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Botello-Marabotto M, Martínez-Bisbal MC, Pinazo-Durán MD, Martínez-Máñez R. Tear metabolomics for the diagnosis of primary open-angle glaucoma. Talanta 2024; 273:125826. [PMID: 38479028 DOI: 10.1016/j.talanta.2024.125826] [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: 11/03/2023] [Revised: 02/14/2024] [Accepted: 02/21/2024] [Indexed: 04/09/2024]
Abstract
Primary Open-Angle Glaucoma (POAG) is the most prevalent glaucoma type, and the leading cause of irreversible visual impairment and blindness worldwide. Identification of early POAG biomarkers is of enormous value, as there is not an effective treatment for the glaucomatous optic nerve degeneration (OND). In this pilot study, a metabolomic analysis, by using proton (1H) nuclear magnetic resonance (NMR) spectroscopy was conducted in tears, in order to determine the changes of specific metabolites in the initial glaucoma eyes and to discover potential diagnostic biomarkers. A classification model, based on the metabolomic fingerprint in tears was generated as a non-invasive tool to support the preclinical and clinical POAG diagnosis. 1H NMR spectra were acquired from 30 tear samples corresponding to the POAG group (n = 11) and the control group (n = 19). Data were analysed by multivariate statistics (partial least squares-discriminant analysis: PLS-DA) to determine a model capable of differentiating between groups. The whole data set was split into calibration (65%)/validation (35%), to test the performance and the ability for glaucoma discrimination. The calculated PLS-DA model showed an area under the curve (AUC) of 1, as well as a sensitivity of 100% and a specificity of 83.3% to distinguish POAG group versus control group tear data. This model included 11 metabolites, potential biomarkers of the disease. When comparing the study groups, a decrease in the tear concentration of phenylalanine, phenylacetate, leucine, n-acetylated compounds, formic acid, and uridine, was found in the POAG group. Moreover, an increase in the tear concentration of taurine, glycine, urea, glucose, and unsaturated fatty acids was observed in the POAG group. These results highlight the potential of tear metabolomics by 1H NMR spectroscopy as a non-invasive approach to support early POAG diagnosis and in order to prevent visual loss.
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Affiliation(s)
- Marina Botello-Marabotto
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València - Universitat de València, Valencia, Spain; Unidad Mixta de Investigación en Nanomedicina y Sensores, Instituto de Investigación Sanitaria La Fe (IISLAFE) - Universitat Politècnica de València, Valencia, Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, Spain
| | - M Carmen Martínez-Bisbal
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València - Universitat de València, Valencia, Spain; Unidad Mixta de Investigación en Nanomedicina y Sensores, Instituto de Investigación Sanitaria La Fe (IISLAFE) - Universitat Politècnica de València, Valencia, Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, Spain; Departamento de Química Física, Universitat de València, Valencia, Spain.
| | - M Dolores Pinazo-Durán
- Ophthalmic Research Unit "Santiago Grisolia"/FISABIO, Valencia, Spain; Cellular and Molecular Ophthalmobiology Research Group at the University of Valencia, Valencia, Spain; Spanish Net of Inflammatory Research (REI-RICORS: RD21/0002/0032) Institute of Health Carlos III, Madrid, Spain
| | - Ramón Martínez-Máñez
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València - Universitat de València, Valencia, Spain; Unidad Mixta de Investigación en Nanomedicina y Sensores, Instituto de Investigación Sanitaria La Fe (IISLAFE) - Universitat Politècnica de València, Valencia, Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, Spain; Departamento de Química, Universitat Politècnica de València, Valencia, Spain; Unidad Mixta UPV-CIPF de Investigación en Mecanismos de Enfermedades y Nanomedicina, València, Universitat Politècnica de València, Centro de Investigación Príncipe Felipe, Valencia, Spain
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2
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Sluiskes MH, Goeman JJ, Beekman M, Slagboom PE, Putter H, Rodríguez-Girondo M. Clarifying the biological and statistical assumptions of cross-sectional biological age predictors: an elaborate illustration using synthetic and real data. BMC Med Res Methodol 2024; 24:58. [PMID: 38459475 PMCID: PMC10921716 DOI: 10.1186/s12874-024-02181-x] [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: 06/22/2023] [Accepted: 02/15/2024] [Indexed: 03/10/2024] Open
Abstract
BACKGROUND There is divergence in the rate at which people age. The concept of biological age is postulated to capture this variability, and hence to better represent an individual's true global physiological state than chronological age. Biological age predictors are often generated based on cross-sectional data, using biochemical or molecular markers as predictor variables. It is assumed that the difference between chronological and predicted biological age is informative of one's chronological age-independent aging divergence ∆. METHODS We investigated the statistical assumptions underlying the most popular cross-sectional biological age predictors, based on multiple linear regression, the Klemera-Doubal method or principal component analysis. We used synthetic and real data to illustrate the consequences if this assumption does not hold. RESULTS The most popular cross-sectional biological age predictors all use the same strong underlying assumption, namely that a candidate marker of aging's association with chronological age is directly informative of its association with the aging rate ∆. We called this the identical-association assumption and proved that it is untestable in a cross-sectional setting. If this assumption does not hold, weights assigned to candidate markers of aging are uninformative, and no more signal may be captured than if markers would have been assigned weights at random. CONCLUSIONS Cross-sectional methods for predicting biological age commonly use the untestable identical-association assumption, which previous literature in the field had never explicitly acknowledged. These methods have inherent limitations and may provide uninformative results, highlighting the importance of researchers exercising caution in the development and interpretation of cross-sectional biological age predictors.
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Affiliation(s)
- Marije H Sluiskes
- Medical Statistics, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands.
| | - Jelle J Goeman
- Medical Statistics, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Marian Beekman
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - P Eline Slagboom
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
- Max Planck Institute for the Biology of Ageing, Cologne, Germany
| | - Hein Putter
- Medical Statistics, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Mar Rodríguez-Girondo
- Medical Statistics, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
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3
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Bizzarri D, Reinders MJT, Beekman M, Slagboom PE, van den Akker EB. Technical Report: A Comprehensive Comparison between Different Quantification Versions of Nightingale Health's 1H-NMR Metabolomics Platform. Metabolites 2023; 13:1181. [PMID: 38132863 PMCID: PMC10745109 DOI: 10.3390/metabo13121181] [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: 10/11/2023] [Revised: 11/07/2023] [Accepted: 11/17/2023] [Indexed: 12/23/2023] Open
Abstract
1H-NMR metabolomics data is increasingly used to track health and disease. Nightingale Health, a major supplier of 1H-NMR metabolomics, has recently updated the quantification strategy to further align with clinical standards. Such updates, however, might influence backward replicability, particularly affecting studies with repeated measures. Using data from BBMRI-NL consortium (~28,000 samples from 28 cohorts), we compared Nightingale data, originally released in 2014 and 2016, with a re-quantified version released in 2020, of which both versions were based on the same NMR spectra. Apart from two discontinued and twenty-three new analytes, we generally observe a high concordance between quantification versions with 73 out of 222 (33%) analytes showing a mean ρ > 0.9 across all cohorts. Conversely, five analytes consistently showed lower Spearman's correlations (ρ < 0.7) between versions, namely acetoacetate, LDL-L, saturated fatty acids, S-HDL-C, and sphingomyelins. Furthermore, previously trained multi-analyte scores, such as MetaboAge or MetaboHealth, might be particularly sensitive to platform changes. Whereas MetaboHealth replicated well, the MetaboAge score had to be retrained due to use of discontinued analytes. Notably, both scores in the re-quantified data recapitulated mortality associations observed previously. Concluding, we urge caution in utilizing different platform versions to avoid mixing analytes, having different units, or simply being discontinued.
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Affiliation(s)
- Daniele Bizzarri
- Molecular Epidemiology, Department of Biomedical Data Science, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands
- Leiden Computational Biology Center, Department of Biomedical Data Science, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands
- Delft Bioinformatics Lab., Department of Intelligent Systems, TU Delft, 2628 XE Delft, The Netherlands
| | - Marcel J. T. Reinders
- Leiden Computational Biology Center, Department of Biomedical Data Science, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands
- Delft Bioinformatics Lab., Department of Intelligent Systems, TU Delft, 2628 XE Delft, The Netherlands
| | - Marian Beekman
- Molecular Epidemiology, Department of Biomedical Data Science, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands
| | - P. Eline Slagboom
- Molecular Epidemiology, Department of Biomedical Data Science, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands
- Max Planck Institute for the Biology of Ageing, 50931 Cologne, Germany
| | - Erik B. van den Akker
- Molecular Epidemiology, Department of Biomedical Data Science, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands
- Leiden Computational Biology Center, Department of Biomedical Data Science, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands
- Delft Bioinformatics Lab., Department of Intelligent Systems, TU Delft, 2628 XE Delft, The Netherlands
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4
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Dey A, Charrier B, Ribay V, Dumez JN, Giraudeau P. Hyperpolarized 1H and 13C NMR Spectroscopy in a Single Experiment for Metabolomics. Anal Chem 2023; 95:16861-16867. [PMID: 37947414 DOI: 10.1021/acs.analchem.3c02614] [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] [Indexed: 11/12/2023]
Abstract
The application of NMR spectroscopy to complex mixture analysis and, in particular, to metabolomics is limited by the low sensitivity of NMR. We recently showed that dissolution dynamic nuclear polarization (d-DNP) could enhance the sensitivity of 13C NMR for complex metabolite mixtures, leading to the detection of highly sensitive 13C NMR fingerprints of complex samples such as plant extracts or urine. While such experiments provide heteronuclear spectra, which are complementary to conventional NMR, hyperpolarized 1H NMR spectra would also be highly useful, with improved limits of detection and compatibility with the existing metabolomics workflow and databases. In this technical note, we introduce an approach capable of recording both 1H and 13C hyperpolarized spectra of metabolite mixtures in a single experiment and on the same hyperpolarized sample. We investigate the analytical performance of this method in terms of sensitivity and repeatability, and then we show that it can be efficiently applied to a plant extract. Significant sensitivity enhancements in 1H NMR are reported with a repeatability suitable for metabolomics studies without compromising on the performance of hyperpolarized 13C NMR. This approach provides a way to perform both 1H and 13C hyperpolarized NMR metabolomics with unprecedented sensitivity and throughput.
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Affiliation(s)
- Arnab Dey
- Nantes Université, CEISAM UMR 6230, 44000 Nantes, France
| | | | - Victor Ribay
- Nantes Université, CEISAM UMR 6230, 44000 Nantes, France
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Mäkinen VP, Karsikas M, Kettunen J, Lehtimäki T, Kähönen M, Viikari J, Perola M, Salomaa V, Järvelin MR, Raitakari OT, Ala-Korpela M. Longitudinal profiling of metabolic ageing trends in two population cohorts of young adults. Int J Epidemiol 2022; 51:1970-1983. [PMID: 35441226 DOI: 10.1093/ije/dyac062] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 03/20/2022] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Quantification of metabolic changes over the human life course is essential to understanding ageing processes. Yet longitudinal metabolomics data are rare and long gaps between visits can introduce biases that mask true trends. We introduce new ways to process quantitative time-series population data and elucidate metabolic ageing trends in two large cohorts. METHODS Eligible participants included 1672 individuals from the Cardiovascular Risk in Young Finns Study and 3117 from the Northern Finland Birth Cohort 1966. Up to three time points (ages 24-49 years) were analysed by nuclear magnetic resonance metabolomics and clinical biochemistry (236 measures). Temporal trends were quantified as median change per decade. Sample quality was verified by consistency of shared biomarkers between metabolomics and clinical assays. Batch effects between visits were mitigated by a new algorithm introduced in this report. The results below satisfy multiple testing threshold of P < 0.0006. RESULTS Women gained more weight than men (+6.5% vs +5.0%) but showed milder metabolic changes overall. Temporal sex differences were observed for C-reactive protein (women +5.1%, men +21.1%), glycine (women +5.2%, men +1.9%) and phenylalanine (women +0.6%, men +3.5%). In 566 individuals with ≥+3% weight gain vs 561 with weight change ≤-3%, divergent patterns were observed for insulin (+24% vs -10%), very-low-density-lipoprotein triglycerides (+32% vs -6%), high-density-lipoprotein2 cholesterol (-6.5% vs +4.7%), isoleucine (+5.7% vs -6.0%) and C-reactive protein (+25% vs -22%). CONCLUSION We report absolute and proportional trends for 236 metabolic measures as new reference material for overall age-associated and specific weight-driven changes in real-world populations.
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Affiliation(s)
- Ville-Petteri Mäkinen
- Computational and Systems Biology Program, Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, Australia.,Australian Centre for Precision Health, University of South Australia, Adelaide, Australia.,Computational Medicine, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Mari Karsikas
- Computational Medicine, Faculty of Medicine, University of Oulu, Oulu, Finland.,Biocenter Oulu, Oulu, Finland.,Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Johannes Kettunen
- Computational Medicine, Faculty of Medicine, University of Oulu, Oulu, Finland.,Biocenter Oulu, Oulu, Finland.,Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland.,Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, and Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, and Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Jorma Viikari
- Department of Medicine, University of Turku, Turku, Finland.,Division of Medicine, Turku University Hospital, Turku, Finland
| | - Markus Perola
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland.,Institute for Molecular Medicine (FIMM), University of Helsinki, Helsinki, Finland.,Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Veikko Salomaa
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Marjo-Riitta Järvelin
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland.,Unit of Primary Health Care, Oulu University Hospital, OYS, Oulu, Finland.,Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK.,Department of Life Sciences, College of Health and Life Sciences, Brunel University London, UK
| | - Olli T Raitakari
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland.,Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland.,Centre for Population Health Research, University of Turku and Turku University Hospital
| | - Mika Ala-Korpela
- Computational Medicine, Faculty of Medicine, University of Oulu, Oulu, Finland.,Biocenter Oulu, Oulu, Finland.,Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland.,NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Kuopio, Finland
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6
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LC-MS/MS Insight into Vitamin C Restoration to Metabolic Disorder Evoked by Amyloid β in Caenorhabditis elegans CL2006. Metabolites 2022; 12:metabo12090841. [PMID: 36144245 PMCID: PMC9506573 DOI: 10.3390/metabo12090841] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/01/2022] [Accepted: 09/02/2022] [Indexed: 11/16/2022] Open
Abstract
The transitional expression and aggregation of amyloid β (Aβ) are the most important causative factors leading to the deterioration of Alzheimer’s disease (AD), a commonly occurring metabolic disease among older people. Antioxidant agents such as vitamin C (Vc) have shown potential effects against AD and aging. We applied an liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) method and differential metabolites strategy to explore the metabolic disorders and Vc restoration in a human Aβ transgenic (Punc-54::Aβ1–42) nematode model CL2006. We combined the LC-MS/MS investigation with the KEGG and HMDB databases and the CFM-ID machine-learning model to identify and qualify the metabolites with important physiological roles. The differential metabolites responding to Aβ activation and Vc treatment were filtered out and submitted to enrichment analysis. The enrichment showed that Aβ mainly caused abnormal biosynthesis and metabolism pathways of phenylalanine, tyrosine and tryptophan biosynthesis, as well as arginine and proline metabolism. Vc reversed the abnormally changed metabolites tryptophan, anthranilate, indole and indole-3-acetaldehyde. Vc restoration affected the tryptophan metabolism and the biosynthesis of phenylalanine, tyrosine and tryptophan. Our findings provide supporting evidence for understanding the metabolic abnormalities in neurodegenerative diseases and the repairing effect of drug interventions.
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7
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Niehues A, Bizzarri D, Reinders MJT, Slagboom PE, van Gool AJ, van den Akker EB, 't Hoen PAC. Metabolomic predictors of phenotypic traits can replace and complement measured clinical variables in population-scale expression profiling studies. BMC Genomics 2022; 23:546. [PMID: 35907790 PMCID: PMC9339202 DOI: 10.1186/s12864-022-08771-7] [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: 03/17/2022] [Accepted: 07/12/2022] [Indexed: 11/10/2022] Open
Abstract
Population-scale expression profiling studies can provide valuable insights into biological and disease-underlying mechanisms. The availability of phenotypic traits is essential for studying clinical effects. Therefore, missing, incomplete, or inaccurate phenotypic information can make analyses challenging and prevent RNA-seq or other omics data to be reused. A possible solution are predictors that infer clinical or behavioral phenotypic traits from molecular data. While such predictors have been developed based on different omics data types and are being applied in various studies, metabolomics-based surrogates are less commonly used than predictors based on DNA methylation profiles.In this study, we inferred 17 traits, including diabetes status and exposure to lipid medication, using previously trained metabolomic predictors. We evaluated whether these metabolomic surrogates can be used as an alternative to reported information for studying the respective phenotypes using expression profiling data of four population cohorts. For the majority of the 17 traits, the metabolomic surrogates performed similarly to the reported phenotypes in terms of effect sizes, number of significant associations, replication rates, and significantly enriched pathways.The application of metabolomics-derived surrogate outcomes opens new possibilities for reuse of multi-omics data sets. In studies where availability of clinical metadata is limited, missing or incomplete information can be complemented by these surrogates, thereby increasing the size of available data sets. Additionally, the availability of such surrogates could be used to correct for potential biological confounding. In the future, it would be interesting to further investigate the use of molecular predictors across different omics types and cohorts.
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Affiliation(s)
- Anna Niehues
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud university medical center, Geert Grooteplein Zuid 26-28, Nijmegen, 6525 GA, Netherlands.,Translational Metabolic Laboratory, Department Laboratory Medicine, Radboud university medical center, Geert Grooteplein Zuid 10, Nijmegen, 6525 GA, Netherlands
| | - Daniele Bizzarri
- Molecular Epidemiology, LUMC, Einthovenweg 20, Leiden, 2333 ZC, Netherlands.,Leiden Computational Biology Center, LUMC, Einthovenweg 20, Leiden, 2333 ZC, Netherlands
| | - Marcel J T Reinders
- Leiden Computational Biology Center, LUMC, Einthovenweg 20, Leiden, 2333 ZC, Netherlands.,Delft Bioinformatics Lab, TU Delft, Van Mourik Broekmanweg 6, Delft, 2628 XE, Netherlands
| | - P Eline Slagboom
- Molecular Epidemiology, LUMC, Einthovenweg 20, Leiden, 2333 ZC, Netherlands.,Max Planck Institute for the Biology of Ageing, Cologne, Germany
| | - Alain J van Gool
- Translational Metabolic Laboratory, Department Laboratory Medicine, Radboud university medical center, Geert Grooteplein Zuid 10, Nijmegen, 6525 GA, Netherlands
| | - Erik B van den Akker
- Molecular Epidemiology, LUMC, Einthovenweg 20, Leiden, 2333 ZC, Netherlands.,Leiden Computational Biology Center, LUMC, Einthovenweg 20, Leiden, 2333 ZC, Netherlands.,Delft Bioinformatics Lab, TU Delft, Van Mourik Broekmanweg 6, Delft, 2628 XE, Netherlands
| | | | | | - Peter A C 't Hoen
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud university medical center, Geert Grooteplein Zuid 26-28, Nijmegen, 6525 GA, Netherlands.
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8
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Xiong L, Wang L, Zhang T, Ye X, Huang F, Huang Q, Huang X, Wu J, Zeng J. UHPLC/MS-Based Serum Metabolomics Reveals the Mechanism of Radiation-Induced Thrombocytopenia in Mice. Int J Mol Sci 2022; 23:ijms23147978. [PMID: 35887324 PMCID: PMC9319504 DOI: 10.3390/ijms23147978] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 07/16/2022] [Accepted: 07/18/2022] [Indexed: 11/16/2022] Open
Abstract
Radiation-induced thrombocytopenia is a common and life-threatening side effect of ionizing radiation (IR) therapy. However, the underlying pathological mechanisms remain unclear. In the present study, irradiation was demonstrated to significantly reduce platelet levels, inhibit megakaryocyte differentiation, and promote the apoptosis of bone marrow (BM) cells. A metabolomics approach and a UHPLC-QTOF MS system were subsequently employed for the comprehensive analysis of serum metabolic profiles of normal and irradiated mice. A total of 66 metabolites were significantly altered, of which 56 were up-regulated and 10 were down-regulated in irradiated mice compared to normal mice on day 11 after irradiation. Pathway analysis revealed that disorders in glycerophospholipid metabolism, nicotinate and nicotinamide metabolism, sphingolipid metabolism, inositol phosphate metabolism, and tryptophan metabolism were involved in radiation-induced thrombocytopenia. In addition, three important differential metabolites, namely L-tryptophan, LysoPC (17:0), and D-sphinganine, which were up-regulated in irradiated mice, significantly induced the apoptosis of K562 cells. L-tryptophan inhibited megakaryocyte differentiation of K562 cells. Finally, serum metabolomics was performed on day 30 (i.e., when the platelet levels in irradiated mice recovered to normal levels). The contents of L-tryptophan, LysoPC (17:0), and D-sphinganine in normal and irradiated mice did not significantly differ on day 30 after irradiation. In conclusion, radiation can cause metabolic disorders, which are highly correlated with the apoptosis of hematopoietic cells and inhibition of megakaryocyte differentiation, ultimately resulting in thrombocytopenia. Further, the metabolites, L-tryptophan, LysoPC (17:0), and D-sphinganine can serve as biomarkers for radiation-induced thrombocytopenia.
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Affiliation(s)
- Ling Xiong
- School of Pharmacy, Southwest Medical University, Luzhou 646000, China; (L.X.); (L.W.); (T.Z.); (X.Y.); (F.H.); (Q.H.); (X.H.)
| | - Long Wang
- School of Pharmacy, Southwest Medical University, Luzhou 646000, China; (L.X.); (L.W.); (T.Z.); (X.Y.); (F.H.); (Q.H.); (X.H.)
| | - Ting Zhang
- School of Pharmacy, Southwest Medical University, Luzhou 646000, China; (L.X.); (L.W.); (T.Z.); (X.Y.); (F.H.); (Q.H.); (X.H.)
| | - Xinyuan Ye
- School of Pharmacy, Southwest Medical University, Luzhou 646000, China; (L.X.); (L.W.); (T.Z.); (X.Y.); (F.H.); (Q.H.); (X.H.)
| | - Feihong Huang
- School of Pharmacy, Southwest Medical University, Luzhou 646000, China; (L.X.); (L.W.); (T.Z.); (X.Y.); (F.H.); (Q.H.); (X.H.)
- Education Ministry Key Laboratory of Medical Electrophysiology, Key Medical Laboratory of New Drug Discovery and Druggability Evaluation, Key Laboratory of Activity Screening and Druggability Evaluation for Chinese Materia Medica, Southwest Medical University, Luzhou 646000, China
| | - Qianqian Huang
- School of Pharmacy, Southwest Medical University, Luzhou 646000, China; (L.X.); (L.W.); (T.Z.); (X.Y.); (F.H.); (Q.H.); (X.H.)
- Education Ministry Key Laboratory of Medical Electrophysiology, Key Medical Laboratory of New Drug Discovery and Druggability Evaluation, Key Laboratory of Activity Screening and Druggability Evaluation for Chinese Materia Medica, Southwest Medical University, Luzhou 646000, China
| | - Xinwu Huang
- School of Pharmacy, Southwest Medical University, Luzhou 646000, China; (L.X.); (L.W.); (T.Z.); (X.Y.); (F.H.); (Q.H.); (X.H.)
- Education Ministry Key Laboratory of Medical Electrophysiology, Key Medical Laboratory of New Drug Discovery and Druggability Evaluation, Key Laboratory of Activity Screening and Druggability Evaluation for Chinese Materia Medica, Southwest Medical University, Luzhou 646000, China
| | - Jianming Wu
- School of Pharmacy, Southwest Medical University, Luzhou 646000, China; (L.X.); (L.W.); (T.Z.); (X.Y.); (F.H.); (Q.H.); (X.H.)
- Education Ministry Key Laboratory of Medical Electrophysiology, Key Medical Laboratory of New Drug Discovery and Druggability Evaluation, Key Laboratory of Activity Screening and Druggability Evaluation for Chinese Materia Medica, Southwest Medical University, Luzhou 646000, China
- Correspondence: (J.W.); (J.Z.); Tel./Fax: +86-830-316-2291 (J.Z.)
| | - Jing Zeng
- School of Pharmacy, Southwest Medical University, Luzhou 646000, China; (L.X.); (L.W.); (T.Z.); (X.Y.); (F.H.); (Q.H.); (X.H.)
- Correspondence: (J.W.); (J.Z.); Tel./Fax: +86-830-316-2291 (J.Z.)
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9
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Bizzarri D, Reinders MJT, Beekman M, Slagboom PE, van den Akker EB. MiMIR: R-shiny application to infer risk factors and endpoints from Nightingale Health's 1H-NMR Metabolomics data. Bioinformatics 2022; 38:3847-3849. [PMID: 35695757 PMCID: PMC9344846 DOI: 10.1093/bioinformatics/btac388] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 06/02/2022] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION 1H-NMR metabolomics is rapidly becoming a standard resource in large epidemiological studies to acquire metabolic profiles in large numbers of samples in a relatively low-priced and standardized manner. Concomitantly, metabolomics-based models are increasingly developed that capture disease risk or clinical risk factors. These developments raise the need for user-friendly toolbox to inspect new 1H-NMR metabolomics data and project a wide array of previously established risk models. RESULTS We present MiMIR (Metabolomics-based Models for Imputing Risk), a graphical user interface that provides an intuitive framework for ad-hoc statistical analysis of Nightingale Health's 1H-NMR metabolomics data and allows for the projection and calibration of 24 pre-trained metabolomics-based models, without any pre-required programming knowledge. AVAILABILITY The R-shiny package is available in CRAN or downloadable at https://github.com/DanieleBizzarri/MiMIR, together with an extensive user manual (also available as Supplementary Documents to the paper). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- D Bizzarri
- Molecular Epidemiology, LUMC, Leiden, The Netherlands.,Leiden Computational Biology Center, LUMC, Leiden, The Netherlands
| | - M J T Reinders
- Leiden Computational Biology Center, LUMC, Leiden, The Netherlands.,Delft Bioinformatics Lab, TU Delft, Delft, The Netherlands
| | - M Beekman
- Molecular Epidemiology, LUMC, Leiden, The Netherlands
| | - P E Slagboom
- Molecular Epidemiology, LUMC, Leiden, The Netherlands.,Max Planck Institute for the Biology of Ageing, Cologne, Germany
| | - E B van den Akker
- Molecular Epidemiology, LUMC, Leiden, The Netherlands.,Leiden Computational Biology Center, LUMC, Leiden, The Netherlands.,Delft Bioinformatics Lab, TU Delft, Delft, The Netherlands
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Kwon DH, Hwang JS, Kim SG, Jang YE, Shin TH, Lee G. Cerebrospinal Fluid Metabolome in Parkinson's Disease and Multiple System Atrophy. Int J Mol Sci 2022; 23:ijms23031879. [PMID: 35163800 PMCID: PMC8836409 DOI: 10.3390/ijms23031879] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/04/2022] [Accepted: 02/04/2022] [Indexed: 11/16/2022] Open
Abstract
Parkinson’s disease (PD) and multiple system atrophy (MSA) belong to the neurodegenerative group of synucleinopathies; differential diagnosis between PD and MSA is difficult, especially at early stages, owing to their clinical and biological similarities. Thus, there is a pressing need to identify metabolic biomarkers for these diseases. The metabolic profile of the cerebrospinal fluid (CSF) is reported to be altered in PD and MSA; however, the altered metabolites remain unclear. We created a single network with altered metabolites in PD and MSA based on the literature and assessed biological functions, including metabolic disorders of the nervous system, inflammation, concentration of ATP, and neurological disorder, through bioinformatics methods. Our in-silico prediction-based metabolic networks are consistent with Parkinsonism events. Although metabolomics approaches provide a more quantitative understanding of biochemical events underlying the symptoms of PD and MSA, limitations persist in covering molecules related to neurodegenerative disease pathways. Thus, omics data, such as proteomics and microRNA, help understand the altered metabolomes mechanism. In particular, integrated omics and machine learning approaches will be helpful to elucidate the pathological mechanisms of PD and MSA. This review discusses the altered metabolites between PD and MSA in the CSF and omics approaches to discover diagnostic biomarkers.
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Affiliation(s)
- Do Hyeon Kwon
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea; (D.H.K.); (J.S.H.); (S.G.K.); (Y.E.J.)
| | - Ji Su Hwang
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea; (D.H.K.); (J.S.H.); (S.G.K.); (Y.E.J.)
| | - Seok Gi Kim
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea; (D.H.K.); (J.S.H.); (S.G.K.); (Y.E.J.)
| | - Yong Eun Jang
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea; (D.H.K.); (J.S.H.); (S.G.K.); (Y.E.J.)
| | - Tae Hwan Shin
- Department of Physiology, Ajou University School of Medicine, Suwon 16499, Korea
- Correspondence: (T.H.S.); (G.L.)
| | - Gwang Lee
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea; (D.H.K.); (J.S.H.); (S.G.K.); (Y.E.J.)
- Department of Physiology, Ajou University School of Medicine, Suwon 16499, Korea
- Correspondence: (T.H.S.); (G.L.)
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