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Pharmacogenomics Volume 7, 2006 - Issue 7
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Review

Monitoring the Health to Disease Continuum with Global Metabolic Profiling and Systems Biology

Laura K Schnackenberg1 Division of Systems Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR72079-9502, USA. Tel: +1 870 543 7986; Fax: +1 870 543 7686; [email protected]View further author information
&
Richard D Beger1 Division of Systems Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR72079-9502, USA. Tel: +1 870 543 7986; Fax: +1 870 543 7686; [email protected]View further author information
Pages 1077-1086 | Published online: 20 Oct 2006

Bibliography

  • Fiehn O : Combining genomics, metabolome analysis, and biochemical modeling to understand metabolic networks.Comp. Funct. Genomics2(3) , 155–168 (2001).
  • German JB , BaumanDE, BurrinDG et al.: Metabolomics in the opening decade of the 21st century: building the roads to individual health. J. Nutr.134(10) , 2729–2732 (2004).
  • Nicholson JK , HolmesE, LindonJC, WilsonID: The challenges of modeling mammalian biocomplexity.Nature Biotechnol.22(10) , 1268–1274 (2004).
  • Fiehn O : Metabolomics – the link between genotypes and phenotypes.Plant Mol. Biol.48(1–2) , 155–171 (2002).
  • Nicholson JK , LindonJC, HolmesE: ‘Metabonomics‘: understanding the metabolic responses of living systems to pathophysiological stimuli via multivariate statistical analysis of biological NMR spectroscopic data.Xenobiotica29(11) , 1181–1189 (1999).
  • Lindon JC , HolmesE, NicholsonJK: Metabonomics: systems biology in pharmaceutical research and development.Curr. Opin. Mol. Ther.6(3) , 265–272 (2004).
  • Urbanczyk-Wochniak E , LuedemannA, KopkaJ et al.: Parallel analysis of transcript and metabolic profiles: a new approach in systems biology. EMBO Rep.4(10) , 989–993 (2003).
  • Nicholson JK , WilsonID: Opinion: understanding ’global’ systems biology: metabonomics and the continuum of metabolism.Nat. Rev. Drug Discov.2(8) , 668–677 (2003).
  • Goodacre R , VaidyanathanS, DunnWB, HarriganGG, KellDB: Metabolomics by numbers: acquiring and understanding global metabolite data.Trends Biotechnol.22(5) , 245–252 (2004).
  • Hall N , KarrasM, RaineJD et al.: A comprehensive survey of the Plasmodium life cycle by genomic, transcriptomic, and proteomic analyses. Science307(5706) , 82–86 (2005).
  • Coen M , LenzEM, NicholsonJK, Wilson ID, Pognan F, Lindon JC: An integrated metabonomic investigation of acetaminophen toxicity in the mouse using NMR spectroscopy. Chem. Res. Toxicol.16(3) , 295–303 (2003).
  • Lenz EM , BrightJ, WilsonID, MorganSR, NashAF: A 1H NMR-based metabonomic study of urine and plasma samples obtained from healthy human subjects.J. Pharm. Biomed. Anal.33(5) , 1103–1115 (2003).
  • Nicholson JK , ConnellyJ, LindonJC, HolmesE: Metabonomics: a platform for studying drug toxicity and gene function.Nat. Rev. Drug Discov.1(2) , 153–161 (2002).
  • Ebbels T , KeunH, BeckonertO: Toxicity classification from metabonomic data using a density superposition approach: ’CLOUDS’.Anal. Chim. Acta490(1–2) , 109–122 (2003).
  • Heijne WH , LamersRJ, van Bladeren PJ, Groten JP, van Nesselrooij JH, van Ommen B: Profiles of metabolites and gene expression in rats with chemically induced hepatic necrosis. Toxicol. Pathol.33(4) , 425–433 (2005).
  • Robertson DG : Metabonomics in toxicology: a review.Toxicol. Sci.85(2) , 809–822 (2005).
  • Crockford DJ , HolmesE, LindonJC et al.: Statististical heterospectroscopy, an approach to the integrated analysis of NMR and UPLC-MS data sets: application in metabonomic toxicology studies. Anal. Chem.78(2) , 363–371 (2006).
  • Sandusky P , RafteryD: Use of selective TOCSY NMR experiments for quantifying minor components in complex mixtures: application to the metabonomics of amino acids in honey.Anal. Chem.77(8) , 2455–2463 (2005).
  • Sandusky P , RafteryD: Use of semiselective TOCSY and the Pearson correlation for the metabonomic analysis of biofluid mixtures: application to urine.Anal. Chem.77(23) , 7717–7723 (2005).
  • Lindon JC , KeunHC, EbbelsTM, Pearce JM, Holmes E, Nicholson JK: The Consortium for Metabonomic Technology (COMET): aims, activities, and achievements. Pharmacogenomics6(7) , 691–699 (2005).
  • Plumb RS , GrangerJH, StumpfCL et al.: A rapid screening approach to metabonomics using UPLC and oa-TOF mass spectrometry: application to age, gender and diurnal variation in normal/Zucker obese rats and black, white and nude mice. Analyst130(6) , 844–849 (2005).
  • Wilson ID , PlumbR, GrangerJ, MajorH, WilliamsR, LenzEM: HPLC-MS-based methods for the study of metabonomics.J. Chromatogr. B Analyt. Technol. Biomed. Life Sci.817(1) , 67–76 (2005).
  • Vaidyanathan S , GaskellS, GoodacreR: Matrix-suppressed laser desorption/ionisation mass spectrometry and its suitability for metabolome analyses.Rapid Commun. Mass Spectrom.20(8) , 1192–1198 (2006).
  • Umezu-Goto M , TanyiJ, LahadJ et al.: Lysophosphatidic acid production and action: validated targets in cancer? J. Cell. Biochem.92(6) , 1115–1140 (2004).
  • Wang C , KongH, GuanY et al.: Plasma phospholipid metabolic profiling and biomarkers of Type 2 diabetes mellitus based on high-performance liquid chromatography/electrospray mass spectrometry and multivariate statistical analysis. Anal. Chem.77(13) , 4108–4116 (2005).
  • Yang J , XuG, HongQ et al.: Discrimination of Type 2 diabetic patients from healthy controls by using metabonomics method based on their serum fatty acid profiles. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci.813(1–2) , 53–58 (2004).
  • Yang J , XuG, ZhengY: Strategy for metabonomics research based on high-performance liquid chromatography and liquid chromatography coupled with tandem mass spectrometry.J. Chromatogr. A1084(1–2) , 214–221 (2005).
  • Iles RA , HindAJ, ChalmersRA: Use of proton nuclear magnetic resonance spectroscopy in detection and study of organic acidurias.Clin. Chem.31(11) , 1795–1801 (1985).
  • Lehnert W , HunklerD: Possibilities of selective screening for inborn errors of metabolism using high-resolution 1H-FT-NMR spectrometry.Eur. J. Pediatr.145(4) , 260–266 (1986).
  • Sweetman L , HoffmannG, AramakiS: New diagnostic techniques for the detection of organic acidemias.Enzyme38(1–4) , 124–131 (1987).
  • Chace DH , KalasTA, NaylorEW: The application of tandem mass spectrometry to neonatal screening for inherited disorders of intermediary metabolism.Annu. Rev. Genomics Hum. Genet.3 , 17–45 (2002).
  • Constantinou MA , PapakonstantinouE, SpraulM et al.: 1H NMR-based metabonomics for the diagnosis of inborn errors of metabolism in urine. Anal. Chim. Acta,511 , 303–312 (2005).
  • Kuhara T : Gas chromatographic-mass spectrometric urinary metabolome analysis to study mutations of inborn errors of metabolism.Mass Spectrom. Rev.24(6) , 814–827 (2005).
  • Wevers RA , EngelkeUF, MoolenaarSH et al.: 1H-NMR spectroscopy of body fluids: inborn errors of purine and pyrimidine metabolism. Clin. Chem.45(4) , 539–548 (1999).
  • Van Coster RN , GerloEA, GiardinaTG et al.: Aminoacylase I deficiency: a novel inborn error of metabolism. Biochem. Biophys. Res. Commun.338(3) , 1322–1326 (2005).
  • Perez B , DesviatLR, Rodriguez-PomboP et al.: Propionic acidemia: identification of 24 novel mutations in Europe and North America. Mol. Genet. Metab.78(1) , 59–67 (2003).
  • Andresen BS , DobrowolskiSF, O’ReillyL et al.: Medium-chain acyl-CoA dehydrogenase (MCAD) mutations identified by MS/MS-based prospective screening of newborns differ from those observed in patients with clinical symptoms: identification and characterization of a new, prevalent mutation that results in mild MCAD deficiency. Am. J. Hum. Genet.68(6) , 1408–1418 (2001).
  • Dougherty FE , LevyHL: Present newborn screening for phenylketonuria.Ment. Retard. Dev. Disabil. Res. Rev.5(2) , 144–149 (1999).
  • Serkova N , FullerTF, KlawitterJ, FreiseCE, NiemannCU: 1H-NMR -based metabolic signatures of mild and severe ischemia/reperfusion injury in rat kidney transplants.Kidney Int.67(3) , 1142–1151 (2005).
  • Silva MA , JambulingamPS, GunsonBK et al.: Hepatic artery thrombosis following orthotopic liver transplantation: a 10-year experience from a single centre in the United Kingdom. Liver Transpl.12(1) , 146–151 (2006).
  • Wishart DS : Metabolomics: the principles and potential applications to transplantation.Am. J. Transplant.5(12) , 2814–2820 (2005).
  • Bell JD , LeeJA, LeeHA, SadlerPJ, Wilkie DR, Woodham RH: Nuclear magnetic resonance studies of blood plasma and urine from subjects with chronic renal failure: identification of trimethylamine-N-oxide. Biochim. Biophys. Acta1096(2) , 101–107 (1991).
  • Foxall PJ , MellotteGJ, BendingMR, LindonJC, NicholsonJK: NMR spectroscopy as a novel approach to the monitoring of renal transplant function.Kidney Int.43(1) , 234–245 (1993).
  • Gibelin H , EugeneM, HebrardW, Henry C, Carretier M, Hauet T: A new approach to the evaluation of liver graft function by nuclear magnetic resonance spectroscopy. A comparative study between Euro-Collins and University of Wisconsin solutions. Clin. Chem. Lab. Med.38(11) , 1133–1136 (2000).
  • Barshop BA : Metabolomic approaches to mitochondrial disease: correlation of urine organic acids.Mitochondrion4(5–6) , 521–527 (2004).
  • Yang J , XuG, ZhengY et al.: Diagnosis of liver cancer using HPLC-based metabonomics avoiding false-positive result from hepatitis and hepatocirrhosis diseases. J. Chromatogr. B813(1–2) , 59–65 (2004).
  • Fan TW , LaneAN, HigashiRM: The promise of metabolomics in cancer molecular therapeutics.Curr. Opin. Mol. Ther.6(6) , 584–592 (2004).
  • Odunsi K , WollmanRM, AmbrosoneCB et al.: Detection of epithelial ovarian cancer using 1H-NMR-based metabonomics. Int. J. Cancer113(5) , 782–788 (2005).
  • Whitehead TL , Monzavi-KarbassiB, JousheghanyF, ArtaudC, ElbeinA, Kieber-EmmonsT: 1H-NMR metabolic markers of malignancy correlate with spontaneous metastases in murine mammary tumor model.Int. J. Oncol.27(1) , 257–263 (2005).
  • Holmes E , FoxallPJ, NicholsonJK: Proton NMR analysis of plasma from renal failure patients: evaluation of sample preparation and spectral-editing methods.J. Pharm. Biomed. Anal.8(8–12) , 955–958 (1990).
  • Coen M , O’SullivanM, BubbWA, Kuchel PW, Sorrell T: Proton nuclear magnetic resonance-based metabonomics for rapid detection of meningitis and ventriculitis. Clin. Infect. Dis.41(11) , 1582–1590 (2005).
  • Bijlsma S , BobeldijkI, VerheijER et al.: Large-scale human metabolomics studies: a strategy for data (pre-) processing and validation. Anal. Chem.78(2) , 567–574 (2006).
  • Moolenaar SH , EngelkeUF, WeversRA: Proton nuclear magnetic resonance spectroscopy of body fluids in the field of inborn errors of metabolism.Ann. Clin. Biochem.40(1) , 16–24 (2003).
  • Brindle JT , AnttiH, HolmesE et al.: Rapid and noninvasive diagnosis of the presence and severity of coronary heart disease using 1H-NMR-based metabonomics. Nat. Med.8(12) , 1439–1445 (2002).
  • Rozen S , CudkowiczME, BogdanovM et al.: Metabolomic analysis and signatures in motor neuron disease. Metabolomics1(2) , 101–108 (2005).
  • Beger RD , SchnackenbergLK, LiD, DraganY: Metabonomic models of human pancreatic cancer using 1D proton NMR spectra of lipids in plasma.Metabolomics (2006) (Epub ahead of print).
  • Watkins SM , GermanJB: Metabolomics and biochemical profiling in drug discovery and development.Curr. Opin. Mol. Ther.4(3) , 224–228 (2002).
  • Morris M , WatkinsSM: Focused metabolomic profiling in the drug development process: advances from lipid profiling.Curr. Opin. Chem. Biol.9(4) , 407–412 (2005).
  • Stoughton RB , FriendSH: How molecular profiling could revolutionize drug discovery.Nature Rev. Drug Discov.4(4) , 345–350 (2005).
  • Portilla D , LiS, NagothuKK et al.: Metabolomic study of cisplatin-induced nephrotoxicity. Kidney Int.69(12) , 2194–2204 (2006).
  • Schnackenberg LK , JonesRC, Thyparambil S et al.: An integrated study of acute effects of valproic acid in the liver using metabonomics, proteomics, and transcriptomics platforms. OMICS10(1) , 1–14 (2006).
  • Schnackenberg L , BegerRD, DraganY: NMR-based metabonomic evaluation of livers from rats chronically treated with tamoxifen, mestranol, and phenobarbital.Metabonomics1(1) , 87–94 (2005).
  • Robertson DG , Reily,MD, AlbassamM, DethloffLA: Metabonomics assessment of vasculitis in rats.Cardiovasc. Toxicol.1(1) , 7–19 (2001).
  • Slim RM , RobertsonDG, AlbassamM, ReilyMD, RoboskyL, DethloffLA: Effect of dexamethasone on the metabonomics profile associated with phosphodiesterase inhibitor-induced vascular lesions in rats.Toxicol. Appl. Pharmacol.183(2) , 108–116 (2002).
  • Zhang J , HermanEH, RobertsonDG et al.: Mechanisms and biomarkers of cardiovascular injury induced by phosphodiesterase inhibitor III SK&F 95654 in the spontaneously hypertensive rat. Toxicol. Pathol.34(2) , 152–163 (2006).
  • Antti H , BollardME, EbbelsTM et al.: Batch statistical processing of 1H NMR-derived urinary spectral data. J. Chemometrics16(8–10) , 461–468 (2002).
  • Keun HC , EbbelsTM, BollardME et al.: Geometric trajectory analysis of metabolic responses to toxicity can define treatment specific profiles. Chem. Res. Toxicol.17(5) , 578–587 (2004).
  • Coen M , RueppSU, LindonJC et al.: Integrated application of transcriptomics and metabonomics yields new insight into the toxicity due to paracetamol in the mouse. J. Pharm. Biomed. Anal.35(1) , 93–105 (2004).
  • Whitfield PD , GermanAJ, NoblePJ: Metabolomics: an emerging post-genomic tool for nutrition.Br. J. Nutr.92(4) , 549–555 (2004).
  • Gibney MJ , WalshM, BrennanL, Roche HM, German B, van Ommen B: Metabolomics in human nutrition: opportunities and challenges. Am. J. Clin. Nutr.82(3) , 497–503 (2005).
  • Kaput J , OrdovasJM, FergusonL et al.: The case for strategic international alliances to harness nutritional genomics for public and personal health. Br. J. Nutr.94(5) , 623–632 (2005).
  • Zeisel SH , FreakeHC, BaumanDE et al.: The nutritional phenotype in the age of metabolomics. J. Nutr.135(7) , 1613–1616 (2005).
  • Solanky KS , BaileyNJ, Beckwidth-HallBM et al.: Biofluid 1H NMR-based metabonomic techniques in nutrition research - metabolic effects of dietary isoflavones in humans. J. Nutr. Biochem.16 , 236–244 (2005).
  • Singh RH , RheadWJ, SmithW, LeeB, KingLS, SummarM: Nutritional management of urea cycle disorders.Crit. Care Clin.21(4 Suppl) , S27–S35 (2005).
  • Lamb DJ , ZhangL: Challenges in prostate cancer research: animal models for nutritional studies of chemoprevention and disease progression.J. Nutr.135(12 Suppl.) , 3009S–S3015 (2005).
  • Bessems JG , VermeulenNP: Paracetamol (acetaminophen)-induced toxicity: molecular and biochemical mechanisms, analogues and protective approaches.Crit. Rev. Toxicol.31(1) , 55–138 (2001).
  • Rist MJ , WenzelU, DanielH: Nutrition and food science go genomic.Trends Biotechnol.24(4) , 172–178 (2006).
  • Al-Hasani H , JoostHG: Nutrition-/diet-induced changes in gene expression in white adipose tissue.Best Pract. Res. Clin. Endocrinol. Metab.19(4) , 589–603 (2005).
  • Yang K , YangW, MariadasonJ, VelcichA, LipkinM, AugenlichtL: Dietary components modify gene expression: implications for carcinogenesis.J. Nutr.135(11) , 2710–2714 (2005).
  • Han X , GrossRW: Global analyses of cellular lipidomes directly from crude extracts of biological samples by ESI mass spectrometry: a bridge to lipidomics.J. Lipid Res.44(6) , 1071–1079 (2003).
  • Taguchi R , HoujouT, NakanishiH et al.: Focused lipidomics by tandem mass spectrometry. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci.823(1) , 26–36 (2005).
  • Fahy E , SubramaniamS, BrownHA et al.: A comprehensive classification system for lipids. J. Lipid Res.46(5) , 839–861 (2005).
  • Dhawan V , SchwalbDJ, ShumwayMJ et al.: Selective nitros(yl)ation induced in vivo by a nitric oxide-donating cycloxygenase-2 inhibitor: a NObonomic analysis. Free Radic. Biol. Med.39(9) , 1191–1207 (2005).
  • Sanford K , SoucailleP, WhitedG, Chotani G: Genomics to fluxomics and physiomics – pathway engineering. Curr. Opin. Microbiol.5(3) , 318–322 (2002).
  • Boros LG , LernerMR, MorganDL et al.: [1,2–13C2]-D-Glucose profiles of the serum, liver, pancreas, and DMBA-induced pancreatic tumors of rats. Pancreas31(4) , 337–343 (2005).
  • Ruepp SU , TongeRP, ShawJ, WallisN, PognanF: Genomics and proteomics analysis of acetaminophen toxicity in mouse liver.Toxicol. Sci.65(1) , 135–150 (2002).
  • Kleno TG , KiehrB, BaunsgaardD, SidelmannUG: combination of ‘omics‘ data to investigate the mechanism(s) of hydrazine-induced hepatotoxicity in rats and to identify potential biomarkers.Biomarkers9(2) , 116–138 (2004).
  • Craig A , SidawayJ, HolmesE et al.: Systems toxicology: integrated genomic, proteomic and metabonomic analysis of methapyrilene induced hepatotoxicity in the rat. J. Proteome Res.5(7) , 1586–1601 (2006).
  • Jenkins H , HardyN, BeckmannM et al.: A proposed framework for the description of plant metabolomics experiments and their results. Nat. Biotechnol.22(12) , 1601–1606 (2004).
  • Lindon JC , NicholsonJK, HolmesE et al.: Summary recommendations for standardization and reporting of metabolic analyses. Nat. Biotechnol.23(7) , 833–838 (2005).
  • Tong W , HarrisS, CaoX et al.: Development of public toxicogenomics software for microarray data management and analysis. Mutat. Res.549(1–2) , 241–253 (2004).
  • Clayton TA , LindonJC, CloarecO et al.: Pharmaco-metabonomic phenotyping and personalized drug treatment. Nature440(7087) , 1073–1077 (2006).

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