1
|
Li J, Wei X, Sun Y, Chen X, Zhang Y, Cui X, Shu J, Li D, Cai C. Phosphoserine aminotransferase deficiency diagnosed by whole-exome sequencing and LC-MS/MS reanalysis: A case report and review of literature. Mol Genet Genomic Med 2024; 12:e2400. [PMID: 38546032 PMCID: PMC10976427 DOI: 10.1002/mgg3.2400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 12/26/2023] [Accepted: 02/05/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Phosphoserine aminotransferase deficiency (PSATD) is an autosomal recessive disorder associated with hypertonia, psychomotor retardation, and acquired microcephaly. Patients with PSATD have low concentrations of serine in plasma and cerebrospinal fluid. METHODS We reported a 2-year-old female child with developmental delay, dyskinesia, and microcephaly. LC-MS/MS was used to detect amino acid concentration in the blood and whole-exome sequencing (WES) was used to identify the variants. PolyPhen-2 web server and PyMol were used to predict the pathogenicity and changes in the 3D model molecular structure of protein caused by variants. RESULTS WES demonstrated compound heterozygous variants in PSAT1, which is associated with PSATD, with a paternal likely pathogenic variant (c.235G>A, Gly79Arg) and a maternal likely pathogenic variant (c.43G>C, Ala15Pro). Reduced serine concentration in LC-MS/MS further confirmed the diagnosis of PSATD in this patient. CONCLUSIONS Our findings demonstrate the importance of WES combined with LC-MS/MS reanalysis in the diagnosis of genetic diseases and expand the PSAT1 variant spectrum in PSATD. Moreover, we summarize all the cases caused by PSAT1 variants in the literature. This case provides a vital reference for the diagnosis of future cases.
Collapse
Affiliation(s)
- Jiaci Li
- Tianjin Children's Hospital (Children's Hospital, Tianjin University)TianjinChina
- Tianjin Pediatric Research InstituteTianjinChina
- Tianjin Key Laboratory of Birth Defects for Prevention and TreatmentTianjinChina
| | - Xinping Wei
- Tianjin Children's Hospital (Children's Hospital, Tianjin University)TianjinChina
- Department of NeurologyTianjin Children's HospitalTianjinChina
| | - Yuchen Sun
- College of Traditional Chinese medicineTianjin University of Traditional Chinese MedicineTianjinChina
| | - Xiaofang Chen
- Tianjin Children's Hospital (Children's Hospital, Tianjin University)TianjinChina
| | - Ying Zhang
- Tianjin Children's Hospital (Children's Hospital, Tianjin University)TianjinChina
- Tianjin Medical UniversityGraduate College of Tianjin Medical UniversityTianjinChina
| | - Xiaoyu Cui
- Tianjin Children's Hospital (Children's Hospital, Tianjin University)TianjinChina
| | - Jianbo Shu
- Tianjin Children's Hospital (Children's Hospital, Tianjin University)TianjinChina
- Tianjin Pediatric Research InstituteTianjinChina
- Tianjin Key Laboratory of Birth Defects for Prevention and TreatmentTianjinChina
| | - Dong Li
- Tianjin Children's Hospital (Children's Hospital, Tianjin University)TianjinChina
- Department of NeurologyTianjin Children's HospitalTianjinChina
| | - Chunquan Cai
- Tianjin Children's Hospital (Children's Hospital, Tianjin University)TianjinChina
- Tianjin Pediatric Research InstituteTianjinChina
- Tianjin Key Laboratory of Birth Defects for Prevention and TreatmentTianjinChina
| |
Collapse
|
2
|
Wurth R, Turgeon C, Stander Z, Oglesbee D. An evaluation of untargeted metabolomics methods to characterize inborn errors of metabolism. Mol Genet Metab 2024; 141:108115. [PMID: 38181458 PMCID: PMC10843816 DOI: 10.1016/j.ymgme.2023.108115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/19/2023] [Accepted: 12/12/2023] [Indexed: 01/07/2024]
Abstract
Inborn errors of metabolism (IEMs) encompass a diverse group of disorders that can be difficult to classify due to heterogenous clinical, molecular, and biochemical manifestations. Untargeted metabolomics platforms have become a popular approach to analyze IEM patient samples because of their ability to detect many metabolites at once, accelerating discovery of novel biomarkers, and metabolic mechanisms of disease. However, there are concerns about the reproducibility of untargeted metabolomics research due to the absence of uniform reporting practices, data analyses, and experimental design guidelines. Therefore, we critically evaluated published untargeted metabolomic platforms used to characterize IEMs to summarize the strengths and areas for improvement of this technology as it progresses towards the clinical laboratory. A total of 96 distinct IEMs were collectively evaluated by the included studies. However, most of these IEMs were evaluated by a single untargeted metabolomic method, in a single study, with a limited cohort size (55/96, 57%). The goals of the included studies generally fell into two, often overlapping, categories: detecting known biomarkers from many biochemically distinct IEMs using a single platform, and detecting novel metabolites or metabolic pathways. There was notable diversity in the design of the untargeted metabolomic platforms. Importantly, the majority of studies reported adherence to quality metrics, including the use of quality control samples and internal standards in their experiments, as well as confirmation of at least some of their feature annotations with commercial reference standards. Future applications of untargeted metabolomics platforms to the study of IEMs should move beyond single-subject analyses, and evaluate reproducibility using a prospective, or validation cohort.
Collapse
Affiliation(s)
- Rachel Wurth
- Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, 200 1(st) St SW, Rochester, MN 55905, USA
| | - Coleman Turgeon
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 1st St SW, Rochester, MN 55905, USA
| | - Zinandré Stander
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 1st St SW, Rochester, MN 55905, USA
| | - Devin Oglesbee
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 1st St SW, Rochester, MN 55905, USA.
| |
Collapse
|
3
|
Xie MJ, Cromie GA, Owens K, Timour MS, Tang M, Kutz JN, El-Hattab AW, McLaughlin RN, Dudley AM. Constructing and interpreting a large-scale variant effect map for an ultrarare disease gene: Comprehensive prediction of the functional impact of PSAT1 genotypes. PLoS Genet 2023; 19:e1010972. [PMID: 37812589 PMCID: PMC10561871 DOI: 10.1371/journal.pgen.1010972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 09/13/2023] [Indexed: 10/11/2023] Open
Abstract
Reduced activity of the enzymes encoded by PHGDH, PSAT1, and PSPH causes a set of ultrarare, autosomal recessive diseases known as serine biosynthesis defects. These diseases present in a broad phenotypic spectrum: at the severe end is Neu-Laxova syndrome, in the intermediate range are infantile serine biosynthesis defects with severe neurological manifestations and growth deficiency, and at the mild end is childhood disease with intellectual disability. However, L-serine supplementation, especially if started early, can ameliorate and in some cases even prevent symptoms. Therefore, knowledge of pathogenic variants can improve clinical outcomes. Here, we use a yeast-based assay to individually measure the functional impact of 1,914 SNV-accessible amino acid substitutions in PSAT. Results of our assay agree well with clinical interpretations and protein structure-function relationships, supporting the inclusion of our data as functional evidence as part of the ACMG variant interpretation guidelines. We use existing ClinVar variants, disease alleles reported in the literature and variants present as homozygotes in the primAD database to define assay ranges that could aid clinical variant interpretation for up to 98% of the tested variants. In addition to measuring the functional impact of individual variants in yeast haploid cells, we also assay pairwise combinations of PSAT1 alleles that recapitulate human genotypes, including compound heterozygotes, in yeast diploids. Results from our diploid assay successfully distinguish the genotypes of affected individuals from those of healthy carriers and agree well with disease severity. Finally, we present a linear model that uses individual allele measurements to predict the biallelic function of ~1.8 million allele combinations corresponding to potential human genotypes. Taken together, our work provides an example of how large-scale functional assays in model systems can be powerfully applied to the study of ultrarare diseases.
Collapse
Affiliation(s)
- Michael J. Xie
- Pacific Northwest Research Institute, Seattle, Washington, United States of America
- Molecular Engineering Graduate Program, University of Washington, Seattle, Washington, United States of America
| | - Gareth A. Cromie
- Pacific Northwest Research Institute, Seattle, Washington, United States of America
| | - Katherine Owens
- Pacific Northwest Research Institute, Seattle, Washington, United States of America
- Department of Applied Mathematics, University of Washington, Seattle, Washington, United States of America
| | - Martin S. Timour
- Pacific Northwest Research Institute, Seattle, Washington, United States of America
| | - Michelle Tang
- Pacific Northwest Research Institute, Seattle, Washington, United States of America
| | - J. Nathan Kutz
- Department of Applied Mathematics, University of Washington, Seattle, Washington, United States of America
| | - Ayman W. El-Hattab
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | | | - Aimée M. Dudley
- Pacific Northwest Research Institute, Seattle, Washington, United States of America
- Molecular Engineering Graduate Program, University of Washington, Seattle, Washington, United States of America
| |
Collapse
|
4
|
Lu Y, Xing H, Liu C, Huang D, Sun C, Yu M, Meng L, Lv H, Zhang W, Wang Z, Yuan Y, Xie Z. Pathogenic PSAT1 Variants and Autosomal Recessive Axonal Charcot-Marie-Tooth Disease With Ichthyosis. Pediatr Neurol 2023; 140:25-34. [PMID: 36599231 DOI: 10.1016/j.pediatrneurol.2022.11.013] [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: 06/27/2022] [Revised: 09/26/2022] [Accepted: 11/21/2022] [Indexed: 11/27/2022]
Abstract
BACKGROUND Biallelic pathogenic phosphoserine aminotransferase 1 (PSAT1) variants generally cause a severe phenotype predominantly involving the central nervous system. Here, for the first time, we report two patients harboring pathogenic PSAT1 variants only manifested as polyneuropathy and ichthyosis. METHODS Two patients from unrelated families presenting with polyneuropathy and ichthyosis were enrolled. Whole exome sequencing was performed to identify possible disease-causing variants. Their clinical, electrophysiological, imaging, biochemical, and pathologic changes were in detail assessed and investigated. RESULTS Homozygous variant c.43G>C and compound heterozygous variants c.112A>C and c.43G>C in PSAT1 were identified in patients 1 and 2, respectively. Nerve conduction studies revealed preserved or mild slowing motor nerve conduction velocities of the median nerves in the two patients, whereas the compound motor action potential in patient 1 was severely decreased. Brain magnetic resonance imaging of the two patients found no abnormalities. Median nerve enlargement was observed on ultrasound in patient 1. Both patients had normal level of serine and glycine in plasma and cerebrospinal fluid. Sural nerve biopsy found severe loss of myelinated fibers. Electron microscopy revealed neurofilament accumulation and mitochondrial aggregation in axons. Both variants in PSAT1 were classified as likely pathogenic or pathogenic variants according to the standard guidelines. CONCLUSIONS Our study confirms that pathogenic PSAT1 variants can cause a mild phenotype, predominantly as autosomal recessive axonal Charcot-Marie-Tooth disease.
Collapse
Affiliation(s)
- Yanyu Lu
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Haiying Xing
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Chang Liu
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Diandian Huang
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Chengyue Sun
- Department of Neurology, Peking University People's Hospital, Beijing, China
| | - Meng Yu
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Lingchao Meng
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - He Lv
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Wei Zhang
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Zhaoxia Wang
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Yun Yuan
- Department of Neurology, Peking University First Hospital, Beijing, China.
| | - Zhiying Xie
- Department of Neurology, Peking University First Hospital, Beijing, China.
| |
Collapse
|
5
|
Marchesani F, Zangelmi E, Murtas G, Costanzi E, Ullah R, Peracchi A, Bruno S, Pollegioni L, Mozzarelli A, Storici P, Campanini B. L-Serine Biosynthesis in The Human Central Nervous System: Structure and Function of Phosphoserine Aminotransferase. Protein Sci 2023; 32:e4609. [PMID: 36851825 PMCID: PMC10031235 DOI: 10.1002/pro.4609] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 01/12/2023] [Accepted: 02/23/2023] [Indexed: 03/01/2023]
Abstract
Organisms from all kingdoms of life synthesize L-serine from 3-phosphoglycerate through the phosphorylated pathway, a three-step diversion of glycolysis. Phosphoserine aminotransferase (PSAT) catalyzes the intermediate step, the pyridoxal 5'-phosphate-dependent transamination of 3-phosphohydroxypyruvate and L-glutamate to O-phosphoserine and α-ketoglutarate. PSAT is particularly relevant in the central nervous system of mammals because L-serine is the metabolic precursor of D-serine, cysteine, phospholipids, and nucleotides. Several mutations in the human psat gene have been linked to serine deficiency disorders, characterized by severe neurological symptoms. Furthermore, PSAT is overexpressed in many tumors and this overexpression has been associated with poor clinical outcomes. Here, we report the detailed functional and structural characterization of the recombinant human PSAT. The reaction catalyzed by PSAT is reversible, with an equilibrium constant of about 10, and the enzyme is very efficient, with a kcat /Km of 5.9 × 106 M-1 s-1 , thus contributing in driving the pathway towards the products despite the extremely unfavorable first step catalyzed by 3-phosphoglycerate dehydrogenase. The three-dimensional X-ray crystal structure of PSAT was solved in the substrate-free as well as in the O-phosphoserine-bound forms. Both structures contain eight protein molecules in the asymmetric unit, arranged in four dimers, with a bound cofactor in each subunit. In the substrate-free form, the active site of PSAT contains a sulfate ion that, in the substrate-bound form, is replaced by the phosphate group of O-phosphoserine. Interestingly, fast crystal soaking used to produce the substrate-bound form allowed the trapping of different intermediates along the catalytic cycle. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
| | - Erika Zangelmi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Giulia Murtas
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Elisa Costanzi
- Protein Facility, Elettra Sincrotrone Trieste S.C.p.A., Trieste, Italy
| | - Raheem Ullah
- Protein Facility, Elettra Sincrotrone Trieste S.C.p.A., Trieste, Italy
- Present address: Structural Biology Lab, NIBGE, Faisalabad, Pakistan
| | - Alessio Peracchi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Stefano Bruno
- Department of Food and Drug, University of Parma, Parma, Italy
| | - Loredano Pollegioni
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | | | - Paola Storici
- Protein Facility, Elettra Sincrotrone Trieste S.C.p.A., Trieste, Italy
| | | |
Collapse
|
6
|
Sulukan E, Baran A, Şenol O, Kankaynar M, Yıldırım S, Bolat İ, Ceyhun HA, Toraman E, Ceyhun SB. Global warming and glyphosate toxicity (I): Adult zebrafish modelling with behavioural, immunohistochemical and metabolomic approaches. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 858:160086. [PMID: 36356745 DOI: 10.1016/j.scitotenv.2022.160086] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 10/24/2022] [Accepted: 11/05/2022] [Indexed: 06/16/2023]
Abstract
Global warming further increases the toxic threat of environmental pollutants on organisms. In order to reveal the dimensions of this threat more clearly, it is of great importance that the studies be carried out with temperature differences as close as possible to the temperature values that will represent the global climate projection. In our study, how the toxicity of glyphosate, which is widely used around the world, on zebrafish changes with temperature increases of 0.5° was investigated on behavioral and molecular basis. For this purpose, adult zebrafish were exposed to glyphosate at concentrations of 1 ppm and 5 ppm for 96 h in four environments with a temperature difference of 0.5° (28.5; 29.0; 29.5; 30.0 °C). At the end of the exposure, half of the zebrafish were sampled and remaining half were left for a 10-day recovery process. At the end of the trials, zebrafish were subjected to circadian rhythm and anxiety tests. In addition, histopathological, immunohistochemical and metabolome analyses were performed on brain tissues. As a result, it has been detected that anxiety and circadian rhythm were disrupted in parallel with the increased temperature and glyphosate concentration, and increased histopathological findings and 5-HT4R and GNAT2 immunopositivity in the brain. As a result of metabolome analysis, more than thirty annotated metabolites have been determined due to the synergistic effect of temperature increase and glyphosate exposure. As a conclusion, it was concluded that even a temperature increase of 0.5° caused an increasing effect of glyphosate toxicity in the zebrafish model.
Collapse
Affiliation(s)
- Ekrem Sulukan
- Aquatic Biotechnology Laboratory, Fisheries Faculty, Atatürk University, Erzurum, Turkey; Aquaculture Department, Fisheries Faculty, Atatürk University, Erzurum, Turkey; Department of Aquaculture Engineering, Graduate School of Natural and Applied Science, Atatürk University, Erzurum, Turkey
| | - Alper Baran
- Aquatic Biotechnology Laboratory, Fisheries Faculty, Atatürk University, Erzurum, Turkey; Department of Food Quality Control and Analysis, Technical Vocational School, Atatürk University, Erzurum, Turkey
| | - Onur Şenol
- Department of Analytical Chemistry, Faculty of Pharmacy, Atatürk University, Erzurum, Turkey
| | - Meryem Kankaynar
- Aquatic Biotechnology Laboratory, Fisheries Faculty, Atatürk University, Erzurum, Turkey; Department of Nanoscience and Nanoengineering, Graduate School of Natural and Applied Science, Atatürk University, Erzurum, Turkey
| | - Serkan Yıldırım
- Department of Pathology, Faculty of Veterinary, Atatürk University, Erzurum, Turkey
| | - İsmail Bolat
- Department of Pathology, Faculty of Veterinary, Atatürk University, Erzurum, Turkey
| | - Hacer Akgül Ceyhun
- Department of Psychiatry, Faculty of Medicine, Atatürk University, Erzurum, Turkey
| | - Emine Toraman
- Department of Molecular Biology and Genetics, Faculty of Science, Atatürk University, Erzurum, Turkey
| | - Saltuk Buğrahan Ceyhun
- Aquatic Biotechnology Laboratory, Fisheries Faculty, Atatürk University, Erzurum, Turkey; Aquaculture Department, Fisheries Faculty, Atatürk University, Erzurum, Turkey; Department of Aquaculture Engineering, Graduate School of Natural and Applied Science, Atatürk University, Erzurum, Turkey; Department of Nanoscience and Nanoengineering, Graduate School of Natural and Applied Science, Atatürk University, Erzurum, Turkey.
| |
Collapse
|
7
|
Fu J, Chen L, Su T, Xu S, Liu Y. Mild phenotypes of phosphoglycerate dehydrogenase deficiency by a novel mutation of PHGDH gene: Case report and literature review. Int J Dev Neurosci 2023; 83:44-52. [PMID: 36308023 DOI: 10.1002/jdn.10236] [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: 06/12/2022] [Revised: 10/09/2022] [Accepted: 10/24/2022] [Indexed: 02/04/2023] Open
Abstract
Phosphoglycerate dehydrogenase (PHGDH) deficiency is a rare autosomal recessive genetic disease of serine biosynthesis. Its typical features are congenital microcephaly, epileptic seizures, and psychomotor developmental delay. Here, we reported the first Chinese familial cases with genetically confirmed PHGDH deficiency and reviewed several previous reports. Two siblings in this family presented with microcephaly, psychomotor retardation, and epilepsy in early juvenile. Brain magnetic resonance imaging (MRI) showed only a slight change of enlarged ventricle. Biochemical investigations revealed low serum serine and glycine concentrations. The whole-exome sequencing (WES) results identified a missense variant in the PHGDH gene (NM_006623.4: exon11: c.1211T>A, p. Val404Asp). Although two patients in this Chinese family carried the same pathogenic mutation in the PHGDH, their symptoms and responses to treatment were not exactly the same. We found a novel variant in the PHGDH gene and expanded the genotypic and phenotypic spectrum of serine biosynthesis disorders.
Collapse
Affiliation(s)
- Junyi Fu
- Department of Pediatrics, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Liqing Chen
- Department of Pediatrics, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tangfeng Su
- Department of Pediatrics, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Sanqing Xu
- Department of Pediatrics, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yan Liu
- Department of Pediatrics, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| |
Collapse
|
8
|
Hertzog A, Selvanathan A, Devanapalli B, Ho G, Bhattacharya K, Tolun AA. A narrative review of metabolomics in the era of "-omics": integration into clinical practice for inborn errors of metabolism. Transl Pediatr 2022; 11:1704-1716. [PMID: 36345452 PMCID: PMC9636448 DOI: 10.21037/tp-22-105] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 08/23/2022] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND AND OBJECTIVE Traditional targeted metabolomic investigations identify a pre-defined list of analytes in samples and have been widely used for decades in the diagnosis and monitoring of inborn errors of metabolism (IEMs). Recent technological advances have resulted in the development and maturation of untargeted metabolomics: a holistic, unbiased, analytical approach to detecting metabolic disturbances in human disease. We aim to provide a summary of untargeted metabolomics [focusing on tandem mass spectrometry (MS-MS)] and its application in the field of IEMs. METHODS Data for this review was identified through a literature search using PubMed, Google Scholar, and personal repositories of articles collected by the authors. Findings are presented within several sections describing the metabolome, the current use of targeted metabolomics in the diagnostic pathway of patients with IEMs, the more recent integration of untargeted metabolomics into clinical care, and the limitations of this newly employed analytical technique. KEY CONTENT AND FINDINGS Untargeted metabolomic investigations are increasingly utilized in screening for rare disorders, improving understanding of cellular and subcellular physiology, discovering novel biomarkers, monitoring therapy, and functionally validating genomic variants. Although the untargeted metabolomic approach has some limitations, this "next generation metabolic screening" platform is becoming increasingly affordable and accessible. CONCLUSIONS When used in conjunction with genomics and the other promising "-omic" technologies, untargeted metabolomics has the potential to revolutionize the diagnostics of IEMs (and other rare disorders), improving both clinical and health economic outcomes.
Collapse
Affiliation(s)
- Ashley Hertzog
- NSW Biochemical Genetics Service, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Arthavan Selvanathan
- Genetic Metabolic Disorders Service, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Beena Devanapalli
- NSW Biochemical Genetics Service, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Gladys Ho
- Sydney Genome Diagnostics, The Children's Hospital at Westmead, Westmead, NSW, Australia.,Specialty of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Kaustuv Bhattacharya
- Genetic Metabolic Disorders Service, The Children's Hospital at Westmead, Westmead, NSW, Australia.,Specialty of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Adviye Ayper Tolun
- NSW Biochemical Genetics Service, The Children's Hospital at Westmead, Westmead, NSW, Australia.,Specialty of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| |
Collapse
|
9
|
Shen Y, Peng Y, Huang P, Zheng Y, Li S, Jiang K, Zhou M, Deng J, Zhu M, Hong D. Juvenile-onset PSAT1-related neuropathy: A milder phenotype of serine deficiency disorder. Front Genet 2022; 13:949038. [PMID: 36061210 PMCID: PMC9428789 DOI: 10.3389/fgene.2022.949038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 06/28/2022] [Indexed: 12/03/2022] Open
Abstract
Background: Primary serine deficiency disorders have a broad range of the phenotypic spectrum. As an inborn error of metabolism, individuals with severe phenotype may be easily recognized with Neu-Laxova syndrome. However, late-onset mild phenotypes may be underdiagnosed and will lead to disastrous consequences due to treatment delays. Materials and Methods: Clinical features of patients with serine deficiency disorders were summarized in two unrelated patients. Skin and sural nerve biopsies were conducted on the patients. Whole exome sequencing (WES) was performed in the index patients. Sanger sequencing was used to analyze family cosegregation. Results: Patient 1 was a 19-year-old male presenting with infancy-onset ichthyosis and juvenile-onset neuropathy. Patient 2 was a 17-year-old male manifesting childhood-onset ichthyosis and juvenile-onset neuropathy. Except for nystagmus, no other developmental or neurodegenerative disorders were found in the patients. Electrophysiological studies indicated a severe sensorimotor axonal neuropathy with a possible demyelinating component. High-dose oral L-serine and glycine completely alleviated skin lesions and only slightly improved neuropathy symptoms. Skin biopsies showed typical features consistent with ichthyosis and severe loss of unmyelinated axons. Sural biopsies revealed a severe loss of axons and a few thinly myelinated fibers. WES found the same homozygous variant c.43G > C (p.A15P) in the PSAT1 gene, which was cosegregated in the two families. Conclusions: The skin and nervous system may be the main affected targets in serine deficiency disorders. Our patients show a more simple and mild phenotype of PSAT1-related serine deficiency disorder. The pathological changes and regenerative ability of skin and peripheral nerves determine their response to serine supplements.
Collapse
Affiliation(s)
- Yu Shen
- Department of Neurology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yun Peng
- Department of Neurology, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Department of Medical Genetics, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Pengcheng Huang
- Department of Neurology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yilei Zheng
- Department of Neurology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Shumeng Li
- Department of Neurology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Kaiyan Jiang
- Department of Neurology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Meihong Zhou
- Department of Neurology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jianwen Deng
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Min Zhu
- Department of Neurology, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Department of Medical Genetics, The First Affiliated Hospital of Nanchang University, Nanchang, China
- *Correspondence: Min Zhu, ; Daojun Hong,
| | - Daojun Hong
- Department of Neurology, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Department of Medical Genetics, The First Affiliated Hospital of Nanchang University, Nanchang, China
- *Correspondence: Min Zhu, ; Daojun Hong,
| |
Collapse
|
10
|
Saleh DA, Attia AAEM. Shedding light on the phenotypic–genotypic correlation of rare treatable and potentially treatable pediatric movement disorders. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2022. [DOI: 10.1186/s43042-022-00286-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Advances in genetic science have led to the identification of many rare treatable pediatric movements disorders (MDs). We explored the phenotypic–genotypic spectrum of pediatric patients presenting with MDs. By this, we aimed at raising awareness about such rare disorders, especially in our region. Over the past 3 years, we reviewed the demographic data, clinical profile, molecular genetics and other diagnostic workups of pediatric patients presenting with MDs.
Results
Twelve patients were identified; however, only six patients were genetically confirmed. The phenomenology of MDs ranged from paroxysmal kinesigenic choreoathetosis (1 patient), exercise-induced dyskinesia (2 patients), ataxia (2 patients) and dystonia (2 patients). Whole-exome sequencing in addition to the functional studies for some patients revealed a specific genetic diagnosis being responsible for their MDs. The genetic diagnosis of our patients included infantile convulsions and paroxysmal choreoathetosis syndrome and episodic ataxia due to “pathogenic homozygous mutation of PRRT2 gene,” glucose transporter type 1 deficiency-exercise induced dyskinesia due to “De Novo pathogenic heterozygous missense mutation of exon 4 of SLC2A1 gene,” aromatic L amino acid decarboxylase deficiency due to “pathogenic homozygous mutation of the DDC gene,” myopathy with extrapyramidal signs due to “likely pathogenic homozygous mutations of the MICU1 gene,” mitochondrial trifunctional protein deficiency due to “homozygous variant of uncertain significance (VUS) of HADHB gene” and glutaric aciduria II with serine deficiency due to “homozygous VUS for both ETFDH and PHGDH genes.” After receiving the treatment as per recognized treatment protocols, two patients showed complete resolution of symptoms and the rest showed variable responses.
Conclusion
Identifying the genetic etiology of our patients guided us to provide either disease-specific treatment or redirected our management plan. Hence, highlighting the value of molecular genetic analysis to avoid the diagnostic odyssey and identify treatable MDs.
Collapse
|
11
|
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.
Collapse
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.
| |
Collapse
|
12
|
Odom JD, Sutton VR. Metabolomics in Clinical Practice: Improving Diagnosis and Informing Management. Clin Chem 2021; 67:1606-1617. [PMID: 34633032 DOI: 10.1093/clinchem/hvab184] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 08/17/2021] [Indexed: 11/14/2022]
Abstract
BACKGROUND Metabolomics is the study of small molecules to simultaneously identify multiple low molecular weight molecules in a system. Broadly speaking, metabolomics can be subdivided into targeted and untargeted types of analysis, each type having advantages and drawbacks. Targeted metabolomics can quantify analytes but only looks for known or expected analytes related to particular disease(s), whereas untargeted metabolomics is typically nonquantitative but can detect thousands of analytes from an agnostic or nonhypothesis driven perspective, allowing for novel discoveries. CONTENT One application of metabolomics is the study of inborn errors of metabolism (IEM). The biochemical hallmark of IEMs is decreased concentrations of analytes distal to the enzymatic defect and buildup of analytes proximal to the defect. Metabolomics can detect these changes with one test and is effective in screening for and diagnosis of IEMs. Metabolomics has also been used to study many nonmetabolic diseases such as autism spectrum disorder, various cancers, and multiple congenital anomalies syndromes. Metabolomics has led to the discovery of many novel biomarkers of disease. Recent publications demonstrate how metabolomics can be useful clinically in the diagnosis and management of patients, as well as for research and clinical discovery. SUMMARY Metabolomics has proved to be a useful tool clinically for screening and diagnostic purposes and from a research perspective for the detection of novel biomarkers. In the future, metabolomics will likely become a routine part of the evaluation for many diseases as either a supplementary test or it may simply replace historical analyses that require several individual tests and sample types.
Collapse
Affiliation(s)
- John D Odom
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - V Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX.,Baylor Genetics Laboratory, Houston, TX
| |
Collapse
|
13
|
He L, Liu Y, Long J, Zhou X, Zeng S, Li T, Yin Y. Maternal serine supply from late pregnancy to lactation improves offspring performance through modulation of metabolic pathways. Food Funct 2021; 11:8089-8098. [PMID: 32856649 DOI: 10.1039/d0fo01594f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Maternal dietary serine affects free amino acid content in milk and the antioxidant ability of progeny. However, whether maternal dietary serine has any effects on offspring performance in pigs and related metabolic consequences remains unknown. This study was conducted to investigate the effects of different levels of maternal dietary serine from late pregnancy to lactation on sow reproductive performance and offspring performance, and on the metabolome of milk and the serum of sows and their offspring. The results showed that sows fed a diet supplemented with 25% serine of the basal diet (l-Ser) had a higher litter weight, and higher average piglet weight at birth and aged 21 days when compared with sows fed the basal diet (CON). We found a large number of metabolites in both colostrum and milk that differed significantly between sows in the CON and l-Ser groups. Additionally, twenty metabolites differed in the serum of piglets aged 21 days between the CON and l-Ser groups. Most of these metabolites are involved in purine and pyrimidine metabolism, glutathione and taurine metabolism, as well as phospholipid and sphingolipid metabolism, which may contribute to the growth-promoting effects of serine on offspring. Our results imply that maternal serine has the potential to improve offspring outcomes.
Collapse
Affiliation(s)
- Liuqin He
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, College of Life Sciences, Hunan Normal University, Changsha 410081, China and CAS Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Changsha 410125, China. and Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Changsha 410125, China.
| | - Yonghui Liu
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Jing Long
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Xihong Zhou
- CAS Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Changsha 410125, China. and Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Changsha 410125, China.
| | - Sijing Zeng
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, College of Life Sciences, Hunan Normal University, Changsha 410081, China and CAS Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Changsha 410125, China.
| | - Tiejun Li
- CAS Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Changsha 410125, China. and Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Changsha 410125, China.
| | - Yulong Yin
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, College of Life Sciences, Hunan Normal University, Changsha 410081, China and CAS Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Changsha 410125, China. and Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, Changsha 410125, China.
| |
Collapse
|
14
|
Liu N, Xiao J, Gijavanekar C, Pappan KL, Glinton KE, Shayota BJ, Kennedy AD, Sun Q, Sutton VR, Elsea SH. Comparison of Untargeted Metabolomic Profiling vs Traditional Metabolic Screening to Identify Inborn Errors of Metabolism. JAMA Netw Open 2021; 4:e2114155. [PMID: 34251446 PMCID: PMC8276086 DOI: 10.1001/jamanetworkopen.2021.14155] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
IMPORTANCE Recent advances in newborn screening (NBS) have improved the diagnosis of inborn errors of metabolism (IEMs); however, many potentially treatable IEMs are not included on NBS panels, nor are they covered in standard, first-line biochemical testing. OBJECTIVE To examine the utility of untargeted metabolomics as a primary screening tool for IEMs by comparing the diagnostic rate of clinical metabolomics with the recommended traditional metabolic screening approach. DESIGN, SETTING, AND PARTICIPANTS This cross-sectional study compares data from 4464 clinical samples received from 1483 unrelated families referred for trio testing of plasma amino acids, plasma acylcarnitine profiling, and urine organic acids (June 2014 to October 2018) and 2000 consecutive plasma samples from 1807 unrelated families (July 2014 to February 2019) received for clinical metabolomic screening at a College of American Pathologists and Clinical Laboratory Improvement Amendments-certified biochemical genetics laboratory. Data analysis was performed from September 2019 to August 2020. EXPOSURES Metabolic and molecular tests performed at a genetic testing reference laboratory in the US and available clinical information for each patient were assessed to determine diagnostic rate. MAIN OUTCOMES AND MEASURES The diagnostic rate of traditional metabolic screening compared with clinical metabolomic profiling was assessed in the context of expanded NBS. RESULTS Of 1483 cases screened by the traditional approach, 912 patients (61.5%) were male and 1465 (98.8%) were pediatric (mean [SD] age, 4.1 [6.0] years; range, 0-65 years). A total of 19 families were identified with IEMs, resulting in a 1.3% diagnostic rate. A total of 14 IEMs were detected, including 3 conditions not included in the Recommended Uniform Screening Panel for NBS. Of the 1807 unrelated families undergoing plasma metabolomic profiling, 1059 patients (58.6%) were male, and 1665 (92.1%) were pediatric (mean [SD] age, 8.1 [10.4] years; range, 0-80 years). Screening identified 128 unique cases with IEMs, giving an overall diagnostic rate of 7.1%. In total, 70 different metabolic conditions were identified, including 49 conditions not presently included on the Recommended Uniform Screening Panel for NBS. CONCLUSIONS AND RELEVANCE These findings suggest that untargeted metabolomics provided a 6-fold higher diagnostic yield compared with the conventional screening approach and identified a broader spectrum of IEMs. Notably, with the expansion of NBS programs, traditional metabolic testing approaches identify few disorders beyond those covered on the NBS. These data support the capability of clinical untargeted metabolomics in screening for IEMs and suggest that broader screening approaches should be considered in the initial evaluation for metabolic disorders.
Collapse
Affiliation(s)
- Ning Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics, Houston, Texas
| | - Jing Xiao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | | | - Kirk L Pappan
- Metabolon, Inc, Durham, North Carolina
- Now with Owlstone Medical, Inc, Research Triangle Park, North Carolina
| | - Kevin E Glinton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Brian J Shayota
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Now with Division of Medical Genetics, Department of Pediatrics, University of Utah, Salt Lake City
| | | | - Qin Sun
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics, Houston, Texas
| | - V Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics, Houston, Texas
| | - Sarah H Elsea
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics, Houston, Texas
| |
Collapse
|
15
|
Ford L, Kennedy AD, Goodman KD, Pappan KL, Evans AM, Miller LAD, Wulff JE, Wiggs BR, Lennon JJ, Elsea S, Toal DR. Precision of a Clinical Metabolomics Profiling Platform for Use in the Identification of Inborn Errors of Metabolism. J Appl Lab Med 2021; 5:342-356. [PMID: 32445384 DOI: 10.1093/jalm/jfz026] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 09/09/2019] [Indexed: 01/29/2023]
Abstract
BACKGROUND The application of whole-exome sequencing for the diagnosis of genetic disease has paved the way for systems-based approaches in the clinical laboratory. Here, we describe a clinical metabolomics method for the screening of metabolic diseases through the analysis of a multi-pronged mass spectrometry platform. By simultaneously measuring hundreds of metabolites in a single sample, clinical metabolomics offers a comprehensive approach to identify metabolic perturbations across multiple biochemical pathways. METHODS We conducted a single- and multi-day precision study on hundreds of metabolites in human plasma on 4, multi-arm, high-throughput metabolomics platforms. RESULTS The average laboratory coefficient of variation (CV) on the 4 platforms was between 9.3 and 11.5% (median, 6.5-8.4%), average inter-assay CV on the 4 platforms ranged from 9.9 to 12.6% (median, 7.0-8.3%) and average intra-assay CV on the 4 platforms ranged from 5.7 to 6.9% (median, 3.5-4.4%). In relation to patient sample testing, the precision of multiple biomarkers associated with IEM disorders showed CVs that ranged from 0.2 to 11.0% across 4 analytical batches. CONCLUSIONS This evaluation describes single and multi-day precision across 4 identical metabolomics platforms, comprised each of 4 independent method arms, and reproducibility of the method for the measurement of key IEM metabolites in patient samples across multiple analytical batches, providing evidence that the method is robust and reproducible for the screening of patients with inborn errors of metabolism.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Sarah Elsea
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | | |
Collapse
|
16
|
Debs S, Ferreira CR, Groden C, Kim HJ, King KA, King MC, Lehky T, Cowen EW, Brown LH, Merideth M, Owen CM, Macnamara E, Toro C, Gahl WA, Soldatos A. Adult diagnosis of congenital serine biosynthesis defect: A treatable cause of progressive neuropathy. Am J Med Genet A 2021; 185:2102-2107. [PMID: 34089226 DOI: 10.1002/ajmg.a.62245] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/09/2020] [Accepted: 11/14/2020] [Indexed: 11/07/2022]
Abstract
A woman with ichthyosis, contractures, and progressive neuropathy represents the first case of phosphoserine aminotransferase deficiency diagnosed and treated in an adult. She has novel compound heterozygous mutations in the gene PSAT1. Treatment with high dose oral L-serine completely resolved the ichthyosis. Consideration of this diagnosis is important because early treatment with L-serine repletion can halt progression of neurodegeneration and potentially improve neurological disabilities. As exome sequencing becomes more widely implemented in the diagnostic evaluation of progressive neurodegenerative phenotypes, adult neurologists and geneticists will increasingly encounter later onset manifestations of inborn errors of metabolism classically considered in infancy and early childhood.
Collapse
Affiliation(s)
- Sarah Debs
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA.,Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
| | - Carlos R Ferreira
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Catherine Groden
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - H Jeffrey Kim
- National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland, USA
| | - Kelly A King
- National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland, USA
| | - Monique C King
- Rehabilitation Medicine Department, National Institutes of Health Clinical Center, Bethesda, Maryland, USA
| | - Tanya Lehky
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Edward W Cowen
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Laura H Brown
- Johns Hopkins Community Physicians_North Bethesda, Rockville, MD, USA
| | - Melissa Merideth
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Carter M Owen
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Ellen Macnamara
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Camilo Toro
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - William A Gahl
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Ariane Soldatos
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| |
Collapse
|
17
|
Characterization of ETFDH and PHGDH Mutations in a Patient with Mild Glutaric Aciduria Type II and Serine Deficiency. Genes (Basel) 2021; 12:genes12050703. [PMID: 34066864 PMCID: PMC8150808 DOI: 10.3390/genes12050703] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 04/29/2021] [Accepted: 05/05/2021] [Indexed: 12/20/2022] Open
Abstract
Glutaric aciduria type II (GA-II) is a rare autosomal recessive disease caused by defects in electron transfer flavoprotein (ETF), ultimately causing insufficiencies in multiple acyl-CoA dehydrogenase (MAD). 3-phosphoglycerate dehydrogenase (3-PHGDH) deficiency, is another rare autosomal disorder that appears due to a defect in the synthesis of L-serine amino acid. Several mutations of ETFDH and PHGDH genes have been associated with different forms of GA-II and serine deficiency, respectively. In this study, we report a unique case of GA-II with serine deficiency using biochemical, genetic, and in silico approaches. The proband of Syrian descent had positive newborn screening (NBS) for GA-II. At two years of age, the patient presented with developmental regression, ataxia, and intractable seizures. Results of amino acid profiling demonstrated extremely low levels of serine. Confirmatory tests for GA-II and whole exome sequencing (WES) were performed to determine the etiology of intractable seizure. Sequencing results indicated a previously reported homozygous missense mutation, c.679 C>A (p.Pro227Thr) in the ETFDH gene and a novel missense homozygous mutation c.1219 T>C (p.Ser407Pro) in the PHGDH gene. In silico tools predicted these mutations as deleterious. Here, the clinical and biochemical investigations indicate that ETFDH:p.Pro227Thr and PHGDH:p.Ser407Pro variants likely underlie the pathogenesis of GA-II and serine deficiency, respectively. This study indicates that two rare autosomal recessive disorders should be considered in consanguineous families, more specifically in those with atypical presentation.
Collapse
|
18
|
Kennedy AD, Ford L, Wittmann B, Conner J, Wulff J, Mitchell M, Evans AM, Toal DR. Global biochemical analysis of plasma, serum and whole blood collected using various anticoagulant additives. PLoS One 2021; 16:e0249797. [PMID: 33831088 PMCID: PMC8031419 DOI: 10.1371/journal.pone.0249797] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 03/25/2021] [Indexed: 01/23/2023] Open
Abstract
Introduction Analysis of blood for the evaluation of clinically relevant biomarkers requires precise collection and sample handling by phlebotomists and laboratory staff. An important consideration for the clinical application of metabolomics are the different anticoagulants utilized for sample collection. Most studies that have characterized differences in metabolite levels in various blood collection tubes have focused on single analytes. We define analyte levels on a global metabolomics platform following blood sampling using five different, but commonly used, clinical laboratory blood collection tubes (i.e., plasma anticoagulated with either EDTA, lithium heparin or sodium citrate, along with no additive (serum), and EDTA anticoagulated whole blood). Methods Using an untargeted metabolomics platform we analyzed five sample types after all had been collected and stored at -80°C. The biochemical composition was determined and differences between the samples established using matched-pair t-tests. Results We identified 1,117 biochemicals across all samples and detected a mean of 1,036 in the sample groups. Compared to the levels of metabolites in EDTA plasma, the number of biochemicals present at statistically significant different levels (p<0.05) ranged from 452 (serum) to 917 (whole blood). Several metabolites linked to screening assays for rare diseases including acylcarnitines, bilirubin and heme metabolites, nucleosides, and redox balance metabolites varied significantly across the sample collection types. Conclusions Our study highlights the widespread effects and importance of using consistent additives for assessing small molecule levels in clinical metabolomics. The biochemistry that occurs during the blood collection process creates a reproducible signal that can identify specimens collected with different anticoagulants in metabolomic studies. Impact statement In this manuscript, normal/healthy donors had peripheral blood collected using multiple anticoagulants as well as serum during a fasted blood draw. Global metabolomics is a new technology being utilized to draw clinical conclusions and we interrogated the effects of different anticoagulants on the levels of biochemicals from each of the donors. Characterizing the effects of the anticoagulants on biochemical levels will help researchers leverage the information using global metabolomics in order to make conclusions regarding important disease biomarkers.
Collapse
Affiliation(s)
- Adam D. Kennedy
- Metabolon, Morrisville, North Carolina, United States of America
- * E-mail:
| | - Lisa Ford
- Metabolon, Morrisville, North Carolina, United States of America
| | - Bryan Wittmann
- Metabolon, Morrisville, North Carolina, United States of America
| | - Jesse Conner
- Metabolon, Morrisville, North Carolina, United States of America
| | - Jacob Wulff
- Metabolon, Morrisville, North Carolina, United States of America
| | - Matthew Mitchell
- Metabolon, Morrisville, North Carolina, United States of America
| | - Anne M. Evans
- Metabolon, Morrisville, North Carolina, United States of America
| | - Douglas R. Toal
- Metabolon, Morrisville, North Carolina, United States of America
| |
Collapse
|
19
|
Goodman K, Mitchell M, Evans AM, Miller LAD, Ford L, Wittmann B, Kennedy AD, Toal D. Assessment of the effects of repeated freeze thawing and extended bench top processing of plasma samples using untargeted metabolomics. Metabolomics 2021; 17:31. [PMID: 33704583 DOI: 10.1007/s11306-021-01782-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 02/26/2021] [Indexed: 12/14/2022]
Abstract
INTRODUCTION Clinical metabolomics has utility as a screen for inborn errors of metabolism (IEM) and variant classification in patients with rare disease. It is important to understand and characterize preanalytical factors that influence assay performance during patient sample testing. OBJECTIVES To evaluate the impact of extended thawing of human EDTA plasma samples on ice prior to extraction as well as repeated freeze-thaw cycling of samples to identify compounds that are unstable prior to metabolomic analysis. METHODS Twenty-four (24) donor EDTA plasma samples were collected and immediately frozen at - 80 °C. Twelve samples were thawed on ice and extracted for analysis at time 0, 2, 4, and 6 h. Twelve other donor samples were repeatedly thawed and frozen up to four times and analyzed at each cycle. Compound levels at each time point/freeze-thaw cycle were compared to the control samples using matched-paired t tests to identify analytes affected by each condition. RESULTS We identified 1026 biochemicals across all samples. Incubation of thawed EDTA plasma samples on ice for up to 6 h resulted in < 1% of biochemicals changing significantly. Freeze-thaw cycles affected a greater percentage of the metabolome; ~ 2% of biochemicals changed after 3 freeze-thaw cycles. CONCLUSIONS Our study highlights that the number and magnitude of these changes are not as widespread as other aspects of improper sample handling. In total, < 3% of the metabolome detected on our clinical metabolomics platform should be disqualified when multiple freeze-thaw cycles or extended thawing at 4 °C are performed on a given sample.
Collapse
Affiliation(s)
- Kelli Goodman
- Metabolon, 617 Davis Drive, Suite 100, Morrisville, NC, 27560, USA
| | - Matthew Mitchell
- Metabolon, 617 Davis Drive, Suite 100, Morrisville, NC, 27560, USA
| | - Anne M Evans
- Metabolon, 617 Davis Drive, Suite 100, Morrisville, NC, 27560, USA
| | - Luke A D Miller
- Metabolon, 617 Davis Drive, Suite 100, Morrisville, NC, 27560, USA
| | - Lisa Ford
- Metabolon, 617 Davis Drive, Suite 100, Morrisville, NC, 27560, USA
| | - Bryan Wittmann
- Metabolon, 617 Davis Drive, Suite 100, Morrisville, NC, 27560, USA
| | - Adam D Kennedy
- Metabolon, 617 Davis Drive, Suite 100, Morrisville, NC, 27560, USA
| | - Douglas Toal
- Metabolon, 617 Davis Drive, Suite 100, Morrisville, NC, 27560, USA.
| |
Collapse
|
20
|
Murtas G, Marcone GL, Sacchi S, Pollegioni L. L-serine synthesis via the phosphorylated pathway in humans. Cell Mol Life Sci 2020; 77:5131-5148. [PMID: 32594192 PMCID: PMC11105101 DOI: 10.1007/s00018-020-03574-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 06/03/2020] [Accepted: 06/12/2020] [Indexed: 12/12/2022]
Abstract
L-serine is a nonessential amino acid in eukaryotic cells, used for protein synthesis and in producing phosphoglycerides, glycerides, sphingolipids, phosphatidylserine, and methylenetetrahydrofolate. Moreover, L-serine is the precursor of two relevant coagonists of NMDA receptors: glycine (through the enzyme serine hydroxymethyltransferase), which preferentially acts on extrasynaptic receptors and D-serine (through the enzyme serine racemase), dominant at synaptic receptors. The cytosolic "phosphorylated pathway" regulates de novo biosynthesis of L-serine, employing 3-phosphoglycerate generated by glycolysis and the enzymes 3-phosphoglycerate dehydrogenase, phosphoserine aminotransferase, and phosphoserine phosphatase (the latter representing the irreversible step). In the human brain, L-serine is primarily found in glial cells and is supplied to neurons for D-serine synthesis. Serine-deficient patients show severe neurological symptoms, including congenital microcephaly, psychomotor retardation, and intractable seizures, thus highlighting the relevance of de novo production of this amino acid in brain development and morphogenesis. Indeed, the phosphorylated pathway is strictly linked to cancer. Moreover, L-serine has been suggested as a ready-to-use treatment, as also recently proposed for Alzheimer's disease. Here, we present our current state of knowledge concerning the three mammalian enzymes of the phosphorylated pathway and known mutations related to pathological conditions: although the structure of these enzymes has been solved, how enzyme activity is regulated remains largely unknown. We believe that an in-depth investigation of these enzymes is crucial to identify the molecular mechanisms involved in modulating concentrations of the serine enantiomers and for studying the interplay between glial and neuronal cells and also to determine the most suitable therapeutic approach for various diseases.
Collapse
Affiliation(s)
- Giulia Murtas
- Department of Biotechnology and Life Sciences, University of Insubria, Via J. H. Dunant 3, 21100, Varese, Italy
| | - Giorgia Letizia Marcone
- Department of Biotechnology and Life Sciences, University of Insubria, Via J. H. Dunant 3, 21100, Varese, Italy
| | - Silvia Sacchi
- Department of Biotechnology and Life Sciences, University of Insubria, Via J. H. Dunant 3, 21100, Varese, Italy
| | - Loredano Pollegioni
- Department of Biotechnology and Life Sciences, University of Insubria, Via J. H. Dunant 3, 21100, Varese, Italy.
| |
Collapse
|
21
|
Douglas TD, Newby LK, Eckstrand J, Wixted D, Singh RH. Lipid changes in the metabolome of a single case study with maple syrup urine disease (MSUD) after five days of improved diet adherence of controlled branched-chain amino acids (BCAA). Mol Genet Metab Rep 2020; 25:100651. [PMID: 33088714 PMCID: PMC7567947 DOI: 10.1016/j.ymgmr.2020.100651] [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: 09/17/2020] [Accepted: 09/19/2020] [Indexed: 11/19/2022] Open
Abstract
Background Distinguishing systemic metabolic disruptions in maple syrup urine disease (MSUD) beyond amino acid pathways is under-investigated, yet important to understanding disease pathology and treatment options. Methods An adolescent female (15 years) with MSUD without liver transplant, attended 2 study visits, 5 days apart. Medical diet adherence was determined based on her 3-day diet records and plasma branched-chain amino acid (BCAA) concentrations at both study visits. Plasma from a single age- and sex-matched control (MURDOCK Study, Duke University) and the case patient were analyzed with UPLC/MS/MS for intensity (m/z), annotated, and normalized against a median of 1 (Metabolon, Morrisville NC). Differences between case/control and 5-day comparisons were defined as ≥ ǀ 0.5 ǀ. Results 434 lipid metabolites were identified across samples; 90 (20.7%) were higher and 120 (27.6%) lower in the MSUD case at baseline compared with control. By study visit 2, plasma BCAA had declined, while 48 (53%) of elevated lipids and 14 (11.7%) of lower lipid values had moved to within ǀ 0.5 ǀ of control. Most shifts towards control by day 5 were seen in long-chain fatty acid intermediates (42%) and acylcarnitines (32%). Although androgenic (28%) and bile acid (23%) metabolites increased towards control, neither reached control level by day 5. Discussion This comparative metabolomics study in a single MSUD case and healthy control suggests intrinsic differences in MSUD lipid metabolism potentially influenced by therapeutic diet. Findings suggest influences on hormone regulation, fatty acid oxidation, and bile acid synthesis, but further studies are needed to confirm an association between MSUD and lipid dysregulation. Synopsis Within 5 days of improved dietary adherence, a single MSUD case experienced substantial changes in lipid markers potentially related to changes in plasma branched-chain amino acids.
Collapse
Affiliation(s)
- Teresa D. Douglas
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
- Corresponding author.
| | - L. Kristin Newby
- Duke Clinical and Translational Science Institute (CTSI), Duke University School of Medicine, Durham, NC, USA
| | - Julie Eckstrand
- Duke Clinical and Translational Science Institute (CTSI), Duke University School of Medicine, Durham, NC, USA
| | - Douglas Wixted
- Duke Clinical and Translational Science Institute (CTSI), Duke University School of Medicine, Durham, NC, USA
| | - Rani H. Singh
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| |
Collapse
|
22
|
Abdelfattah F, Kariminejad A, Kahlert AK, Morrison PJ, Gumus E, Mathews KD, Darbro BW, Amor DJ, Walsh M, Sznajer Y, Weiß L, Weidensee S, Chitayat D, Shannon P, Bermejo-Sánchez E, Riaño-Galán I, Hayes I, Poke G, Rooryck C, Pennamen P, Khung-Savatovsky S, Toutain A, Vuillaume ML, Ghaderi-Sohi S, Kariminejad MH, Weinert S, Sticht H, Zenker M, Schanze D. Expanding the genotypic and phenotypic spectrum of severe serine biosynthesis disorders. Hum Mutat 2020; 41:1615-1628. [PMID: 32579715 DOI: 10.1002/humu.24067] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/31/2020] [Accepted: 06/22/2020] [Indexed: 12/21/2022]
Abstract
Serine biosynthesis disorders comprise a spectrum of very rare autosomal recessive inborn errors of metabolism with wide phenotypic variability. Neu-Laxova syndrome represents the most severe expression and is characterized by multiple congenital anomalies and pre- or perinatal lethality. Here, we present the mutation spectrum and a detailed phenotypic analysis in 15 unrelated families with severe types of serine biosynthesis disorders. We identified likely disease-causing variants in the PHGDH and PSAT1 genes, several of which have not been reported previously. Phenotype analysis and a comprehensive review of the literature corroborates the evidence that serine biosynthesis disorders represent a continuum with varying degrees of phenotypic expression and suggest that even gradual differences at the severe end of the spectrum may be correlated with particular genotypes. We postulate that the individual residual enzyme activity of mutant proteins is the major determinant of the phenotypic variability, but further functional studies are needed to explore effects at the enzyme protein level.
Collapse
Affiliation(s)
- Fatima Abdelfattah
- Institute of Human Genetics, University Hospital Magdeburg, Magdeburg, Germany
| | | | - Anne-Karin Kahlert
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Patrick J Morrison
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Evren Gumus
- Division of Medical Genetics, School of Medicine, Harran University, Sanliurfa, Turkey
| | | | | | - David J Amor
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia.,Royal Children's Hospital, Parkville, Victoria, Australia
| | - Maie Walsh
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Yves Sznajer
- Centre de Génétique Humaine, Cliniques Universitaires Saint Luc, Université Catholique de Louvain, Brussels, Belgium
| | - Luisa Weiß
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | | | - David Chitayat
- Department of Obstetrics and Gynecology, The Prenatal Diagnosis and Medical Genetics Program, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada.,Division of Clinical and Metabolic Genetics, The Hospital for SickKids, University of Toronto, Toronto, Ontario, Canada
| | - Patrick Shannon
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Eva Bermejo-Sánchez
- ECEMC (Spanish Collaborative Study of Congenital Malformations), Research Unit on Congenital Anomalies (UIAC), Institute of Rare Diseases Research (IIER), Institute of Health Carlos III, Ministry of Science and Innovation, Madrid, Spain
| | - Isolina Riaño-Galán
- AGC de Pediatría, Hospital Universitario Central de Asturias, Oviedo, Spain.,IUOPA-Departamento de Medicina-ISPA, Universidad de Oviedo, Oviedo, Spain.,CIBER de Epidemiologia y Salud Pública, Madrid, Spain
| | - Ian Hayes
- Genetic Health Service New Zealand, Auckland Hospital, Auckland, New Zealand
| | - Gemma Poke
- Genetic Health Service New Zealand, Wellington Regional Hospital, Wellington, New Zealand
| | - Caroline Rooryck
- MRGM INSERM U1211, CHU de Bordeaux, Service de Génétique Médicale, University of Bordeaux, Bordeaux, France
| | - Perrine Pennamen
- MRGM INSERM U1211, CHU de Bordeaux, Service de Génétique Médicale, University of Bordeaux, Bordeaux, France
| | | | - Annick Toutain
- Service de Génétique, CHU de Tours, UMR 1253, iBrain, Université de Tours, INSERM, Tours, France
| | - Marie-Laure Vuillaume
- Service de Génétique, CHU de Tours, UMR 1253, iBrain, Université de Tours, INSERM, Tours, France
| | | | | | - Sönke Weinert
- Department of Cardiology and Angiology, Internal Medicine, University Hospital Magdeburg, Magdeburg, Germany
| | - Heinrich Sticht
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Martin Zenker
- Institute of Human Genetics, University Hospital Magdeburg, Magdeburg, Germany
| | - Denny Schanze
- Institute of Human Genetics, University Hospital Magdeburg, Magdeburg, Germany
| |
Collapse
|
23
|
Zhou C, He M, Peng C, Yu J, Li Z, Zhou M, Li Y, Yang S, Ouyang H, Feng Y. Pharmacokinetic and Lipidomic Assessment of the In Vivo Effects of Parishin A-Isorhynchophylline in Rat Migraine Models. JOURNAL OF ANALYTICAL METHODS IN CHEMISTRY 2020; 2020:9101598. [PMID: 32695549 PMCID: PMC7362284 DOI: 10.1155/2020/9101598] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 03/27/2020] [Indexed: 06/11/2023]
Abstract
Migraine is a chronic brain disease that leads to periodic neurological attacks. Parishin A and isorhynchophylline (PI) is the active monomer component extracted from the traditional antimigraine Chinese medicinal combination of Gastrodia and Uncaria, respectively. In this study, using high-performance liquid chromatography coupled with tandem mass spectrometry (HPLC-MS/MS) technology, we performed pharmacokinetic and lipidomic study on migraine model rats after administration of PI. For the detection of the compounds in plasma, AB Sciex Triple Quad™ 4500 was applied for quantitative analysis, and the COSMOSIL C18 column (2.1 × 100 mm, 2.6 μm) was used for separation. Isorhynchophylline (ISO: m/z 384.8-241.2) and its main metabolite rhynchophylline (RHY: m/z 384.8-160.2) were simultaneously detected under positive ion modes. Besides, parishin A (PA: m/z 995.1-726.9) and its main metabolite gastrodin (GAS: m/z 331.1-123.0) were simultaneously detected with negative ion modes. For the analysis of endogenous lipid components, Dionex Ultimate 3000 (UHPLC) Thermo Orbitrap Elite was applied for the detection, and the Waters UPLCRBEH C18 column (1.7 μm 100 ∗ 2.1 mm) was used for separation. Chloroform/methanol (2 : 1, v : v) was used for extraction. The results demonstrated that PI exists significant difference in metabolism between single- and coadministration and can regulate lipid levels associated with migraine.
Collapse
Affiliation(s)
- Chaoqun Zhou
- Jiangxi University of Traditional Chinese Medicine, Nanchang, China
| | - Mingzhen He
- Jiangxi University of Traditional Chinese Medicine, Nanchang, China
- State Key Laboratory of Innovative Drug and Efficient Energy-Saving Pharmaceutical Equipment, Nanchang, China
| | - Chunyan Peng
- Jiangxi University of Traditional Chinese Medicine, Nanchang, China
| | - Jianjun Yu
- Jiangxi University of Traditional Chinese Medicine, Nanchang, China
| | - Zhifeng Li
- Jiangxi University of Traditional Chinese Medicine, Nanchang, China
- State Key Laboratory of Innovative Drug and Efficient Energy-Saving Pharmaceutical Equipment, Nanchang, China
| | - Maofu Zhou
- Jiangxi University of Traditional Chinese Medicine, Nanchang, China
| | - Yan Li
- Jiangxi University of Traditional Chinese Medicine, Nanchang, China
| | - Shilin Yang
- State Key Laboratory of Innovative Drug and Efficient Energy-Saving Pharmaceutical Equipment, Nanchang, China
| | - Hui Ouyang
- Jiangxi University of Traditional Chinese Medicine, Nanchang, China
| | - Yulin Feng
- Jiangxi University of Traditional Chinese Medicine, Nanchang, China
- State Key Laboratory of Innovative Drug and Efficient Energy-Saving Pharmaceutical Equipment, Nanchang, China
| |
Collapse
|
24
|
Sirr A, Lo RS, Cromie GA, Scott AC, Ashmead J, Heyesus M, Dudley AM. A yeast-based complementation assay elucidates the functional impact of 200 missense variants in human PSAT1. J Inherit Metab Dis 2020; 43:758-769. [PMID: 32077105 PMCID: PMC7444316 DOI: 10.1002/jimd.12227] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 02/12/2020] [Accepted: 02/17/2020] [Indexed: 11/10/2022]
Abstract
Defects in serine biosynthesis resulting from loss of function mutations in PHGDH, PSAT1, and PSPH cause a set of rare, autosomal recessive diseases known as Neu-Laxova syndrome (NLS) or serine-deficiency disorders. The diseases present with a broad range of phenotypes including lethality, severe neurological manifestations, seizures, and intellectual disability. However, because L-serine supplementation, especially if started prenatally, can ameliorate and in some cases even prevent symptoms, knowledge of pathogenic variants is medically actionable. Here, we describe a functional assay that leverages the evolutionary conservation of an enzyme in the serine biosynthesis pathway, phosphoserine aminotransferase, and the ability of the human protein-coding sequence (PSAT1) to functionally replace its yeast ortholog (SER1). Results from our quantitative, yeast-based assay agree well with clinical annotations and expectations based on the disease literature. Using this assay, we have measured the functional impact of the 199 PSAT1 variants currently listed in ClinVar, gnomAD, and the literature. We anticipate that the assay could be used to comprehensively assess the functional impact of all SNP-accessible amino acid substitution mutations in PSAT1, a resource that could aid variant interpretation and identify potential NLS carriers.
Collapse
Affiliation(s)
- Amy Sirr
- Pacific Northwest Research Institute, Seattle, Washington, USA
| | - Russell S. Lo
- Pacific Northwest Research Institute, Seattle, Washington, USA
| | | | - Adrian C. Scott
- Pacific Northwest Research Institute, Seattle, Washington, USA
| | - Julee Ashmead
- Pacific Northwest Research Institute, Seattle, Washington, USA
| | - Mirutse Heyesus
- Pacific Northwest Research Institute, Seattle, Washington, USA
| | - Aimée M. Dudley
- Pacific Northwest Research Institute, Seattle, Washington, USA
| |
Collapse
|
25
|
Almontashiri NAM, Zha L, Young K, Law T, Kellogg MD, Bodamer OA, Peake RWA. Clinical Validation of Targeted and Untargeted Metabolomics Testing for Genetic Disorders: A 3 Year Comparative Study. Sci Rep 2020; 10:9382. [PMID: 32523032 PMCID: PMC7287104 DOI: 10.1038/s41598-020-66401-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 05/19/2020] [Indexed: 02/04/2023] Open
Abstract
Global untargeted metabolomics (GUM) has entered clinical diagnostics for genetic disorders. We compared the clinical utility of GUM with traditional targeted metabolomics (TM) as a screening tool in patients with established genetic disorders and determined the scope of GUM as a discovery tool in patients with no diagnosis under investigation. We compared TM and GUM data in 226 patients. The first cohort (n = 87) included patients with confirmed inborn errors of metabolism (IEM) and genetic syndromes; the second cohort (n = 139) included patients without diagnosis who were undergoing evaluation for a genetic disorder. In patients with known disorders (n = 87), GUM performed with a sensitivity of 86% (95% CI: 78–91) compared with TM for the detection of 51 diagnostic metabolites. The diagnostic yield of GUM in patients under evaluation with no established diagnosis (n = 139) was 0.7%. GUM successfully detected the majority of diagnostic compounds associated with known IEMs. The diagnostic yield of both targeted and untargeted metabolomics studies is low when assessing patients with non-specific, neurological phenotypes. GUM shows promise as a validation tool for variants of unknown significance in candidate genes in patients with non-specific phenotypes.
Collapse
Affiliation(s)
- Naif A M Almontashiri
- Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Faculty of Applied Medical Sciences and the Center for Genetics and Inherited Disorders, Taibah University, Almadinah Almunwarah, Saudi Arabia
| | - Li Zha
- Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Kim Young
- Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Terence Law
- Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Mark D Kellogg
- Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Olaf A Bodamer
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Broad Institute of Harvard University and MIT, Cambridge, Massachusetts, USA
| | - Roy W A Peake
- Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.
| |
Collapse
|
26
|
Vaz FM, McDermott JH, Alders M, Wortmann SB, Kölker S, Pras-Raves ML, Vervaart MAT, van Lenthe H, Luyf ACM, Elfrink HL, Metcalfe K, Cuvertino S, Clayton PE, Yarwood R, Lowe MP, Lovell S, Rogers RC, van Kampen AHC, Ruiter JPN, Wanders RJA, Ferdinandusse S, van Weeghel M, Engelen M, Banka S. Mutations in PCYT2 disrupt etherlipid biosynthesis and cause a complex hereditary spastic paraplegia. Brain 2020; 142:3382-3397. [PMID: 31637422 PMCID: PMC6821184 DOI: 10.1093/brain/awz291] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 06/07/2019] [Accepted: 07/16/2019] [Indexed: 11/14/2022] Open
Abstract
CTP:phosphoethanolamine cytidylyltransferase (ET), encoded by PCYT2, is the rate-limiting enzyme for phosphatidylethanolamine synthesis via the CDP-ethanolamine pathway. Phosphatidylethanolamine is one of the most abundant membrane lipids and is particularly enriched in the brain. We identified five individuals with biallelic PCYT2 variants clinically characterized by global developmental delay with regression, spastic para- or tetraparesis, epilepsy and progressive cerebral and cerebellar atrophy. Using patient fibroblasts we demonstrated that these variants are hypomorphic, result in altered but residual ET protein levels and concomitant reduced enzyme activity without affecting mRNA levels. The significantly better survival of hypomorphic CRISPR-Cas9 generated pcyt2 zebrafish knockout compared to a complete knockout, in conjunction with previously described data on the Pcyt2 mouse model, indicates that complete loss of ET function may be incompatible with life in vertebrates. Lipidomic analysis revealed profound lipid abnormalities in patient fibroblasts impacting both neutral etherlipid and etherphospholipid metabolism. Plasma lipidomics studies also identified changes in etherlipids that have the potential to be used as biomarkers for ET deficiency. In conclusion, our data establish PCYT2 as a disease gene for a new complex hereditary spastic paraplegia and confirm that etherlipid homeostasis is important for the development and function of the brain.
Collapse
Affiliation(s)
- Frédéric M Vaz
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry, Amsterdam Gastroenterology and Metabolism, Meibergdreef 9, AZ Amsterdam, The Netherlands
| | - John H McDermott
- Manchester Centre for Genomics Medicine, St Mary's Hospital, Manchester University Hospital Foundation Trust, Health Innovation Manchester, Oxford Road, Manchester, UK
| | - Mariëlle Alders
- Laboratory Genome Diagnostics, Amsterdam UMC, University of Amsterdam, Department of Clinical Genetics, Amsterdam Reproduction and Development, Meibergdreef 9, AZ Amsterdam, The Netherlands
| | - Saskia B Wortmann
- Institute of Human Genetics, Technical University München, Munich, Germany.,Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany.,University Children's Hospital, Paracelsus Medical University, Salzburg, Austria
| | - Stefan Kölker
- Division of Pediatric Neurology and Metabolic Medicine, Centre for Pediatric and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Mia L Pras-Raves
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry, Amsterdam Gastroenterology and Metabolism, Meibergdreef 9, AZ Amsterdam, The Netherlands.,Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam Public Health research institute, Amsterdam UMC, University of Amsterdam, Amsterdam AZ, The Netherlands
| | - Martin A T Vervaart
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry, Amsterdam Gastroenterology and Metabolism, Meibergdreef 9, AZ Amsterdam, The Netherlands
| | - Henk van Lenthe
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry, Amsterdam Gastroenterology and Metabolism, Meibergdreef 9, AZ Amsterdam, The Netherlands
| | - Angela C M Luyf
- Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam Public Health research institute, Amsterdam UMC, University of Amsterdam, Amsterdam AZ, The Netherlands
| | - Hyung L Elfrink
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry, Amsterdam Gastroenterology and Metabolism, Meibergdreef 9, AZ Amsterdam, The Netherlands
| | - Kay Metcalfe
- Manchester Centre for Genomics Medicine, St Mary's Hospital, Manchester University Hospital Foundation Trust, Health Innovation Manchester, Oxford Road, Manchester, UK
| | - Sara Cuvertino
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Peter E Clayton
- Department of Pediatric Endocrinology, Royal Manchester Children's Hospital, Manchester University Hospital Foundation Trust, Oxford Road, Manchester, UK
| | - Rebecca Yarwood
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Martin P Lowe
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Simon Lovell
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Richard C Rogers
- Greenwood Genetic Center, 14 Edgewood Drive, Greenville, SC, USA
| | | | - Antoine H C van Kampen
- Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam Public Health research institute, Amsterdam UMC, University of Amsterdam, Amsterdam AZ, The Netherlands.,Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, XH Amsterdam, The Netherlands
| | - Jos P N Ruiter
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry, Amsterdam Gastroenterology and Metabolism, Meibergdreef 9, AZ Amsterdam, The Netherlands
| | - Ronald J A Wanders
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry, Amsterdam Gastroenterology and Metabolism, Meibergdreef 9, AZ Amsterdam, The Netherlands
| | - Sacha Ferdinandusse
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry, Amsterdam Gastroenterology and Metabolism, Meibergdreef 9, AZ Amsterdam, The Netherlands
| | - Michel van Weeghel
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry, Amsterdam Gastroenterology and Metabolism, Meibergdreef 9, AZ Amsterdam, The Netherlands
| | - Marc Engelen
- Department of (Pediatric) Neurology, Emma Children's Hospital, Amsterdam UMC, Amsterdam, The Netherlands
| | - Siddharth Banka
- Manchester Centre for Genomics Medicine, St Mary's Hospital, Manchester University Hospital Foundation Trust, Health Innovation Manchester, Oxford Road, Manchester, UK.,Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| |
Collapse
|
27
|
Mordaunt D, Cox D, Fuller M. Metabolomics to Improve the Diagnostic Efficiency of Inborn Errors of Metabolism. Int J Mol Sci 2020; 21:ijms21041195. [PMID: 32054038 PMCID: PMC7072749 DOI: 10.3390/ijms21041195] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 02/08/2020] [Accepted: 02/09/2020] [Indexed: 12/21/2022] Open
Abstract
Early diagnosis of inborn errors of metabolism (IEM)—a large group of congenital disorders—is critical, given that many respond well to targeted therapy. Newborn screening programs successfully capture a proportion of patients enabling early recognition and prompt initiation of therapy. For others, the heterogeneity in clinical presentation often confuses diagnosis with more common conditions. In the absence of family history and following clinical suspicion, the laboratory diagnosis typically begins with broad screening tests to circumscribe specialised metabolite and/or enzyme assays to identify the specific IEM. Confirmation of the biochemical diagnosis is usually achieved by identifying pathogenic genetic variants that will also enable cascade testing for family members. Unsurprisingly, this diagnostic trajectory is too often a protracted and lengthy process resulting in delays in diagnosis and, importantly, therapeutic intervention for these rare conditions is also postponed. Implementation of mass spectrometry technologies coupled with the expanding field of metabolomics is changing the landscape of diagnosing IEM as numerous metabolites, as well as enzymes, can now be measured collectively on a single mass spectrometry-based platform. As the biochemical consequences of impaired metabolism continue to be elucidated, the measurement of secondary metabolites common across groups of IEM will facilitate algorithms to further increase the efficiency of diagnosis.
Collapse
Affiliation(s)
- Dylan Mordaunt
- Genetics and Molecular Pathology, SA Pathology at Women’s and Children’s Hospital, 72 King William Road, North Adelaide, SA 5006, Australia; (D.M.); (D.C.)
- School of Medicine, University of Adelaide, Adelaide, SA 5000, Australia
| | - David Cox
- Genetics and Molecular Pathology, SA Pathology at Women’s and Children’s Hospital, 72 King William Road, North Adelaide, SA 5006, Australia; (D.M.); (D.C.)
| | - Maria Fuller
- Genetics and Molecular Pathology, SA Pathology at Women’s and Children’s Hospital, 72 King William Road, North Adelaide, SA 5006, Australia; (D.M.); (D.C.)
- School of Medicine, University of Adelaide, Adelaide, SA 5000, Australia
- Correspondence: ; Tel.: +61-8-8161-6741
| |
Collapse
|
28
|
Nguyen JH, Chung JD, Lynch GS, Ryall JG. The Microenvironment Is a Critical Regulator of Muscle Stem Cell Activation and Proliferation. Front Cell Dev Biol 2019; 7:254. [PMID: 31737625 PMCID: PMC6828616 DOI: 10.3389/fcell.2019.00254] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 10/14/2019] [Indexed: 12/21/2022] Open
Abstract
Skeletal muscle has a remarkable capacity to regenerate following injury, a property conferred by a resident population of muscle stem cells (MuSCs). In response to injury, MuSCs must double their cellular content to divide, a process requiring significant new biomass in the form of nucleotides, phospholipids, and amino acids. This new biomass is derived from a series of intracellular metabolic cycles and alternative routing of carbon. In this review, we examine the link between metabolism and skeletal muscle regeneration with particular emphasis on the role of the cellular microenvironment in supporting the production of new biomass and MuSC proliferation.
Collapse
Affiliation(s)
- John H Nguyen
- Department of Physiology, Centre for Muscle Research, The University of Melbourne, Melbourne, VIC, Australia
| | - Jin D Chung
- Department of Physiology, Centre for Muscle Research, The University of Melbourne, Melbourne, VIC, Australia
| | - Gordon S Lynch
- Department of Physiology, Centre for Muscle Research, The University of Melbourne, Melbourne, VIC, Australia
| | - James G Ryall
- Department of Physiology, Centre for Muscle Research, The University of Melbourne, Melbourne, VIC, Australia
| |
Collapse
|
29
|
Haijes HA, van der Ham M, Gerrits J, van Hasselt PM, Prinsen HCMT, de Sain-van der Velden MGM, Verhoeven-Duif NM, Jans JJM. Direct-infusion based metabolomics unveils biochemical profiles of inborn errors of metabolism in cerebrospinal fluid. Mol Genet Metab 2019; 127:51-57. [PMID: 30926434 DOI: 10.1016/j.ymgme.2019.03.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 03/11/2019] [Accepted: 03/14/2019] [Indexed: 12/14/2022]
Abstract
BACKGROUND For inborn errors of metabolism (IEM), metabolomics is performed for three main purposes: 1) development of next generation metabolic screening platforms, 2) identification of new biomarkers in predefined patient cohorts and 3) for identification of new IEM. To date, plasma, urine and dried blood spots are used. We anticipate that cerebrospinal fluid (CSF) holds additional - valuable - information, especially for IEM with neurological involvement. To expand metabolomics to CSF, we here tested whether direct-infusion high-resolution mass spectrometry (DI-HRMS) based non-quantitative metabolomics could correctly capture the biochemical profile of patients with an IEM in CSF. METHODS Eleven patient samples, harboring eight different IEM, and thirty control samples were analyzed using DI-HRMS. First we assessed whether the biochemical profile of the control samples represented the expected profile in CSF. Next, each patient sample was assigned a 'most probable diagnosis' by an investigator blinded for the known diagnoses of the patients. RESULTS the biochemical profile identified using DI-HRMS in CSF samples resembled the known profile, with - among others - the highest median intensities for mass peaks annotated with glucose, lactic acid, citric acid and glutamine. Subsequent analysis of patient CSF profiles resulted in correct 'most probable diagnoses' for all eleven patients, including non-ketotic hyperglycinaemia, propionic aciduria, purine nucleoside phosphorylase deficiency, argininosuccinic aciduria, tyrosinaemia type I, hyperphenylalaninemia and hypermethioninaemia. CONCLUSION We here demonstrate that DI-HRMS based non-quantitative metabolomics accurately captures the biochemical profile of this set of patients in CSF, opening new ways for using metabolomics in CSF in the metabolic diagnostic laboratory.
Collapse
Affiliation(s)
- Hanneke A Haijes
- Section Metabolic Diagnostics, Department of Biomedical Genetics, Centre for Molecular Medicine, University Medical Centre Utrecht, Utrecht University, Lundlaan 6, 3584 EA Utrecht, The Netherlands; Section Metabolic Diseases, Department of Child Health, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht University, Lundlaan 6, 3584 EA Utrecht, The Netherlands
| | - Maria van der Ham
- Section Metabolic Diagnostics, Department of Biomedical Genetics, Centre for Molecular Medicine, University Medical Centre Utrecht, Utrecht University, Lundlaan 6, 3584 EA Utrecht, The Netherlands
| | - Johan Gerrits
- Section Metabolic Diagnostics, Department of Biomedical Genetics, Centre for Molecular Medicine, University Medical Centre Utrecht, Utrecht University, Lundlaan 6, 3584 EA Utrecht, The Netherlands
| | - Peter M van Hasselt
- Section Metabolic Diseases, Department of Child Health, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht University, Lundlaan 6, 3584 EA Utrecht, The Netherlands
| | - Hubertus C M T Prinsen
- Section Metabolic Diagnostics, Department of Biomedical Genetics, Centre for Molecular Medicine, University Medical Centre Utrecht, Utrecht University, Lundlaan 6, 3584 EA Utrecht, The Netherlands
| | - Monique G M de Sain-van der Velden
- Section Metabolic Diagnostics, Department of Biomedical Genetics, Centre for Molecular Medicine, University Medical Centre Utrecht, Utrecht University, Lundlaan 6, 3584 EA Utrecht, The Netherlands
| | - Nanda M Verhoeven-Duif
- Section Metabolic Diagnostics, Department of Biomedical Genetics, Centre for Molecular Medicine, University Medical Centre Utrecht, Utrecht University, Lundlaan 6, 3584 EA Utrecht, The Netherlands
| | - Judith J M Jans
- Section Metabolic Diagnostics, Department of Biomedical Genetics, Centre for Molecular Medicine, University Medical Centre Utrecht, Utrecht University, Lundlaan 6, 3584 EA Utrecht, The Netherlands.
| |
Collapse
|
30
|
Direct Infusion Based Metabolomics Identifies Metabolic Disease in Patients' Dried Blood Spots and Plasma. Metabolites 2019; 9:metabo9010012. [PMID: 30641898 PMCID: PMC6359237 DOI: 10.3390/metabo9010012] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/04/2019] [Accepted: 01/08/2019] [Indexed: 01/17/2023] Open
Abstract
In metabolic diagnostics, there is an emerging need for a comprehensive test to acquire a complete view of metabolite status. Here, we describe a non-quantitative direct-infusion high-resolution mass spectrometry (DI-HRMS) based metabolomics method and evaluate the method for both dried blood spots (DBS) and plasma. 110 DBS of 42 patients harboring 23 different inborn errors of metabolism (IEM) and 86 plasma samples of 38 patients harboring 21 different IEM were analyzed using DI-HRMS. A peak calling pipeline developed in R programming language provided Z-scores for ~1875 mass peaks corresponding to ~3835 metabolite annotations (including isomers) per sample. Based on metabolite Z-scores, patients were assigned a ‘most probable diagnosis’ by an investigator blinded for the known diagnoses of the patients. Based on DBS sample analysis, 37/42 of the patients, corresponding to 22/23 IEM, could be correctly assigned a ‘most probable diagnosis’. Plasma sample analysis, resulted in a correct ‘most probable diagnosis’ in 32/38 of the patients, corresponding to 19/21 IEM. The added clinical value of the method was illustrated by a case wherein DI-HRMS metabolomics aided interpretation of a variant of unknown significance (VUS) identified by whole-exome sequencing. In summary, non-quantitative DI-HRMS metabolomics in DBS and plasma is a very consistent, high-throughput and nonselective method for investigating the metabolome in genetic disease.
Collapse
|
31
|
Diop F, Vial T, Ferraris P, Wichit S, Bengue M, Hamel R, Talignani L, Liegeois F, Pompon J, Yssel H, Marti G, Missé D. Zika virus infection modulates the metabolomic profile of microglial cells. PLoS One 2018; 13:e0206093. [PMID: 30359409 PMCID: PMC6201926 DOI: 10.1371/journal.pone.0206093] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 10/06/2018] [Indexed: 11/25/2022] Open
Abstract
Zika virus (ZIKV) is an emerging arbovirus of the Flaviviridae family. Although infection with ZIKV generally leads to mild disease, its recent emergence in the Americas has been associated with an increase in the development of the Guillain-Barré syndrome in adults, as well as with neurological complications, in particular congenital microcephaly, in new-borns. To date, little information is available on neuroinflammation induced by ZIKV, notably in microglial cells in the context of their metabolic activity, a series of chemical transformations that are essential for their growth, reproduction, structural maintenance and environmental responses. Therefore, in the present study we investigated the metabolomic profile of ZIKV-infected microglia. Microglial cells were exposed to ZIKV at different time points and were analyzed by a Liquid Chromatography-High Resolution mass spectrometry-based metabolomic approach. The results show that ZIKV infection in microglia leads to modulation of the expression of numerous metabolites, including lysophospholipids, particulary Lysophosphatidylcholine, and phospholipids such as Phosphatidylcholine, Phosphatidylserine, Ceramide and Sphingomyelin, and carboxylicic acids as Undecanedioic and Dodecanedioic acid. Some of these metabolites are involved in neuronal differentiation, regulation of apoptosis, virion architecture and viral replication. ZIKV infection was associated with concomitant secretion of inflammatory mediators linked with central nervous system inflammation such as IL-6, TNF-α, IL-1β, iNOS and NO. It also resulted in the upregulation of the expression of the gene encoding CX3CR1, a chemokine receptor known to regulate functional synapse plasticity and signaling between microglial cells. These findings highlight an important role for microglia and their metabolites in the process of neuroinflammation that occurs during ZIKV pathogenesis.
Collapse
Affiliation(s)
- Fodé Diop
- MIVEGEC UMR 224, Univ Montpellier, IRD, CNRS, Montpellier, France
| | - Thomas Vial
- PHARMADEV UMR 152, Université de Toulouse, IRD, Toulouse, France
| | - Pauline Ferraris
- MIVEGEC UMR 224, Univ Montpellier, IRD, CNRS, Montpellier, France
| | - Sineewanlaya Wichit
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Salaya, Thailand
| | - Michèle Bengue
- MIVEGEC UMR 224, Univ Montpellier, IRD, CNRS, Montpellier, France
| | - Rodolphe Hamel
- MIVEGEC UMR 224, Univ Montpellier, IRD, CNRS, Montpellier, France
| | - Loïc Talignani
- MIVEGEC UMR 224, Univ Montpellier, IRD, CNRS, Montpellier, France
| | - Florian Liegeois
- MIVEGEC UMR 224, Univ Montpellier, IRD, CNRS, Montpellier, France
| | - Julien Pompon
- MIVEGEC UMR 224, Univ Montpellier, IRD, CNRS, Montpellier, France
| | - Hans Yssel
- Centre d’Immunologie et des Maladies Infectieuses, Inserm, U1135, Sorbonne Universités, UPMC, APHP Hôpital Pitié-Salpêtrière, Paris, France
| | - Guillaume Marti
- PHARMADEV UMR 152, Université de Toulouse, IRD, Toulouse, France
| | - Dorothée Missé
- MIVEGEC UMR 224, Univ Montpellier, IRD, CNRS, Montpellier, France
- * E-mail:
| |
Collapse
|
32
|
Ferreira CR, Goorden SMI, Soldatos A, Byers HM, Ghauharali-van der Vlugt JMM, Beers-Stet FS, Groden C, van Karnebeek CD, Gahl WA, Vaz FM, Jiang X, Vernon HJ. Deoxysphingolipid precursors indicate abnormal sphingolipid metabolism in individuals with primary and secondary disturbances of serine availability. Mol Genet Metab 2018; 124:204-209. [PMID: 29789193 PMCID: PMC6057808 DOI: 10.1016/j.ymgme.2018.05.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 05/02/2018] [Accepted: 05/03/2018] [Indexed: 12/27/2022]
Abstract
Patients with primary serine biosynthetic defects manifest with intellectual disability, microcephaly, ichthyosis, seizures and peripheral neuropathy. The underlying pathogenesis of peripheral neuropathy in these patients has not been elucidated, but could be related to a decrease in the availability of certain classical sphingolipids, or to an increase in atypical sphingolipids. Here, we show that patients with primary serine deficiency have a statistically significant elevation in specific atypical sphingolipids, namely deoxydihydroceramides of 18-22 carbons in acyl length. We also show that patients with aberrant plasma serine and alanine levels secondary to mitochondrial disorders also display peripheral neuropathy along with similar elevations of atypical sphingolipids. We hypothesize that the etiology of peripheral neuropathy in patients with primary mitochondrial disorders is related to this elevation of deoxysphingolipids, in turn caused by increased availability of alanine and decreased availability of serine. These findings could have important therapeutic implications for the management of these patients.
Collapse
Affiliation(s)
- C R Ferreira
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA; Division of Genetics and Metabolism, Children's National Health System, Washington, DC, USA
| | - S M I Goorden
- Laboratory Genetic Metabolic Diseases, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - A Soldatos
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - H M Byers
- Division of Medical Genetics, Stanford University, Palo Alto, CA, USA
| | | | - F S Beers-Stet
- Laboratory Genetic Metabolic Diseases, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - C Groden
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - C D van Karnebeek
- Departments of Pediatrics and Clinical Genetics, Academic Medical Centre, Amsterdam, The Netherlands
| | - W A Gahl
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - F M Vaz
- Laboratory Genetic Metabolic Diseases, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - X Jiang
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - H J Vernon
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| |
Collapse
|