Abstract
Purpose of Review
Metabolomics is the systematic and comparative study of the levels of small-molecule metabolites in samples under various conditions. In biological system, metabolites play a critical role in a diversity of cellular functions. Metabolomics has been widely employed in toxicology and other fields. The purpose of this review is to summarize recent literatures on the application of LC–MS-based metabolomics in drug bioactivation and drug-induced liver injury (DILI) and to discuss their challenges in the field of toxicology.
Recent Findings
The emerging metabolomics could provide us a comprehensive view of novel biochemical sequelae in the cells, tissues, and organisms following toxicant administration. This article reviews LC–MS-based metabolomics in identification of biomarkers of drug toxicity and elucidating mechanisms of toxicity reported in recent years. This review also discusses the application of metabolomics combined with genomics or proteomics in the research field of DILI.
Summary
LC–MS-based metabolomics has a great potential in drug metabolism, identification of biomarkers of cause and/or effect, and revealing the novel mechanisms of drug toxicity. In the future, metabolomics integrating with other omics can serve as an effective tool for investigating the mechanisms of drug toxicity.
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Abbreviations
- AcHZ:
-
Acetylhydrazine
- AGM:
-
Agomelatine
- ALAS:
-
Aminolevulinic acid synthase
- ALA:
-
Aminolevulinic acid
- ALT:
-
Alanine aminotransferase
- APAP:
-
Acetaminophen
- Cd:
-
Cadmium
- CYP450:
-
Cytochromes P450
- DILI:
-
Drug-induced liver injury
- ESI:
-
Electrospray ionization
- GSH:
-
Glutathione
- HLM:
-
Human liver microsomes
- hPXR:
-
Pregnane X receptor humanized
- INH:
-
Isoniazid
- MDA:
-
Multivariate data analysis
- MDF:
-
Mass defect filtering
- MRM:
-
Multiple reaction monitoring
- NADPH:
-
Reduced nicotinamide adenine dinucleotide phosphate
- OPLS-DA:
-
Orthogonal projection to latent structures-discriminant analysis
- PMCol:
-
Pentamethyl-6-chromanol
- PPIX:
-
Protoporphyrin IX
- QTOFMS:
-
Quadrupole time of flight mass spectrometry
- RIF:
-
Rifampicin
- UPLC:
-
Ultra-performance liquid chromatography
References
Papers of particular interest, published recently, have been highlighted as: • Of importance •• Of major importance
Nicholson JK, Lindon JC. Systems biology: metabonomics. Nature. 2008;455:1054–6.
• Gonzalez FJ, Fang ZZ, Ma X. Transgenic mice and metabolomics for study of hepatic xenobiotic metabolism and toxicity. Expert Opin Drug Metab Toxicol. 2015;11:869–81. This paper reviews the application of metabolomics in xenobiotic metabolism and toxicity by the use of genetically modified mouse models.
•• Bouhifd M, Hartung T, Hogberg HT, Kleensang A, Zhao L. Review: toxicometabolomics. J Appl Toxicol. 2013;33:1365–83. This review summarizes the status of metabolomics technologies and principles, their uses in toxicology till 2013 and provides a comprehensive overview on pathway identification, metabolomics and bioinformatics.
O'Connell TM, Watkins PB. The application of metabonomics to predict drug-induced liver injury. Clin Pharmacol Ther. 2010;88:394–9.
Yu M, Zhu Y, Cong Q, Wu C. Metabonomics research progress on liver diseases. Can J Gastroenterol Hepatol. 2017;2017:8467192.
Mishur RJ, Rea SL. Applications of mass spectrometry to metabolomics and metabonomics: detection of biomarkers of aging and of age-related diseases. Mass Spectrom Rev. 2012;31:70–95.
Larrey D. Drug-induced liver diseases. J Hepatol. 2000;32:77–88.
Lee WM. Drug-induced hepatotoxicity. N Engl J Med. 1995;333:1118–27.
Navarro VJ, Senior JR. Drug-related hepatotoxicity. N Engl J Med. 2006;354:731–9.
Welch KD, Reilly TP, Bourdi M, Hays T, Pise-Masison CA, Radonovich MF, et al. Genomic identification of potential risk factors during acetaminophen-induced liver disease in susceptible and resistant strains of mice. Chem Res Toxicol. 2006;19:223–33.
Welch KD, Wen B, Goodlett DR, Yi EC, Lee H, Reilly TP, et al. Proteomic identification of potential susceptibility factors in drug-induced liver disease. Chem Res Toxicol. 2005;18:924–33.
Eun JW, Bae HJ, Shen Q, Park SJ, Kim HS, Shin WC, et al. Characteristic molecular and proteomic signatures of drug-induced liver injury in a rat model. J Appl Toxicol: JAT. 2015;35:152–64.
Aithal GP, Grove JI. Genome-wide association studies in drug-induced liver injury: step change in understanding the pathogenesis. Semin Liver Dis. 2015;35:421–31.
Bell LN, Vuppalanchi R, Watkins PB, Bonkovsky HL, Serrano J, Fontana RJ, et al. Serum proteomic profiling in patients with drug-induced liver injury. Aliment Pharmacol Ther. 2012;35:600–12.
•• Chen C, Gonzalez FJ, Idle JR. LC-MS-based metabolomics in drug metabolism. Drug Metab Rev. 2007;39:581–97. This review describes and discuss the applicable approaches of using LC-MS-base metabolomic techniques to resolve practical issues in drug metabolism for the first time
• Fang ZZ, Gonzalez FJ. LC-MS-based metabolomics: an update. Arch Toxicol. 2014;88:1491–502. This paper updates the application of liquid chromatography-mass spectrometry (LC-MS)-based metabolomics in multiple research fields, especially when combined with other technologies.
Griffiths WJ, Koal T, Wang Y, Kohl M, Enot DP, Deigner HP. Targeted metabolomics for biomarker discovery. Angew Chem Int Ed Engl. 2010;49:5426–45.
Hollywood K, Brison DR, Goodacre R. Metabolomics: current technologies and future trends. Proteomics. 2006;6:4716–23.
Issaq HJ, Fox SD, Chan KC, Veenstra TD. Global proteomics and metabolomics in cancer biomarker discovery. J Sep Sci. 2011;34:3484–92.
Li F, Gonzalez FJ, Ma X. LC–MS-based metabolomics in profiling of drug metabolism and bioactivation. Acta Pharm Sin B. 2012;2:118–25.
Lin L, Huang Z, Gao Y, Yan X, Xing J, Hang W. LC-MS based serum metabonomic analysis for renal cell carcinoma diagnosis, staging, and biomarker discovery. J Proteome Res. 2011;10:1396–405.
Merrick BA. Toxicoproteomics in liver injury and inflammation. Ann N Y Acad Sci. 2006;1076:707–17.
Zhang L, Hatzakis E, Patterson AD. NMR-based metabolomics and its application in drug metabolism and cancer research. Curr Pharmacol Rep. 2016;2:231–40.
Bedair M, Sumner LW. Current and emerging mass-spectrometry technologies for metabolomics. Trends Anal Chem. 2008;27:238–50.
Dettmer K, Aronov PA, Hammock BD. Mass spectrometry-based metabolomics. Mass Spectrom Rev. 2007;26:51–78.
Dunn WB, Ellis DI. Metabolomics: current analytical platforms and methodologies. Trends Anal Chem. 2005;24:285–94.
Kim HK, Choi YH, Verpoorte R. NMR-based plant metabolomics: where do we stand, where do we go? Trends Biotechnol. 2011;29:267–75.
Reo NV. NMR-based metabolomics. Drug Chem Toxicol. 2002;25:375–82.
Wishart DS. Quantitative metabolomics using NMR. TrAC Trends Anal Chem. 2008;27:228–37.
Hu C, van Dommelen J, van der Heijden R, Spijksma G, Reijmers TH, Wang M, et al. RPLC-ion-trap-FTMS method for lipid profiling of plasma: method validation and application to p53 mutant mouse model. J Proteome Res. 2008;7:4982–91.
Bajad SU, Lu W, Kimball EH, Yuan J, Peterson C, Rabinowitz JD. Separation and quantitation of water soluble cellular metabolites by hydrophilic interaction chromatography-tandem mass spectrometry. J Chromatogr A. 2006;1125:76–88.
Banerjee S, Mazumdar S. Electrospray ionization mass spectrometry: a technique to access the information beyond the molecular weight of the analyte. Int J Anal Chem. 2012;2012:282574.
Gunawan BK, Kaplowitz N. Mechanisms of drug-induced liver disease. Clin Liver Dis. 2007;11:459–75. v
Bleibel W, Kim S, D'Silva K, Lemmer ER. Drug-induced liver injury: review article. Dig Dis Sci. 2007;52:2463–71.
Xu JJ, Diaz D, O'Brien PJ. Applications of cytotoxicity assays and pre-lethal mechanistic assays for assessment of human hepatotoxicity potential. Chem Biol Interact. 2004;150:115–28.
Russmann S, Kullak-Ublick GA, Grattagliano I. Current concepts of mechanisms in drug-induced hepatotoxicity. Curr Med Chem. 2009;16:3041–53.
Roth RA, Ganey PE. Intrinsic versus idiosyncratic drug-induced hepatotoxicity—two villains or one? J Pharmacol Exp Ther. 2010;332:692–7.
Katarey D, Verma S. Drug-induced liver injury. Clinical Med. 2016;16:s104–9.
Tujios SR, Lee WM. Acute liver failure induced by idiosyncratic reaction to drugs: challenges in diagnosis and therapy. Liver Int. 2018;38:6–14.
Lee WM. Drug-induced hepatotoxicity. N Engl J Med. 2003;349:474–85.
Ostapowicz G, Fontana RJ, Schiodt FV, Larson A, Davern TJ, Han SH, et al. Results of a prospective study of acute liver failure at 17 tertiary care centers in the United States. Ann Intern Med. 2002;137:947–54.
Baillie TA. Metabolism and toxicity of drugs. Two decades of progress in industrial drug metabolism. Chem Res Toxicol. 2008;21:129–37.
Tang W, Lu AY. Metabolic bioactivation and drug-related adverse effects: current status and future directions from a pharmaceutical research perspective. Drug Metab Rev. 2010;42:225–49.
Leung L, Kalgutkar AS, Obach RS. Metabolic activation in drug-induced liver injury. Drug Metab Rev. 2012;44:18–33.
Juran BD, Lazaridis KN. Genomics and complex liver disease: challenges and opportunities. Hepatology. 2006;44:1380–90.
Gray J, Chattopadhyay D, Beale GS, Patman GL, Miele L, King BP, et al. A proteomic strategy to identify novel serum biomarkers for liver cirrhosis and hepatocellular cancer in individuals with fatty liver disease. BMC Cancer. 2009;9:271.
Baillie TA, Rettie AE. Role of biotransformation in drug-induced toxicity: influence of intra- and inter-species differences in drug metabolism. Drug Metab Pharmacokinet. 2011;26:15–29.
Srivastava A, Maggs JL, Antoine DJ, Williams DP, Smith DA, Park BK. Role of reactive metabolites in drug-induced hepatotoxicity. Handb Exp Pharmacol 2010:165–194.
Regan SL, Maggs JL, Hammond TG, Lambert C, Williams DP, Park BK. Acyl glucuronides: the good, the bad and the ugly. Biopharm Drug Dispos. 2010;31:367–95.
Thurman R, Kauffman F, Baron J. Biotransformation and zonal toxicity. In: Thurman R, Kauffman F, Jungermann K, editors. Regulation of Hepatic Metabolism: Springer US; 1986. p. 321–382.
Kalgutkar AS, Soglia JR. Minimising the potential for metabolic activation in drug discovery. Expert Opin Drug Metab Toxicol. 2005;1:91–142.
Kalgutkar AS, Didiuk MT. Structural alerts, reactive metabolites, and protein covalent binding: how reliable are these attributes as predictors of drug toxicity? Chem Biodivers. 2009;6:2115–37.
Guengerich FP, MacDonald JS. Applying mechanisms of chemical toxicity to predict drug safety. Chem Res Toxicol. 2007;20:344–69.
Holt MP, Ju C. Mechanisms of drug-induced liver injury. AAPS J. 2006;8:E48–54.
Argoti D, Liang L, Conteh A, Chen L, Bershas D, Yu CP, et al. Cyanide trapping of iminium ion reactive intermediates followed by detection and structure identification using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Chem Res Toxicol. 2005;18:1537–44.
Evans DC, Watt AP, Nicoll-Griffith DA, Baillie TA. Drug-protein adducts: an industry perspective on minimizing the potential for drug bioactivation in drug discovery and development. Chem Res Toxicol. 2004;17:3–16.
Gan J, Harper TW, Hsueh MM, Qu Q, Humphreys WG. Dansyl glutathione as a trapping agent for the quantitative estimation and identification of reactive metabolites. Chem Res Toxicol. 2005;18:896–903.
Kalgutkar AS, Dalvie DK, O'Donnell JP, Taylor TJ, Sahakian DC. On the diversity of oxidative bioactivation reactions on nitrogen-containing xenobiotics. Curr Drug Metab. 2002;3:379–424.
Dieckhaus CM, Fernandez-Metzler CL, King R, Krolikowski PH, Baillie TA. Negative ion tandem mass spectrometry for the detection of glutathione conjugates. Chem Res Toxicol. 2005;18:630–8.
Zhu M, Ma L, Zhang H, Humphreys WG. Detection and structural characterization of glutathione-trapped reactive metabolites using liquid chromatography-high-resolution mass spectrometry and mass defect filtering. Anal Chem. 2007;79:8333–41.
Zheng J, Ma L, Xin B, Olah T, Humphreys WG, Zhu M. Screening and identification of GSH-trapped reactive metabolites using hybrid triple quadruple linear ion trap mass spectrometry. Chem Res Toxicol. 2007;20:757–66.
Li F, Wang L, Guo GL, Ma X. Metabolism-mediated drug interactions associated with ritonavir-boosted tipranavir in mice. Drug Metab Dispos. 2010;38:871–8.
Ma X, Chen C, Krausz KW, Idle JR, Gonzalez FJ. A metabolomic perspective of melatonin metabolism in the mouse. Endocrinology. 2008;149:1869–79.
Li F, Lu J, Ma X. Profiling the reactive metabolites of xenobiotics using metabolomic technologies. Chem Res Toxicol. 2011;24:744–51.
Bessems JG, Vermeulen NP. Paracetamol (acetaminophen)-induced toxicity: molecular and biochemical mechanisms, analogues and protective approaches. Crit Rev Toxicol. 2001;31:55–138.
Han D, Hanawa N, Saberi B, Kaplowitz N. Mechanisms of liver injury. III. Role of glutathione redox status in liver injury. Am J Physiol Gastrointest Liver Physiol. 2006;291:G1–7.
Liu X, Lu YF, Guan X, Zhao M, Wang J, Li F. Characterizing novel metabolic pathways of melatonin receptor agonist agomelatine using metabolomic approaches. Biochem Pharmacol. 2016;109:70–82.
Li F, Lu J, Wang L, Ma X. CYP3A-mediated generation of aldehyde and hydrazine in atazanavir metabolism. Drug Metab Dispos. 2011;39:394–401.
Li F, Lu J, Ma X. Metabolomic screening and identification of the bioactivation pathways of ritonavir. Chem Res Toxicol. 2011;24:2109–14.
Li F, Lu J, Ma X. CPY3A4-mediated alpha-hydroxyaldehyde formation in saquinavir metabolism. Drug Metab Dispos. 2014;42:213–20.
Liu X, Lu Y, Guan X, Dong B, Chavan H, Wang J, et al. Metabolomics reveals the formation of aldehydes and iminium in gefitinib metabolism. Biochem Pharmacol. 2015;97:111–21.
Yao D, Shi X, Wang L, Gosnell BA, Chen C. Characterization of differential cocaine metabolism in mouse and rat through metabolomics-guided metabolite profiling. Drug Metab Dispos. 2013;41:79–88.
Li F, Pang X, Krausz KW, Jiang C, Chen C, Cook JA, et al. Stable isotope- and mass spectrometry-based metabolomics as tools in drug metabolism: a study expanding tempol pharmacology. J Proteome Res. 2013;12:1369–76.
Yang X-N, Lv Q-Q, Zhao Q, Li X-M, Yan D-M, Yang X-W, et al. Metabolic profiling of myrislignan by UPLC-ESI-QTOFMS-based metabolomics. RSC Adv. 2017;7:40131–40.
Wang P, Shehu AI, Liu K, Lu J, Ma X. Biotransformation of Cobicistat: metabolic pathways and enzymes. Drug Metab Lett. 2016;10:111–23.
Shi J, Xie C, Liu H, Krausz KW, Bewley CA, Zhang S, et al. Metabolism and bioactivation of fluorochloridone, a novel selective herbicide, in vivo and in vitro. Environ Sci Technol. 2016;50:9652–60.
Kim JH, Choi WG, Lee S, Lee HS. Revisiting the metabolism and bioactivation of ketoconazole in human and mouse using liquid chromatography-mass spectrometry-based metabolomics. Int J Mol Sci 2017;18.
Kim JH, Jo JH, Seo KA, Hwang H, Lee HS, Lee S. Non-targeted metabolomics-guided sildenafil metabolism study in human liver microsomes. J Chromatogr B Anal Technol Biomed Life Sci. 2018;1072:86–93.
Xie C, Gao X, Sun D, Zhang Y, Krausz KW, Qin X, et al. Metabolic profiling of the novel hypoxia-inducible factor 2alpha inhibitor PT2385 in vivo and in vitro. Drug Metab Dispos. 2018;46:336–45.
Kim JH, Choi WG, Moon JY, Lee JY, Lee S, Lee HS. Metabolomics-assisted metabolite profiling of itraconazole in human liver preparations. J Chromatogr B Anal Technol Biomed Life Sci. 2018;1083:68–74.
Zhao Q, Li XM, Liu HN, Gonzalez FJ, Li F. Metabolic map of osthole and its effect on lipids. Xenobiotica. 2018;48:285–99.
•• Araujo AM, Carvalho M, Carvalho F, Bastos ML, Guedes de Pinho P. Metabolomic approaches in the discovery of potential urinary biomarkers of drug-induced liver injury (DILI). Crit Rev Toxicol. 2017;47:633–49. This review describes the current status of the application of metabolomics to the early prognosis and diagnosis of drug-induced liver injury and in the discovery of potential biomarkers of liver injury in urine.
Yew WW, Leung CC. Antituberculosis drugs and hepatotoxicity. Respirology. 2006;11:699–707.
Chowdhury A, Santra A, Bhattacharjee K, Ghatak S, Saha DR, Dhali GK. Mitochondrial oxidative stress and permeability transition in isoniazid and rifampicin induced liver injury in mice. J Hepatol. 2006;45:117–26.
Tasduq SA, Kaiser P, Sharma SC, Johri RK. Potentiation of isoniazid-induced liver toxicity by rifampicin in a combinational therapy of antitubercular drugs (rifampicin, isoniazid and pyrazinamide) in Wistar rats: a toxicity profile study. Hepatol Res. 2007;37:845–53.
Kliewer SA, Moore JT, Wade L, Staudinger JL, Watson MA, Jones SA, et al. An orphan nuclear receptor activated by pregnanes defines a novel steroid signaling pathway. Cell. 1998;92:73–82.
Lehmann JM, McKee DD, Watson MA, Willson TM, Moore JT, Kliewer SA. The human orphan nuclear receptor PXR is activated by compounds that regulate CYP3A4 gene expression and cause drug interactions. J Clin Invest. 1998;102:1016–23.
Li F, Lu J, Cheng J, Wang L, Matsubara T, Csanaky IL, et al. Human PXR modulates hepatotoxicity associated with rifampicin and isoniazid co-therapy. Nat Med. 2013;19:418–20.
Gangadharam PR. Isoniazid, rifampin, and hepatotoxicity. Am Rev Respir Dis. 1986;133:963–5.
Huang YS, Chern HD, Su WJ, Wu JC, Chang SC, Chiang CH, et al. Cytochrome P450 2E1 genotype and the susceptibility to antituberculosis drug-induced hepatitis. Hepatology. 2003;37:924–30.
Miguet JP, Mavier P, Soussy CJ, Dhumeaux D. Induction of hepatic microsomal enzymes after brief administration of rifampicin in man. Gastroenterology. 1977;72:924–6.
Slatter JG, Templeton IE, Castle JC, Kulkarni A, Rushmore TH, Richards K, et al. Compendium of gene expression profiles comprising a baseline model of the human liver drug metabolism transcriptome. Xenobiotica. 2006;36:938–62.
Rosenfeld JM, Vargas R Jr, Xie W, Evans RM. Genetic profiling defines the xenobiotic gene network controlled by the nuclear receptor pregnane X receptor. Mol Endocrinol. 2003;17:1268–82.
Sarich TC, Youssefi M, Zhou T, Adams SP, Wall RA, Wright JM. Role of hydrazine in the mechanism of isoniazid hepatotoxicity in rabbits. Arch Toxicol. 1996;70:835–40.
Mitchell JR, Zimmerman HJ, Ishak KG, Thorgeirsson UP, Timbrell JA, Snodgrass WR, et al. Isoniazid liver injury: clinical spectrum, pathology, and probable pathogenesis. Ann Intern Med. 1976;84:181–92.
Casanova-Gonzalez MJ, Trapero-Marugan M, Jones EA, Moreno-Otero R. Liver disease and erythropoietic protoporphyria: a concise review. World J Gastroenterol. 2010;16:4526–31.
Fraser DJ, Zumsteg A, Meyer UA. Nuclear receptors constitutive androstane receptor and pregnane X receptor activate a drug-responsive enhancer of the murine 5-aminolevulinic acid synthase gene. J Biol Chem. 2003;278:39392–401.
Sachar M, Li F, Liu K, Wang P, Lu J, Ma X. Chronic treatment with isoniazid causes protoporphyrin IX accumulation in mouse liver. Chem Res Toxicol. 2016;29:1293–7.
Parman T, Bunin DI, Ng HH, McDunn JE, Wulff JE, Wang A, et al. Toxicogenomics and metabolomics of pentamethylchromanol (PMCol)-induced hepatotoxicity. Toxicol Sci. 2011;124:487–501.
Go YM, Roede JR, Orr M, Liang Y, Jones DP. Integrated redox proteomics and metabolomics of mitochondria to identify mechanisms of Cd toxicity. Toxicol Sci. 2014;139:59–73.
Garcia-Canaveras JC, Castell JV, Donato MT, Lahoz A. A metabolomics cell-based approach for anticipating and investigating drug-induced liver injury. Sci Rep. 2016;6:27239.
Mattes W, Davis K, Fabian E, Greenhaw J, Herold M, Looser R, et al. Detection of hepatotoxicity potential with metabolite profiling (metabolomics) of rat plasma. Toxicol Lett. 2014;230:467–78.
Ramirez T, Strigun A, Verlohner A, Huener HA, Peter E, Herold M, et al. Prediction of liver toxicity and mode of action using metabolomics in vitro in HepG2 cells. Arch Toxicol. 2018;92:893–906.
Acknowledgements
We would like to thank Dr. Xiaochao Ma at University of Pittsburgh for his kind suggestion and support for this research.
Funding
This work was supported by the Cancer Prevention & Research Institute of Texas (RP160805), Welch Foundation Grant (H-Q-0042) to Dr. Martin M. Matzuk, and NIH R01 (AR063686) to Zhaoyong Hu.
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Lu, Y., Zhao, XM., Hu, Z. et al. LC–MS-Based Metabolomics in the Study of Drug-Induced Liver Injury. Curr Pharmacol Rep 5, 56–67 (2019). https://doi.org/10.1007/s40495-018-0144-3
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DOI: https://doi.org/10.1007/s40495-018-0144-3