MetabolomicsanditsapplicationsBaichuanDengUniversityofBergen鄧百川Contents1.Background2.Workflow3.Application4.ChallengeContents1.Background2.Workflow3.Application4.ChallengeManhattanProject(1942-1946)ApolloProject(1961-1972)HumanGenomeProject(1990-2003)HumanGenomeProjectThe“omics”familyWeakWeakWeakHumandiseaseriskAdvantageofmetabolomicsLowComplexityNoninvasivebiofuidsHighSensitivityGenomicsProteomicsMetabolomicsMetabolicchangeEnzymaticchangeGenomicchangeAmplifyingUrineSerumPlasmaThetotalnumberofmetabolitesismuchlessthanthatofproteinsandgenesThestructureofmetabolitesismuchsimplerthanthatofproteinsandgenesAliteraturesurveyinWebofScience(June10th,2015).‘Metabolomics’wasusedasakeyword.PublicationsandcitationsrelatedtometabolomicsYearYearNumberNumber(A)Publications(B)CitationsContents1.Background2.Workflow3.Application4.ChallengeAlternateworkflows1Targetedmetabolomics2NontargetedmetabolomicsAlternateworkflows1Targetedmetabolomics2NontargetedmetabolomicsSelectanalyticaltargetsSelectanalyticalmethodsConductexperimentsAnalyzesamplesandperformstatisticalanalysisAlternateworkflows1Targetedmetabolomics2NontargetedmetabolomicsPosescientificquestionSamplecollectionHighresolutiondetectionanddataanalysisSignificantmetabolitesandpathwaysWorkflowofmetabolomicsG.A.NaganaGowdaetal.ExpertRevMolDiagn.2008Keysteps:SamplecollectionSamplepreparationDataacquisitionDatapreprocessingStatisticalanalysisBiomarkeridentificationPathwayanalysisWorkflowofmetabolomicsG.A.NaganaGowdaetal.ExpertRevMolDiagn.2008Keysteps:SamplecollectionSamplepreparationDataacquisitionDatapreprocessingStatisticalanalysisBiomarkeridentificationPathwayanalysisClinicTrialsWorkflowofNutritionalMetabolomicsGaschromatography-massspectrometry(GC-MS)Nuclearmagneticresonance(NMR)Liquidchromatography-massspectrometry(LC-MS)RetentiontimeChemicalshiftRetentiontimeNMRDataaquisitionNMRMSNon-destructiveHighsensitivityApplicabletointactbiomaterialsRelativelowsensitivityHighselectivityDestructiveNeedsamplepreparationLittlesamplepreparationComparisonofNMRandMSplatformsRelativepoorsensitivityGoodatquantificationAdvantagesDisadvantagesDatapreprocessingBaselinecorrectionRawdataAfterbaselinecorrectionLiuetal.ChemometrIntellLab.2014PeakalignmentLiebekeetal.AnalyticalChemistry.2013DeconvolutionBernsteinetal.AnalyticalChemistry.2013RawdataAfterbaselinecorrectionDataintegrationStatisticalanalysis

Principalcomponentanalysis(PCA)Hierarchicalclusteranalysis(HCA)Softindependentmodelingofclassanalogies(SIMCA)Self-organizingmapping(SOM)

Partialleastsquares-discriminantanalysis(PLS-DA)Artificialneuralnetworks(ANN)Supportvectormachines(SVM)Randomforests(RF)UnsupervisedSupervisedPC1PCAPC2PLS-DAModelvalidationMethods:IndependenttestsetCross-validationPermutationtestCriteria:AccuracyrateAUROCR2andQ2A:BadmodelB:GoodmodelPermutationtestBiomarkerdiscoveryStatisticaltest:StudentttestVariableimportance:LoadingweightsRegressioncoefficients(RC)Variableinprojection(VIP)Selectiveratio(SR)TarjaRajalahtietal.ChemometrIntellLab.2009MetabolitesidentificationMetabolicpathwayshttp://www.genome.jp/kegg/MetabolicpathwayspossiblyaffectedindiabetesUpregulatedPintoetal.JProteomeResearch.2015Blue:EarlystageRed:LatestageDownregulatedContents1.Background2.Workflow3.Application4.ChallengeFactorsthatinfluencemetabolomeClaudinoetal.Journalofclinicaloncology.2007Principlecomponentanalysis(PCA)ofmetabolitesof4differentplantspeciesobtainedbyGC-MS.Roessneretal.Biotechniques.2009BarleyWheatMossArabldopsisGeneticbackgroundMetabolicpatternsforpeoplefromdifferentregionsDumasetal.AnalyticalChemistry.2006600MHz1HNMRspectraofhumanurinePrincipalcomponentanalysis(PCA)JapaneseChineseAmericanDietThemetabolicfootprintofaginginmiceHoutkooperetal.Scientificreports.2011AgeLungcancerdiagnosisAbdul-HamidM.Emwasetal.Metabolomics.2013DiseaseDSWishart.DrugsinR&D.2008DrugdiscoveryTomonitordrugmetabolismandtoxicity.CostincreasesSuccessratedecreaseDrugsContents1.Background2.Workflow3.Application4.ChallengeChallengeBiomarkerdiscoveryHighdimensionaldata(Curseofdimensionality)Synergyeffectofmetabolites(Combinatorialexplosion)IntegrationofdifferentinstrumentalplatformsIntegrationofdifferent-omicstechniquesMatteoCassottietc.Chemometr.Intell.Lab.2014Assuming10000modelspersecond.CombinatorialexplosionChallengeBiomarkerdiscoveryIntegrationofdifferentinstrumentalplatformsIntegrationofdifferent-omicstechniquesTheoverlapofserummetabolitesdetectedbyNMR,GC–MS,TLC/GC-FID,LC-ESI-MS/MSandDFI-MSmethodsNikolaosPsychogiosetal.Plosone2011TheoverlapofurinemetabolitesdetectedbyNMR,GC–MS,ICP-MS,DFI/LC-M