Skip to main content
SpringerLink
Log in

Unbiased Lipidomics and Metabolomics of Human Brain Samples

  • Protocol
  • First Online:
Biomarkers for Alzheimer’s Disease Drug Development

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1750))

Abstract

Mass spectrometry (MS)-based lipidomics and metabolomics approaches have been used to discover new diagnostic and therapeutic targets of neurodegenerative disorders. Here, we describe a protocol to conduct an integrated metabolomics and lipidomics profiling of postmortem brains of frozen tissue samples from clinically characterized patients and age-matched controls. Metabolites and lipids can be extracted from each brain tissue sample, using a biphasic liquid/liquid extraction method. An unbiased liquid chromatography MS-based lipidomics and metabolomics workflows allows to screen for the content and composition of lipids and polar metabolites for each brain tissue. Data processing and statistical analysis are then used to compare the molecular content of all the samples, grouping them into cluster based on molecular similarities. The final results highlight classes of metabolites and biochemical pathways that are altered in brain samples from diseased brains compared to those from healthy subjects, helping to generate novel hypotheses on their mechanistic and functional significance.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 69.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 89.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 119.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Toledo JB, Arnold M, Kastenmuller G, Chang R, Baillie RA, Han X, Thambisetty M, Tenenbaum JD, Suhre K, Thompson JW, John-Williams LS, MahmoudianDehkordi S, Rotroff DM, Jack JR, Motsinger-Reif A, Risacher SL, Blach C, Lucas JE, Massaro T, Louie G, Zhu H, Dallmann G, Klavins K, Koal T, Kim S, Nho K, Shen L, Casanova R, Varma S, Legido-Quigley C, Moseley MA, Zhu K, Henrion MY, van der Lee SJ, Harms AC, Demirkan A, Hankemeier T, van Duijn CM, Trojanowski JQ, Shaw LM, Saykin AJ, Weiner MW, Doraiswamy PM, Kaddurah-Daouk R, Alzheimer’s Disease Neuroimaging I, the Alzheimer Disease Metabolomics C (2017) Metabolic network failures in Alzheimer’s disease-A biochemical road map. Alzheimer’s Dement 13:965. https://doi.org/10.1016/j.jalz.2017.01.020

    Article  Google Scholar 

  2. Paglia G, Stocchero M, Cacciatore S, Lai S, Angel P, Alam MT, Keller M, Ralser M, Astarita G (2016) Unbiased metabolomic investigation of Alzheimer’s disease brain points to dysregulation of mitochondrial aspartate metabolism. J Proteome Res 15(2):608–618. https://doi.org/10.1021/acs.jproteome.5b01020

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  3. Fonteh AN, Harrington RJ, Huhmer AF, Biringer RG, Riggins JN, Harrington MG (2006) Identification of disease markers in human cerebrospinal fluid using lipidomic and proteomic methods. Dis Markers 22(1–2):39–64

    Article  CAS  PubMed  Google Scholar 

  4. Astarita G, Jung KM, Vasilevko V, Dipatrizio NV, Martin SK, Cribbs DH, Head E, Cotman CW, Piomelli D (2011) Elevated stearoyl-CoA desaturase in brains of patients with Alzheimer’s disease. PLoS One 6(10):e24777. https://doi.org/10.1371/journal.pone.0024777

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  5. Astarita G, Jung KM, Berchtold NC, Nguyen VQ, Gillen DL, Head E, Cotman CW, Piomelli D (2010) Deficient liver biosynthesis of docosahexaenoic acid correlates with cognitive impairment in Alzheimer’s disease. PLoS One 5(9):e12538. https://doi.org/10.1371/journal.pone.0012538

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  6. Inoue K, Tsutsui H, Akatsu H, Hashizume Y, Matsukawa N, Yamamoto T, Toyo’oka T (2013) Metabolic profiling of Alzheimer’s disease brains. Sci Rep 3:2364. https://doi.org/10.1038/srep02364

    Article  PubMed  PubMed Central  Google Scholar 

  7. Graham SF, Chevallier OP, Roberts D, Holscher C, Elliott CT, Green BD (2013) Investigation of the human brain metabolome to identify potential markers for early diagnosis and therapeutic targets of Alzheimer’s disease. Anal Chem 85(3):1803–1811. https://doi.org/10.1021/ac303163f

    Article  PubMed  CAS  Google Scholar 

  8. Zhu ZJ, Schultz AW, Wang J, Johnson CH, Yannone SM, Patti GJ, Siuzdak G (2013) Liquid chromatography quadrupole time-of-flight mass spectrometry characterization of metabolites guided by the METLIN database. Nat Protoc 8(3):451–460. https://doi.org/10.1038/nprot.2013.004

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  9. Wishart DS, Jewison T, Guo AC, Wilson M, Knox C, Liu Y, Djoumbou Y, Mandal R, Aziat F, Dong E, Bouatra S, Sinelnikov I, Arndt D, Xia J, Liu P, Yallou F, Bjorndahl T, Perez-Pineiro R, Eisner R, Allen F, Neveu V, Greiner R, Scalbert A (2013) HMDB 3.0—the human metabolome database in 2013. Nucleic Acids Res 41(Database issue):D801–D807. https://doi.org/10.1093/nar/gks1065

    Article  PubMed  CAS  Google Scholar 

  10. Fahy E, Subramaniam S, Murphy RC, Nishijima M, Raetz CR, Shimizu T, Spener F, van Meer G, Wakelam MJ, Dennis EA (2009) Update of the LIPID MAPS comprehensive classification system for lipids. J Lipid Res 50(Suppl):S9–14. https://doi.org/10.1194/jlr.R800095-JLR200

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  11. Lau OW, Wong SK (2000) Contamination in food from packaging material. J Chromatogr A 882(1–2):255–270

    Article  CAS  PubMed  Google Scholar 

  12. Lin JH, Liu LY, Yang MH, Lee MH (2004) Ethyl acetate/ethyl alcohol mixtures as an alternative to folch reagent for extracting animal lipids. J Agric Food Chem 52(16):4984–4986. https://doi.org/10.1021/jf049360m

    Article  PubMed  CAS  Google Scholar 

  13. Hara A, Radin NS (1978) Lipid extraction of tissues with a low-toxicity solvent. Anal Biochem 90(1):420–426

    Article  CAS  PubMed  Google Scholar 

  14. Bian L, Yang J, Sun Y (2015) Isolation and purification of monosialotetrahexosylgangliosides from pig brain by extraction and liquid chromatography. Biomed Chromatogr 29(10):1604–1611. https://doi.org/10.1002/bmc.3467

    Article  PubMed  CAS  Google Scholar 

  15. Garcia AD, Chavez JL, Mechref Y (2014) Rapid and sensitive LC-ESI-MS of gangliosides. J Chromatogr B Anal Technol Biomed Life Sci 947-948:1–7. https://doi.org/10.1016/j.jchromb.2013.11.025

    Article  CAS  Google Scholar 

  16. Fu W, Magnusdottir M, Brynjolfson S, Palsson BO, Paglia G (2012) UPLC-UV-MS(E) analysis for quantification and identification of major carotenoid and chlorophyll species in algae. Anal Bioanal Chem 404(10):3145–3154. https://doi.org/10.1007/s00216-012-6434-4

    Article  PubMed  CAS  Google Scholar 

  17. Pluskal T, Castillo S, Villar-Briones A, Oresic M (2010) MZmine 2: modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data. BMC Bioinformatics 11:395. https://doi.org/10.1186/1471-2105-11-395

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  18. Huan T, Forsberg EM, Rinehart D, Johnson CH, Ivanisevic J, Benton HP, Fang M, Aisporna A, Hilmers B, Poole FL, Thorgersen MP, Adams MWW, Krantz G, Fields MW, Robbins PD, Niedernhofer LJ, Ideker T, Majumder EL, Wall JD, Rattray NJW, Goodacre R, Lairson LL, Siuzdak G (2017) Systems biology guided by XCMS online metabolomics. Nat Methods 14(5):461–462. https://doi.org/10.1038/nmeth.4260

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  19. Xia J, Wishart DS (2016) Using MetaboAnalyst 3.0 for comprehensive metabolomics data analysis. Curr Protoc Bioinformatics 55:14.10.11–14.10.91. https://doi.org/10.1002/cpbi.11

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Biochemistry and Molecular and Cellular Biology, Georgetown University, Washington, DC, USA

    Giuseppe Astarita

  2. Department of Women’s and Children’s Health, University of Padova, Padova, Italy

    Matteo Stocchero

  3. EURAC Institute For Biomedicine, Institute for Biomedicine, European Academy of Bolzano/Bozen, Bolzano, Italy

    Giuseppe Paglia

Authors
  1. Giuseppe Astarita
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Matteo Stocchero
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Giuseppe Paglia
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Giuseppe Paglia .

Editor information

Editors and Affiliations

  1. Department of Psychiatry and Psychotherapy, Ludwig-Maximilians-Universität München, Munich, Germany

    Robert Perneczky

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer Science+Business Media, LLC

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Astarita, G., Stocchero, M., Paglia, G. (2018). Unbiased Lipidomics and Metabolomics of Human Brain Samples. In: Perneczky, R. (eds) Biomarkers for Alzheimer’s Disease Drug Development. Methods in Molecular Biology, vol 1750. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7704-8_17

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-7704-8_17

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7703-1

  • Online ISBN: 978-1-4939-7704-8

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation