Metabolomics and Its Impact on Health and Diseases

384 Pages·2023·9.706 MB·English

by  Veronica Ghini, Kathleen A. Stringer, Claudio Luchinat

Handbook of Experimental Pharmacology 277
Veronica Ghini
Kathleen A. Stringer
Claudio Luchinat   Editors
Metabolomics
and Its Impact
on Health and
Diseases
Handbook of Experimental Pharmacology
Volume 277
Editor-in-Chief
MartinC.Michel,DeptofPharmacology,JohannesGutenbergUniversität,Mainz,
Germany
EditorialBoardMembers
James E. Barrett, Center for Substance Abuse Research, Lewis Katz School of
MedicineatTempleUniversity,Philadelphia,PA,USA
David Centurión, Dept. of Pharmabiology, Center for Research and Advanced
Studies,Col.Granjas-Coapa,Mexico
Veit Flockerzi, Institutefor Experimental and Clinical Pharmacology and Toxicol-
ogy,SaarlandUniversity,Homburg,Germany
PierangeloGeppetti,HeadacheCenter,UniversityofFlorence,Florence,Italy
Franz B. Hofmann, Forschergruppe 923 Carvas, Technical University, München,
Germany
KathrynElaineMeier,Dept.ofPharmaceuticalSciences,WashingtonStateUniver-
sitySpokane,Spokane,USA
CliveP.Page,SIPP,KingsCollegeLondon,London,UK
KeWeiWang,SchoolofPharmacy,QingdaoUniversity,Qingdao,China
TheHandbookofExperimentalPharmacologyisoneofthemostauthoritativeand
influential book series in pharmacology. It provides critical and comprehensive
discussions of the most significant areas of pharmacological research, written by
leading international authorities. Each volume in the series represents the most
informative and contemporary account of its subject available, making it an unri-
valledreferencesource.
HEPisindexedinPubMedandScopus.
(cid:129) (cid:129)
Veronica Ghini Kathleen A. Stringer
Claudio Luchinat
Editors
Metabolomics and Its
Impact on Health
and Diseases
Editors
VeronicaGhini KathleenA.Stringer
DepartmentofChemistry DepartmentofClinicalPharmacy
UniversityofFlorence UniversityofMichigan–AnnArbor
SestoFiorentino,Florence,Italy AnnArbor,MI,USA
ClaudioLuchinat
DepartmentofChemistry
UniversityofFlorence
SestoFiorentino,Florence,Italy
ISSN0171-2004 ISSN1865-0325 (electronic)
HandbookofExperimentalPharmacology
ISBN978-3-031-26858-8 ISBN978-3-031-26859-5 (eBook)
https://doi.org/10.1007/978-3-031-26859-5
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AG2023
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Preface
ThisvolumeoftheHandbookofExperimentalPharmacology,whichcelebratedits
100th anniversary in 2019, addresses the rapidly growing and evolving field of
metabolomics. It has been compiled and designed to broaden and enrich your
understanding as well as simplify a complicated picture of the diverse field of
metabolomics. This is accomplished by chapters from experts in the field on basic
principlesas well as reviews and updatesof analytical techniques.The varietyand
differentperspectivesofthenuclearmagneticresonanceapproachesaredescribedin
thechaptersauthoredbyDavidS.Wishartandco-authors,G.A.NaganaGowdaand
DanielRaftery,andRyanT.McKay.Advancesinmassspectrometryarecoveredby
CharlesR.Evansandco-authorsandStefanKempaandco-authors.Thisbookalso
reflectsthestateoftheartintheapplicationofmetabolomicstocellbiology(Ulrich
L. Günther and co-authors) and chapters that share insights into the application of
metabolomics. These include the assessment of treatment response (Paola Turano
and co-authors) and the phenotyping of various diseases (Rachel S. Kelly and co-
authors, Paige Lacy and co-authors, and Angela J. Rogers and co-author).
Relationshipsofmetabolomicsanddrugs arehighlightedbyRobertVerpoorteand
co-authors,OscarMilletandco-authors, andDanielL.Hertzandco-author. Given
the diverse topics addressed, we believe this book has interdisciplinary appeal and
scholarswithaninterestintheroleofmetabolomicsinachievingprecisionmedicine
willfinditofparticularorspecialinterest.
WewanttothanktheauthorsfortheircontributionsasthisHandbookwouldnot
be possible without them. We also express our appreciation to the many
investigators who work in the field of metabolomics and strive to advance the
science.Its analytical advancement aswellas its translationto theclinic isof vital
importance to the field. It is our belief that metabolomics will continue to provide
newandnovelinsightsintocomplexillnessesandenablemoreaccurateandprecise
therapies in the future. We would also like to express our sincere appreciation to
Susanne Dathe, Springer Editor for Neurosciences/Pharmaceutical Sciences/
Protocols,whosecommitmentandcompetencehavehelpedtocontinuethetradition
v
vi Preface
of this remarkable series, and tothe past and current editorial board members who
have dedicated time and effort into establishing this series as one of the most
recognizedpublicationsinpharmacology.
Florence,Italy VeronicaGhini
AnnArbor,MI,USA KathleenA.Stringer
Florence,Italy ClaudioLuchinat
Contents
PracticalAspectsofNMR-BasedMetabolomics. . . . . . . . . . . . . . . . . . . 1
DavidS.Wishart,ManojRout,BrianL.Lee,MarkBerjanskii,
MarciaLeVatte,andMatthiasLipfert
CompoundIdentificationStrategiesinMassSpectrometry-Based
MetabolomicsandPharmacometabolomics. . . . . . . . . . . . . . . . . . . . . . 43
RylanHissong,KendraR.Evans,andCharlesR.Evans
MetabolomicsandNMR. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
RyanT.McKay
NaturalProductsDrugDiscovery:OnSilicaorIn-Silico?. . . . . . . . . . . 117
HyeKyongKim,YoungHaeChoi,andRobertVerpoorte
QuantitativeNMRMethodsinMetabolomics. . . . . . . . . . . . . . . . . . . . . 143
G.A.NaganaGowdaandDanielRaftery
AdvancementsinPulsedStableIsotope-ResolvedMetabolomics. . . . . . . 165
MartinForbes,SabrinaGeisberger,MatthiasPietzke,GuidoMastrobuoni,
andStefanKempa
MetabolomicsinCellBiology. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181
ZuhalEraslan,MartaCascante,andUlrichL.Günther
NMR-BasedMetabolomicstoEvaluateIndividualResponse
toTreatments. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 209
AlessiaVignoli,GaiaMeoni,VeronicaGhini,FrancescaDiCesare,
LeonardoTenori,ClaudioLuchinat,andPaolaTurano
PharmacometabolomicsofAsthmaasaRoadMaptoPrecision
Medicine. . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . 247
RachelS.Kelly,MargaretF.Cote,SofinaBegum,andJessicaLasky-Su
ProspectiveMetabolomicStudiesinPrecisionMedicine:
TheAKRIBEAProject. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 275
MaiderBizkarguenaga,RubénGil-Redondo,ChiaraBruzzone,
GanekoBernardo-Seisdedos,AnaLaín,BeatrizGonzález-Valle,
NievesEmbade,JoséM.Mato,andOscarMillet
vviiii
viii Contents
Chemotherapy-InducedPeripheralNeuropathy. . . . . . . . . . . . . . . . . . . 299
Ciao-SinChenandDanielL.Hertz
MetabolomicsofRespiratoryDiseases. . . . . . . . . . . . . . . . . . . . . . . . . . 339
SubhabrataMoitra,ArghyaBandyopadhyay,andPaigeLacy
TheMetabolomicsofCriticalIllness. . . . . . . . . . . . . . . . . . . . . . . . . . . . 367
AnaE.Pacheco-NavarroandAngelaJ.Rogers
Practical Aspects of NMR-Based
Metabolomics
David S. Wishart, Manoj Rout, Brian L. Lee, Mark Berjanskii,
Marcia LeVatte, and Matthias Lipfert
Contents
1 Introduction................................................................................... 2
2 AShortHistoryofNMR-BasedMetabolomics.............................................. 5
3 PracticalAspectsofNMR-BasedMetabolomics............................................ 6
3.1 SamplePreparation..................................................................... 6
3.2 ChoosingtheRightPulseSequence.................................................... 10
3.3 SpectralAcquisitionandProcessing................................................... 14
4 DataAnalysis................................................................................. 18
4.1 DataAnalysisforTargetedMetabolomics............................................. 18
4.2 DataAnalysisforUntargetedMetabolomics.......................................... 22
4.3 TargetedorUntargeted?................................................................ 24
5 BiologicalInterpretation...................................................................... 24
6 ConclusionandFutureProspects............................................................. 27
References......................................................................................... 31
✉
D.S.Wishart( )
DepartmentofBiologicalSciences,UniversityofAlberta,Edmonton,AB,Canada
DepartmentofComputingScience,UniversityofAlberta,Edmonton,AB,Canada
DepartmentofLaboratoryMedicineandPathology,UniversityofAlberta,Edmonton,AB,Canada
FacultyofPharmacyandPharmaceuticalSciences,UniversityofAlberta,Edmonton,AB,Canada
e-mail:[email protected]
M.Rout·B.L.Lee·M.Berjanskii·M.LeVatte
DepartmentofBiologicalSciences,UniversityofAlberta,Edmonton,AB,Canada
e-mail:[email protected];[email protected];[email protected];[email protected]
M.Lipfert
DepartmentofBiologicalSciences,UniversityofAlberta,Edmonton,AB,Canada
ReferenceStandardManagement&NMRQC,LonzaGroupAG,Visp,Switzerland
e-mail:[email protected]
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