Abstract
Lipids play critical roles in developmental processes, and alterations in lipid metabolism are linked to a wide range of human diseases, including neurodegeneration, cancer, metabolic diseases, and microbial infections. Drosophila melanogaster, more commonly known as the fruit fly, is a powerful organism for developmental biology and human disease research. We have previously developed a comprehensive biochemical tool, based on liquid chromatography-mass spectrometry (LC-MS), to probe the dynamics of lipid remodeling during D. melanogaster development. This chapter introduces a step-by-step protocol for extracting and analyzing lipids across all developmental stages (embryo, larvae, pupa, and adult) of D. melanogaster. The targeted semi-quantitative approach offers a comprehensive coverage of more than 400 lipid species spanning the lipid classes, glycerophospholipids, sphingolipids, triacylglycerols, and sterols.
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References
Ugur B, Chen K, Bellen HJ (2016) Drosophila tools and assays for the study of human diseases. Dis Model Mech 9(3):235–244. https://doi.org/10.1242/dmm.023762
Yamamoto S, Jaiswal M, Charng WL, Gambin T, Karaca E, Mirzaa G, Wiszniewski W, Sandoval H, Haelterman NA, Xiong B, Zhang K, Bayat V, David G, Li T, Chen K, Gala U, Harel T, Pehlivan D, Penney S, Vissers L, de Ligt J, Jhangiani SN, Xie Y, Tsang SH, Parman Y, Sivaci M, Battaloglu E, Muzny D, Wan YW, Liu Z, Lin-Moore AT, Clark RD, Curry CJ, Link N, Schulze KL, Boerwinkle E, Dobyns WB, Allikmets R, Gibbs RA, Chen R, Lupski JR, Wangler MF, Bellen HJ (2014) A drosophila genetic resource of mutants to study mechanisms underlying human genetic diseases. Cell 159(1):200–214. https://doi.org/10.1016/j.cell.2014.09.002
Acharya U, Patel S, Koundakjian E, Nagashima K, Han X, Acharya JK (2003) Modulating sphingolipid biosynthetic pathway rescues photoreceptor degeneration. Science (New York, NY) 299(5613):1740–1743. https://doi.org/10.1126/science.1080549
Carvalho M, Sampaio JL, Palm W, Brankatschk M, Eaton S, Shevchenko A (2012) Effects of diet and development on the Drosophila lipidome. Mol Syst Biol 8:600. https://doi.org/10.1038/msb.2012.29
Guan XL, Cestra G, Shui G, Kuhrs A, Schittenhelm RB, Hafen E, van der Goot FG, Robinett CC, Gatti M, Gonzalez-Gaitan M, Wenk MR (2013) Biochemical membrane lipidomics during Drosophila development. Dev Cell 24(1):98–111. https://doi.org/10.1016/j.devcel.2012.11.012
Huang Y, Huang S, Lam SM, Liu Z, Shui G, Zhang YQ (2016) Acsl, the Drosophila ortholog of intellectual-disability-related ACSL4, inhibits synaptic growth by altered lipids. J Cell Sci 129(21):4034–4045. https://doi.org/10.1242/jcs.195032
Kohler K, Brunner E, Guan XL, Boucke K, Greber UF, Mohanty S, Barth JM, Wenk MR, Hafen E (2009) A combined proteomic and genetic analysis identifies a role for the lipid desaturase Desat1 in starvation-induced autophagy in Drosophila. Autophagy 5(7):980–990. https://doi.org/10.4161/auto.5.7.9325
Laurinyecz B, Peter M, Vedelek V, Kovacs AL, Juhasz G, Maroy P, Vigh L, Balogh G, Sinka R (2016) Reduced expression of CDP-DAG synthase changes lipid composition and leads to male sterility in Drosophila. Open Biol 6(1):50169. https://doi.org/10.1098/rsob.150169
Niehoff AC, Kettling H, Pirkl A, Chiang YN, Dreisewerd K, Yew JY (2014) Analysis of Drosophila lipids by matrix-assisted laser desorption/ionization mass spectrometric imaging. Anal Chem 86(22):11086–11092. https://doi.org/10.1021/ac503171f
Carvalho M, Schwudke D, Sampaio JL, Palm W, Riezman I, Dey G, Gupta GD, Mayor S, Riezman H, Shevchenko A, Kurzchalia TV, Eaton S (2010) Survival strategies of a sterol auxotroph. Development 137(21):3675–3685. https://doi.org/10.1242/dev.044560
Chung H, Carroll SB (2015) Wax, sex and the origin of species: dual roles of insect cuticular hydrocarbons in adaptation and mating. Bioessays 37(7):822–830. https://doi.org/10.1002/bies.201500014
Scott D (1986) Sexual mimicry regulates the attractiveness of mated Drosophila melanogaster females. Proc Natl Acad Sci U S A 83(21):8429–8433. https://doi.org/10.1073/PNAS.83.21.8429
Brankatschk M, Gutmann T, Knittelfelder O, Palladini A, Prince E, Grzybek M, Brankatschk B, Shevchenko A, Coskun U, Eaton S (2018) A temperature-dependent switch in feeding preference improves Drosophila development and survival in the cold. Dev Cell 46(6):781–793. e784. https://doi.org/10.1016/j.devcel.2018.05.028
Katewa SD, Akagi K, Bose N, Rakshit K, Camarella T, Zheng X, Hall D, Davis S, Nelson CS, Brem RB, Ramanathan A, Sehgal A, Giebultowicz JM, Kapahi P (2016) Peripheral circadian clocks mediate dietary restriction-dependent changes in lifespan and fat metabolism in Drosophila. Cell Metab 23(1):143–154. https://doi.org/10.1016/j.cmet.2015.10.014
Chin JSR, Ellis SR, Pham HT, Blanksby SJ, Mori K, Koh QL, Etges WJ, Yew JY (2014) Sex-specific triacylglycerides are widely conserved in Drosophila and mediate mating behavior. eLife 3:e01751. https://doi.org/10.7554/eLife.01751
Wenk MR (2005) The emerging field of lipidomics. Nat Rev Drug Discov 4(7):594–610. https://doi.org/10.1038/nrd1776
Murphy RC, Gaskell SJ (2011) New applications of mass spectrometry in lipid analysis. J Biol Chem 286(29):25427–25433. https://doi.org/10.1074/jbc.R111.233478
Wang C, Wang M, Han X (2015) Applications of mass spectrometry for cellular lipid analysis. Mol BioSyst 11(3):698–713. https://doi.org/10.1039/c4mb00586d
Hsu FF, Turk J (2009) Electrospray ionization with low-energy collisionally activated dissociation tandem mass spectrometry of glycerophospholipids: mechanisms of fragmentation and structural characterization. J Chromatogr B Anal Technol Biomed Life Sci 877(26):2673–2695. https://doi.org/10.1016/j.jchromb.2009.02.033
Harkewicz R, Dennis EA (2011) Applications of mass spectrometry to lipids and membranes. Annu Rev Biochem 80:301–325. https://doi.org/10.1146/annurev-biochem-060409-092612
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
Pluskal T, Castillo S, Villar-Briones A, Orešič M (2010) MZmine 2: modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data. BMC Bioinformatics 11(1):395. https://doi.org/10.1186/1471-2105-11-395
Tsugawa H, Cajka T, Kind T, Ma Y, Higgins B, Ikeda K, Kanazawa M, VanderGheynst J, Fiehn O, Arita M (2015) MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis. Nat Methods 12(6):523–526. https://doi.org/10.1038/nmeth.3393
Sud M, Fahy E, Cotter D, Brown A, Dennis EA, Glass CK, Merrill AH Jr, Murphy RC, Raetz CR, Russell DW, Subramaniam S (2007) LMSD: LIPID MAPS structure database. Nucleic Acids Res 35(Database issue):D527–D532. https://doi.org/10.1093/nar/gkl838
Kind T, Liu KH, Lee DY, DeFelice B, Meissen JK, Fiehn O (2013) LipidBlast in silico tandem mass spectrometry database for lipid identification. Nat Methods 10(8):755–758. https://doi.org/10.1038/nmeth.2551
Wolrab D, Chocholoušková M, Jirásko R, Peterka O, Holčapek M (2020) Validation of lipidomic analysis of human plasma and serum by supercritical fluid chromatography-mass spectrometry and hydrophilic interaction liquid chromatography-mass spectrometry. Anal Bioanal Chem 412(10):2375–2388. https://doi.org/10.1007/s00216-020-02473-3
Takeda H, Izumi Y, Takahashi M, Paxton T, Tamura S, Koike T, Yu Y, Kato N, Nagase K, Shiomi M, Bamba T (2018) Widely-targeted quantitative lipidomics method by supercritical fluid chromatography triple quadrupole mass spectrometry. J Lipid Res 59(7):1283–1293. https://doi.org/10.1194/jlr.D083014
Lísa M, Holčapek M (2018) UHPSFC/ESI-MS analysis of lipids. Methods Mol Biol 1730:73–82. https://doi.org/10.1007/978-1-4939-7592-1_5
Züllig T, Trötzmüller M, Köfeler HC (2020) Lipidomics from sample preparation to data analysis: a primer. Anal Bioanal Chem 412(10):2191–2209. https://doi.org/10.1007/s00216-019-02241-y
Wang J, Wang C, Han X (2019) Tutorial on lipidomics. Anal Chim Acta 1061:28–41. https://doi.org/10.1016/j.aca.2019.01.043
Wu Z, Bagarolo GI, Thoroe-Boveleth S, Jankowski J (2020) “Lipidomics”: mass spectrometric and chemometric analyses of lipids. Adv Drug Deliv Rev 159:294. https://doi.org/10.1016/j.addr.2020.06.009
Han X, Yang K, Yang J, Fikes KN, Cheng H, Gross RW (2006) Factors influencing the electrospray intrasource separation and selective ionization of glycerophospholipids. J Am Soc Mass Spectrom 17(2):264–274. https://doi.org/10.1016/j.jasms.2005.11.003
Han X, Gross RW (2005) Shotgun lipidomics: electrospray ionization mass spectrometric analysis and quantitation of cellular lipidomes directly from crude extracts of biological samples. Mass Spectrom Rev 24(3):367–412. https://doi.org/10.1002/mas.20023
Han X, Gross RW (2008) Chapter 5: New developments in multi-dimensional mass spectrometry based shotgun lipidomics. In: Metabolomics, Metabonomics and metabolite profiling. The Royal Society of Chemistry, London, pp 134–160. https://doi.org/10.1039/9781847558107-00134
Han X, Yang K, Gross RW (2012) Multi-dimensional mass spectrometry-based shotgun lipidomics and novel strategies for lipidomic analyses. Mass Spectrom Rev 31(1):134–178. https://doi.org/10.1002/mas.20342
Wang M, Wang C, Han RH, Han X (2016) Novel advances in shotgun lipidomics for biology and medicine. Prog Lipid Res 61:83–108. https://doi.org/10.1016/j.plipres.2015.12.002
Hsu FF (2018) Mass spectrometry-based shotgun lipidomics – a critical review from the technical point of view. Anal Bioanal Chem 410(25):6387–6409. https://doi.org/10.1007/s00216-018-1252-y
Shui G, Guan XL, Gopalakrishnan P, Xue Y, Goh JS, Yang H, Wenk MR (2010) Characterization of substrate preference for Slc1p and Cst26p in Saccharomyces cerevisiae using lipidomic approaches and an LPAAT activity assay. PLoS One 5(8):e11956. https://doi.org/10.1371/journal.pone.0011956
Shui G, Guan XL, Low CP, Chua GH, Goh JS, Yang H, Wenk MR (2010) Toward one step analysis of cellular lipidomes using liquid chromatography coupled with mass spectrometry: application to Saccharomyces cerevisiae and Schizosaccharomyces pombe lipidomics. Mol Biosyst 6(6):1008–1017. https://doi.org/10.1039/b913353d
Bligh EG, Dyer WJ (1959) A rapid method of total lipid extraction and purification. Can J Biochem Physiol 37(8):911–917. https://doi.org/10.1139/o59-099
Acknowledgments
X.L.G. is supported by the Nanyang Assistant Professorship from Lee Kong Chian School of Medicine, Nanyang Technological University.
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Goh, E.X.Y., Guan, X.L. (2021). Targeted Lipidomics of Drosophila melanogaster During Development. In: Hsu, FF. (eds) Mass Spectrometry-Based Lipidomics. Methods in Molecular Biology, vol 2306. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1410-5_13
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