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Application of Metabolomics in Lung Research

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Lung Innate Immunity and Inflammation

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1809))

Abstract

Advancements in omics technologies have increased our potential to evaluate molecular changes in a rapid and comprehensive manner. This is especially true in mass spectrometry-based metabolomics where improvements, including ease of use, in high-performance liquid chromatography (HPLC), column chemistries, instruments, software, and molecular databases, have advanced the field considerably. Applications of this relatively new omics technology in clinical research include discovering disease biomarkers, finding new drug targets, and elucidating disease mechanisms. Here we describe a typical clinical metabolomics workflow, which includes the following steps: (1) extraction of metabolites from the lung, plasma, bronchoalveolar lavage, or cells; (2) sample analysis via liquid chromatography-mass spectrometry; and (3) data analysis using commercial and freely available software packages. Overall, the methods delineated here can help investigators use metabolomics to discovery novel biomarkers and to understand lung diseases.

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References

  1. Snowden S, Dahlen SE, Wheelock CE (2012) Application of metabolomics approaches to the study of respiratory diseases. Bioanalysis 4(18):2265–2290. https://doi.org/10.4155/bio.12.218

    Article  PubMed  CAS  Google Scholar 

  2. Mattarucchi E, Baraldi E, Guillou C (2012) Metabolomics applied to urine samples in childhood asthma; differentiation between asthma phenotypes and identification of relevant metabolites. Biomed Chromatogr 26(1):89–94. https://doi.org/10.1002/bmc.1631

    Article  PubMed  CAS  Google Scholar 

  3. Reisdorph N, Wechsler ME (2013) Utilizing metabolomics to distinguish asthma phenotypes: strategies and clinical implications. Allergy 68(8):959–962. https://doi.org/10.1111/all.12238

    Article  PubMed  CAS  Google Scholar 

  4. Bowler RP, Bahr TM, Hughes G, Lutz S, Kim YI, Coldren CD, Reisdorph N, Kechris KJ (2013) Integrative omics approach identifies interleukin-16 as a biomarker of emphysema. OMICS 17(12):619–626. https://doi.org/10.1089/omi.2013.0038

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  5. Bowler RP, Jacobson S, Cruickshank C, Hughes GJ, Siska C, Ory DS, Petrache I, Schaffer JE, Reisdorph N, Kechris K (2015) Plasma sphingolipids associated with chronic obstructive pulmonary disease phenotypes. Am J Respir Crit Care Med 191(3):275–284. https://doi.org/10.1164/rccm.201410-1771OC

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  6. Cruickshank-Quinn CI, Mahaffey S, Justice MJ, Hughes G, Armstrong M, Bowler RP, Reisdorph R, Petrache I, Reisdorph N (2014) Transient and persistent metabolomic changes in plasma following chronic cigarette smoke exposure in a mouse model. PLoS One 9(7):e101855. https://doi.org/10.1371/journal.pone.0101855

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  7. Ho WE, Xu YJ, Xu F, Cheng C, Peh HY, Tannenbaum SR, Wong WS, Ong CN (2013) Metabolomics reveals altered metabolic pathways in experimental asthma. Am J Respir Cell Mol Biol 48(2):204–211. https://doi.org/10.1165/rcmb.2012-0246OC

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  8. Jung J, Kim SH, Lee HS, Choi GS, Jung YS, Ryu DH, Park HS, Hwang GS (2013) Serum metabolomics reveals pathways and biomarkers associated with asthma pathogenesis. Clin Exp Allergy 43(4):425–433. https://doi.org/10.1111/cea.12089

    Article  PubMed  CAS  Google Scholar 

  9. Quinn KD, Schedel M, Nkrumah-Elie Y, Joetham A, Armstrong M, Cruickshank-Quinn C, Reisdorph R, Gelfand EW, Reisdorph N (2017) Dysregulation of metabolic pathways in a mouse model of allergic asthma. Allergy. https://doi.org/10.1111/all.13144

  10. Ried JS, Baurecht H, Stuckler F, Krumsiek J, Gieger C, Heinrich J, Kabesch M, Prehn C, Peters A, Rodriguez E, Schulz H, Strauch K, Suhre K, Wang-Sattler R, Wichmann HE, Theis FJ, Illig T, Adamski J, Weidinger S (2013) Integrative genetic and metabolite profiling analysis suggests altered phosphatidylcholine metabolism in asthma. Allergy 68(5):629–636. https://doi.org/10.1111/all.12110

    Article  PubMed  CAS  Google Scholar 

  11. Armstrong M, Liu AH, Harbeck R, Reisdorph R, Rabinovitch N, Reisdorph N (2009) Leukotriene-E4 in human urine: comparison of on-line purification and liquid chromatography-tandem mass spectrometry to affinity purification followed by enzyme immunoassay. J Chromatogr B Analyt Technol Biomed Life Sci 877(27):3169–3174. https://doi.org/10.1016/j.jchromb.2009.08.011

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  12. Rabinovitch N, Reisdorph N, Silveira L, Gelfand EW (2011) Urinary leukotriene E(4) levels identify children with tobacco smoke exposure at risk for asthma exacerbation. J Allergy Clin Immunol 128(2):323–327. https://doi.org/10.1016/j.jaci.2011.05.035

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  13. Levy BD (2012) Resolvin D1 and resolvin E1 promote the resolution of allergic airway inflammation via shared and distinct molecular counter-regulatory pathways. Front Immunol 3:390. https://doi.org/10.3389/fimmu.2012.00390

    Article  PubMed  PubMed Central  Google Scholar 

  14. Armstrong M, Jonscher K, Reisdorph NA (2007) Analysis of 25 underivatized amino acids in human plasma using ion-pairing reversed-phase liquid chromatography/time-of-flight mass spectrometry. Rapid Commun Mass Spectrom 21(16):2717–2726. https://doi.org/10.1002/rcm.3124

    Article  PubMed  CAS  Google Scholar 

  15. Smith CA, Want EJ, O'Maille G, Abagyan R, Siuzdak G (2006) XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. Anal Chem 78(3):779–787. https://doi.org/10.1021/ac051437y

    Article  PubMed  CAS  Google Scholar 

  16. Kuhl C, Tautenhahn R, Bottcher C, Larson TR, Neumann S (2012) CAMERA: an integrated strategy for compound spectra extraction and annotation of liquid chromatography/mass spectrometry data sets. Anal Chem 84(1):283–289. https://doi.org/10.1021/ac202450g

    Article  PubMed  CAS  Google Scholar 

  17. Cruickshank-Quinn C, Quinn KD, Powell R, Yang Y, Armstrong M, Mahaffey S, Reisdorph R, Reisdorph N (2014) Multi-step preparation technique to recover multiple metabolite compound classes for in-depth and informative metabolomic analysis. J Vis Exp 89:e51670. https://doi.org/10.3791/51670

    Article  CAS  Google Scholar 

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Author information

Authors and Affiliations

  1. Department of Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA

    Nichole A. Reisdorph, Charmion Cruickshank-Quinn, Yasmeen Nkrumah-Elie & Richard Reisdorph

Authors
  1. Nichole A. Reisdorph
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  2. Charmion Cruickshank-Quinn
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  3. Yasmeen Nkrumah-Elie
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  4. Richard Reisdorph
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Corresponding author

Correspondence to Nichole A. Reisdorph .

Editor information

Editors and Affiliations

  1. Department of Immunology and Microbiology University of Colorado School of Medicine, Department of Biomedical Research and Center for Genes Environment and Health, National Jewish Health Denver, CO, USA, Aurora,, Colorado, USA

    Scott Alper

  2. Division of Pulmonary Sciences and Critical Care Medicine Department of Medicine University of Colorado Denver, Division of Pulmonary, Critical Care and Sleep Medicine Department of Medicine National Jewish Health Denver, CO, USA, Aurora, Colorado, USA

    William J. Janssen

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Reisdorph, N.A., Cruickshank-Quinn, C., Nkrumah-Elie, Y., Reisdorph, R. (2018). Application of Metabolomics in Lung Research. In: Alper, S., Janssen, W. (eds) Lung Innate Immunity and Inflammation. Methods in Molecular Biology, vol 1809. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8570-8_17

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  • DOI: https://doi.org/10.1007/978-1-4939-8570-8_17

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-8569-2

  • Online ISBN: 978-1-4939-8570-8

  • eBook Packages: Springer Protocols

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