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Grijseels S, Vasskog T, Heinsvig PJ, Myhre TN, Hansen T, Mardal M. Validation of two LCHRMS methods for large-scale untargeted metabolomics of serum samples: Strategy to establish method fitness-for-purpose. J Chromatogr A 2024; 1732:465230. [PMID: 39142167 DOI: 10.1016/j.chroma.2024.465230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 07/22/2024] [Accepted: 08/06/2024] [Indexed: 08/16/2024]
Abstract
Untargeted metabolomics by LCHRMS is a powerful tool to enhance our knowledge of pathophysiological processes. Whereas validation of a bioanalytical method is customary in most analytical chemistry fields, it is rarely performed for untargeted metabolomics. This study aimed to establish and validate an analytical platform for a long-term, clinical metabolomics study. Sample preparation was performed with an automated liquid handler and four analytical methods were developed and evaluated. The validation study spanned three batches with twelve runs using individual serum samples and various quality control samples. Data was acquired with untargeted acquisition and only metabolites identified at level 1 were evaluated. Validation parameters were set to evaluate key performance metrics relevant for the intended application: reproducibility, repeatability, stability, and identification selectivity, emphasizing dataset intrinsic variance. Concordance of semi-quantitative results between methods was evaluated to identify potential bias. Spearman rank correlation coefficients (rs) were calculated from individual serum samples. Of the four methods tested, two were selected for validation. A total of 47 and 55 metabolites (RPLC-ESI+- and HILIC-ESI--HRMS, respectively) met specified validation criteria. Quality assurance involved system suitability testing, sample release, run release, and batch release. The median repeatability and within-run reproducibility as coefficient of variation% for metabolites that passed validation on RPLC-ESI+- and HILIC-ESI--HRMS were 4.5 and 4.6, and 1.5 and 3.8, respectively. Metabolites that passed validation on RPLC-ESI+-HRMS had a median D-ratio of 1.91, and 89 % showed good signal intensity after ten-fold dilution. The corresponding numbers for metabolites with the HILIC-ESI--HRMS method was 1.45 and 45 %, respectively. The rs median ({range}) for metabolites that passed validation on RPLC-ESI+- was 0.93 (N = 9 {0.69-0.98}) and on HILIC-ESI--HRMS was 0.93 (N = 22 {0.55-1.00}). The validated methods proved fit-for-purpose and the laboratory thus demonstrated its capability to produce reliable results for a large-scale, untargeted metabolomics study. This validation not only bolsters the reliability of the assays but also significantly enhances the impact and credibility of the hypotheses generated from the studies. Therefore, this validation study serves as a benchmark in the documentation of untargeted metabolomics, potentially guiding future endeavors in the field.
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Affiliation(s)
- Sietske Grijseels
- Proteomics and Metabolomics Core Facility, Department of Medical Biology, UiT - the Arctic University of Norway, Tromsø, Norway
| | - Terje Vasskog
- Natural Products and Medicinal Chemistry Research Group, Department of Pharmacy, UiT - the Arctic University of Norway, Tromsø, Norway
| | - Pia J Heinsvig
- Section of Forensic Chemistry, Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Torbjørn N Myhre
- Natural Products and Medicinal Chemistry Research Group, Department of Pharmacy, UiT - the Arctic University of Norway, Tromsø, Norway
| | - Terkel Hansen
- Natural Products and Medicinal Chemistry Research Group, Department of Pharmacy, UiT - the Arctic University of Norway, Tromsø, Norway; Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Marie Mardal
- Natural Products and Medicinal Chemistry Research Group, Department of Pharmacy, UiT - the Arctic University of Norway, Tromsø, Norway; Section of Forensic Chemistry, Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark.
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Cui M, Guo Q, Zhao S, Liu X, Yang C, Liu P, Wang L. An untargeted comparative metabolomics analysis of infants with and without late-onset breast milk jaundice. PLoS One 2024; 19:e0308710. [PMID: 39133689 PMCID: PMC11318923 DOI: 10.1371/journal.pone.0308710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Accepted: 07/29/2024] [Indexed: 08/15/2024] Open
Abstract
BACKGROUND Late-onset breast milk jaundice (LBMJ) is a common form of hyperbilirubinemia, which can result in serious complications for newborns with persistently high bilirubin levels. The aim of this study was to investigate the differences in fecal metabolites between breastfed infants with and without LBMJ in order to elucidate potential biological mechanisms. METHODS Biological samples were collected from 12 infants with LBMJ and 12 healthy individuals. Ultra-high performance liquid chromatography quadrupole time-of-flight tandem mass spectrometry (UHPLC-Q-TOF/MS) was utilized for non-targeted determination of fecal metabolites. Principal components analysis (PCA), cluster analysis, and differential metabolite analysis were performed in both positive ion mode and negative ion mode for the two groups. Additionally, the KEGG database was employed to comprehensively analyze the pathways of differential metabolites. RESULTS There were no significant differences in maternal and neonatal demographic characteristics between the two groups (p > 0.05). The results of PCA and cluster heat map analysis in both modes showed that there were significant differences in metabolites between the two groups. Among 751 differential metabolites (DMs) detected in positive ion mode, 720 were up-regulated in the case group while 31 were down-regulated. In negative ion mode, 1891 DMs were detected, including 817 up-regulated metabolites and 1074 down-regulated metabolites in the case group. Analysis of differential metabolic pathways showed that the DMs of the two groups were mainly annotated and enriched in Biotin metabolism, N-Glycan biosynthesis, Taurine and hypotaurine metabolism, Pyrimidine metabolism, and Pentose and glucuronate interconversions. CONCLUSION Significant differences exist in fecal metabolites between LBMJ infants and healthy controls. The study of differential metabolic pathways provides insights into the mechanism of LBMJ.
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Affiliation(s)
- Mingxuan Cui
- Department of Clinical Nutrition, Peking University People’s Hospital, Beijing, China
| | - Qianying Guo
- Department of Clinical Nutrition, Peking University People’s Hospital, Beijing, China
| | - Shilong Zhao
- Department of Clinical Nutrition, Peking University People’s Hospital, Beijing, China
| | - Xinran Liu
- Department of Clinical Nutrition, Peking University People’s Hospital, Beijing, China
| | - Chen Yang
- Institute of Reproductive and Child Health/National Health Commission Key Laboratory of Reproductive Health, School of Public Health, Peking University, Beijing, China
| | - Peng Liu
- Department of Clinical Nutrition, Peking University People’s Hospital, Beijing, China
| | - Linlin Wang
- Institute of Reproductive and Child Health/National Health Commission Key Laboratory of Reproductive Health, School of Public Health, Peking University, Beijing, China
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Beger RD, Goodacre R, Jones CM, Lippa KA, Mayboroda OA, O'Neill D, Najdekr L, Ntai I, Wilson ID, Dunn WB. Analysis types and quantification methods applied in UHPLC-MS metabolomics research: a tutorial. Metabolomics 2024; 20:95. [PMID: 39110307 PMCID: PMC11306277 DOI: 10.1007/s11306-024-02155-6] [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: 02/07/2024] [Accepted: 07/16/2024] [Indexed: 08/10/2024]
Abstract
BACKGROUND Different types of analytical methods, with different characteristics, are applied in metabolomics and lipidomics research and include untargeted, targeted and semi-targeted methods. Ultra High Performance Liquid Chromatography-Mass Spectrometry is one of the most frequently applied measurement instruments in metabolomics because of its ability to detect a large number of water-soluble and lipid metabolites over a wide range of concentrations in short analysis times. Methods applied for the detection and quantification of metabolites differ and can either report a (normalised) peak area or an absolute concentration. AIM OF REVIEW In this tutorial we aim to (1) define similarities and differences between different analytical approaches applied in metabolomics and (2) define how amounts or absolute concentrations of endogenous metabolites can be determined together with the advantages and limitations of each approach in relation to the accuracy and precision when concentrations are reported. KEY SCIENTIFIC CONCEPTS OF REVIEW The pre-analysis knowledge of metabolites to be targeted, the requirement for (normalised) peak responses or absolute concentrations to be reported and the number of metabolites to be reported define whether an untargeted, targeted or semi-targeted method is applied. Fully untargeted methods can only provide (normalised) peak responses and fold changes which can be reported even when the structural identity of the metabolite is not known. Targeted methods, where the analytes are known prior to the analysis, can also report fold changes. Semi-targeted methods apply a mix of characteristics of both untargeted and targeted assays. For the reporting of absolute concentrations of metabolites, the analytes are not only predefined but optimized analytical methods should be developed and validated for each analyte so that the accuracy and precision of concentration data collected for biological samples can be reported as fit for purpose and be reviewed by the scientific community.
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Affiliation(s)
- Richard D Beger
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Royston Goodacre
- Department of Biochemistry, Cell and Systems Biology, Centre for Metabolomics Research, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Christina M Jones
- Office of Advanced Manufacturing, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
| | - Katrice A Lippa
- Office of Weights and Measures, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
| | - Oleg A Mayboroda
- Center for Proteomics and Metabolomics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Donna O'Neill
- School of Biosciences and Phenome Centre Birmingham, University of Birmingham, Birmingham, UK
| | - Lukas Najdekr
- Faculty of Medicine and Dentistry, Institute of Molecular and Translational Medicine, Palacký University Olomouc, 779 00, Olomouc, Czech Republic
| | - Ioanna Ntai
- BioMarin Pharmaceutical Inc., San Rafael, CA, USA
| | - Ian D Wilson
- Department of Biochemistry, Cell and Systems Biology, Centre for Metabolomics Research, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
- Computational and Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Warwick B Dunn
- Department of Biochemistry, Cell and Systems Biology, Centre for Metabolomics Research, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
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He Y, Wang X, Liu Q, Liu H, Yang S. Exploring the mechanism of clomiphene citrate to improve ovulation disorder in PCOS rats based on follicular fluid metabolomics. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024; 397:2281-2296. [PMID: 37815607 DOI: 10.1007/s00210-023-02750-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 09/26/2023] [Indexed: 10/11/2023]
Abstract
To examine the effects of clomiphene citrate (CC) on follicular fluid metabolites and related metabolic pathways in rats with polycystic ovary syndrome (PCOS) using non-targeted metabolomics and determine how CC treats ovulation disorder in PCOS. The Sprague Dawley rats were randomly divided into control, model, and CC groups. A PCOS model was established with letrozole. Body weight, ovarian weight, estrus cycles, serum hormone levels, and ovary histopathology of the rats were collected for further evaluation. Moreover, through ultra-performance liquid chromatography-mass spectrometry, the study of follicular fluid metabolites revealed the mechanism of action of CC. CC reduced ovarian weight and regulated estrous cycles and serum hormone levels in PCOS rats but did not affect their body weight. Moreover, the metabolomic results showed that CC adjusted 153 metabolites, among which 16 cross metabolites like testosterone, androstenedione, 17α-hydroxyprogesterone, and cholic acid were considered as potential biomarkers for CC to improve ovulation disorders in PCOS rats. Kyoto Encyclopedia of Genes and Genomes pathway enrichment also showed that the CC group mainly engaged in tryptophan metabolism and steroid hormone biosynthesis. CC can improve ovulation disorders in rats, and its mechanism is related to the regulation of the secretion of serum hormone and follicular fluid metabolites and the amelioration of multi-metabolic pathways.
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Affiliation(s)
- Yiqing He
- College of Integrated Traditional Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha, 410208, Hunan, China
| | - Xi Wang
- College of Integrated Traditional Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha, 410208, Hunan, China
| | - Quan Liu
- College of Integrated Traditional Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha, 410208, Hunan, China
| | - Huiping Liu
- Hunan University of Chinese Medicine, Changsha, 410208, Hunan, China
| | - Shuo Yang
- Hunan University of Chinese Medicine, Changsha, 410208, Hunan, China.
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Yurkovich JT, Evans SJ, Rappaport N, Boore JL, Lovejoy JC, Price ND, Hood LE. The transition from genomics to phenomics in personalized population health. Nat Rev Genet 2024; 25:286-302. [PMID: 38093095 DOI: 10.1038/s41576-023-00674-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/03/2023] [Indexed: 03/21/2024]
Abstract
Modern health care faces several serious challenges, including an ageing population and its inherent burden of chronic diseases, rising costs and marginal quality metrics. By assessing and optimizing the health trajectory of each individual using a data-driven personalized approach that reflects their genetics, behaviour and environment, we can start to address these challenges. This assessment includes longitudinal phenome measures, such as the blood proteome and metabolome, gut microbiome composition and function, and lifestyle and behaviour through wearables and questionnaires. Here, we review ongoing large-scale genomics and longitudinal phenomics efforts and the powerful insights they provide into wellness. We describe our vision for the transformation of the current health care from disease-oriented to data-driven, wellness-oriented and personalized population health.
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Affiliation(s)
- James T Yurkovich
- Phenome Health, Seattle, WA, USA
- Center for Phenomic Health, The Buck Institute for Research on Aging, Novato, CA, USA
- Department of Bioengineering, University of Texas at Dallas, Richardson, TX, USA
| | - Simon J Evans
- Phenome Health, Seattle, WA, USA
- Center for Phenomic Health, The Buck Institute for Research on Aging, Novato, CA, USA
| | - Noa Rappaport
- Center for Phenomic Health, The Buck Institute for Research on Aging, Novato, CA, USA
- Institute for Systems Biology, Seattle, WA, USA
| | - Jeffrey L Boore
- Phenome Health, Seattle, WA, USA
- Center for Phenomic Health, The Buck Institute for Research on Aging, Novato, CA, USA
| | - Jennifer C Lovejoy
- Phenome Health, Seattle, WA, USA
- Center for Phenomic Health, The Buck Institute for Research on Aging, Novato, CA, USA
- Institute for Systems Biology, Seattle, WA, USA
| | - Nathan D Price
- Institute for Systems Biology, Seattle, WA, USA
- Thorne HealthTech, New York, NY, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA
| | - Leroy E Hood
- Phenome Health, Seattle, WA, USA.
- Center for Phenomic Health, The Buck Institute for Research on Aging, Novato, CA, USA.
- Institute for Systems Biology, Seattle, WA, USA.
- Department of Bioengineering, University of Washington, Seattle, WA, USA.
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA.
- Department of Immunology, University of Washington, Seattle, WA, USA.
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Garcia-Viñola V, Ruiz-de-Villa C, Gombau J, Poblet M, Bordons A, Reguant C, Rozès N. Simultaneous Analysis of Organic Acids, Glycerol and Phenolic Acids in Wines Using Gas Chromatography-Mass Spectrometry. Foods 2024; 13:186. [PMID: 38254487 PMCID: PMC10814861 DOI: 10.3390/foods13020186] [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: 12/04/2023] [Revised: 12/30/2023] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
Fermented beverages, particularly wines, exhibit variable concentrations of organic and phenolic acids, posing challenges in their accurate determination. Traditionally, enzymatic methods or chromatographic analyses, mainly high-performance liquid chromatography (HPLC), have been employed to quantify these compounds individually in the grape must or wine. However, chromatographic analyses face limitations due to the high sugar content in the grape must. Meanwhile, phenolic acids, found in higher quantities in red wines than in white wines, are typically analyzed using HPLC. This study presents a novel method for the quantification of organic acids (OAs), glycerol, and phenolic acids in grape musts and wines. The approach involves liquid-liquid extraction with ethyl acetate, followed by sample derivatization and analysis using gas chromatography-mass spectrometry (GC-MS) in selected ion monitoring (SIM) detection mode. The results indicated successful detection and quantification of all analyzed compounds without the need for sample dilution. However, our results showed that the method of adding external standards was more suitable for quantifying wine compounds, owing to the matrix effect. Furthermore, this method is promising for quantifying other metabolites present in wines, depending on their extractability with ethyl acetate. Fermented beverages, particularly wines, exhibit variable concentrations of organic and phenolic acids, posing challenges in their accurate determination. Traditionally, enzymatic methods or chromatographic analyses, mainly high-performance liquid chromatography (HPLC), have been employed to quantify these compounds individually in the grape must or wine. The approach of this proposed method involves (i) methoximation of wine compounds in a basic medium, (ii) acidification with HCl, (iii) liquid-liquid extraction with ethyl acetate, and (iv) silyl derivatization to analyze samples with gas chromatography-mass spectrometry (GC-MS) in ion monitoring detection mode (SIM). The results indicated successful detection and quantification of all analyzed compounds without the need for sample dilution. However, our results showed that the method of adding external standards was more suitable for quantifying wine compounds, owing to the matrix effect. Furthermore, this method is promising for quantifying other metabolites present in wines, depending on their extractability with ethyl acetate. In other words, the proposed method may be suitable for profiling (targeted) or fingerprinting (untargeted) strategies to quantify wine metabolites or to classify wines according to the type of winemaking process, grape, or fermentation.
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Affiliation(s)
- Violeta Garcia-Viñola
- Grup de Biotecnologia Microbiana dels Aliments, Departament de Bioquímica i Biotecnologia, Facultat d’Enologia, Universitat Rovira i Virgili, c/Marcel·lí Domingo s/n, 43007 Tarragona, Catalonia, Spain; (V.G.-V.); (C.R.-d.-V.); (M.P.)
| | - Candela Ruiz-de-Villa
- Grup de Biotecnologia Microbiana dels Aliments, Departament de Bioquímica i Biotecnologia, Facultat d’Enologia, Universitat Rovira i Virgili, c/Marcel·lí Domingo s/n, 43007 Tarragona, Catalonia, Spain; (V.G.-V.); (C.R.-d.-V.); (M.P.)
| | - Jordi Gombau
- Grup de Tecnologia Enològica, Departament de Bioquímica i Biotecnologia, Facultat d’Enologia, Universitat Rovira i Virgili, c/Marcel·lí Domingo s/n, 43007 Tarragona, Catalonia, Spain;
| | - Montse Poblet
- Grup de Biotecnologia Microbiana dels Aliments, Departament de Bioquímica i Biotecnologia, Facultat d’Enologia, Universitat Rovira i Virgili, c/Marcel·lí Domingo s/n, 43007 Tarragona, Catalonia, Spain; (V.G.-V.); (C.R.-d.-V.); (M.P.)
| | - Albert Bordons
- Grup de Biotecnologia Enològica, Departament de Bioquímica i Biotecnologia, Facultat d’Enologia, Universitat Rovira i Virgili, c/Marcel·lí Domingo s/n, 43007 Tarragona, Catalonia, Spain; (A.B.); (C.R.)
| | - Cristina Reguant
- Grup de Biotecnologia Enològica, Departament de Bioquímica i Biotecnologia, Facultat d’Enologia, Universitat Rovira i Virgili, c/Marcel·lí Domingo s/n, 43007 Tarragona, Catalonia, Spain; (A.B.); (C.R.)
| | - Nicolas Rozès
- Grup de Biotecnologia Microbiana dels Aliments, Departament de Bioquímica i Biotecnologia, Facultat d’Enologia, Universitat Rovira i Virgili, c/Marcel·lí Domingo s/n, 43007 Tarragona, Catalonia, Spain; (V.G.-V.); (C.R.-d.-V.); (M.P.)
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Calame DG, Emrick LT. Functional genomics and small molecules in mitochondrial neurodevelopmental disorders. Neurotherapeutics 2024; 21:e00316. [PMID: 38244259 PMCID: PMC10903096 DOI: 10.1016/j.neurot.2024.e00316] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 12/16/2023] [Accepted: 01/02/2024] [Indexed: 01/22/2024] Open
Abstract
Mitochondria are critical for brain development and homeostasis. Therefore, pathogenic variation in the mitochondrial or nuclear genome which disrupts mitochondrial function frequently results in developmental disorders and neurodegeneration at the organismal level. Large-scale application of genome-wide technologies to individuals with mitochondrial diseases has dramatically accelerated identification of mitochondrial disease-gene associations in humans. Multi-omic and high-throughput studies involving transcriptomics, proteomics, metabolomics, and saturation genome editing are providing deeper insights into the functional consequence of mitochondrial genomic variation. Integration of deep phenotypic and genomic data through allelic series continues to uncover novel mitochondrial functions and permit mitochondrial gene function dissection on an unprecedented scale. Finally, mitochondrial disease-gene associations illuminate disease mechanisms and thereby direct therapeutic strategies involving small molecules and RNA-DNA therapeutics. This review summarizes progress in functional genomics and small molecule therapeutics in mitochondrial neurodevelopmental disorders.
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Affiliation(s)
- Daniel G Calame
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| | - Lisa T Emrick
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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Gan J, Chen J, Ma RL, Deng Y, Ding XS, Zhu SY, Sun AJ. Action Mechanisms of Metformin Combined with Exenatide and Metformin Only in the Treatment of PCOS in Obese Patients. Int J Endocrinol 2023; 2023:4288004. [PMID: 38131036 PMCID: PMC10735721 DOI: 10.1155/2023/4288004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 07/14/2023] [Accepted: 10/28/2023] [Indexed: 12/23/2023] Open
Abstract
Background Polycystic ovary syndrome (PCOS) is the most common endocrine disease in women of reproductive age, whose clinical characteristics are hyperandrogenism (HA), ovulatory dysfunction, and polycystic ovary, often accompanied by insulin resistance (IR) and metabolic abnormalities. Glucagon-like peptide (GLP)-1 receptor agonists (GLP-1Ra), such as exenatide, can bind to specific receptors on tissues such as the ovaries to improve the clinical phenotype of PCOS, while insulin-sensitizing agents, such as metformin, can also benefit to metabolic abnormalities in PCOS. Liquid chromatography-mass spectrometry (LC/MS) metabolomics revealed differences between the mechanisms of exenatide and metformin treatment of PCOS to some extent. Methods In this study, 50 obese subjects with PCOS were randomly divided into the exenatide combined with metformin group (COM group, n = 28) and the metformin group (MF group, n = 22) for 12-week treatment. Before and after, serum samples were subjected to LC/MS analysis. Results After treatment, there were 153 named differential metabolites in the COM group and 99 in the MF group. Most phosphatidylcholines (PC) and deoxycholic acid 3-glucuronide (DA3G) were significantly upregulated, while most glycerophosphoethanolamine (PE-NMe2), glycerophosphocholine (GPC), and threonine were downregulated in both groups. Only the decrease of neuromedin B, glutamate, and glutamyl groups and the increase of chenodeoxycholic acid sulfate docosadienoate (22: 2n6), and prostaglandin E2 have been observed in the COM group. In addition, salicylic acid and spisulosine increased and decanoylcarnitine decreased in the MF group. Both groups were enriched in glycerophospholipid, choline, and sphingolipid metabolism, while the COM group was especially superior in the glutamine and glutamate, bile secretion, and amino acid metabolism. Conclusion Compared with metformin alone in the treatment of PCOS, the differential metabolites of the exenatide combined with metformin group are more extensive. The COM group may act on the hypothalamic-pituitary-gonadal axis (HPO) and its bypass, regulate multiple metabolism pathways such as phospholipids, amino acids, fatty acids, carnitine, bile acids, and glucose directly or indirectly in obese PCOS patients.
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Affiliation(s)
- Jingwen Gan
- National Clinical Research Center for Obstetric & Gynecologic Diseases, Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 1 Shuaifuyuan, Dongcheng District, Beijing 100730, China
| | - Jie Chen
- National Clinical Research Center for Obstetric & Gynecologic Diseases, Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 1 Shuaifuyuan, Dongcheng District, Beijing 100730, China
| | - Rui-lin Ma
- Department of Ultrasound, Qilu Hospital of Shandong University, Jinan, Shandong 250012, China
| | - Yan Deng
- National Clinical Research Center for Obstetric & Gynecologic Diseases, Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 1 Shuaifuyuan, Dongcheng District, Beijing 100730, China
| | - Xue-song Ding
- National Clinical Research Center for Obstetric & Gynecologic Diseases, Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 1 Shuaifuyuan, Dongcheng District, Beijing 100730, China
| | - Shi-yang Zhu
- National Clinical Research Center for Obstetric & Gynecologic Diseases, Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 1 Shuaifuyuan, Dongcheng District, Beijing 100730, China
| | - Ai-jun Sun
- National Clinical Research Center for Obstetric & Gynecologic Diseases, Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 1 Shuaifuyuan, Dongcheng District, Beijing 100730, China
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Lekka P, Fragopoulou E, Terpou A, Dasenaki M. Exploring Human Metabolome after Wine Intake-A Review. Molecules 2023; 28:7616. [PMID: 38005338 PMCID: PMC10673339 DOI: 10.3390/molecules28227616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 10/21/2023] [Accepted: 10/24/2023] [Indexed: 11/26/2023] Open
Abstract
Wine has a rich history dating back to 2200 BC, originally recognized for its medicinal properties. Today, with the aid of advanced technologies like metabolomics and sophisticated analytical techniques, we have gained remarkable insights into the molecular-level changes induced by wine consumption in the human organism. This review embarks on a comprehensive exploration of the alterations in human metabolome associated with wine consumption. A great number of 51 studies from the last 25 years were reviewed; these studies systematically investigated shifts in metabolic profiles within blood, urine, and feces samples, encompassing both short-term and long-term studies of the consumption of wine and wine derivatives. Significant metabolic alterations were observed in a wide variety of metabolites belonging to different compound classes, such as phenolic compounds, lipids, organic acids, and amino acids, among others. Within these classes, both endogenous metabolites as well as diet-related metabolites that exhibited up-regulation or down-regulation following wine consumption were included. The up-regulation of short-chain fatty acids and the down-regulation of sphingomyelins after wine intake, as well as the up-regulation of gut microbial fermentation metabolites like vanillic and syringic acid are some of the most important findings reported in the reviewed literature. Our results confirm the intact passage of certain wine compounds, such as tartaric acid and other wine acids, to the human organism. In an era where the health effects of wine consumption are of growing interest, this review offers a holistic perspective on the metabolic underpinnings of this centuries-old tradition.
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Affiliation(s)
- Pelagia Lekka
- Food Chemistry Laboratory, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zographou, 15771 Athens, Greece;
| | - Elizabeth Fragopoulou
- School of Health Science and Education, Department of Nutrition and Dietetics, Harokopio University, 17671 Athens, Greece;
| | - Antonia Terpou
- Department of Agricultural Development, Agrofood and Management of Natural Resources, School of Agricultural Development, Nutrition & Sustainability, National and Kapodistrian University of Athens, 34400 Psachna, Greece;
| | - Marilena Dasenaki
- Food Chemistry Laboratory, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zographou, 15771 Athens, Greece;
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10
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Han X, Wang W, Ma LH, AI-Ramahi I, Botas J, MacKenzie K, Allen GI, Young DW, Liu Z, Maletic-Savatic M. SPA-STOCSY: an automated tool for identifying annotated and non-annotated metabolites in high-throughput NMR spectra. Bioinformatics 2023; 39:btad593. [PMID: 37792497 PMCID: PMC10568371 DOI: 10.1093/bioinformatics/btad593] [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: 01/24/2023] [Revised: 07/31/2023] [Accepted: 10/02/2023] [Indexed: 10/06/2023] Open
Abstract
MOTIVATION Nuclear magnetic resonance spectroscopy (NMR) is widely used to analyze metabolites in biological samples, but the analysis requires specific expertise, it is time-consuming, and can be inaccurate. Here, we present a powerful automate tool, SPatial clustering Algorithm-Statistical TOtal Correlation SpectroscopY (SPA-STOCSY), which overcomes challenges faced when analyzing NMR data and identifies metabolites in a sample with high accuracy. RESULTS As a data-driven method, SPA-STOCSY estimates all parameters from the input dataset. It first investigates the covariance pattern among datapoints and then calculates the optimal threshold with which to cluster datapoints belonging to the same structural unit, i.e. the metabolite. Generated clusters are then automatically linked to a metabolite library to identify candidates. To assess SPA-STOCSY's efficiency and accuracy, we applied it to synthesized spectra and spectra acquired on Drosophila melanogaster tissue and human embryonic stem cells. In the synthesized spectra, SPA outperformed Statistical Recoupling of Variables (SRV), an existing method for clustering spectral peaks, by capturing a higher percentage of the signal regions and the close-to-zero noise regions. In the biological data, SPA-STOCSY performed comparably to the operator-based Chenomx analysis while avoiding operator bias, and it required <7 min of total computation time. Overall, SPA-STOCSY is a fast, accurate, and unbiased tool for untargeted analysis of metabolites in the NMR spectra. It may thus accelerate the use of NMR for scientific discoveries, medical diagnostics, and patient-specific decision making. AVAILABILITY AND IMPLEMENTATION The codes of SPA-STOCSY are available at https://github.com/LiuzLab/SPA-STOCSY.
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Affiliation(s)
- Xu Han
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX 77030, United States
- Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Wanli Wang
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX 77030, United States
- Graduate Program of Quantitative & Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, United States
| | - Li-Hua Ma
- Advanced Technology Cores, Baylor College of Medicine, Houston, TX 77030, United States
| | - Ismael AI-Ramahi
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX 77030, United States
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, United States
| | - Juan Botas
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX 77030, United States
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, United States
| | - Kevin MacKenzie
- Advanced Technology Cores, Baylor College of Medicine, Houston, TX 77030, United States
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX 77030, United States
| | - Genevera I Allen
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX 77030, United States
- Department of Electrical and Computer Engineering, Statistics, and Computer Science, Rice University, Houston, TX 77005-1827, United States
| | - Damian W Young
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX 77030, United States
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX 77030, United States
| | - Zhandong Liu
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX 77030, United States
- Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Mirjana Maletic-Savatic
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX 77030, United States
- Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX 77030, United States
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11
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Zhang Y, Barupal DK, Fan S, Gao B, Zhu C, Flenniken AM, McKerlie C, Nutter LMJ, Lloyd KCK, Fiehn O. Sexual Dimorphism of the Mouse Plasma Metabolome Is Associated with Phenotypes of 30 Gene Knockout Lines. Metabolites 2023; 13:947. [PMID: 37623890 PMCID: PMC10456929 DOI: 10.3390/metabo13080947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/03/2023] [Accepted: 08/08/2023] [Indexed: 08/26/2023] Open
Abstract
Although metabolic alterations are observed in many monogenic and complex genetic disorders, the impact of most mammalian genes on cellular metabolism remains unknown. Understanding the effect of mouse gene dysfunction on metabolism can inform the functions of their human orthologues. We investigated the effect of loss-of-function mutations in 30 unique gene knockout (KO) lines on plasma metabolites, including genes coding for structural proteins (11 of 30), metabolic pathway enzymes (12 of 30) and protein kinases (7 of 30). Steroids, bile acids, oxylipins, primary metabolites, biogenic amines and complex lipids were analyzed with dedicated mass spectrometry platforms, yielding 827 identified metabolites in male and female KO mice and wildtype (WT) controls. Twenty-two percent of 23,698 KO versus WT comparison tests showed significant genotype effects on plasma metabolites. Fifty-six percent of identified metabolites were significantly different between the sexes in WT mice. Many of these metabolites were also found to have sexually dimorphic changes in KO lines. We used plasma metabolites to complement phenotype information exemplified for Dhfr, Idh1, Mfap4, Nek2, Npc2, Phyh and Sra1. The association of plasma metabolites with IMPC phenotypes showed dramatic sexual dimorphism in wildtype mice. We demonstrate how to link metabolomics to genotypes and (disease) phenotypes. Sex must be considered as critical factor in the biological interpretation of gene functions.
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Affiliation(s)
- Ying Zhang
- West Coast Metabolomics Center, University of California Davis, Davis, CA 95616, USA
- Department of Chemistry, University of California Davis, Davis, CA 95616, USA
| | - Dinesh K. Barupal
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
| | - Sili Fan
- West Coast Metabolomics Center, University of California Davis, Davis, CA 95616, USA
| | - Bei Gao
- School of Marine Sciences, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Chao Zhu
- College of Medicine & Nursing, Dezhou University, Dezhou 253023, China
| | - Ann M. Flenniken
- The Centre for Phenogenomics, Toronto, ON M5T 3H7, Canada; (A.M.F.); (C.M.); (L.M.J.N.)
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Colin McKerlie
- The Centre for Phenogenomics, Toronto, ON M5T 3H7, Canada; (A.M.F.); (C.M.); (L.M.J.N.)
- The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Lauryl M. J. Nutter
- The Centre for Phenogenomics, Toronto, ON M5T 3H7, Canada; (A.M.F.); (C.M.); (L.M.J.N.)
- The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Kevin C. Kent Lloyd
- Department of Surgery, School of Medicine, and Mouse Biology Program, University of California Davis, Davis, CA 95616, USA;
| | - Oliver Fiehn
- West Coast Metabolomics Center, University of California Davis, Davis, CA 95616, USA
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12
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Konopka MJ, Sperlich B, Rietjens G, Zeegers MP. Genetics and athletic performance: a systematic SWOT analysis of non-systematic reviews. Front Genet 2023; 14:1232987. [PMID: 37621703 PMCID: PMC10445150 DOI: 10.3389/fgene.2023.1232987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 07/26/2023] [Indexed: 08/26/2023] Open
Abstract
Exercise genetics/genomics is a growing research discipline comprising several Strengths and Opportunities but also deals with Weaknesses and Threats. This "systematic SWOT overview of non-systematic reviews" (sSWOT) aimed to identify the Strengths, Weaknesses, Opportunities, and Threats linked to exercise genetics/genomics. A systematic search was conducted in the Medline and Embase databases for non-systematic reviews to provide a comprehensive overview of the current literature/research area. The extracted data was thematically analyzed, coded, and categorized into SWOT clusters. In the 45 included reviews five Strengths, nine Weaknesses, six Opportunities, and three Threats were identified. The cluster of Strengths included "advances in technology", "empirical evidence", "growing research discipline", the "establishment of consortia", and the "acceptance/accessibility of genetic testing". The Weaknesses were linked to a "low research quality", the "complexity of exercise-related traits", "low generalizability", "high costs", "genotype scores", "reporting bias", "invasive methods", "research progress", and "causality". The Opportunities comprised of "precision exercise", "omics", "multicenter studies", as well as "genetic testing" as "commercial"-, "screening"-, and "anti-doping" detection tool. The Threats were related to "ethical issues", "direct-to-consumer genetic testing companies", and "gene doping". This overview of the present state of the art research in sport genetics/genomics indicates a field with great potential, while also drawing attention to the necessity for additional advancement in methodological and ethical guidance to mitigate the recognized Weaknesses and Threats. The recognized Strengths and Opportunities substantiate the capability of genetics/genomics to make significant contributions to the performance and wellbeing of athletes.
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Affiliation(s)
- Magdalena Johanna Konopka
- Care and Public Health Research Institute, Maastricht University, Maastricht, Netherlands
- Department of Epidemiology, Maastricht University, Maastricht, Netherlands
| | - Billy Sperlich
- Integrative and Experimental Exercise Science and Training, Institute of Sport Science, University of Würzburg, Würzburg, Germany
| | - Gerard Rietjens
- Human Physiology and Sports Physiotherapy Research Group, Vrije Universiteit Brussel, Brussels, Belgium
| | - Maurice Petrus Zeegers
- Care and Public Health Research Institute, Maastricht University, Maastricht, Netherlands
- Department of Epidemiology, Maastricht University, Maastricht, Netherlands
- School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, Netherlands
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13
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Rahman M, Schellhorn HE. Metabolomics of infectious diseases in the era of personalized medicine. Front Mol Biosci 2023; 10:1120376. [PMID: 37275959 PMCID: PMC10233009 DOI: 10.3389/fmolb.2023.1120376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 05/08/2023] [Indexed: 06/07/2023] Open
Abstract
Infectious diseases continue to be a major cause of morbidity and mortality worldwide. Diseases cause perturbation of the host's immune system provoking a response that involves genes, proteins and metabolites. While genes are regulated by epigenetic or other host factors, proteins can undergo post-translational modification to enable/modify function. As a result, it is difficult to correlate the disease phenotype based solely on genetic and proteomic information only. Metabolites, however, can provide direct information on the biochemical activity during diseased state. Therefore, metabolites may, potentially, represent a phenotypic signature of a diseased state. Measuring and assessing metabolites in large scale falls under the omics technology known as "metabolomics". Comprehensive and/or specific metabolic profiling in biological fluids can be used as biomarkers of disease diagnosis. In addition, metabolomics together with genomics can be used to differentiate patients with differential treatment response and development of host targeted therapy instead of pathogen targeted therapy where pathogens are more prone to mutation and lead to antimicrobial resistance. Thus, metabolomics can be used for patient stratification, personalized drug formulation and disease control and management. Currently, several therapeutics and in vitro diagnostics kits have been approved by US Food and Drug Administration (FDA) for personalized treatment and diagnosis of infectious diseases. However, the actual number of therapeutics or diagnostics kits required for tailored treatment is limited as metabolomics and personalized medicine require the involvement of personnel from multidisciplinary fields ranging from technological development, bioscience, bioinformatics, biostatistics, clinicians, and biotechnology companies. Given the significance of metabolomics, in this review, we discussed different aspects of metabolomics particularly potentials of metabolomics as diagnostic biomarkers and use of small molecules for host targeted treatment for infectious diseases, and their scopes and challenges in personalized medicine.
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14
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DeBalsi KL, Newman JH, Sommerville LJ, Phillips JA, Hamid R, Cogan J, Fessel JP, Evans AM, Network UD, Kennedy AD. A Case Study of Dysfunctional Nicotinamide Metabolism in a 20-Year-Old Male. Metabolites 2023; 13:399. [PMID: 36984839 PMCID: PMC10055858 DOI: 10.3390/metabo13030399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/24/2023] [Accepted: 03/04/2023] [Indexed: 03/10/2023] Open
Abstract
We present a case study of a 20-year-old male with an unknown neurodegenerative disease who was referred to the Undiagnosed Diseases Network Vanderbilt Medical Center site. A previous metabolic panel showed that the patient had a critical deficiency in nicotinamide intermediates that are generated during the biosynthesis of NAD(H). We followed up on these findings by evaluating the patient's ability to metabolize nicotinamide. We performed a global metabolic profiling analysis of plasma samples that were collected: (1) under normal fed conditions (baseline), (2) after the patient had fasted, and (3) after he was challenged with a 500 mg nasogastric tube bolus of nicotinamide following the fast. Our findings showed that the patient's nicotinamide N-methyltransferase (NNMT), a key enzyme in NAD(H) biosynthesis and methionine metabolism, was not functional under normal fed or fasting conditions but was restored in response to the nicotinamide challenge. Altered levels of metabolites situated downstream of NNMT and in neighboring biochemical pathways provided further evidence of a baseline defect in NNMT activity. To date, this is the only report of a critical defect in NNMT activity manifesting in adulthood and leading to neurodegenerative disease. Altogether, this study serves as an important reference in the rare disease literature and also demonstrates the utility of metabolomics as a diagnostic tool for uncharacterized metabolic diseases.
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Affiliation(s)
| | - John H. Newman
- Vanderbilt University Medical Center, Nashville, TN 37235, USA
| | | | | | - Rizwan Hamid
- Vanderbilt University Medical Center, Nashville, TN 37235, USA
| | - Joy Cogan
- Vanderbilt University Medical Center, Nashville, TN 37235, USA
| | - Joshua P. Fessel
- National Institutes of Health, National Center for Advancing Translational Sciences, Bethesda, MD 20892, USA
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15
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Han X, Wang W, Ma LH, Al-Ramahi I, Botas J, MacKenzie K, Allen GI, Young DW, Liu Z, Maletic-Savatic M. SPA-STOCSY: An Automated Tool for Identification of Annotated and Non-Annotated Metabolites in High-Throughput NMR Spectra. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.22.529564. [PMID: 36865102 PMCID: PMC9980041 DOI: 10.1101/2023.02.22.529564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Nuclear Magnetic Resonance (NMR) spectroscopy is widely used to analyze metabolites in biological samples, but the analysis can be cumbersome and inaccurate. Here, we present a powerful automated tool, SPA-STOCSY (Spatial Clustering Algorithm - Statistical Total Correlation Spectroscopy), which overcomes the challenges by identifying metabolites in each sample with high accuracy. As a data-driven method, SPA-STOCSY estimates all parameters from the input dataset, first investigating the covariance pattern and then calculating the optimal threshold with which to cluster data points belonging to the same structural unit, i.e. metabolite. The generated clusters are then automatically linked to a compound library to identify candidates. To assess SPA-STOCSY’s efficiency and accuracy, we applied it to synthesized and real NMR data obtained from Drosophila melanogaster brains and human embryonic stem cells. In the synthesized spectra, SPA outperforms Statistical Recoupling of Variables, an existing method for clustering spectral peaks, by capturing a higher percentage of the signal regions and the close-to-zero noise regions. In the real spectra, SPA-STOCSY performs comparably to operator-based Chenomx analysis but avoids operator bias and performs the analyses in less than seven minutes of total computation time. Overall, SPA-STOCSY is a fast, accurate, and unbiased tool for untargeted analysis of metabolites in the NMR spectra. As such, it might accelerate the utilization of NMR for scientific discoveries, medical diagnostics, and patient-specific decision making.
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Affiliation(s)
- Xu Han
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, 77030, USA
- Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Wanli Wang
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, 77030, USA
- Graduate Program of Quantitative & Computational Biosciences, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Li-Hua Ma
- Advanced Technology Cores, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ismael Al-Ramahi
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Juan Botas
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Kevin MacKenzie
- Advanced Technology Cores, Baylor College of Medicine, Houston, TX, 77030, USA
- Center for Drug Discovery, Department of Pathology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Genevera I. Allen
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, 77030, USA
- Department of Statistics, Rice University, 6100 Main Street, Houston, TX 77005-1827, USA
| | - Damian W. Young
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Zhandong Liu
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, 77030, USA
- Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Mirjana Maletic-Savatic
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, 77030, USA
- Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX, 77030, USA
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16
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Lokhov PG, Balashova EE, Trifonova OP, Maslov DL, Grigoriev AI, Ponomarenko EA, Archakov AI. Mass Spectrometric Blood Metabogram: Acquisition, Characterization, and Prospects for Application. Int J Mol Sci 2023; 24:ijms24021736. [PMID: 36675249 PMCID: PMC9861083 DOI: 10.3390/ijms24021736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 01/04/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023] Open
Abstract
In metabolomics, many metabolites are measured simultaneously in a single run. Such analytical performance opens up prospects for clinical laboratory diagnostics. In this work, a mass spectrometric metabogram was developed as a simplified and clinically applicable way of measuring the blood plasma metabolome. To develop the metabogram, blood plasma samples from healthy male volunteers (n = 48) of approximately the same age, direct infusion mass spectrometry (DIMS) of the low molecular fraction of samples, and principal component analysis (PCA) of the mass spectra were used. The seven components of the metabogram defined by PCA, which cover ~70% of blood plasma metabolome variability, were characterized using a metabolite set enrichment analysis (MSEA) and clinical test results of participating volunteers. It has been established that the components of the metabogram are functionally related groups of the blood metabolome associated with regulation, lipid-carbohydrate, and lipid-amine blood components, eicosanoids, lipid intake into the organism, and liver function thereby providing a lot of clinically relevant information. Therefore, metabogram provides the possibility to apply the metabolomics performance in the clinic. The features of the metabogram are also discussed in comparison with the thin-layer chromatography and with the analysis of blood metabolome by liquid chromatography combined with mass spectrometry.
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Affiliation(s)
- Petr G. Lokhov
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia
- Correspondence:
| | - Elena E. Balashova
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia
| | - Oxana P. Trifonova
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia
| | - Dmitry L. Maslov
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia
| | - Anatoly I. Grigoriev
- Institute of Biomedical Problems, Russian Federation State Scientific Research Center, Russian Academy of Sciences, 123007 Moscow, Russia
| | - Elena A. Ponomarenko
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia
| | - Alexander I. Archakov
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia
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17
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Trifonova OP, Maslov DL, Balashova EE, Lokhov PG. Current State and Future Perspectives on Personalized Metabolomics. Metabolites 2023; 13:metabo13010067. [PMID: 36676992 PMCID: PMC9863827 DOI: 10.3390/metabo13010067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 12/27/2022] [Accepted: 12/29/2022] [Indexed: 01/03/2023] Open
Abstract
Metabolomics is one of the most promising 'omics' sciences for the implementation in medicine by developing new diagnostic tests and optimizing drug therapy. Since in metabolomics, the end products of the biochemical processes in an organism are studied, which are under the influence of both genetic and environmental factors, the metabolomics analysis can detect any changes associated with both lifestyle and pathological processes. Almost every case-controlled metabolomics study shows a high diagnostic accuracy. Taking into account that metabolomics processes are already described for most nosologies, there are prerequisites that a high-speed and comprehensive metabolite analysis will replace, in near future, the narrow range of chemical analyses used today, by the medical community. However, despite the promising perspectives of personalized metabolomics, there are currently no FDA-approved metabolomics tests. The well-known problem of complexity of personalized metabolomics data analysis and their interpretation for the end-users, in addition to a traditional need for analytical methods to address the quality control, standardization, and data treatment are reported in the review. Possible ways to solve the problems and change the situation with the introduction of metabolomics tests into clinical practice, are also discussed.
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18
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Blood Plasma Metabolome Profiling at Different Stages of Renal Cell Carcinoma. Cancers (Basel) 2022; 15:cancers15010140. [PMID: 36612136 PMCID: PMC9818272 DOI: 10.3390/cancers15010140] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 12/23/2022] [Accepted: 12/24/2022] [Indexed: 12/28/2022] Open
Abstract
Early diagnostics significantly improves the survival of patients with renal cell carcinoma (RCC), which is the prevailing type of adult kidney cancer. However, the absence of clinically obvious symptoms and effective screening strategies at the early stages result to disease progression and survival rate reducing. The study was focused on revealing of potential low molecular biomarkers for early-stage RCC. The untargeted direct injection mass spectrometry-based metabolite profiling of blood plasma samples from 51 non-cancer volunteers (control) and 78 patients with different RCC subtypes and stages (early stages of clear cell RCC (ccRCC), papillary RCC (pRCC), chromophobe RCC (chrRCC) and advanced stages of ccRCC) was performed. Comparative analysis of the blood plasma metabolites between the control and cancer groups provided the detection of metabolites associated with different tumor stages. The designed model based on the revealed metabolites demonstrated high diagnostic power and accuracy. Overall, using the metabolomics approach the study revealed the metabolites demonstrating a high value for design of plasma-based test to improve early ccRCC diagnosis.
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19
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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.
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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
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20
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Mildau K, van der Hooft JJJ, Flasch M, Warth B, El Abiead Y, Koellensperger G, Zanghellini J, Büschl C. Homologue series detection and management in LC-MS data with homologueDiscoverer. Bioinformatics 2022; 38:5139-5140. [PMID: 36165687 PMCID: PMC9665864 DOI: 10.1093/bioinformatics/btac647] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/20/2022] [Accepted: 09/23/2022] [Indexed: 12/24/2022] Open
Abstract
SUMMARY Untargeted metabolomics data analysis is highly labour intensive and can be severely frustrated by both experimental noise and redundant features. Homologous polymer series is a particular case of features that can either represent large numbers of noise features or alternatively represent features of interest with large peak redundancy. Here, we present homologueDiscoverer, an R package that allows for the targeted and untargeted detection of homologue series as well as their evaluation and management using interactive plots and simple local database functionalities. AVAILABILITY AND IMPLEMENTATION homologueDiscoverer is freely available at GitHub https://github.com/kevinmildau/homologueDiscoverer. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Kevin Mildau
- To whom correspondence should be addressed. or or
| | - Justin J J van der Hooft
- Bioinformatics Group, Wageningen University, Wageningen 6708PB, the Netherlands,Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa
| | - Mira Flasch
- Department of Food Chemistry and Toxicology, University of Vienna, Vienna A-1090, Austria
| | - Benedikt Warth
- Department of Food Chemistry and Toxicology, University of Vienna, Vienna A-1090, Austria
| | - Yasin El Abiead
- Department of Analytical Chemistry, University of Vienna, Vienna A-1090, Austria
| | - Gunda Koellensperger
- Department of Analytical Chemistry, University of Vienna, Vienna A-1090, Austria
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21
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Innovative Application of Metabolomics on Bioactive Ingredients of Foods. Foods 2022; 11:foods11192974. [PMID: 36230049 PMCID: PMC9562173 DOI: 10.3390/foods11192974] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/12/2022] [Accepted: 09/20/2022] [Indexed: 11/17/2022] Open
Abstract
Metabolomics, as a new omics technology, has been widely accepted by researchers and has shown great potential in the field of nutrition and health in recent years. This review briefly introduces the process of metabolomics analysis, including sample preparation and extraction, derivatization, separation and detection, and data processing. This paper focuses on the application of metabolomics in food-derived bioactive ingredients. For example, metabolomics techniques are used to analyze metabolites in food to find bioactive substances or new metabolites in food materials. Moreover, bioactive substances have been tested in vitro and in vivo, as well as in humans, to investigate the changes of metabolites and the underlying metabolic pathways, among which metabolomics is used to find potential biomarkers and targets. Metabolomics provides a new approach for the prevention and regulation of chronic diseases and the study of the underlying mechanisms. It also provides strong support for the development of functional food or drugs. Although metabolomics has some limitations such as low sensitivity, poor repeatability, and limited detection range, it is developing rapidly in general, and also in the field of nutrition and health. At the end of this paper, we put forward our own insights on the development prospects of metabolomics in the application of bioactive ingredients in food.
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22
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Roth HE, Powers R. Meta-Analysis Reveals Both the Promises and the Challenges of Clinical Metabolomics. Cancers (Basel) 2022; 14:3992. [PMID: 36010984 PMCID: PMC9406125 DOI: 10.3390/cancers14163992] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 08/09/2022] [Accepted: 08/16/2022] [Indexed: 11/17/2022] Open
Abstract
Clinical metabolomics is a rapidly expanding field focused on identifying molecular biomarkers to aid in the efficient diagnosis and treatment of human diseases. Variations in study design, metabolomics methodologies, and investigator protocols raise serious concerns about the accuracy and reproducibility of these potential biomarkers. The explosive growth of the field has led to the recent availability of numerous replicate clinical studies, which permits an evaluation of the consistency of biomarkers identified across multiple metabolomics projects. Pancreatic ductal adenocarcinoma (PDAC) is the third-leading cause of cancer-related death and has the lowest five-year survival rate primarily due to the lack of an early diagnosis and the limited treatment options. Accordingly, PDAC has been a popular target of clinical metabolomics studies. We compiled 24 PDAC metabolomics studies from the scientific literature for a detailed meta-analysis. A consistent identification across these multiple studies allowed for the validation of potential clinical biomarkers of PDAC while also highlighting variations in study protocols that may explain poor reproducibility. Our meta-analysis identified 10 metabolites that may serve as PDAC biomarkers and warrant further investigation. However, 87% of the 655 metabolites identified as potential biomarkers were identified in single studies. Differences in cohort size and demographics, p-value choice, fold-change significance, sample type, handling and storage, data collection, and analysis were all factors that likely contributed to this apparently large false positive rate. Our meta-analysis demonstrated the need for consistent experimental design and normalized practices to accurately leverage clinical metabolomics data for reliable and reproducible biomarker discovery.
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Affiliation(s)
- Heidi E. Roth
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
- Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
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23
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Adil N, Siddiqui AJ, Musharraf SG. Metabolomics‐based Researches in Autoimmune Liver Disease: A
Mini‐Review. Scand J Immunol 2022. [DOI: 10.1111/sji.13208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Nurmeen Adil
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences University of Karachi Karachi Pakistan
| | - Amna Jabbar Siddiqui
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences University of Karachi Karachi Pakistan
| | - Syed Ghulam Musharraf
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences University of Karachi Karachi Pakistan
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences University of Karachi Karachi Pakistan
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24
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Mapar M, Rydzak T, Groves RA, Lewis IA. Biomarker enrichment medium: A defined medium for metabolomic analysis of microbial pathogens. Front Microbiol 2022; 13:957158. [PMID: 35935218 PMCID: PMC9354526 DOI: 10.3389/fmicb.2022.957158] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022] Open
Abstract
Microbes have diverse metabolic capabilities and differences in these phenotypes are critical for differentiating strains, species, and broader taxa of microorganisms. Recent advances in liquid chromatography-mass spectrometry (LC-MS) allow researchers to track the complex combinations of molecules that are taken up by each cell type and to quantify the rates that individual metabolites enter or exit the cells. This metabolomics-based approach allows complex metabolic phenotypes to be captured in a single assay, enables computational models of microbial metabolism to be constructed, and can serve as a diagnostic approach for clinical microbiology. Unfortunately, metabolic phenotypes are directly affected by the molecular composition of the culture medium and many traditional media are subject to molecular-level heterogeneity. Herein, we show that commercially sourced Mueller Hinton (MH) medium, a Clinical and Laboratory Standards Institute (CLSI) approved medium for clinical microbiology, has significant lot-to-lot and supplier-to-supplier variability in the concentrations of individual nutrients. We show that this variability does not affect microbial growth rates but does affect the metabolic phenotypes observed in vitro—including metabolic phenotypes that distinguish six common pathogens. To address this, we used a combination of isotope-labeling, substrate exclusion, and nutritional supplementation experiments using Roswell Park Memorial Institute (RPMI) medium to identify the specific nutrients used by the microbes to produce diagnostic biomarkers, and to formulate a Biomarker Enrichment Medium (BEM) as an alternative to complex undefined media for metabolomics research, clinical diagnostics, antibiotic susceptibility testing, and other applications where the analysis of stable microbial metabolic phenotypes is important.
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25
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A Comprehensive Metabolomics Analysis of Fecal Samples from Advanced Adenoma and Colorectal Cancer Patients. Metabolites 2022; 12:metabo12060550. [PMID: 35736483 PMCID: PMC9229737 DOI: 10.3390/metabo12060550] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 06/08/2022] [Accepted: 06/14/2022] [Indexed: 12/14/2022] Open
Abstract
Accurate diagnosis of colorectal cancer (CRC) still relies on invasive colonoscopy. Noninvasive methods are less sensitive in detecting the disease, particularly in the early stage. In the current work, a metabolomics analysis of fecal samples was carried out by ultra-high-performance liquid chromatography–tandem mass spectroscopy (UPLC-MS/MS). A total of 1380 metabolites were analyzed in a cohort of 120 fecal samples from patients with normal colonoscopy, advanced adenoma (AA) and CRC. Multivariate analysis revealed that metabolic profiles of CRC and AA patients were similar and could be clearly separated from control individuals. Among the 25 significant metabolites, sphingomyelins (SM), lactosylceramides (LacCer), secondary bile acids, polypeptides, formiminoglutamate, heme and cytidine-containing pyrimidines were found to be dysregulated in CRC patients. Supervised random forest (RF) and logistic regression algorithms were employed to build a CRC accurate predicted model consisting of the combination of hemoglobin (Hgb) and bilirubin E,E, lactosyl-N-palmitoyl-sphingosine, glycocholenate sulfate and STLVT with an accuracy, sensitivity and specificity of 91.67% (95% Confidence Interval (CI) 0.7753–0.9825), 0.7 and 1, respectively.
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26
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Wang Y, Chen Z, Shima K, Zhong D, Yang L, Wang Q, Jiang R, Dong J, Lei Y, Li X, Cao L. Rapid diagnosis of papillary thyroid carcinoma with machine learning and probe electrospray ionization mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2022; 57:e4831. [PMID: 35562642 DOI: 10.1002/jms.4831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 04/21/2022] [Accepted: 04/22/2022] [Indexed: 06/15/2023]
Abstract
Frozen section examination could provide pathological diagnosis for surgery of thyroid nodules, which is time-consuming, skill- and experience-dependent. This study developed a rapid classification method for thyroid nodules and machine learning. Total 69 tissues were collected including 43 nodules and 26 nodule-adjacent tissues. Intraoperative frozen section was first performed to give accurate diagnosis, and the rest frozen specimen were pretreated for probe electrospray ionization mass measurement. By multivariate analysis of mass scan data, a series compounds were found downregulated in the extraction solution of papillary thyroid carcinoma (PTC), but some were found upregulated by mass spectrometry imaging. m/z 758.5713 ([PC[34:2] + H]+ ), m/z 772.5845 ([PC[32:0] + K]+ ), and m/z 786.6037 ([PC[36:2] + H]+ ) were firstly identified as potential biomarkers for nodular goiter (NG). Machine learning was employed by means of support vector machine (SVM) and random forest (RF) algorithms. For classification of PTC from NG, SVM and RF algorithms exhibited the same performance and the concordance was 94.2% and 94.4% between prediction and pathological diagnosis with positive and negative mass dataset, respectively. For the classification of PTC from PTC adjacent tissues, SVM was better than RF and the concordance was 93.8% and 83.3% with positive and negative mass dataset, respectively. With the identified compounds as training features, the sensitivity and specificity are 87.5% and 88.9% for the test set. The developed method could also correctly predict the malignancy of one medullary thyroid carcinoma and one adenomatous goiter (benign). The diagnosis time is about 10 min for one specimen, and it is very promising for the intraoperative diagnosis of papillary thyroid carcinoma.
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Affiliation(s)
- Ye Wang
- Department of Pathology, China-Japan Friendship Hospital, Beijing, China
| | - Zhenhe Chen
- Shimadzu China Innovation Center, Shimadzu Corporation, Beijing, China
| | - Keisuke Shima
- Shimadzu China Innovation Center, Shimadzu Corporation, Beijing, China
| | - Dingrong Zhong
- Department of Pathology, China-Japan Friendship Hospital, Beijing, China
| | - Lei Yang
- Department of Pathology, China-Japan Friendship Hospital, Beijing, China
| | - Qingyang Wang
- Department of Pathology, China-Japan Friendship Hospital, Beijing, China
| | - Ruiying Jiang
- Department of Pathology, China-Japan Friendship Hospital, Beijing, China
| | - Jing Dong
- Shimadzu China Innovation Center, Shimadzu Corporation, Beijing, China
| | - Yajuan Lei
- Shimadzu China Innovation Center, Shimadzu Corporation, Beijing, China
| | - Xiaodong Li
- Shimadzu China Innovation Center, Shimadzu Corporation, Beijing, China
| | - Lei Cao
- Shimadzu China Innovation Center, Shimadzu Corporation, Beijing, China
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27
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Gandhi S, Chinnadurai V, Bhadra K, Gupta I, Kanwar RS. Urinary metabolic modulation in human participants residing in Siachen: a 1H NMR metabolomics approach. Sci Rep 2022; 12:9070. [PMID: 35641596 PMCID: PMC9156790 DOI: 10.1038/s41598-022-13031-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 05/19/2022] [Indexed: 12/15/2022] Open
Abstract
The main physiological challenge in high altitude environment is hypoxia which affects the aerobic metabolism reducing the energy supply. These changes may further progress toward extreme environment-related diseases. These are further reflected in changes in small molecular weight metabolites and metabolic pathways. In the present study, metabolic changes due to chronic environmental hypoxia were assessed using 1H NMR metabolomics by analysing the urinary metabolic profile of 70 people at sea level and 40 people at Siachen camp (3700 m) for 1 year. Multivariate statistical analysis was carried out, and PLSDA detected 15 metabolites based on VIP score > 1. ROC analysis detected cis-aconitate, Nicotinamide Mononucleotide, Tyrosine, Choline and Creatinine metabolites with a high range of sensitivity and specificity. Pathway analysis revealed 16 pathways impact > 0.05, and phenylalanine tyrosine and tryptophan biosynthesis was the most prominent altered pathway indicating metabolic remodelling to meet the energy requirements. TCA cycle, Glycine serine and Threonine metabolism, Glutathione metabolism and Cysteine alterations were other metabolic pathways affected during long-term high-altitude hypoxia exposure. Present findings will help unlock a new dimension for the potential application of NMR metabolomics to address extreme environment-related health problems, early detection and developing strategies to combat high altitude hypoxia.
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Affiliation(s)
- Sonia Gandhi
- Metabolomics Research Facility, Institute of Nuclear Medicine and Allied Sciences (INMAS), Lucknow Road, Timarpur, Delhi, 110054, India.
| | - Vijayakumar Chinnadurai
- Cognitive Control and Machine Learning Centre, Institute of Nuclear Medicine and Allied Sciences, Delhi, 110054, India
| | - Kuntal Bhadra
- Department of Endocrinology and Thyroid Research Centre, Institute of Nuclear Medicine and Allied Sciences, Delhi, 110054, India
| | - Isha Gupta
- Metabolomics Research Facility, Institute of Nuclear Medicine and Allied Sciences (INMAS), Lucknow Road, Timarpur, Delhi, 110054, India
| | - Ratnesh Singh Kanwar
- Department of Endocrinology and Thyroid Research Centre, Institute of Nuclear Medicine and Allied Sciences, Delhi, 110054, India
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28
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Tallis E, Karsenty CL, Grimes AB, Karam LB, Elsea SH, Sutton VR, Rawls‐Castillo BL, Liu N, Soler‐Alfonso C. Untargeted metabolomic profiling in a patient with glycogen storage disease
Ib
receiving empagliflozin treatment. JIMD Rep 2022; 63:309-315. [PMID: 35822097 PMCID: PMC9259396 DOI: 10.1002/jmd2.12304] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/09/2022] [Accepted: 05/11/2022] [Indexed: 11/29/2022] Open
Abstract
Glycogen storage disease type Ib (GSD‐Ib) is a rare inborn error of glycogen metabolism uniquely associated with neutropenia and neutrophil dysfunction, causing severe infections, inflammatory bowel disease (IBD), and impaired wound healing. Recently, kidney sodium‐glucose co‐transporter‐2 (SGLT2) inhibitors such as empagliflozin known to reduce plasma levels of 1,5‐anhydroglucitol (1,5‐AG) and its toxic derivatives in neutrophils, have been described as a new treatment option in case reports of patients with GSD‐Ib from Europe and Asia. We report our experience with an 11‐year‐old girl with GSD‐Ib presenting with short fasting hypoglycemia, neutropenia with neutrophil dysfunction, recurrent infections, suboptimal growth, iron‐deficiency anemia, and IBD. Treatment with daily empagliflozin improved neutrophil counts and function with a significant reduction in G‐CSF needs. Significant improvement in IBD has led to weight gain with improved nutritional markers and improved fasting tolerance. Reduction of maximum empagliflozin dose was needed due to arthralgia. No other significant side effects of empagliflozin were observed. This report uniquely highlights the novel use of untargeted metabolomics profiling for monitoring plasma levels of 1,5‐AG to assess empagliflozin dose responsiveness and guide dietary management and G‐CSF therapy. Clinical improvement correlated to rapid normalization of 1,5‐AG levels in plasma sustained after dose reduction. In conclusion, empagliflozin appeared to be a safe treatment option for GSD‐Ib‐associated neutropenia and neutrophil dysfunction. Global untargeted metabolomics is an efficient method to assess biochemical responsiveness to treatment.
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Affiliation(s)
- Eran Tallis
- Department of Molecular and Human Genetics Baylor College of Medicine Houston Texas USA
| | - Cecile L. Karsenty
- Department of Pediatrics Baylor College of Medicine Houston Texas USA
- Texas Children's Cancer and Hematology Centers Houston Texas USA
| | - Amanda B. Grimes
- Department of Pediatrics Baylor College of Medicine Houston Texas USA
- Texas Children's Cancer and Hematology Centers Houston Texas USA
| | - Lina B. Karam
- Department of Pediatrics‐Gastroenterology Baylor College of Medicine Houston Texas USA
| | - Sarah H. Elsea
- Department of Molecular and Human Genetics Baylor College of Medicine Houston Texas USA
- Baylor Genetics Houston Texas USA
| | - Vernon Reed Sutton
- Department of Molecular and Human Genetics Baylor College of Medicine Houston Texas USA
- Baylor Genetics Houston Texas USA
| | | | - Ning Liu
- Department of Molecular and Human Genetics Baylor College of Medicine Houston Texas USA
- Baylor Genetics Houston Texas USA
| | - Claudia Soler‐Alfonso
- Department of Molecular and Human Genetics Baylor College of Medicine Houston Texas USA
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29
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Thistlethwaite LR, Li X, Burrage LC, Riehle K, Hacia JG, Braverman N, Wangler MF, Miller MJ, Elsea SH, Milosavljevic A. Clinical diagnosis of metabolic disorders using untargeted metabolomic profiling and disease-specific networks learned from profiling data. Sci Rep 2022; 12:6556. [PMID: 35449147 PMCID: PMC9023513 DOI: 10.1038/s41598-022-10415-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 03/14/2022] [Indexed: 02/06/2023] Open
Abstract
Untargeted metabolomics is a global molecular profiling technology that can be used to screen for inborn errors of metabolism (IEMs). Metabolite perturbations are evaluated based on current knowledge of specific metabolic pathway deficiencies, a manual diagnostic process that is qualitative, has limited scalability, and is not equipped to learn from accumulating clinical data. Our purpose was to improve upon manual diagnosis of IEMs in the clinic by developing novel computational methods for analyzing untargeted metabolomics data. We employed CTD, an automated computational diagnostic method that "connects the dots" between metabolite perturbations observed in individual metabolomics profiling data and modules identified in disease-specific metabolite co-perturbation networks learned from prior profiling data. We also extended CTD to calculate distances between any two individuals (CTDncd) and between an individual and a disease state (CTDdm), to provide additional network-quantified predictors for use in diagnosis. We show that across 539 plasma samples, CTD-based network-quantified measures can reproduce accurate diagnosis of 16 different IEMs, including adenylosuccinase deficiency, argininemia, argininosuccinic aciduria, aromatic L-amino acid decarboxylase deficiency, cerebral creatine deficiency syndrome type 2, citrullinemia, cobalamin biosynthesis defect, GABA-transaminase deficiency, glutaric acidemia type 1, maple syrup urine disease, methylmalonic aciduria, ornithine transcarbamylase deficiency, phenylketonuria, propionic acidemia, rhizomelic chondrodysplasia punctata, and the Zellweger spectrum disorders. Our approach can be used to supplement information from biochemical pathways and has the potential to significantly enhance the interpretation of variants of uncertain significance uncovered by exome sequencing. CTD, CTDdm, and CTDncd can serve as an essential toolset for biological interpretation of untargeted metabolomics data that overcomes limitations associated with manual diagnosis to assist diagnosticians in clinical decision-making. By automating and quantifying the interpretation of perturbation patterns, CTD can improve the speed and confidence by which clinical laboratory directors make diagnostic and treatment decisions, while automatically improving performance with new case data.
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Affiliation(s)
- Lillian R Thistlethwaite
- Quantitative and Computational Biosciences Program, Baylor College of Medicine, One Baylor Plaza, 400D, Houston, TX, 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Xiqi Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Lindsay C Burrage
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Hospital, Houston, TX, USA
| | - Kevin Riehle
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Joseph G Hacia
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Nancy Braverman
- Department of Pediatrics and Human Genetics, McGill University, Montreal, QC, Canada
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Hospital, Houston, TX, USA
- Jan and Dan Duncan Texas Children's Hospital Neurological Research Institute, Houston, TX, USA
| | - Marcus J Miller
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Sarah H Elsea
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Aleksandar Milosavljevic
- Quantitative and Computational Biosciences Program, Baylor College of Medicine, One Baylor Plaza, 400D, Houston, TX, 77030, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
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30
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Ford L, Mitchell M, Wulff J, Evans A, Kennedy A, Elsea S, Wittmann B, Toal D. Clinical metabolomics for inborn errors of metabolism. Adv Clin Chem 2022; 107:79-138. [PMID: 35337606 DOI: 10.1016/bs.acc.2021.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Metabolism is a highly regulated process that provides nutrients to cells and essential building blocks for the synthesis of protein, DNA and other macromolecules. In healthy biological systems, metabolism maintains a steady state in which the concentrations of metabolites are relatively constant yet are subject to metabolic demands and environmental stimuli. Rare genetic disorders, such as inborn errors of metabolism (IEM), cause defects in regulatory enzymes or proteins leading to metabolic pathway disruption and metabolite accumulation or deficiency. Traditionally, the laboratory diagnosis of IEMs has been limited to analytical methods that target specific metabolites such as amino acids and acyl carnitines. This approach is effective as a screening method for the most common IEM disorders but lacks the comprehensive coverage of metabolites that is necessary to identify rare disorders that present with nonspecific clinical symptoms. Fortunately, advancements in technology and data analytics has introduced a new field of study called metabolomics which has allowed scientists to perform comprehensive metabolite profiling of biological systems to provide insight into mechanism of action and gene function. Since metabolomics seeks to measure all small molecule metabolites in a biological specimen, it provides an innovative approach to evaluating disease in patients with rare genetic disorders. In this review we provide insight into the appropriate application of metabolomics in clinical settings. We discuss the advantages and limitations of the method and provide details related to the technology, data analytics and statistical modeling required for metabolomic profiling of patients with IEMs.
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Affiliation(s)
- Lisa Ford
- Metabolon, Inc., Morrisville, NC, United States
| | | | - Jacob Wulff
- Metabolon, Inc., Morrisville, NC, United States
| | - Annie Evans
- Metabolon, Inc., Morrisville, NC, United States
| | | | - Sarah Elsea
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | | | - Douglas Toal
- Metabolon, Inc., Morrisville, NC, United States.
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31
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Pienkowski T, Kowalczyk T, Garcia-Romero N, Ayuso-Sacido A, Ciborowski M. Proteomics and metabolomics approach in adult and pediatric glioma diagnostics. Biochim Biophys Acta Rev Cancer 2022; 1877:188721. [PMID: 35304294 DOI: 10.1016/j.bbcan.2022.188721] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/10/2022] [Accepted: 03/11/2022] [Indexed: 12/26/2022]
Abstract
The diagnosis of glioma is mainly based on imaging methods that do not distinguish between stage and subtype prior to histopathological analysis. Patients with gliomas are generally diagnosed in the symptomatic stage of the disease. Additionally, healing scar tissue may be mistakenly identified based on magnetic resonance imaging (MRI) as a false positive tumor recurrence in postoperative patients. Current knowledge of molecular alterations underlying gliomagenesis and identification of tumoral biomarkers allow for their use as discriminators of the state of the organism. Moreover, a multiomics approach provides the greatest spectrum and the ability to track physiological changes and can serve as a minimally invasive method for diagnosing asymptomatic gliomas, preceding surgery and allowing for the initiation of prophylactic treatment. It is important to create a vast biomarker library for adults and pediatric patients due to their metabolic differences. This review focuses on the most promising proteomic, metabolomic and lipidomic glioma biomarkers, their pathways, the interactions, and correlations that can be considered characteristic of tumor grade or specific subtype.
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Affiliation(s)
- Tomasz Pienkowski
- Clinical Research Centre, Medical University of Bialystok, M. Sklodowskiej-Curie 24a, 15-276 Bialystok, Poland.
| | - Tomasz Kowalczyk
- Clinical Research Centre, Medical University of Bialystok, M. Sklodowskiej-Curie 24a, 15-276 Bialystok, Poland; Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Bialystok, Mickiewicza 2C, 15-222 Bialystok, Poland
| | - Noemi Garcia-Romero
- Faculty of Experimental Sciences, Universidad Francisco de Vitoria, 28223 Madrid, Spain; Brain Tumor Laboratory, Fundación Vithas, Grupo Hospitales Vithas, 28043 Madrid, Spain
| | - Angel Ayuso-Sacido
- Faculty of Experimental Sciences, Universidad Francisco de Vitoria, 28223 Madrid, Spain; Brain Tumor Laboratory, Fundación Vithas, Grupo Hospitales Vithas, 28043 Madrid, Spain; Faculty of Medicine, Universidad Francisco de Vitoria, 28223 Madrid, Spain
| | - Michal Ciborowski
- Clinical Research Centre, Medical University of Bialystok, M. Sklodowskiej-Curie 24a, 15-276 Bialystok, Poland
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32
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Castelli FA, Rosati G, Moguet C, Fuentes C, Marrugo-Ramírez J, Lefebvre T, Volland H, Merkoçi A, Simon S, Fenaille F, Junot C. Metabolomics for personalized medicine: the input of analytical chemistry from biomarker discovery to point-of-care tests. Anal Bioanal Chem 2022; 414:759-789. [PMID: 34432105 PMCID: PMC8386160 DOI: 10.1007/s00216-021-03586-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/24/2021] [Accepted: 07/27/2021] [Indexed: 12/30/2022]
Abstract
Metabolomics refers to the large-scale detection, quantification, and analysis of small molecules (metabolites) in biological media. Although metabolomics, alone or combined with other omics data, has already demonstrated its relevance for patient stratification in the frame of research projects and clinical studies, much remains to be done to move this approach to the clinical practice. This is especially true in the perspective of being applied to personalized/precision medicine, which aims at stratifying patients according to their risk of developing diseases, and tailoring medical treatments of patients according to individual characteristics in order to improve their efficacy and limit their toxicity. In this review article, we discuss the main challenges linked to analytical chemistry that need to be addressed to foster the implementation of metabolomics in the clinics and the use of the data produced by this approach in personalized medicine. First of all, there are already well-known issues related to untargeted metabolomics workflows at the levels of data production (lack of standardization), metabolite identification (small proportion of annotated features and identified metabolites), and data processing (from automatic detection of features to multi-omic data integration) that hamper the inter-operability and reusability of metabolomics data. Furthermore, the outputs of metabolomics workflows are complex molecular signatures of few tens of metabolites, often with small abundance variations, and obtained with expensive laboratory equipment. It is thus necessary to simplify these molecular signatures so that they can be produced and used in the field. This last point, which is still poorly addressed by the metabolomics community, may be crucial in a near future with the increased availability of molecular signatures of medical relevance and the increased societal demand for participatory medicine.
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Affiliation(s)
- Florence Anne Castelli
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), Gif-sur-Yvette cedex, 91191, France
- MetaboHUB, Gif-sur-Yvette, France
| | - Giulio Rosati
- Institut Català de Nanociència i Nanotecnologia (ICN2), Edifici ICN2 Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Christian Moguet
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), Gif-sur-Yvette cedex, 91191, France
| | - Celia Fuentes
- Institut Català de Nanociència i Nanotecnologia (ICN2), Edifici ICN2 Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Jose Marrugo-Ramírez
- Institut Català de Nanociència i Nanotecnologia (ICN2), Edifici ICN2 Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Thibaud Lefebvre
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), Gif-sur-Yvette cedex, 91191, France
- Centre de Recherche sur l'Inflammation/CRI, Université de Paris, Inserm, Paris, France
- CRMR Porphyrie, Hôpital Louis Mourier, AP-HP Nord - Université de Paris, Colombes, France
| | - Hervé Volland
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), Gif-sur-Yvette cedex, 91191, France
| | - Arben Merkoçi
- Institut Català de Nanociència i Nanotecnologia (ICN2), Edifici ICN2 Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Stéphanie Simon
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), Gif-sur-Yvette cedex, 91191, France
| | - François Fenaille
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), Gif-sur-Yvette cedex, 91191, France
- MetaboHUB, Gif-sur-Yvette, France
| | - Christophe Junot
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), Gif-sur-Yvette cedex, 91191, France.
- MetaboHUB, Gif-sur-Yvette, France.
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Defining Blood Plasma and Serum Metabolome by GC-MS. Metabolites 2021; 12:metabo12010015. [PMID: 35050137 PMCID: PMC8779220 DOI: 10.3390/metabo12010015] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/18/2021] [Accepted: 12/21/2021] [Indexed: 01/04/2023] Open
Abstract
Metabolomics uses advanced analytical chemistry methods to analyze metabolites in biological samples. The most intensively studied samples are blood and its liquid components: plasma and serum. Armed with advanced equipment and progressive software solutions, the scientific community has shown that small molecules’ roles in living systems are not limited to traditional “building blocks” or “just fuel” for cellular energy. As a result, the conclusions based on studying the metabolome are finding practical reflection in molecular medicine and a better understanding of fundamental biochemical processes in living systems. This review is not a detailed protocol of metabolomic analysis. However, it should support the reader with information about the achievements in the whole process of metabolic exploration of human plasma and serum using mass spectrometry combined with gas chromatography.
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Guo L, Li L, Xu Z, Meng F, Guo H, Liu P, Liu P, Tian Y, Xu F, Zhang Z, Zhang S, Huang Y. Metabolic network-based identification of plasma markers for non-small cell lung cancer. Anal Bioanal Chem 2021; 413:7421-7430. [PMID: 34617154 DOI: 10.1007/s00216-021-03699-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 09/01/2021] [Accepted: 09/27/2021] [Indexed: 12/01/2022]
Abstract
Metabolic markers, offering sensitive information on biological dysfunction, play important roles in diagnosing and treating cancers. However, the discovery of effective markers is limited by the lack of well-established metabolite selection approaches. Here, we propose a network-based strategy to uncover the metabolic markers with potential clinical availability for non-small cell lung cancer (NSCLC). First, an integrated mass spectrometry-based untargeted metabolomics was used to profile the plasma samples from 43 NSCLC patients and 43 healthy controls. We found that a series of 39 metabolites were altered significantly. Relying on the human metabolic network assembled from Kyoto Encyclopedia of Genes and Genomes (KEGG) database, we mapped these differential metabolites to the network and constructed an NSCLC-related disease module containing 23 putative metabolic markers. By measuring the PageRank centrality of molecules in this module, we computationally evaluated the network-based importance of the 23 metabolites and demonstrated that the metabolism pathways of aromatic amino acids and long-chain fatty acids provided potential molecular targets of NSCLC (i.e., IL4l1 and ACOT2). Combining network-based ranking and support-vector machine modeling, we further found a panel of eight metabolites (i.e., pyruvate, tryptophan, and palmitic acid) that showed a high capability to differentiate patients from controls (accuracy > 97.7%). In summary, we present a meaningful network method for metabolic marker discovery and have identified eight strong candidate metabolites for NSCLC diagnosis.
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Affiliation(s)
- Linling Guo
- Key Laboratory of Drug Quality Control and Pharmacovigilance, China Pharmaceutical University, Ministry of Education, Nanjing, 210009, Jaingsu, China
| | - Linrui Li
- Key Laboratory of Drug Quality Control and Pharmacovigilance, China Pharmaceutical University, Ministry of Education, Nanjing, 210009, Jaingsu, China
| | - Zhiyun Xu
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital of Jiangsu Province, Nanjing, 210009, Jiangsu, China
| | - Fanchen Meng
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital of Jiangsu Province, Nanjing, 210009, Jiangsu, China
| | - Huimin Guo
- Center for Biological Technology, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Peijia Liu
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150001, Heilongjiang, China
| | - Peifang Liu
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150001, Heilongjiang, China
| | - Yuan Tian
- Key Laboratory of Drug Quality Control and Pharmacovigilance, China Pharmaceutical University, Ministry of Education, Nanjing, 210009, Jaingsu, China
| | - Fengguo Xu
- Key Laboratory of Drug Quality Control and Pharmacovigilance, China Pharmaceutical University, Ministry of Education, Nanjing, 210009, Jaingsu, China
| | - Zunjian Zhang
- Key Laboratory of Drug Quality Control and Pharmacovigilance, China Pharmaceutical University, Ministry of Education, Nanjing, 210009, Jaingsu, China
| | - Shuai Zhang
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital of Jiangsu Province, Nanjing, 210009, Jiangsu, China.
| | - Yin Huang
- Key Laboratory of Drug Quality Control and Pharmacovigilance, China Pharmaceutical University, Ministry of Education, Nanjing, 210009, Jaingsu, China.
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Katz L, Tata A, Woolman M, Zarrine-Afsar A. Lipid Profiling in Cancer Diagnosis with Hand-Held Ambient Mass Spectrometry Probes: Addressing the Late-Stage Performance Concerns. Metabolites 2021; 11:metabo11100660. [PMID: 34677375 PMCID: PMC8537725 DOI: 10.3390/metabo11100660] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/18/2021] [Accepted: 09/22/2021] [Indexed: 02/06/2023] Open
Abstract
Untargeted lipid fingerprinting with hand-held ambient mass spectrometry (MS) probes without chromatographic separation has shown promise in the rapid characterization of cancers. As human cancers present significant molecular heterogeneities, careful molecular modeling and data validation strategies are required to minimize late-stage performance variations of these models across a large population. This review utilizes parallels from the pitfalls of conventional protein biomarkers in reaching bedside utility and provides recommendations for robust modeling as well as validation strategies that could enable the next logical steps in large scale assessment of the utility of ambient MS profiling for cancer diagnosis. Six recommendations are provided that range from careful initial determination of clinical added value to moving beyond just statistical associations to validate lipid involvements in disease processes mechanistically. Further guidelines for careful selection of suitable samples to capture expected and unexpected intragroup variance are provided and discussed in the context of demographic heterogeneities in the lipidome, further influenced by lifestyle factors, diet, and potential intersect with cancer lipid pathways probed in ambient mass spectrometry profiling studies.
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Affiliation(s)
- Lauren Katz
- Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada; (L.K.); (M.W.)
- Techna Institute for the Advancement of Technology for Health, University Health Network, 100 College Street, Toronto, ON M5G 1P5, Canada
| | - Alessandra Tata
- Laboratorio di Chimica Sperimentale, Istituto Zooprofilattico delle Venezie, Viale Fiume 78, 36100 Vicenza, Italy;
| | - Michael Woolman
- Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada; (L.K.); (M.W.)
- Techna Institute for the Advancement of Technology for Health, University Health Network, 100 College Street, Toronto, ON M5G 1P5, Canada
| | - Arash Zarrine-Afsar
- Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada; (L.K.); (M.W.)
- Techna Institute for the Advancement of Technology for Health, University Health Network, 100 College Street, Toronto, ON M5G 1P5, Canada
- Department of Surgery, University of Toronto, 149 College Street, Toronto, ON M5T 1P5, Canada
- Keenan Research Center for Biomedical Science & the Li Ka Shing Knowledge Institute, St. Michael’s Hospital, 30 Bond Street, Toronto, ON M5B 1W8, Canada
- Correspondence: ; Tel.: +1-416-581-8473
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Metabolomics-Based Screening of Inborn Errors of Metabolism: Enhancing Clinical Application with a Robust Computational Pipeline. Metabolites 2021; 11:metabo11090568. [PMID: 34564390 PMCID: PMC8470724 DOI: 10.3390/metabo11090568] [Citation(s) in RCA: 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: 07/15/2021] [Revised: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 11/17/2022] Open
Abstract
Inborn errors of metabolism (IEM) are inherited conditions caused by genetic defects in enzymes or cofactors. These defects result in a specific metabolic fingerprint in patient body fluids, showing accumulation of substrate or lack of an end-product of the defective enzymatic step. Untargeted metabolomics has evolved as a high throughput methodology offering a comprehensive readout of this metabolic fingerprint. This makes it a promising tool for diagnostic screening of IEM patients. However, the size and complexity of metabolomics data have posed a challenge in translating this avalanche of information into knowledge, particularly for clinical application. We have previously established next-generation metabolic screening (NGMS) as a metabolomics-based diagnostic tool for analyzing plasma of individual IEM-suspected patients. To fully exploit the clinical potential of NGMS, we present a computational pipeline to streamline the analysis of untargeted metabolomics data. This pipeline allows for time-efficient and reproducible data analysis, compatible with ISO:15189 accredited clinical diagnostics. The pipeline implements a combination of tools embedded in a workflow environment for large-scale clinical metabolomics data analysis. The accompanying graphical user interface aids end-users from a diagnostic laboratory for efficient data interpretation and reporting. We also demonstrate the application of this pipeline with a case study and discuss future prospects.
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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: 30] [Impact Index Per Article: 10.0] [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.
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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
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Lichtenberg S, Trifonova OP, Maslov DL, Balashova EE, Lokhov PG. Metabolomic Laboratory-Developed Tests: Current Status and Perspectives. Metabolites 2021; 11:423. [PMID: 34206934 PMCID: PMC8305461 DOI: 10.3390/metabo11070423] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/11/2021] [Accepted: 06/25/2021] [Indexed: 12/18/2022] Open
Abstract
Laboratory-developed tests (LDTs) are a subset of in vitro diagnostic devices, which the US Food and Drug Administration defines as "tests that are manufactured by and used within a single laboratory". The review describes the emergence and history of LDTs. The current state and development prospects of LDTs based on metabolomics are analyzed. By comparing LDTs with the scientific metabolomics study of human bio samples, the characteristic features of metabolomic LDT are shown, revealing its essence, strengths, and limitations. The possibilities for further developments and scaling of metabolomic LDTs and their potential significance for healthcare are discussed. The legal aspects of LDT regulation in the United States, European Union, and Singapore, demonstrating different approaches to this issue, are also provided. Based on the data presented in the review, recommendations were made on the feasibility and ways of further introducing metabolomic LDTs into practice.
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Affiliation(s)
- Steven Lichtenberg
- Metabometrics, Inc., 651 N Broad St, Suite 205 #1370, Middletown, DE 19709, USA
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; (O.P.T.); (D.L.M.); (E.E.B.)
| | - Oxana P. Trifonova
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; (O.P.T.); (D.L.M.); (E.E.B.)
| | - Dmitry L. Maslov
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; (O.P.T.); (D.L.M.); (E.E.B.)
| | - Elena E. Balashova
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; (O.P.T.); (D.L.M.); (E.E.B.)
| | - Petr G. Lokhov
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; (O.P.T.); (D.L.M.); (E.E.B.)
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Gawor JP, Wilczak J, Svensson UK, Jank M. Influence of Dietary Supplementation With a Powder Containing A.N. ProDen™ ( Ascophyllum Nodosum) Algae on Dog Saliva Metabolome. Front Vet Sci 2021; 8:681951. [PMID: 34239914 PMCID: PMC8258245 DOI: 10.3389/fvets.2021.681951] [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: 03/17/2021] [Accepted: 05/18/2021] [Indexed: 11/13/2022] Open
Abstract
The objective of this placebo-controlled, double-blind, randomized study (designed according to evidence-based medicine standards) was to determine the effect of 30-day administration of powdered brown algae, Ascophyllum nodosum (ProDen PlaqueOff, SwedenCare AB, Sweden), on saliva metabolomes in dogs. Sixty client-owned dogs underwent professional dental cleaning and were randomly subdivided into two groups receiving daily powdered brown algae A. nodosum, or a placebo (microcrystalline cellulose in powder), adjusted to their bodyweight. After a comprehensive oral health assessment and professional dental cleaning, which were both performed under general anesthesia, clinical assessments for gingivitis, plaque, and calculus were conducted. Saliva samples were collected at Day 0 and Day 30 of supplementation. Whole saliva is a mixed fluid that is derived predominantly from the major salivary glands but it also contains numerous other constituents. Additionally, its composition varies on whether salivary secretion is basal or stimulated. Authors put efforts to avoid contamination of saliva by other constituents and character of saliva was basal. Quadrupole time-of-flight (QTOF) mass spectrometer was used to conduct analysis of the saliva samples. Metabolomic analyses identified clear changes after 30 days of supplementation, and the direction of these changes was completely different than in dogs that received a placebo treatment during the same period. The positive clinical effect of 30 days of A. nodosum supplementation on oral health status in dogs described in previous publication combined with the absence of some metabolites in the saliva of dogs on day 30 of supplementation suggest that brown algae inhibit or turn off some pathways that could enhance plaque or calculus development. The exact mechanism of A. nodosum is still unclear and warrants further study.
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Affiliation(s)
| | - Jacek Wilczak
- Institute of Veterinary Medicine, Department of Physiological Sciences, Warsaw University of Life Sciences, Warsaw, Poland
| | | | - Michal Jank
- Institute of Veterinary Medicine, Department of Pre-Clinical Sciences, Warsaw University of Life Sciences, Warsaw, Poland
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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.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Sarah Elsea
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
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Valko-Rokytovská M, Očenáš P, Salayová A, Kostecká Z. Breast Cancer: Targeting of Steroid Hormones in Cancerogenesis and Diagnostics. Int J Mol Sci 2021; 22:ijms22115878. [PMID: 34070921 PMCID: PMC8199112 DOI: 10.3390/ijms22115878] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/26/2021] [Accepted: 05/27/2021] [Indexed: 12/14/2022] Open
Abstract
Breast cancer is the most common malignancy in women with high mortality. Sensitive and specific methods for the detection, characterization and quantification of endogenous steroids in body fluids or tissues are needed for the diagnosis, treatment and prognosis of breast cancer and many other diseases. At present, non-invasive diagnostic methods are gaining more and more prominence, which enable a relatively fast and painless way of detecting many diseases. Metabolomics is a promising analytical method, the principle of which is the study and analysis of metabolites in biological material. It represents a comprehensive non-invasive diagnosis, which has a high potential for use in the diagnosis and prognosis of cancers, including breast cancer. This short review focuses on the targeted metabolomics of steroid hormones, which play an important role in the development and classification of breast cancer. The most commonly used diagnostic tool is the chromatographic method with mass spectrometry detection, which can simultaneously determine several steroid hormones and metabolites in one sample. This analytical procedure has a high potential in effective diagnosis of steroidogenesis disorders. Due to the association between steroidogenesis and breast cancer progression, steroid profiling is an important tool, as well as in monitoring disease progression, improving prognosis, and minimizing recurrence.
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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: 10] [Impact Index Per Article: 3.3] [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.
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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.
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43
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Trifonova OP, Maslov DL, Balashova EE, Lokhov PG. Mass spectrometry-based metabolomics diagnostics - myth or reality? Expert Rev Proteomics 2021; 18:7-12. [PMID: 33653222 DOI: 10.1080/14789450.2021.1893695] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
ABSTACTIntroduction: Metabolomics, one of the most high-promising technologies, is the most recently developed post-genomics discipline for developing new diagnostic tests for future implementation in medicine. More than 2,000 scientific papers, using mass spectrometry-based (MS-based) metabolomics analysis for human disease diagnostics, have been published during the past two decades, and almost every metabolomics study shows high diagnostic accuracy. However, despite the great results and promising perspectives, there are currently no diagnostic tests based on metabolomics that have been approved and introduced into clinics.Areas covered: In this report, the advantages and challenges of MS-based metabolomics are discussed with a focus on its developing role in diagnostics, and the current trends in implementing metabolomics diagnostics in the clinic.Expert opinion: In the development of new clinical diagnostics tests, MS-based metabolomics has potential as both a preliminary discovery base for routine testing and a multi-test prototype, which is hoped to be introduced into clinical practice in the near future. A laboratory-developed test (LDT) is one possible way that multi-testing could be developed.
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Affiliation(s)
- Oxana P Trifonova
- Analytical Branch, Laboratory of Mass Spectrometry-based Metabolomic Diagnostic, Institute of Biomedical Chemistry, Moscow, Russia
| | - Dmitri L Maslov
- Analytical Branch, Laboratory of Mass Spectrometry-based Metabolomic Diagnostic, Institute of Biomedical Chemistry, Moscow, Russia
| | - Elena E Balashova
- Analytical Branch, Laboratory of Mass Spectrometry-based Metabolomic Diagnostic, Institute of Biomedical Chemistry, Moscow, Russia
| | - Petr G Lokhov
- Analytical Branch, Laboratory of Mass Spectrometry-based Metabolomic Diagnostic, Institute of Biomedical Chemistry, Moscow, Russia
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Lokhov PG, Maslov DL, Lichtenberg S, Trifonova OP, Balashova EE. Holistic Metabolomic Laboratory-Developed Test (LDT): Development and Use for the Diagnosis of Early-Stage Parkinson's Disease. Metabolites 2020; 11:metabo11010014. [PMID: 33383698 PMCID: PMC7824177 DOI: 10.3390/metabo11010014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/24/2020] [Accepted: 12/24/2020] [Indexed: 02/04/2023] Open
Abstract
A laboratory-developed test (LDT) is a type of in vitro diagnostic test that is developed and used within a single laboratory. The holistic metabolomic LDT integrating the currently available data on human metabolic pathways, changes in the concentrations of low-molecular-weight compounds in the human blood during diseases and other conditions, and their prevalent location in the body was developed. That is, the LDT uses all of the accumulated metabolic data relevant for disease diagnosis and high-resolution mass spectrometry with data processing by in-house software. In this study, the LDT was applied to diagnose early-stage Parkinson's disease (PD), which currently lacks available laboratory tests. The use of the LDT for blood plasma samples confirmed its ability for such diagnostics with 73% accuracy. The diagnosis was based on relevant data, such as the detection of overrepresented metabolite sets associated with PD and other neurodegenerative diseases. Additionally, the ability of the LDT to detect normal composition of low-molecular-weight compounds in blood was demonstrated, thus providing a definition of healthy at the molecular level. This LDT approach as a screening tool can be used for the further widespread testing for other diseases, since 'omics' tests, to which the metabolomic LDT belongs, cover a variety of them.
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Affiliation(s)
- Petr G. Lokhov
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; (D.L.M.); (O.P.T.); (E.E.B.)
- Correspondence:
| | - Dmitry L. Maslov
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; (D.L.M.); (O.P.T.); (E.E.B.)
| | - Steven Lichtenberg
- Metabometrics, Inc, 651 N Broad St, Suite 205 #1370, Middletown, DE 19709, USA;
| | - Oxana P. Trifonova
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; (D.L.M.); (O.P.T.); (E.E.B.)
| | - Elena E. Balashova
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; (D.L.M.); (O.P.T.); (E.E.B.)
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45
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Sobering AK, Li D, Beighley JS, Carey JC, Donald T, Elsea SH, Figueroa KP, Gerdts J, Hamlet A, Mirzaa GM, Nelson B, Pulst SM, Smith JL, Tassone F, Toriello HV, Walker RH, Yearwood KR, Bhoj EJ. Experiences with offering pro bono medical genetics services in the West Indies: Benefits to patients, physicians, and the community. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2020; 184:1030-1041. [PMID: 33274544 DOI: 10.1002/ajmg.c.31871] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/21/2020] [Accepted: 11/25/2020] [Indexed: 12/16/2022]
Abstract
We describe our experiences with organizing pro bono medical genetics and neurology outreach programs on several different resource-limited islands in the West Indies. Due to geographic isolation, small population sizes, and socioeconomic disparities, most Caribbean islands lack medical services for managing, diagnosing, and counseling individuals with genetic disorders. From 2015 to 2019, we organized 2-3 clinics per year on various islands in the Caribbean. We also organized a week-long clinic to provide evaluations for children suspected of having autism spectrum disorder. Consultations for over 100 different individuals with suspected genetic disorders were performed in clinics or during home visits following referral by locally registered physicians. When possible, follow-up visits were attempted. When available and appropriate, clinical samples were shipped to collaborating laboratories for molecular analysis. Laboratory tests included karyotyping, cytogenomic microarray analysis, exome sequencing, triplet repeat expansion testing, blood amino acid level determination, biochemical assaying, and metabolomic profiling. We believe that significant contributions to healthcare by genetics professionals can be made even if availability is limited. Visiting geneticists may help by providing continuing medical education seminars. Clinical teaching rounds help to inform local physicians regarding the management of genetic disorders with the aim of generating awareness of genetic conditions. Even when only periodically available, a visiting geneticist may benefit affected individuals, their families, their local physicians, and the community at large.
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Affiliation(s)
- Andrew K Sobering
- Department of Biochemistry, St. George's University School of Medicine, St. George's, Grenada.,Windward Islands Research and Education Foundation, True Blue, St. George's, Grenada
| | - Dong Li
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jennifer S Beighley
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, Washington, USA
| | - John C Carey
- Department of Pediatrics, University of Utah Health, Salt Lake City, Utah, USA
| | - Tyhiesia Donald
- Grenada General Hospital, Pediatrics Ward, St. George's, Grenada.,Clinical Teaching Unit, St. George's University School of Medicine, St. George's, Grenada
| | - Sarah H Elsea
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Karla P Figueroa
- Department of Neurology, University of Utah, Salt Lake City, Utah, USA
| | - Jennifer Gerdts
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, Washington, USA
| | - Andre Hamlet
- Grenada General Hospital, Pediatrics Ward, St. George's, Grenada.,Clinical Teaching Unit, St. George's University School of Medicine, St. George's, Grenada
| | - Ghayda M Mirzaa
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, USA.,Department of Pediatrics, University of Washington, Seattle, Washington, USA.,Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
| | - Beverly Nelson
- Clinical Teaching Unit, St. George's University School of Medicine, St. George's, Grenada
| | - Stefan M Pulst
- Department of Neurology, University of Utah, Salt Lake City, Utah, USA
| | - Janice L Smith
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Flora Tassone
- Department of Biochemistry and Molecular Medicine, University of California Davis, School of Medicine, Sacramento, California, USA.,MIND Institute, University of California Davis Medical Center, Sacramento, California, USA
| | - Helga V Toriello
- Department of Pediatrics/Human Development College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA
| | - Ruth H Walker
- Department of Neurology, James J. Peters Veterans Affairs Medical Center, Bronx, New York, USA.,Department of Neurology, Mount Sinai School of Medicine, New York City, New York, USA
| | | | - Elizabeth J Bhoj
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
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46
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Esperanza MG, Wrobel K, Ojeda AG, Garay-Sevilla ME, Escobosa ARC, Barrientos EY, Wrobel K. Liquid chromatography-mass spectrometry untargeted metabolomics reveals increased levels of tryptophan indole metabolites in urine of metabolic syndrome patients. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2020; 26:379-387. [PMID: 33295818 DOI: 10.1177/1469066720964632] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Metabolic syndrome (MetS) is a multifactor condition predisposing for diabetes, cardiovascular diseases and other degenerative disorders. Although several diagnostic criteria have been established, none of them is specific and there is a call for better pathophysiological explanation of MetS and for the discovery of molecular biomarkers. Phenotype characterization at metabolome level might be useful for both purposes. To this end, our aim was to perform comparative untargeted metabolomics of urines from MetS patients and from the control group. The study participants included 52 diagnosticated and 50 healthy individuals from Leon city in central Mexico; 23 anthropometric and clinical parameters were measured and submitted to Principal Component Analysis (PCA). The obtained PCA model allowed us for selection of 11 MetS patients and 13 control subjects, correspondingly representative for each of the two groups (clearly separated in PCA). The first morning urines from these subjects were ambulatory collected and, after methanol extraction and acidification, were submitted to capillary liquid chromatography-high resolution mass spectrometry (LC-HRMS). The obtained data were analyzed on MetaboScape® platform (Bruker Daltonics). Specifically, t-test applied to LC-HRMS data revealed several ions presenting at least 3-fold higher intensities in MetS with respect to the control samples (p < 0.05). Data analysis and complementary experiments yielded the identification of the following metabolites: indole-3-acetic acid, indole-3-acetic acid-O-glucuronide, N-(indol-3-ylacetyl) glutamine, indole-3-carbaldehyde and hydroxyhexanoycarnitine. Additionally, indole-3-carboxylic acid was annotated with 2.13-fold higher abundance in MetS patients. To assess the contribution of individual metabolites in the difference between two groups of subjects, partial least square discriminant analysis was performed for LC-HRMS data and the obtained values of variable importance in projection (VIP), confirmed the association of six above mentioned compounds with MetS. Overall, this study provides direct evidence on the disturbed catabolism of tryptophan in metabolic syndrome.
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Affiliation(s)
| | - Katarzyna Wrobel
- Department of Chemistry, University of Guanajuato, Guanajuato, Mexico
| | | | | | | | | | - Kazimierz Wrobel
- Department of Chemistry, University of Guanajuato, Guanajuato, Mexico
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47
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Manzi M, Palazzo M, Knott ME, Beauseroy P, Yankilevich P, Giménez MI, Monge ME. Coupled Mass-Spectrometry-Based Lipidomics Machine Learning Approach for Early Detection of Clear Cell Renal Cell Carcinoma. J Proteome Res 2020; 20:841-857. [PMID: 33207877 DOI: 10.1021/acs.jproteome.0c00663] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A discovery-based lipid profiling study of serum samples from a cohort that included patients with clear cell renal cell carcinoma (ccRCC) stages I, II, III, and IV (n = 112) and controls (n = 52) was performed using ultraperformance liquid chromatography coupled to quadrupole-time-of-flight mass spectrometry and machine learning techniques. Multivariate models based on support vector machines and the LASSO variable selection method yielded two discriminant lipid panels for ccRCC detection and early diagnosis. A 16-lipid panel allowed discriminating ccRCC patients from controls with 95.7% accuracy in a training set under cross-validation and 77.1% accuracy in an independent test set. A second model trained to discriminate early (I and II) from late (III and IV) stage ccRCC yielded a panel of 26 compounds that classified stage I patients from an independent test set with 82.1% accuracy. Thirteen species, including cholic acid, undecylenic acid, lauric acid, LPC(16:0/0:0), and PC(18:2/18:2), identified with level 1 exhibited significantly lower levels in samples from ccRCC patients compared to controls. Moreover, 3α-hydroxy-5α-androstan-17-one 3-sulfate, cis-5-dodecenoic acid, arachidonic acid, cis-13-docosenoic acid, PI(16:0/18:1), PC(16:0/18:2), and PC(O-16:0/20:4) contributed to discriminate early from late ccRCC stage patients. The results are auspicious for early ccRCC diagnosis after validation of the panels in larger and different cohorts.
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Affiliation(s)
- Malena Manzi
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD CABA, Argentina.,Departamento de Química Biológica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires. Junín 956, C1113AAD Buenos Aires, Argentina
| | - Martín Palazzo
- LM2S, Université de Technologie de Troyes, 12 rue Marie-Curie, CS42060 Troyes, France.,Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA), CONICET, Instituto Partner de la Sociedad Max Planck, Godoy Cruz 2390, C1425FQD CABA, Argentina
| | - María Elena Knott
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD CABA, Argentina
| | - Pierre Beauseroy
- LM2S, Université de Technologie de Troyes, 12 rue Marie-Curie, CS42060 Troyes, France
| | - Patricio Yankilevich
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA), CONICET, Instituto Partner de la Sociedad Max Planck, Godoy Cruz 2390, C1425FQD CABA, Argentina
| | - María Isabel Giménez
- Departamento de Diagnóstico y Tratamiento, Hospital Italiano de Buenos Aires, Tte. Gral. Juan Domingo Perón 4190, C1199ABB CABA, Argentina
| | - María Eugenia Monge
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD CABA, Argentina
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48
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Duan M, Han ZH, Huang T, Yang Y, Huang B. Characterization of gut microbiota and short-chain fatty acid in breastfed infants with or without breast milk jaundice. Lett Appl Microbiol 2020; 72:60-67. [PMID: 32893879 DOI: 10.1111/lam.13382] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 08/20/2020] [Accepted: 08/22/2020] [Indexed: 12/17/2022]
Abstract
This study aims to investigate the gut microbiota and metabolites in breastfed infants with breast milk jaundice (BMJ) using gut microbiome-metabolomics. Breastfed newborns diagnosed with BMJ and those without BMJ (control group) were enrolled. Faecal samples were collected from the participants and subjected to high-throughput sequencing of the 16s rDNA V3 and V4 regions of the gut flora and metabolomics of short-chain fatty acids (SCFAs). Proteobacteria, Fimicutes and Actinobacteria were the main bacteria at the phylum level. Eshcerichia-Shigella and Enterobacteriacea were the main bacteria at the genus level. The difference between the two groups was compared. Compared to the control group, the amount of Streptococcus was significantly increased while the amount of Enterococcus was significantly decreased in the faeces from infants with BMJ. Functional prediction analysis of 16S found that biosynthesis of penicillin and cephalosporin significantly increased in the BMJ group. Gas chromatography-mass spectrometry detection of SCFAs revealed that levels of acetic acid and propionic acid were significantly lower in the BMJ group than in the control group. The reduced levels of acetic acid and propionic acid may be related to the increase in Streptococcus and decrease in Enterococcus, both of which may contribute to BMJ.
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Affiliation(s)
- M Duan
- Department of Neonate, The Third Affiliated Hospital of Zunyi Medical University/The First People's Hospital of Zunyi, Zunyi, China
| | - Z H Han
- Department of Emergency, The Third Affiliated Hospital of Zunyi Medical University/The First People's Hospital of Zunyi, Zunyi, China
| | - T Huang
- Department of Neonate, The Third Affiliated Hospital of Zunyi Medical University/The First People's Hospital of Zunyi, Zunyi, China
| | - Y Yang
- Department of Neonate, The Third Affiliated Hospital of Zunyi Medical University/The First People's Hospital of Zunyi, Zunyi, China
| | - B Huang
- Department of Pediatrics, The Third Affiliated Hospital of Zunyi Medical University/The First People's Hospital of Zunyi, Zunyi, China
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49
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Heyen S, Scholz-Böttcher BM, Rabus R, Wilkes H. Method development and validation for the quantification of organic acids in microbial samples using anionic exchange solid-phase extraction and gas chromatography-mass spectrometry. Anal Bioanal Chem 2020; 412:7491-7503. [PMID: 32970177 PMCID: PMC7533261 DOI: 10.1007/s00216-020-02883-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/29/2020] [Accepted: 08/13/2020] [Indexed: 11/07/2022]
Abstract
Organic acids play a key role in central metabolic functions of organisms, are crucial for understanding regulatory processes and are ubiquitous inside the cell. Therefore, quantification of these compounds provides a valuable approach for studying dynamics of metabolic processes, in particular when the organism faces changing environmental conditions. However, the extraction and analysis of organic acids can be challenging and validated methods available in this field are limited. In this study, we developed a method for the extraction and quantification of organic acids from microbial samples based on solid-phase extraction on a strong anionic exchange cartridge and gas chromatographic-mass spectrometric analysis. Full method validation was conducted to determine quality parameters of the new method. Recoveries for 12 of the 15 aromatic and aliphatic acids were between 100 and 111% and detection limits between 3 and 272 ng/mL. The ranges for the regression coefficients and process standard deviations for these compound classes were 0.9874–0.9994 and 0.04–0.69 μg/mL, respectively. Limitations were encountered when targeting aliphatic acids with hydroxy, oxo or enol ester functions. Finally, we demonstrated the applicability of the method on cell extracts of the bacterium Escherichia coli and the dinoflagellate Prorocentrum minimum. Graphical abstract ![]()
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Affiliation(s)
- Simone Heyen
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, P.O. Box 2503, 26111, Oldenburg, Germany
| | - Barbara M Scholz-Böttcher
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, P.O. Box 2503, 26111, Oldenburg, Germany
| | - Ralf Rabus
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, P.O. Box 2503, 26111, Oldenburg, Germany
| | - Heinz Wilkes
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, P.O. Box 2503, 26111, Oldenburg, Germany.
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50
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Shayota BJ, Donti TR, Xiao J, Gijavanekar C, Kennedy AD, Hubert L, Rodan L, Vanderpluym C, Nowak C, Bjornsson HT, Ganetzky R, Berry GT, Pappan KL, Sutton VR, Sun Q, Elsea SH. Untargeted metabolomics as an unbiased approach to the diagnosis of inborn errors of metabolism of the non-oxidative branch of the pentose phosphate pathway. Mol Genet Metab 2020; 131:147-154. [PMID: 32828637 PMCID: PMC8630378 DOI: 10.1016/j.ymgme.2020.07.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/31/2020] [Accepted: 07/31/2020] [Indexed: 12/27/2022]
Abstract
Inborn errors of metabolism (IEM) involving the non-oxidative pentose phosphate pathway (PPP) include the two relatively rare conditions, transketolase deficiency and transaldolase deficiency, both of which can be difficult to diagnosis given their non-specific clinical presentations. Current biochemical testing approaches require an index of suspicion to consider targeted urine polyol testing. To determine whether a broad-spectrum biochemical test could accurately identify a specific metabolic pattern defining IEMs of the non-oxidative PPP, we employed the use of clinical metabolomic profiling as an unbiased novel approach to diagnosis. Subjects with molecularly confirmed IEMs of the PPP were included in this study. Targeted quantitative analysis of polyols in urine and plasma samples was accomplished with chromatography and mass spectrometry. Semi-quantitative unbiased metabolomic analysis of urine and plasma samples was achieved by assessing small molecules via liquid chromatography and high-resolution mass spectrometry. Results from untargeted and targeted analyses were then compared and analyzed for diagnostic acuity. Two siblings with transketolase (TKT) deficiency and three unrelated individuals with transaldolase (TALDO) deficiency were identified for inclusion in the study. For both IEMs, targeted polyol testing and untargeted metabolomic testing on urine and/or plasma samples identified typical perturbations of the respective disorder. Additionally, untargeted metabolomic testing revealed elevations in other PPP metabolites not typically measured with targeted polyol testing, including ribonate, ribose, and erythronate for TKT deficiency and ribonate, erythronate, and sedoheptulose 7-phosphate in TALDO deficiency. Non-PPP alternations were also noted involving tryptophan, purine, and pyrimidine metabolism for both TKT and TALDO deficient patients. Targeted polyol testing and untargeted metabolomic testing methods were both able to identify specific biochemical patterns indicative of TKT and TALDO deficiency in both plasma and urine samples. In addition, untargeted metabolomics was able to identify novel biomarkers, thereby expanding the current knowledge of both conditions and providing further insight into potential underlying pathophysiological mechanisms. Furthermore, untargeted metabolomic testing offers the advantage of having a single effective biochemical screening test for identification of rare IEMs, like TKT and TALDO deficiencies, that may otherwise go undiagnosed due to their generally non-specific clinical presentations.
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MESH Headings
- Adult
- Biomarkers/blood
- Carbohydrate Metabolism, Inborn Errors/blood
- Carbohydrate Metabolism, Inborn Errors/genetics
- Carbohydrate Metabolism, Inborn Errors/metabolism
- Carbohydrate Metabolism, Inborn Errors/pathology
- Child
- Child, Preschool
- Chromatography, Liquid
- Female
- Humans
- Infant
- Male
- Mass Spectrometry
- Metabolism, Inborn Errors/blood
- Metabolism, Inborn Errors/genetics
- Metabolism, Inborn Errors/metabolism
- Metabolism, Inborn Errors/pathology
- Metabolomics
- Pentose Phosphate Pathway/genetics
- Transaldolase/blood
- Transaldolase/deficiency
- Transaldolase/genetics
- Transaldolase/metabolism
- Transketolase/blood
- Transketolase/deficiency
- Transketolase/genetics
- Young Adult
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Affiliation(s)
- Brian J Shayota
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Taraka R Donti
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jing Xiao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Baylor Genetics, Houston, TX, USA
| | | | | | - Leroy Hubert
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Lance Rodan
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | | | - Catherine Nowak
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Hans T Bjornsson
- McKusick-Nathans Institute of Genetic Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Faculty of Medicine, University of Iceland, Reykjavik, Iceland; Landspitali University Hospital, Reykjavik, Iceland
| | - Rebecca Ganetzky
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Gerard T Berry
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | | | - V Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Baylor Genetics, Houston, TX, USA
| | - Qin Sun
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Baylor Genetics, Houston, TX, USA
| | - Sarah H Elsea
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Baylor Genetics, Houston, TX, USA.
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