A Systematic Strategy for Screening and Application of Specific Biomarkers in Hepatotoxicity Using Metabolomics Combined With ROC Curves and SVMs.

Current studies that evaluate toxicity based on metabolomics have primarily focused on the screening of biomarkers while largely neglecting further verification and biomarker applications. For this reason, we used drug-induced hepatotoxicity as an example to establish a systematic strategy for screening specific biomarkers and applied these biomarkers to evaluate whether the drugs have potential hepatotoxicity toxicity. Carbon tetrachloride (5 ml/kg), acetaminophen (1500 mg/kg), and atorvastatin (5 mg/kg) are established as rat hepatotoxicity models. Fifteen common biomarkers were screened by multivariate statistical analysis and integration analysis-based metabolomics data. The receiver operating characteristic curve was used to evaluate the sensitivity and specificity of the biomarkers. We obtained 10 specific biomarker candidates with an area under the curve greater than 0.7. Then, a support vector machine model was established by extracting specific biomarker candidate data from the hepatotoxic drugs and nonhepatotoxic drugs; the accuracy of the model was 94.90% (92.86% sensitivity and 92.59% specificity) and the results demonstrated that those ten biomarkers are specific. 6 drugs were used to predict the hepatotoxicity by the support vector machines model; the prediction results were consistent with the biochemical and histopathological results, demonstrating that the model was reliable. Thus, this support vector machine model can be applied to discriminate the between the hepatic or nonhepatic toxicity of drugs. This approach not only presents a new strategy for screening-specific biomarkers with greater diagnostic significance but also provides a new evaluation pattern for hepatotoxicity, and it will be a highly useful tool in toxicity estimation and disease diagnoses.

[1]  D. Amacher,et al.  The discovery and development of proteomic safety biomarkers for the detection of drug-induced liver toxicity. , 2010, Toxicology and applied pharmacology.

[2]  Li Liao,et al.  Clustering exact matches of pairwise sequence alignments by weighted linear regression , 2007, BMC Bioinformatics.

[3]  Sambasivarao Damaraju,et al.  Prediction of skeletal muscle and fat mass in patients with advanced cancer using a metabolomic approach. , 2012, The Journal of nutrition.

[4]  P. Convertini,et al.  The mitochondrial carnitine/acylcarnitine carrier: function, structure and physiopathology. , 2011, Molecular aspects of medicine.

[5]  Xiaohui Lin,et al.  A support vector machine-recursive feature elimination feature selection method based on artificial contrast variables and mutual information. , 2012, Journal of chromatography. B, Analytical technologies in the biomedical and life sciences.

[6]  J. Lindon,et al.  Systems biology: Metabonomics , 2008, Nature.

[7]  B. Allaouchiche,et al.  Metabolic phenotyping of traumatized patients reveals a susceptibility to sepsis. , 2013, Analytical chemistry.

[8]  N. Heaton,et al.  Bile UPLC‐MS fingerprinting and bile acid fluxes during human liver transplantation , 2011, Electrophoresis.

[9]  K. Hajian‐Tilaki,et al.  Receiver Operating Characteristic (ROC) Curve Analysis for Medical Diagnostic Test Evaluation. , 2013, Caspian journal of internal medicine.

[10]  Pengcheng Zhou,et al.  A metabonomics study of Chinese miniature pigs with acute liver failure treated with transplantation of placental mesenchymal stem cells , 2014, Metabolomics.

[11]  Robin H. Schmidt,et al.  Metabolomic analysis of the effects of chronic arsenic exposure in a mouse model of diet-induced Fatty liver disease. , 2014, Journal of proteome research.

[12]  Ming-hui Li,et al.  Insight into biological system responses in goldfish (Carassius auratus) to multiple doses of avermectin exposure by integrated 1H NMR-based metabolomics , 2015 .

[13]  Sai-Sai Xie,et al.  The acute hepatotoxicity of tacrine explained by 1H NMR based metabolomic profiling , 2015 .

[14]  A. Remaley,et al.  Lecithin: cholesterol acyltransferase--from biochemistry to role in cardiovascular disease. , 2009, Current opinion in endocrinology, diabetes, and obesity.

[15]  J. Lindon,et al.  'Metabonomics': understanding the metabolic responses of living systems to pathophysiological stimuli via multivariate statistical analysis of biological NMR spectroscopic data. , 1999, Xenobiotica; the fate of foreign compounds in biological systems.

[16]  小林 隆 A novel serum metabolomics-based diagnostic approach to pancreatic cancer , 2013 .

[17]  Ke Liu,et al.  Characterization and classification of seven citrus herbs by liquid chromatography-quadrupole time-of-flight mass spectrometry and genetic algorithm optimized support vector machines. , 2014, Journal of chromatography. A.

[18]  M. Slomka,et al.  The effects of L-tryptophan and melatonin on selected biochemical parameters in patients with steatohepatitis. , 2010, Journal of physiology and pharmacology : an official journal of the Polish Physiological Society.

[19]  D. Wishart,et al.  Translational biomarker discovery in clinical metabolomics: an introductory tutorial , 2012, Metabolomics.

[20]  Jinhuai Liu,et al.  Detection and direct readout of drugs in human urine using dynamic surface-enhanced Raman spectroscopy and support vector machines. , 2015, Analytical chemistry.

[21]  Deborah I. Bunin,et al.  Toxicogenomics and metabolomics of pentamethylchromanol (PMCol)-induced hepatotoxicity. , 2011, Toxicological sciences : an official journal of the Society of Toxicology.

[22]  K. Nishida,et al.  Therapeutic effect of melatonin on carbon tetrachloride‐induced acute liver injury in rats , 2000, Journal of pineal research.

[23]  Ian H. Witten,et al.  Data mining: practical machine learning tools and techniques, 3rd Edition , 1999 .

[24]  Age K Smilde,et al.  A Critical Assessment of Feature Selection Methods for Biomarker Discovery in Clinical Proteomics* , 2012, Molecular & Cellular Proteomics.

[25]  Xin Lu,et al.  Metabolic characterization of hepatocellular carcinoma using nontargeted tissue metabolomics. , 2013, Cancer research.

[26]  Wei Xu,et al.  Application of ultraperformance liquid chromatography/mass spectrometry-based metabonomic techniques to analyze the joint toxic action of long-term low-level exposure to a mixture of organophosphate pesticides on rat urine profile. , 2013, Toxicological sciences : an official journal of the Society of Toxicology.

[27]  David Broadhurst,et al.  The importance of experimental design and QC samples in large-scale and MS-driven untargeted metabolomic studies of humans. , 2012, Bioanalysis.

[28]  Eberechukwu Onukwugha,et al.  Concordance between administrative claims and registry data for identifying metastasis to the bone: an exploratory analysis in prostate cancer , 2014, BMC Medical Research Methodology.

[29]  E. Fukusaki,et al.  Inflammation and Resolution Are Associated with Upregulation of Fatty Acid β-Oxidation in Zymosan-Induced Peritonitis , 2013, PloS one.

[30]  G. Lou,et al.  Large‐scale profiling of metabolic dysregulation in ovarian cancer , 2014, International journal of cancer.

[31]  David I. Ellis,et al.  A comparative investigation of modern feature selection and classification approaches for the analysis of mass spectrometry data. , 2014, Analytica chimica acta.

[32]  Santosh K. Mishra,et al.  De novo SVM classification of precursor microRNAs from genomic pseudo hairpins using global and intrinsic folding measures , 2007, Bioinform..

[33]  J. Ozer,et al.  The current state of serum biomarkers of hepatotoxicity. , 2008, Toxicology.

[34]  Yubo Li,et al.  Screening, verification, and optimization of biomarkers for early prediction of cardiotoxicity based on metabolomics. , 2015, Journal of proteome research.

[35]  Liang Li,et al.  Development of a universal metabolome-standard method for long-term LC-MS metabolome profiling and its application for bladder cancer urine-metabolite-biomarker discovery. , 2014, Analytical chemistry.

[36]  Cécile Legallais,et al.  Metabolomics-on-a-chip of hepatotoxicity induced by anticancer drug flutamide and Its active metabolite hydroxyflutamide using HepG2/C3a microfluidic biochips. , 2013, Toxicological sciences : an official journal of the Society of Toxicology.

[37]  Svetoslav H. Slavov,et al.  Identification of a metabolic biomarker panel in rats for prediction of acute and idiosyncratic hepatotoxicity , 2014, Computational and structural biotechnology journal.

[38]  Y. Egashira,et al.  Change of tryptophan-niacin metabolism in D-galactosamine-induced liver injury in rat. , 1997, Journal of nutritional science and vitaminology.

[39]  Peng Xie,et al.  Discovery and validation of plasma biomarkers for major depressive disorder classification based on liquid chromatography-mass spectrometry. , 2015, Journal of proteome research.

[40]  Ishan Barman,et al.  Incorporation of support vector machines in the LIBS toolbox for sensitive and robust classification amidst unexpected sample and system variability. , 2012, Analytical chemistry.

[41]  Oliver Kuss,et al.  A modified Wald interval for the area under the ROC curve (AUC) in diagnostic case-control studies , 2014, BMC Medical Research Methodology.

[42]  Peiyuan Yin,et al.  Current state-of-the-art of nontargeted metabolomics based on liquid chromatography-mass spectrometry with special emphasis in clinical applications. , 2014, Journal of chromatography. A.

[43]  Xin Lu,et al.  Metabolomics study of hepatocellular carcinoma: discovery and validation of serum potential biomarkers by using capillary electrophoresis-mass spectrometry. , 2014, Journal of proteome research.

[44]  J. Lindon,et al.  Metabonomics: a platform for studying drug toxicity and gene function , 2002, Nature Reviews Drug Discovery.

[45]  H. Jia,et al.  Metabolic pathways involved in Xin-Ke-Shu protecting against myocardial infarction in rats using ultra high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry. , 2014, Journal of pharmaceutical and biomedical analysis.

[46]  Melanie Hilario,et al.  Approaches to dimensionality reduction in proteomic biomarker studies , 2007, Briefings Bioinform..

[47]  M. Greiner,et al.  Principles and practical application of the receiver-operating characteristic analysis for diagnostic tests. , 2000, Preventive veterinary medicine.

[48]  I. Wilson,et al.  Within-day reproducibility of an HPLC-MS-based method for metabonomic analysis: application to human urine. , 2007, Journal of proteome research.

[49]  A. Smilde,et al.  Fusion of mass spectrometry-based metabolomics data. , 2005, Analytical chemistry.

[50]  Xin Lu,et al.  LC-MS-based metabonomics analysis. , 2008, Journal of chromatography. B, Analytical technologies in the biomedical and life sciences.

[51]  L. Buydens,et al.  Visualization and recovery of the (bio)chemical interesting variables in data analysis with support vector machine classification. , 2010, Analytical chemistry.

[52]  Sirish L. Shah,et al.  Analysis of metabolomic data using support vector machines. , 2008, Analytical chemistry.