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Derivation of metabolic point of departure using high-throughput in vitro metabolomics: investigating the importance of sampling time points on benchmark concentration values in the HepaRG cell line. Arch Toxicol 2023; 97:721-735. [PMID: 36683062 PMCID: PMC9968698 DOI: 10.1007/s00204-022-03439-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 12/21/2022] [Indexed: 01/23/2023]
Abstract
Amongst omics technologies, metabolomics should have particular value in regulatory toxicology as the measurement of the molecular phenotype is the closest to traditional apical endpoints, whilst offering mechanistic insights into the biological perturbations. Despite this, the application of untargeted metabolomics for point-of-departure (POD) derivation via benchmark concentration (BMC) modelling is still a relatively unexplored area. In this study, a high-throughput workflow was applied to derive PODs associated with a chemical exposure by measuring the intracellular metabolome of the HepaRG cell line following treatment with one of four chemicals (aflatoxin B1, benzo[a]pyrene, cyclosporin A, or rotenone), each at seven concentrations (aflatoxin B1, benzo[a]pyrene, cyclosporin A: from 0.2048 μM to 50 μM; rotenone: from 0.04096 to 10 μM) and five sampling time points (2, 6, 12, 24 and 48 h). The study explored three approaches to derive PODs using benchmark concentration modelling applied to single features in the metabolomics datasets or annotated metabolites or lipids: (1) the 1st rank-ordered unannotated feature, (2) the 1st rank-ordered putatively annotated feature (using a recently developed HepaRG-specific library of polar metabolites and lipids), and (3) 25th rank-ordered feature, demonstrating that for three out of four chemical datasets all of these approaches led to relatively consistent BMC values, varying less than tenfold across the methods. In addition, using the 1st rank-ordered unannotated feature it was possible to investigate temporal trends in the datasets, which were shown to be chemical specific. Furthermore, a possible integration of metabolomics-driven POD derivation with the liver steatosis adverse outcome pathway (AOP) was demonstrated. The study highlights that advances in technologies enable application of in vitro metabolomics at scale; however, greater confidence in metabolite identification is required to ensure PODs are mechanistically anchored.
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2
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Kempa J, O’Shea-Stone G, Moss CE, Peters T, Marcotte TK, Tripet B, Eilers B, Bothner B, Copié V, Pincus SH. Distinct Metabolic States Are Observed in Hypoglycemia Induced in Mice by Ricin Toxin or by Fasting. Toxins (Basel) 2022; 14:toxins14120815. [PMID: 36548712 PMCID: PMC9782143 DOI: 10.3390/toxins14120815] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/08/2022] [Accepted: 11/15/2022] [Indexed: 11/23/2022] Open
Abstract
Hypoglycemia may be induced by a variety of physiologic and pathologic stimuli and can result in life-threatening consequences if untreated. However, hypoglycemia may also play a role in the purported health benefits of intermittent fasting and caloric restriction. Previously, we demonstrated that systemic administration of ricin toxin induced fatal hypoglycemia in mice. Here, we examine the metabolic landscape of the hypoglycemic state induced in the liver of mice by two different stimuli: systemic ricin administration and fasting. Each stimulus produced the same decrease in blood glucose and weight loss. The polar metabolome was studied using 1H NMR, quantifying 59 specific metabolites, and untargeted LC-MS on approximately 5000 features. Results were analyzed by multivariate analyses, using both principal component analysis (PCA) and partial least squares-discriminant analysis (PLS-DA), to identify global metabolic patterns, and by univariate analyses (ANOVA) to assess individual metabolites. The results demonstrated that while there were some similarities in the responses to the two stimuli including decreased glucose, ADP, and glutathione, they elicited distinct metabolic states. The metabolite showing the greatest difference was O-phosphocholine, elevated in ricin-treated animals and known to be affected by the pro-inflammatory cytokine TNF-α. Another difference was the alternative fuel source utilized, with fasting-induced hypoglycemia primarily ketotic, while the response to ricin-induced hypoglycemia involves protein and amino acid catabolism.
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Affiliation(s)
- Jacob Kempa
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Galen O’Shea-Stone
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Corinne E. Moss
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Tami Peters
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Tamera K. Marcotte
- Animal Resources Center, Montana State University, Bozeman, MT 59717, USA
| | - Brian Tripet
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Brian Eilers
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Valérie Copié
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
- Correspondence: (V.C.); (S.H.P.)
| | - Seth H. Pincus
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
- Correspondence: (V.C.); (S.H.P.)
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3
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Furlani IL, da Cruz Nunes E, Canuto GAB, Macedo AN, Oliveira RV. Liquid Chromatography-Mass Spectrometry for Clinical Metabolomics: An Overview. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1336:179-213. [PMID: 34628633 DOI: 10.1007/978-3-030-77252-9_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
Metabolomics is a discipline that offers a comprehensive analysis of metabolites in biological samples. In the last decades, the notable evolution in liquid chromatography and mass spectrometry technologies has driven an exponential progress in LC-MS-based metabolomics. Targeted and untargeted metabolomics strategies are important tools in health and medical science, especially in the study of disease-related biomarkers, drug discovery and development, toxicology, diet, physical exercise, and precision medicine. Clinical and biological problems can now be understood in terms of metabolic phenotyping. This overview highlights the current approaches to LC-MS-based metabolomics analysis and its applications in the clinical research.
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Affiliation(s)
- Izadora L Furlani
- Núcleo de Pesquisa em Cromatografia (Separare), Department of Chemistry, Federal University of São Carlos, São Carlos, SP, Brazil
| | - Estéfane da Cruz Nunes
- Department of Analytical Chemistry, Institute of Chemistry, Federal University of Bahia, Salvador, BA, Brazil
| | - Gisele A B Canuto
- Department of Analytical Chemistry, Institute of Chemistry, Federal University of Bahia, Salvador, BA, Brazil
| | - Adriana N Macedo
- Department of Chemistry, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Regina V Oliveira
- Núcleo de Pesquisa em Cromatografia (Separare), Department of Chemistry, Federal University of São Carlos, São Carlos, SP, Brazil.
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Southam AD, Pursell H, Frigerio G, Jankevics A, Weber RJM, Dunn WB. Characterization of Monophasic Solvent-Based Tissue Extractions for the Detection of Polar Metabolites and Lipids Applying Ultrahigh-Performance Liquid Chromatography-Mass Spectrometry Clinical Metabolic Phenotyping Assays. J Proteome Res 2020; 20:831-840. [PMID: 33236910 DOI: 10.1021/acs.jproteome.0c00660] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Metabolic phenotyping of tissues uses metabolomics and lipidomics to measure the relative polar and nonpolar (lipid) metabolite levels in biological samples. This approach aims to understand disease biochemistry and identify biochemical markers of disease. Sample preparation methods must be reproducible, sensitive (high metabolite and lipid yield), and ideally rapid. We evaluated three biphasic methods for polar and nonpolar compound extraction (chloroform/methanol/water, dichloromethane/methanol/water, and methyl tert-butyl ether [MTBE]/methanol/water), a monophasic method for polar compound extraction (acetonitrile/methanol/water), and a monophasic method for nonpolar compound extraction (isopropanol/water). All methods were applied to mammalian heart, kidney, and liver tissues. Polar extracts were analyzed by hydrophilic interaction chromatography (HILIC) ultrahigh-performance liquid chromatography-mass spectrometry (UHPLC-MS) and nonpolar extracts by C18 reversed-phase UHPLC-MS. Method reproducibility and yield were assessed using multiple annotated endogenous compounds (putatively and MS/MS annotated). Monophasic methods had the highest yield and high reproducibility for both polar (positive ion: median relative standard deviation (RSD) < 18%; negative ion: median RSD < 28%) and nonpolar (positive and negative ion: median RSD < 15%) extractions for heart, kidneys, and liver. The polar monophasic method extracted higher levels of lipid than biphasic polar extractions, and these lipids caused minimal detection suppression for other compounds during HILIC UHPLC-MS. The nonpolar monophasic method had similar or greater detection responses of all detected lipid classes compared to biphasic methods (including increased phosphatidylinositol, phosphatidylserine, and cardiolipin responses). Monophasic methods are quicker and simpler than biphasic methods and are therefore most suited for future automation.
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Affiliation(s)
- Andrew D Southam
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom.,Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Harriet Pursell
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Gianfranco Frigerio
- Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan 20122, Italy
| | - Andris Jankevics
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom.,Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Ralf J M Weber
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom.,Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Warwick B Dunn
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom.,Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom.,Institute of Metabolism and Systems Research, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
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Manier SK, Wagmann L, Flockerzi V, Meyer MR. Toxicometabolomics of the new psychoactive substances α-PBP and α-PEP studied in HepaRG cell incubates by means of untargeted metabolomics revealed unexpected amino acid adducts. Arch Toxicol 2020; 94:2047-2059. [PMID: 32313995 PMCID: PMC7303098 DOI: 10.1007/s00204-020-02742-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 04/06/2020] [Indexed: 01/06/2023]
Abstract
Toxicometabolomics, essentially applying metabolomics to toxicology of endogenous compounds such as drugs of abuse or new psychoactive substances (NPS), can be investigated by using different in vitro models and dedicated metabolomics techniques to enhance the number of relevant findings. The present study aimed to study the toxicometabolomics of the two NPS α-pyrrolidinobutiophenone (1-phenyl-2-(pyrrolidin-1-yl)butan-1-one, α-PBP) and α-pyrrolidinoheptaphenone (1-phenyl-2-(pyrrolidin-1-yl)heptan-1-one, α-PEP, PV8) in HepaRG cell line incubates. Evaluation was performed using reversed-phase and normal-phase liquid chromatography coupled with high-resolution mass spectrometry in positive and negative ionization mode, respectively, to analyze cells and cell media. Statistical evaluation was performed using one-way ANOVA, principal component discriminant function analysis, as well as hierarchical clustering. In general, the analysis of cells did not mainly reveal any features, but the parent compounds of the drugs of abuse. For α-PBP an increase in N-methylnicotinamide was found, which may indicate hepatotoxic potential of the substance. After analysis of cell media, significant features led to the identification of several metabolites of both compounds. Amino acid adducts with glycine and alanine were found, and these have not been described in any study before and are likely to appear in vivo. Additionally, significant changes in the metabolism of cholesterol were revealed after incubation with α-PEP. In summary, the application of metabolomics techniques after HepaRG cells exposure to NPS did not lead to an increased number of identified drug metabolites compared to previously published studies, but gave a wider perspective on the physiological effect of the investigated compounds on human liver cells.
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Affiliation(s)
- Sascha K Manier
- Department of Experimental and Clinical Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, Center for Molecular Signaling (PZMS), Saarland University, 66421, Homburg, Germany
| | - Lea Wagmann
- Department of Experimental and Clinical Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, Center for Molecular Signaling (PZMS), Saarland University, 66421, Homburg, Germany
| | - Veit Flockerzi
- Department of Experimental and Clinical Pharmacology, Institute of Experimental and Clinical Pharmacology and Toxicology, Center for Molecular Signaling (PZMS), Saarland University, 66421, Homburg, Germany
| | - Markus R Meyer
- Department of Experimental and Clinical Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, Center for Molecular Signaling (PZMS), Saarland University, 66421, Homburg, Germany.
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Southam AD, Haglington LD, Najdekr L, Jankevics A, Weber RJM, Dunn WB. Assessment of human plasma and urine sample preparation for reproducible and high-throughput UHPLC-MS clinical metabolic phenotyping. Analyst 2020; 145:6511-6523. [DOI: 10.1039/d0an01319f] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
In this study we assess multiple sample preparation methods for UHPLC-MS metabolic phenotyping analysis of human urine and plasma. All methods are discussed in terms of metabolite and lipid coverage and reproducibility.
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Affiliation(s)
- Andrew D. Southam
- School of Biosciences
- University of Birmingham
- Birmingham
- UK
- Phenome Centre Birmingham
| | | | - Lukáš Najdekr
- School of Biosciences
- University of Birmingham
- Birmingham
- UK
- Phenome Centre Birmingham
| | - Andris Jankevics
- School of Biosciences
- University of Birmingham
- Birmingham
- UK
- Phenome Centre Birmingham
| | - Ralf J. M. Weber
- School of Biosciences
- University of Birmingham
- Birmingham
- UK
- Phenome Centre Birmingham
| | - Warwick B. Dunn
- School of Biosciences
- University of Birmingham
- Birmingham
- UK
- Phenome Centre Birmingham
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