers to harness collective capabilities towards developing a strategy for evaluation of these new and novel assessment tools.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Reza M Salek
- International Agency for Research on Cancer, France
| | | | | | | | | | | | | | - Li Tong
- Universities of Georgia Tech and Emory, USA
| | | | | | - Neil Vary
- Canadian Food Inspection Agency, Canada
| | - Tao Wang
- National Medical Products Administration, China
| | | | - May Wang
- Universities of Georgia Tech and Emory, USA
| | - Hairuo Wen
- National Institutes for Food and Drug Control, China
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16
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da Silva Zandonadi F, dos Santos EAF, Marques MS, Sussulini A. Metabolomics: A Powerful Tool to Understand the Schizophrenia Biology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1400:105-119. [DOI: 10.1007/978-3-030-97182-3_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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17
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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.
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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.
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18
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Skogvold H, Sandås EM, Østeby A, Løkken C, Rootwelt H, Rønning PO, Wilson SR, Elgstøen KBP. Bridging the Polar and Hydrophobic Metabolome in Single-Run Untargeted Liquid Chromatography-Mass Spectrometry Dried Blood Spot Metabolomics for Clinical Purposes. J Proteome Res 2021; 20:4010-4021. [PMID: 34296888 PMCID: PMC8397434 DOI: 10.1021/acs.jproteome.1c00326] [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: 04/20/2021] [Indexed: 12/31/2022]
Abstract
Dried blood spot (DBS) metabolite analysis is a central tool for the clinic, e.g., newborn screening. Instead of applying multiple analytical methods, a single liquid chromatography-mass spectrometry (LC-MS) method was developed for metabolites spanning from highly polar glucose to hydrophobic long-chain acylcarnitines. For liquid chromatography, a diphenyl column and a multi-linear solvent gradient operated at elevated flow rates allowed for an even-spread resolution of diverse metabolites. Injecting moderate volumes of DBS organic extracts directly, in contrast to evaporation and reconstitution, provided substantial increases in analyte recovery. Q Exactive MS settings were also tailored for sensitivity increases, and the method allowed for analyte retention time and peak area repeatabilities of 0.1-0.4 and 2-10%, respectively, for a wide polarity range of metabolites (log P -4.4 to 8.8). The method's performance was suited for both untargeted analysis and targeted approaches evaluated in clinically relevant experiments.
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Affiliation(s)
- Hanne
Bendiksen Skogvold
- National
Unit for Screening and Diagnosis of Congenital Pediatric Metabolic
Disorders, Department of Medical Biochemistry, Oslo University Hospital, Rikshospitalet, Sognsvannsveien 20, Oslo 0372, Norway
- Department
of Mechanical, Electronic and Chemical Engineering, Faculty of Technology,
Art and Design, Oslo Metropolitan University, Pilestredet 35, Oslo 0166, Norway
| | - Elise Mørk Sandås
- National
Unit for Screening and Diagnosis of Congenital Pediatric Metabolic
Disorders, Department of Medical Biochemistry, Oslo University Hospital, Rikshospitalet, Sognsvannsveien 20, Oslo 0372, Norway
| | - Anja Østeby
- National
Unit for Screening and Diagnosis of Congenital Pediatric Metabolic
Disorders, Department of Medical Biochemistry, Oslo University Hospital, Rikshospitalet, Sognsvannsveien 20, Oslo 0372, Norway
| | - Camilla Løkken
- National
Unit for Screening and Diagnosis of Congenital Pediatric Metabolic
Disorders, Department of Medical Biochemistry, Oslo University Hospital, Rikshospitalet, Sognsvannsveien 20, Oslo 0372, Norway
| | - Helge Rootwelt
- Department
of Medical Biochemistry, Oslo University
Hospital, Rikshospitalet, Sognsvannsveien 20, Oslo 0372, Norway
| | - Per Ola Rønning
- Department
of Mechanical, Electronic and Chemical Engineering, Faculty of Technology,
Art and Design, Oslo Metropolitan University, Pilestredet 35, Oslo 0166, Norway
| | - Steven Ray Wilson
- Department
of Chemistry, University of Oslo, Sem Sælands vei 26, Oslo 0371, Norway
- Hybrid
Technology Hub-Centre of Excellence, Institute of Basic Medical Sciences,
Faculty of Medicine, University of Oslo, Domus Medica, Gaustad, Sognsvannsveien
9, Oslo 0372, Norway
| | - Katja Benedikte Prestø Elgstøen
- National
Unit for Screening and Diagnosis of Congenital Pediatric Metabolic
Disorders, Department of Medical Biochemistry, Oslo University Hospital, Rikshospitalet, Sognsvannsveien 20, Oslo 0372, Norway
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19
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Bourdin-Pintueles A, Galineau L, Nadal-Desbarats L, Dupuy C, Bodard S, Busson J, Lefèvre A, Emond P, Mavel S. Maternal Rat Metabolomics: Amniotic Fluid and Placental Metabolic Profiling Workflows. J Proteome Res 2021; 20:3853-3864. [PMID: 34282913 DOI: 10.1021/acs.jproteome.1c00145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Studying the metabolome of specific gestational compartments is of growing interest in the context of fetus developmental disorders. However, the metabolomes of the placenta and amniotic fluid (AF) are poorly characterized. Therefore, we present the validation of a fingerprinting methodology. Using pregnant rats, we performed exhaustive and robust extractions of metabolites in the AF and lipids and more polar metabolites in the placenta. For the AF, we compared the extraction capabilities of methanol (MeOH), acetonitrile (ACN), and a mixture of both. For the placenta, we compared (i) the extraction capabilities of dichloromethane, methyl t-butyl ether (MTBE), and butanol, along with (ii) the impact of lyophilization of the placental tissue. Analyses were performed on a C18 and hydrophilic interaction liquid chromatography combined with high-resolution mass spectrometry. The efficiency and the robustness of the extractions were compared based on the number of the features or metabolites (for untargeted or targeted approach, respectively), their mean total intensity, and their coefficient of variation (% CV). The extraction capabilities of MeOH and ACN on the AF metabolome were equivalent. Lyophilization also had no significant impact and usefulness on the placental tissue metabolome profiling. Considering the placental lipidome, MTBE extraction was more informative because it allowed extraction of a slightly higher number of lipids, in higher concentration. This proof-of-concept study assessing the metabolomics and lipidomics of the AF and the placenta revealed changes in both metabolisms, at two different stages of rat gestation, and allowed a detailed prenatal metabolic fingerprinting.
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Affiliation(s)
| | - Laurent Galineau
- UMR 1253 iBrain, Université de Tours, Inserm, Tours 37000, France
| | | | - Camille Dupuy
- UMR 1253 iBrain, Université de Tours, Inserm, Tours 37000, France
| | - Sylvie Bodard
- UMR 1253 iBrain, Université de Tours, Inserm, Tours 37000, France
| | - Julie Busson
- UMR 1253 iBrain, Université de Tours, Inserm, Tours 37000, France
| | - Antoine Lefèvre
- UMR 1253 iBrain, Université de Tours, Inserm, Tours 37000, France
| | - Patrick Emond
- UMR 1253 iBrain, Université de Tours, Inserm, Tours 37000, France.,CHRU de Tours, Service de Médecine Nucléaire In Vitro, Tours 37000, France
| | - Sylvie Mavel
- UMR 1253 iBrain, Université de Tours, Inserm, Tours 37000, France
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20
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Graw S, Chappell K, Washam CL, Gies A, Bird J, Robeson MS, Byrum SD. Multi-omics data integration considerations and study design for biological systems and disease. Mol Omics 2021; 17:170-185. [PMID: 33347526 PMCID: PMC8058243 DOI: 10.1039/d0mo00041h] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
With the advancement of next-generation sequencing and mass spectrometry, there is a growing need for the ability to merge biological features in order to study a system as a whole. Features such as the transcriptome, methylome, proteome, histone post-translational modifications and the microbiome all influence the host response to various diseases and cancers. Each of these platforms have technological limitations due to sample preparation steps, amount of material needed for sequencing, and sequencing depth requirements. These features provide a snapshot of one level of regulation in a system. The obvious next step is to integrate this information and learn how genes, proteins, and/or epigenetic factors influence the phenotype of a disease in context of the system. In recent years, there has been a push for the development of data integration methods. Each method specifically integrates a subset of omics data using approaches such as conceptual integration, statistical integration, model-based integration, networks, and pathway data integration. In this review, we discuss considerations of the study design for each data feature, the limitations in gene and protein abundance and their rate of expression, the current data integration methods, and microbiome influences on gene and protein expression. The considerations discussed in this review should be regarded when developing new algorithms for integrating multi-omics data.
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Affiliation(s)
- Stefan Graw
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (slot 516), Little Rock, AR 72205-7199, USA.
| | - Kevin Chappell
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (slot 516), Little Rock, AR 72205-7199, USA.
| | - Charity L Washam
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (slot 516), Little Rock, AR 72205-7199, USA. and Arkansas Children's Research Institute, 13 Children's Way, Little Rock, AR 72202, USA
| | - Allen Gies
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (slot 516), Little Rock, AR 72205-7199, USA.
| | - Jordan Bird
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (slot 516), Little Rock, AR 72205-7199, USA.
| | - Michael S Robeson
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
| | - Stephanie D Byrum
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (slot 516), Little Rock, AR 72205-7199, USA. and Arkansas Children's Research Institute, 13 Children's Way, Little Rock, AR 72202, USA
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21
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Mussap M, Noto A, Piras C, Atzori L, Fanos V. Slotting metabolomics into routine precision medicine. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2021. [DOI: 10.1080/23808993.2021.1911639] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Michele Mussap
- Department of Surgical Science, University of Cagliari, Monserrato, Italy
| | - Antonio Noto
- Department of Medical Sciences and Public Health, University of Cagliari, Monserrato, Italy
| | - Cristina Piras
- Department of Surgical Science, University of Cagliari, Monserrato, Italy
- Department of Biomedical Sciences, University of Cagliari, Monserrato, Italy
| | - Luigi Atzori
- Department of Biomedical Sciences, University of Cagliari, Monserrato, Italy
| | - Vassilios Fanos
- Department of Surgical Science, University of Cagliari, Monserrato, Italy
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22
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Altamimi E, Khanfar M, Rabab'h O, Dardas Z, Srour L, Mustafa L, Azab B. Effect of Genetic Testing on Diagnosing Gastrointestinal Pediatric Patients with Previously Undiagnosed Diseases. APPLICATION OF CLINICAL GENETICS 2020; 13:221-231. [PMID: 33364809 PMCID: PMC7751587 DOI: 10.2147/tacg.s275992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 11/10/2020] [Indexed: 11/23/2022]
Abstract
Purpose Four consanguineous Jordanian families with affected members of unknown gastrointestinal related diseases were recruited to assess the utility and efficiency of whole exome sequencing (WES) in reaching the definitive diagnosis. Patients and Methods Members from four consanguineous Jordanian families were recruited in this study. Laboratory and imaging tests were used for initial diagnosis, followed by performing WES to test all affected members for the detection of causative variants. Sanger sequencing was used for validation. Results We had a 100% success rate identifying each case presented in this study. Conclusion This is the first study applying a WES testing approach in the diagnosis of pediatric diseases in Jordan. Our results strongly suggest the need to implement WES as an evident diagnostic tool in the clinical setting, as it will subsequently allow for proper disease management and genetic counseling.
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Affiliation(s)
- Eyad Altamimi
- Department of Pediatrics and Neonatology, Jordan University of Science and Technology, Irbid, Jordan
| | - Mariam Khanfar
- Department of Medical Laboratory Sciences, Jordan University of Science and Technology, Irbid, Jordan
| | - Omar Rabab'h
- Center of Cognition and Neuroethics, University of Michigan-Flint, Flint, MI, USA
| | - Zain Dardas
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, University of Jordan, Amman, Jordan.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Luma Srour
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, University of Jordan, Amman, Jordan
| | - Lina Mustafa
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, University of Jordan, Amman, Jordan
| | - Bilal Azab
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, University of Jordan, Amman, Jordan.,Human and Molecular Genetics, Medical College of Virginia, Virginia Commonwealth University, Richmond, VA, USA
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van der Laan T, Dubbelman AC, Duisters K, Kindt A, Harms AC, Hankemeier T. High-Throughput Fractionation Coupled to Mass Spectrometry for Improved Quantitation in Metabolomics. Anal Chem 2020; 92:14330-14338. [PMID: 33054161 PMCID: PMC7871441 DOI: 10.1021/acs.analchem.0c01375] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
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Metabolomics is emerging as an important field in life sciences. However, a weakness of
current mass spectrometry (MS) based metabolomics platforms is the time-consuming
analysis and the occurrence of severe matrix effects in complex mixtures. To overcome
this problem, we have developed an automated and fast fractionation module coupled
online to MS. The fractionation is realized by the implementation of three consecutive
high performance solid-phase extraction columns consisting of a reversed phase,
mixed-mode anion exchange, and mixed-mode cation exchange sorbent chemistry. The
different chemistries resulted in an efficient interaction with a wide range of
metabolites based on polarity, charge, and allocation of important matrix interferences
like salts and phospholipids. The use of short columns and direct solvent switches
allowed for fast screening (3 min per polarity). In total, 50 commonly reported
diagnostic or explorative biomarkers were validated with a limit of quantification that
was comparable with conventional LC–MS(/MS). In comparison with a flow injection
analysis without fractionation, ion suppression decreased from 89% to 25%, and the
sensitivity was 21 times higher. The validated method was used to investigate the
effects of circadian rhythm and food intake on several metabolite classes. The
significant diurnal changes that were observed stress the importance of standardized
sampling times and fasting states when metabolite biomarkers are used. Our method
demonstrates a fast approach for global profiling of the metabolome. This brings
metabolomics one step closer to implementation into the clinic.
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Affiliation(s)
- Tom van der Laan
- Analytical Biosciences and Metabolomics, Division of Systems Biomedicine and Pharmacology, Leiden Academic Center for Drug Research, Leiden University, Leiden 2333 CC, The Netherlands
| | - Anne-Charlotte Dubbelman
- Analytical Biosciences and Metabolomics, Division of Systems Biomedicine and Pharmacology, Leiden Academic Center for Drug Research, Leiden University, Leiden 2333 CC, The Netherlands
| | - Kevin Duisters
- Mathematical Institute, Leiden University, Leiden 2333 CA, The Netherlands
| | - Alida Kindt
- Analytical Biosciences and Metabolomics, Division of Systems Biomedicine and Pharmacology, Leiden Academic Center for Drug Research, Leiden University, Leiden 2333 CC, The Netherlands
| | - Amy C Harms
- Analytical Biosciences and Metabolomics, Division of Systems Biomedicine and Pharmacology, Leiden Academic Center for Drug Research, Leiden University, Leiden 2333 CC, The Netherlands
| | - Thomas Hankemeier
- Analytical Biosciences and Metabolomics, Division of Systems Biomedicine and Pharmacology, Leiden Academic Center for Drug Research, Leiden University, Leiden 2333 CC, The Netherlands
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24
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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.
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High resolution mass spectrometry newborn screening applications for quantitative analysis of amino acids and acylcarnitines from dried blood spots. Anal Chim Acta 2020; 1120:85-96. [PMID: 32475395 PMCID: PMC10046147 DOI: 10.1016/j.aca.2020.04.067] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 04/09/2020] [Accepted: 04/27/2020] [Indexed: 01/03/2023]
Abstract
Amino acid and acylcarnitine first-tier newborn screening typically employs derivatized or non-derivatized sample preparation methods followed by FIA coupled to triple quadrupole (TQ) MS/MS. The low resolving power of TQ instruments results in difficulties distinguishing nominal isobaric metabolites, especially those with identical quantifying product ions such as malonylcarnitine (C3DC) and 4-hydroxybutylcarnitine (C4OH). Twenty-eight amino acids and acylcarnitines extracted from dried blood spots (DBS) were analyzed by direct injection (DI)-HRMS on a Q-Exactive Plus across available mass resolving powers in SIM, in PRM at 17,000 full width at half maximum (FWHM), and a developed SIM/PRM hybrid MS method. Most notably, quantitation of C3DC and C4OH was successful by HRMS in non-derivatized samples, thus, potentially eliminating sample derivatization requirements. Quantitation differed between SIM and PRM acquired data for several metabolites, and it was determined these quantitative differences were due to collision energy differences or kinetic isotope effects between the unlabeled metabolites and the corresponding labeled isotopologue internal standards. Overall quantitative data acquired by HRMS were similar to data acquired on TQ MS/MS platform. A proof-of-concept hybrid DI-HRMS and SIM/PRM/FullScan method was developed demonstrating the ability to hybridize targeted newborn screening with metabolomic screening.
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26
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Klinke G, Richter S, Monostori P, Schmidt-Mader B, García-Cazorla A, Artuch R, Christ S, Opladen T, Hoffmann GF, Blau N, Okun JG. Targeted cerebrospinal fluid analysis for inborn errors of metabolism on an LC-MS/MS analysis platform. J Inherit Metab Dis 2020; 43:712-725. [PMID: 31930732 DOI: 10.1002/jimd.12213] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 12/20/2019] [Accepted: 01/10/2020] [Indexed: 12/27/2022]
Abstract
BACKGROUND Laboratory investigations of cerebrospinal fluid (CSF) are essential when suspecting an inborn error of metabolism (IEM) involving neurological features. Available tests are currently performed on different analytical platforms, requiring a large sample volume and long turnaround time, which often delays timely diagnosis. Therefore, it would be preferable to have an "one-instrument" targeted multi-metabolite approach. METHOD A liquid chromatography-tandem mass spectrometry (LC-MS/MS) platform, based on two different methods for analysing 38 metabolites using positive and negative electrospray ionisation modes, was established. To allow for platform extension, both methods were designed to use the same CSF sample preparation procedure and to be run on the same separation column (ACE C18-PFP). RESULTS Assessment of the LC-MS/MS platform methods was first made by analytical validation, followed by the establishment of literature-based CSF cut-off values and reference ranges, and by the measurement of available samples obtained from patients with confirmed diagnoses of aromatic l-amino acid decarboxylase deficiency, guanidinoacetate methyltransferase deficiency, ornithine aminotransferase deficiency, cerebral folate deficiency and methylenetetrahydrofolate reductase deficiency. CONCLUSION An extendable targeted LC-MS/MS platform was developed for the analysis of multiple metabolites in CSF, thereby distinguishing samples from patients with IEM from non-IEM samples. Reference concentrations for several biomarkers in CSF are provided for the first time. By measurement on a single analytical platform, less sample volume is required (200 μL), diagnostic results are obtained faster, and preanalytical issues are reduced. SYNOPSIS LC-MS/MS platform for CSF analysis consisting of two differentially designed methods.
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Affiliation(s)
- Glynis Klinke
- Department of General Pediatrics, Division of Neuropediatrics and Metabolic Medicine, Centre for Pediatric and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Sylvia Richter
- Department of General Pediatrics, Division of Neuropediatrics and Metabolic Medicine, Centre for Pediatric and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Péter Monostori
- Department of General Pediatrics, Division of Neuropediatrics and Metabolic Medicine, Centre for Pediatric and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Brigitte Schmidt-Mader
- Department of General Pediatrics, Division of Neuropediatrics and Metabolic Medicine, Centre for Pediatric and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Angels García-Cazorla
- Department of Clinical Biochemistry and Pediatric Neurology, Institut de Recerca Sant Joan de Déu, Center for Biomedical Research on Rare Diseases (CIBERER), Barcelona, Spain
| | - Rafael Artuch
- Department of Clinical Biochemistry and Pediatric Neurology, Institut de Recerca Sant Joan de Déu, Center for Biomedical Research on Rare Diseases (CIBERER), Barcelona, Spain
| | - Stine Christ
- Department of General Pediatrics, Division of Neuropediatrics and Metabolic Medicine, Centre for Pediatric and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Thomas Opladen
- Department of General Pediatrics, Division of Neuropediatrics and Metabolic Medicine, Centre for Pediatric and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Georg F Hoffmann
- Department of General Pediatrics, Division of Neuropediatrics and Metabolic Medicine, Centre for Pediatric and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Nenad Blau
- Department of General Pediatrics, Division of Neuropediatrics and Metabolic Medicine, Centre for Pediatric and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Jürgen G Okun
- Department of General Pediatrics, Division of Neuropediatrics and Metabolic Medicine, Centre for Pediatric and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
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27
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López-Hernández Y, Oropeza-Valdez JJ, Blanco-Sandate JO, Herrera-Van Oostdam AS, Zheng J, Chi Guo A, Lima-Rogel V, Rajabzadeh R, Salgado-Bustamante M, Adrian-Lopez J, Castillo CG, Robles Arguelles E, Monárrez-Espino J, Mandal R, Wishart DS. The Urinary Metabolome of Healthy Newborns. Metabolites 2020; 10:E165. [PMID: 32340350 PMCID: PMC7240964 DOI: 10.3390/metabo10040165] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 04/18/2020] [Accepted: 04/21/2020] [Indexed: 02/06/2023] Open
Abstract
The knowledge of normal metabolite values for neonates is key to establishing robust cut-off values to diagnose diseases, to predict the occurrence of new diseases, to monitor a neonate's metabolism, or to assess their general health status. For full term-newborns, many reference biochemical values are available for blood, serum, plasma and cerebrospinal fluid. However, there is a surprising lack of information about normal urine concentration values for a large number of important metabolites in neonates. In the present work, we used targeted tandem mass spectrometry (MS/MS)-based metabolomic assays to identify and quantify 136 metabolites of biomedical interest in the urine from 48 healthy, full-term term neonates, collected in the first 24 h of life. In addition to this experimental study, we performed a literature review (covering the past eight years and over 500 papers) to update the references values in the Human Metabolome Database/Urine Metabolome Database (HMDB/UMDB). Notably, 86 of the experimentally measured urinary metabolites are being reported in neonates/infants for the first time and another 20 metabolites are being reported in human urine for the first time ever. Sex differences were found for 15 metabolites. The literature review allowed us to identify another 78 urinary metabolites with concentration data. As a result, reference concentration values and ranges for 378 neonatal urinary metabolites are now publicly accessible via the HMDB.
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Affiliation(s)
- Yamilé López-Hernández
- CONACyT, Metabolomics and Proteomics Laboratory, Universidad Autónoma de Zacatecas, Zacatecas 98000, Mexico
| | - Juan José Oropeza-Valdez
- Unidad de Investigación Biomédica de Zacatecas, Instituto Mexicano del Seguro Social, Zacatecas 98000, Mexico;
| | - Jorge O. Blanco-Sandate
- CIACYT-Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí 78210, Mexico; (J.O.B.-S.); (C.G.C.)
| | - Ana Sofia Herrera-Van Oostdam
- Biochemistry Department, Faculty of Medicine, Universidad Autónoma de San Luis Potosí, San Luis Potosí 78210, Mexico; (A.S.H.-V.O.); (M.S.-B.)
| | - Jiamin Zheng
- The Metabolomics Innovation Center, University of Alberta, Edmonton, AB T6G1C9, Canada; (J.Z.); (A.C.G.); (R.R.); (R.M.)
| | - An Chi Guo
- The Metabolomics Innovation Center, University of Alberta, Edmonton, AB T6G1C9, Canada; (J.Z.); (A.C.G.); (R.R.); (R.M.)
| | - Victoria Lima-Rogel
- Hospital Central “Dr. Ignacio Morones Prieto”, San Luis Potosí 78290, Mexico;
| | - Rahmatollah Rajabzadeh
- The Metabolomics Innovation Center, University of Alberta, Edmonton, AB T6G1C9, Canada; (J.Z.); (A.C.G.); (R.R.); (R.M.)
| | - Mariana Salgado-Bustamante
- Biochemistry Department, Faculty of Medicine, Universidad Autónoma de San Luis Potosí, San Luis Potosí 78210, Mexico; (A.S.H.-V.O.); (M.S.-B.)
| | - Jesus Adrian-Lopez
- MicroRNAs Laboratory, Unidad Académica de Ciencias Biológicas, Universidad Autónoma de Zacatecas, Zacatecas 98000, Mexico; (J.A.-L.); (E.R.A.)
| | - C. G. Castillo
- CIACYT-Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí 78210, Mexico; (J.O.B.-S.); (C.G.C.)
| | - Emilia Robles Arguelles
- MicroRNAs Laboratory, Unidad Académica de Ciencias Biológicas, Universidad Autónoma de Zacatecas, Zacatecas 98000, Mexico; (J.A.-L.); (E.R.A.)
| | | | - Rupasri Mandal
- The Metabolomics Innovation Center, University of Alberta, Edmonton, AB T6G1C9, Canada; (J.Z.); (A.C.G.); (R.R.); (R.M.)
| | - David S. Wishart
- The Metabolomics Innovation Center, University of Alberta, Edmonton, AB T6G1C9, Canada; (J.Z.); (A.C.G.); (R.R.); (R.M.)
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Sigmarsdóttir Þ, McGarrity S, Rolfsson Ó, Yurkovich JT, Sigurjónsson ÓE. Current Status and Future Prospects of Genome-Scale Metabolic Modeling to Optimize the Use of Mesenchymal Stem Cells in Regenerative Medicine. Front Bioeng Biotechnol 2020; 8:239. [PMID: 32296688 PMCID: PMC7136564 DOI: 10.3389/fbioe.2020.00239] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 03/09/2020] [Indexed: 12/15/2022] Open
Abstract
Mesenchymal stem cells are a promising source for externally grown tissue replacements and patient-specific immunomodulatory treatments. This promise has not yet been fulfilled in part due to production scaling issues and the need to maintain the correct phenotype after re-implantation. One aspect of extracorporeal growth that may be manipulated to optimize cell growth and differentiation is metabolism. The metabolism of MSCs changes during and in response to differentiation and immunomodulatory changes. MSC metabolism may be linked to functional differences but how this occurs and influences MSC function remains unclear. Understanding how MSC metabolism relates to cell function is however important as metabolite availability and environmental circumstances in the body may affect the success of implantation. Genome-scale constraint based metabolic modeling can be used as a tool to fill gaps in knowledge of MSC metabolism, acting as a framework to integrate and understand various data types (e.g., genomic, transcriptomic and metabolomic). These approaches have long been used to optimize the growth and productivity of bacterial production systems and are being increasingly used to provide insights into human health research. Production of tissue for implantation using MSCs requires both optimized production of cell mass and the understanding of the patient and phenotype specific metabolic situation. This review considers the current knowledge of MSC metabolism and how it may be optimized along with the current and future uses of genome scale constraint based metabolic modeling to further this aim.
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Affiliation(s)
- Þóra Sigmarsdóttir
- The Blood Bank, Landspitali – The National University Hospital of Iceland, Reykjavik, Iceland
- School of Science and Engineering, Reykjavik University, Reykjavik, Iceland
| | - Sarah McGarrity
- School of Science and Engineering, Reykjavik University, Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Óttar Rolfsson
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | - Ólafur E. Sigurjónsson
- The Blood Bank, Landspitali – The National University Hospital of Iceland, Reykjavik, Iceland
- School of Science and Engineering, Reykjavik University, Reykjavik, Iceland
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Abstract
In the last years, 'omics' technologies, and especially metabolomics, emerged as expanding scientific disciplines and promising technologies in the characterization of several pathophysiological processes.In detail, metabolomics, able to detect in a dynamic way the whole set of molecules of low molecular weight in cells, tissues, organs, and biological fluids, can provide a detailed phenotypic portray, representing a metabolic "snapshot."Thanks to its numerous strength points, metabolomics could become a fundamental tool in human health, allowing the exact evaluation of individual metabolic responses to pathophysiological stimuli including drugs, environmental changes, lifestyle, a great number of diseases and other epigenetics factors.Moreover, if current metabolomics data will be confirmed on larger samples, such technology could become useful in the early diagnosis of diseases, maybe even before the clinical onset, allowing a clinical monitoring of disease progression and helping in performing the best therapeutic approach, potentially predicting the therapy response and avoiding overtreatments. Moreover, the application of metabolomics in nutrition could provide significant information on the best nutrition regimen, optimal infantile growth and even in the characterization and improvement of commercial products' composition.These are only some of the fields in which metabolomics was applied, in the perspective of a precision-based, personalized care of human health.In this review, we discuss the available literature on such topic and provide some evidence regarding clinical application of metabolomics in heart diseases, auditory disturbance, nephrouropathies, adult and pediatric cancer, obstetrics, perinatal conditions like asphyxia, neonatal nutrition, neonatal sepsis and even some neuropsychiatric disorders, including autism.Our research group has been interested in metabolomics since several years, performing a wide spectrum of experimental and clinical studies, including the first metabolomics analysis of human breast milk. In the future, it is reasonable to predict that the current knowledge could be applied in daily clinical practice, and that sensible metabolomics biomarkers could be easily detected through cheap and accurate sticks, evaluating biofluids at the patient's bed, improving diagnosis, management and prognosis of sick patients and allowing a personalized medicine. A dream? May be I am a dreamer, but I am not the only one.
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Affiliation(s)
- Flaminia Bardanzellu
- Neonatal Intensive Care Unit, Department of Surgical Sciences, AOU University of Cagliari, SS 554 km 4,500, 09042, Monserrato, CA, Italy.
| | - Vassilios Fanos
- Neonatal Intensive Care Unit, Department of Surgical Sciences, AOU University of Cagliari, SS 554 km 4,500, 09042, Monserrato, CA, Italy
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30
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Schuck PF, Ferreira GC, McKenna MC. Recent advances in the pathophysiology of inherited metabolic diseases. Int J Dev Neurosci 2020; 80:50-51. [PMID: 31951034 DOI: 10.1002/jdn.10007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Patricia F Schuck
- Laboratório de Erros Inatos do Metabolismo, Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil.,Programa de Pós-graduação em Biologia Celular e Molecular, Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Gustavo C Ferreira
- Laboratório de Neuroenergética e Erros Inatos do Metabolismo, Programa de Bioquímica e Biofísica Celular, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Mary C McKenna
- Department of Pediatrics and Program in Neuroscience, University of Maryland School of Medicine, Baltimore, MD, USA
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31
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Webb-Robertson BJM, Stratton KG, Kyle JE, Kim YM, Bramer LM, Waters KM, Koeller DM, Metz TO. Statistically Driven Metabolite and Lipid Profiling of Patients from the Undiagnosed Diseases Network. Anal Chem 2020; 92:1796-1803. [PMID: 31742994 PMCID: PMC7183858 DOI: 10.1021/acs.analchem.9b03522] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Advancements in molecular separations coupled with mass spectrometry have enabled metabolome analyses for clinical cohorts. A population of interest for metabolome profiling is patients with rare disease for which abnormal metabolic signatures may yield clues into the genetic basis, as well as mechanistic drivers of the disease and possible treatment options. We undertook the metabolome profiling of a large cohort of patients with mysterious conditions characterized through the Undiagnosed Diseases Network (UDN). Due to the size and enrollment procedures, collection of the metabolomes for UDN patients took place over 2 years. We describe the study designed to adjust for measurements collected over a long time scale and how this enabled statistical analyses to summarize the metabolome of individual patients. We demonstrate the removal of time-based batch effects, overall statistical characteristics of the UDN population, and two case studies of interest that demonstrate the utility of metabolome profiling for rare diseases.
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Affiliation(s)
- Bobbie-Jo M. Webb-Robertson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Kelly G. Stratton
- Computing Analytics Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Jennifer E. Kyle
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Young-Mo Kim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Lisa M. Bramer
- Computing Analytics Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Katrina M. Waters
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - David M. Koeller
- Molecular and Medical Genetics, School of Medicine, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Thomas O. Metz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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32
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Untargeted Metabolomics-Based Screening Method for Inborn Errors of Metabolism using Semi-Automatic Sample Preparation with an UHPLC- Orbitrap-MS Platform. Metabolites 2019; 9:metabo9120289. [PMID: 31779119 PMCID: PMC6950026 DOI: 10.3390/metabo9120289] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/19/2019] [Accepted: 11/22/2019] [Indexed: 02/07/2023] Open
Abstract
Routine diagnostic screening of inborn errors of metabolism (IEM) is currently performed by different targeted analyses of known biomarkers. This approach is time-consuming, targets a limited number of biomarkers and will not identify new biomarkers. Untargeted metabolomics generates a global metabolic phenotype and has the potential to overcome these issues. We describe a novel, single platform, untargeted metabolomics method for screening IEM, combining semi-automatic sample preparation with pentafluorophenylpropyl phase (PFPP)-based UHPLC- Orbitrap-MS. We evaluated analytical performance and diagnostic capability of the method by analysing plasma samples of 260 controls and 53 patients with 33 distinct IEM. Analytical reproducibility was excellent, with peak area variation coefficients below 20% for the majority of the metabolites. We illustrate that PFPP-based chromatography enhances identification of isomeric compounds. Ranked z-score plots of metabolites annotated in IEM samples were reviewed by two laboratory specialists experienced in biochemical genetics, resulting in the correct diagnosis in 90% of cases. Thus, our untargeted metabolomics platform is robust and differentiates metabolite patterns of different IEMs from those of controls. We envision that the current approach to diagnose IEM, using numerous tests, will eventually be replaced by untargeted metabolomics methods, which also have the potential to discover novel biomarkers and assist in interpretation of genetic data.
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33
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Frick MA, Barba I, Fenoy-Alejandre M, López-López P, Baquero-Artigao F, Rodríguez-Molino P, Noguera-Julian A, Nicolás-López M, de la Fuente-Juárez A, Codina-Grau MG, Esperalba Esquerra J, Linde-Sillo Á, Soler-Palacín P. 1H-NMR Urinary Metabolic Profile, A Promising Tool for the Management of Infants with Human Cytomegalovirus-Infection. Metabolites 2019; 9:metabo9120288. [PMID: 31775291 PMCID: PMC6949898 DOI: 10.3390/metabo9120288] [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: 10/09/2019] [Revised: 11/14/2019] [Accepted: 11/23/2019] [Indexed: 02/07/2023] Open
Abstract
Congenital human cytomegalovirus (HCMV) infection is the most common mother-to-child transmitted infection in the developed world. Certain aspects of its management remain a challenge. Urinary metabolic profiling is a promising tool for use in pediatric conditions. The aim of this study was to investigate the urinary metabolic profile in HCMV-infected infants and controls during acute care hospitalization. Urine samples were collected from 53 patients at five hospitals participating in the Spanish congenital HCMV registry. Thirty-one cases of HCMV infection and 22 uninfected controls were included. Proton nuclear magnetic resonance (1H-NMR) spectra were obtained using NOESYPR1D pulse sequence. The dataset underwent orthogonal projection on latent structures discriminant analysis to identify candidate variables affecting the urinary metabolome: HCMV infection, type of infection, sex, chronological age, gestational age, type of delivery, twins, and diet. Statistically significant discriminative models were obtained only for HCMV infection (p = 0.03) and chronological age (p < 0.01). No significant differences in the metabolomic profile were found between congenital and postnatal HCMV infection. When the HCMV-infected group was analyzed according to chronological age, a statistically significant model was obtained only in the neonatal group (p = 0.01), with the differentiating metabolites being betaine, glycine, alanine, and dimethylamine. Despite the considerable variation in urinary metabolic profiles in a real-life setting, clinical application of metabolomics to the study of HCMV infection seems feasible.
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Affiliation(s)
- Marie Antoinette Frick
- Pediatric Infectious Diseases and Primary Immunodeficiencies Unit, Pediatrics Department, Children’s Hospital, Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
| | | | - Marina Fenoy-Alejandre
- Pediatric Infectious Diseases and Primary Immunodeficiencies Unit, Pediatrics Department, Children’s Hospital, Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
| | | | | | | | | | | | | | | | | | | | - Pere Soler-Palacín
- Pediatric Infectious Diseases and Primary Immunodeficiencies Unit, Pediatrics Department, Children’s Hospital, Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
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34
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Ismail IT, Showalter MR, Fiehn O. Inborn Errors of Metabolism in the Era of Untargeted Metabolomics and Lipidomics. Metabolites 2019; 9:metabo9100242. [PMID: 31640247 PMCID: PMC6835511 DOI: 10.3390/metabo9100242] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 10/11/2019] [Accepted: 10/15/2019] [Indexed: 12/30/2022] Open
Abstract
Inborn errors of metabolism (IEMs) are a group of inherited diseases with variable incidences. IEMs are caused by disrupting enzyme activities in specific metabolic pathways by genetic mutations, either directly or indirectly by cofactor deficiencies, causing altered levels of compounds associated with these pathways. While IEMs may present with multiple overlapping symptoms and metabolites, early and accurate diagnosis of IEMs is critical for the long-term health of affected subjects. The prevalence of IEMs differs between countries, likely because different IEM classifications and IEM screening methods are used. Currently, newborn screening programs exclusively use targeted metabolic assays that focus on limited panels of compounds for selected IEM diseases. Such targeted approaches face the problem of false negative and false positive diagnoses that could be overcome if metabolic screening adopted analyses of a broader range of analytes. Hence, we here review the prospects of using untargeted metabolomics for IEM screening. Untargeted metabolomics and lipidomics do not rely on predefined target lists and can detect as many metabolites as possible in a sample, allowing to screen for many metabolic pathways simultaneously. Examples are given for nontargeted analyses of IEMs, and prospects and limitations of different metabolomics methods are discussed. We conclude that dedicated studies are needed to compare accuracy and robustness of targeted and untargeted methods with respect to widening the scope of IEM diagnostics.
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Affiliation(s)
- Israa T Ismail
- National Liver Institute, Menoufia University, Shebeen El Kom 55955, Egypt.
- NIH West Coast Metabolomics Center, University of California Davis, Davis, CA 95616, USA.
| | - Megan R Showalter
- NIH West Coast Metabolomics Center, University of California Davis, Davis, CA 95616, USA.
| | - Oliver Fiehn
- NIH West Coast Metabolomics Center, University of California Davis, Davis, CA 95616, USA.
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35
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Jiao Q, Sun H, Zhang H, Wang R, Li S, Sun D, Yang XA, Jin Y. The combination of whole-exome sequencing and copy number variation sequencing enables the diagnosis of rare neurological disorders. Clin Genet 2019; 96:140-150. [PMID: 30945278 DOI: 10.1111/cge.13548] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 04/01/2019] [Accepted: 04/02/2019] [Indexed: 12/31/2022]
Abstract
This retrospective study aims to investigate the diagnostic yields of multiple strategies of next-generation sequencing (NGS) for children with rare neurological disorders (NDs). A total of 220 pediatric patients with NDs who visited our hospital between Jan 2017 and Dec 2018 and had undergone NGS were included. Most patients were 5 years old or younger, and the number of patients visiting the hospital decreased with age. Seizures were the most common symptom in this cohort. The positive rates for targeted NGS panels (Panel), whole-exome sequencing (WES), and copy number variation sequencing (CNVseq) were 26.5% (9/34), 36.6% (63/172), and 16.7% (22/132), respectively. The positive rate for patients undergoing a combination of WES and CNVseq (WES + CNVseq) was 47.8% (54/113), which was significantly better than the positive rate for patients who underwent WES alone (32.7%, 37/113). A total of 83 variants were found in 42 genes, and SCN1A was the most frequently mutanted gene. Twenty-four CNVs were identified in 22 patients: two CNVs were inherited from the mother; 12 CNVs were de novo; and the CNV origins could not be determined in 10 patients. WES + CNVseq may potentially be the mostly effective NGS approach for diagnosis of rare NDs in pediatric patients.
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Affiliation(s)
- Qingguo Jiao
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, P. R. China.,Key Laboratory of Medical Genetics (Harbin Medical University), Heilongjiang Higher Education Institutions, Harbin, P. R. China
| | - Haiming Sun
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, P. R. China.,Key Laboratory of Medical Genetics (Harbin Medical University), Heilongjiang Higher Education Institutions, Harbin, P. R. China
| | - Haoya Zhang
- School of Medicine, Jianghan University, Wuhan, P. R. China
| | - Ran Wang
- State Key Laboratory of Quality Research in Chinese Medicine and School of Pharmacy, Macau University of Science and Technology, Macau, P. R. China.,Department of Pharmacology, Chengde Medical University, Chengde, P. R. China
| | - Suting Li
- School of Basic Medical Science, Chengde Medical University, Chengde, P. R. China
| | - Dan Sun
- Department of Neurology, Wuhan Children's Hospital (Wuhan Maternal and Child Health Care Hospital), Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Xiu-An Yang
- School of Basic Medical Science, Chengde Medical University, Chengde, P. R. China
| | - Yan Jin
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, P. R. China.,Key Laboratory of Medical Genetics (Harbin Medical University), Heilongjiang Higher Education Institutions, Harbin, P. R. China
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