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Home , Lipidome, Lipidomics, Omics

COMMENTARY

Lipidomics joins the evolution

Edward A. Dennis1 Departments of Chemistry and and Pharmacology, School of Medicine, University of California at San Diego, La Jolla, CA 92093-0601

he end of the 20th century was various combinations the 3 positions on online analysis such as molecular frag- marked by the revolu- the backbone of monoacylglyc- mentation (MSMS), multiple reaction tion, and one might say that the erols (MAGs), diacylglycerols (DAGs), monitoring (MRM), and multiple pre- beginning of the 21st century is and triacylglycerols (TAGs). Similarly, in cursor ion scanning (MPIS). In short, a Tmarked by efforts to bring our knowledge monoacylglycerolphosphates (lysophos- kind of divide-and-conquer strategy. (ii) of a ’s , known as , pholipids) and diacylglycerolphosphates An alternative approach, sometimes re- to a par with our growing knowledge of a (phospholipids), fatty acyl groups can ferred to as ‘‘shotgun ’’ as cell’s transcripts, known as transcriptom- occupy 1 or 2 positions on the glycerol used by Ejsing et al. (5), begins with an ics. Many of us believe that the next evo- backbone, respectively, and the phos- off-line extraction, but then sub- lution of the omics revolution will be to phate can be esterified to a large variety jects these extracts directly to MS analy- map all of the metabolites of a cell, of polar head groups. Thus, the possible sis without LC separation. In the spe- known as . Leading the way number of molecular species for a given cific study reported herein, Ejsing et al. in these efforts is the work in many labo- set of fatty acids (and polar head actually subjected their cells to 2 ratories on one subset of the , groups) is very large and so far it has different extraction protocols, one to the , aimed at mapping all of the not been straightforward to define all of separate the more hydrophobic lipids of a cell, known as lipidomics (1–4). the molecular species and their stereo- The ultimate goal is to evolve an inte- chemistry for a given lipid. Even the and a second extraction with a more grated omics picture (the ‘‘’’) sterol esters that sometimes occur with a polar . In some runs, they first of the genes, transcripts, proteins, and single chain, the sphingolipids acetylated the sample or included meth- metabolites to fully describe cellular func- with a defined fatty acid-derived hydro- ylamine in the procedure to optimize tioning. One leading effort in the lipidom- carbon chain, and an amide-linked fatty the analysis. Additionally, their analysis ics evolution is described in this issue of acid have numerous possibilities. used 2 different types of mass spectrom- PNAS (5). eters, a quadrupole time-of-flight instru- Ejsing et al. (5) have used advanced ment in which they used MRM and (MS) techniques MPIS and a linear ion trap-orbitrap in- combined with state-of-the-art data Genes and transcripts do strument that is capable of providing analysis software to identify 342 lipid extremely accurate mass determinations. molecular species in the yeast lipidome not always predict the With each instrument, they analyzed and to quantify them; they estimate that samples in both negative and positive their findings constitutes 95% of the precise levels of active ionization modes. The extremely compli- lipid molecules present putting its cover- proteins/enzymes. cated data output was then deciphered age on a par with the early efforts at by using sophisticated analysis software. gene sequencing. This effort allowed Their shotgun lipidomics approach al- these authors to describe the major lipid lowed them to identify in yeast some 21 molecular species comprising the yeast Ejsing et al. (5) in choosing yeast have simplified the challenge because these different lipids that were quantitated as membranes. 342 unique molecular species. These include , cells can be grown on a minimal me- dium lacking lipids and this organism is The use of some specialized MS scan sphingolipids, and sterols as well as the modes (e.g., MRM) allows for high sen- neutral glycerolipids. The authors have capable of only synthesizing a limited number of fatty acids, such as palmitic sitivity; however, a drawback is that one described the detailed metabolic path- only finds what one is looking for. Com- ways for the interacting of these diverse acid (16:0), stearic acid (18:0), etc., and ⌬ bined with the use of internal standards, lipid species. can only desaturate in the 9 position to these techniques allow for the identifica- The LIPID MAPS Initiative in lipido- give a limited number of unsaturated tion and quantification of the lipids mics (1, 4) in conjunction with the fatty acids, such as palmitoleic acid (16:1 known to be present, but do not, by International Committee for the Classi- cis-9) and oleic acid (18:1 cis-9). This fication and Nomenclature of Lipids has greatly simplified the task involved themselves, lead to the finding of novel (ICCNL) have defined 8 categories of in studying the lipidome of yeast com- or unexpected molecular species. Ejsing lipids and numerous classes and sub- pared with the challenges of mammalian et al. (5) made critical use of multiple classes (6, 7) to allow one to describe cells, where there are tens of thousands lipid standards obtained from Avanti lipid molecular species. Fig. 1 illustrates of distinct molecular species of lipids. Polar Lipids which had been developed examples of molecular species of lipids There are 2 fundamentally different under LIPID MAPS auspices (14), but in each of 6 of these categories that ex- approaches to lipidomics analysis. (i) they also had to develop their own stan- ist in yeast, although the free fatty acids The LIPID MAPS Consortium has cho- dards for some specific yeast phyto- and prenols were not reported in the sen to develop extraction protocols opti- sphingolipids. The yeast lipidome is present study. (See www.lipidmaps.org.) mized for each lipid category, and in characterized by the usual TAG, DAG, The goal of lipidomics is to define and some cases specific classes of lipids, and quantitate all of the lipid molecular spe- then to use liquid chromatography (LC) cies in a cell, but this is complicated by to optimally separate the specific molec- Author contributions: E.A.D. wrote the paper. the extraordinary number of combina- ular species of lipids present (8–13). The author declares no conflict of interest. tions possible with the large number of The LC eluate is then coupled directly See companion article on page 2136. known fatty acids that can occupy in to a mass spectrometer for further 1E-mail: [email protected].

www.pnas.org͞cgi͞doi͞10.1073͞pnas.0812636106 PNAS ͉ February 17, 2009 ͉ vol. 106 ͉ no. 7 ͉ 2089–2090 Downloaded by guest on September 24, 2021 Fig. 1. Examples of lipid categories present in yeast. Six of the 8 categories of lipids in the LIPID MAPS comprehensive classification system for lipids (6, 7) are illustrated with an example for each drawn by the Structure Drawing Program (www.lipidmaps.org).

and phospholipid species found in mam- quencing and genetic manipulation (15, Furthermore, they have been able to malian cells, but in addition has unusual 16). However, genes and transcripts do demonstrate in quantitative terms the phytosphingolipid species in which the not always predict the precise levels of subtle changes in lipid molecular spe- long-chain base and the fatty acyl amide active proteins/enzymes, and knowl- cies when yeast is grown at different moieties are characterized by hydroxy- edge of the actual lipid metabolite lev- temperatures and the ‘‘ripple’’ effects lated species (e.g., phytoceramides) and els is more predictive of metabolic im- through multiple classes of membrane lipids. an abundance of the sterol ergosterol plications. The article of Ejsing et al. rather than the mammalian cholesterol. (5) provides quantitative information ACKNOWLEDGMENTS. Dr. Eoin Fahy aided in the Much is known about the yeast lipi- on the levels of the lipid metabolites preparation of Fig. 1. This work was supported by dome from prior traditional studies on and their changes with specific gene National Institutes of Health Large Scale Collabora- tive ‘‘Glue’’ Grant U54 GM069338 for the LIPID the enzymes of lipid metabolism and deletions that enhances our under- MAPS initiative and National Institutes of Health enhanced considerably by gene se- standing of metabolism enormously. Grants R01 GM 20,501 and R01 GM 64,611.

1. Dennis EA, et al. (2005) The LIPID MAPS approach to 8. Krank J, Murphy RC, Barkley RM, Duchoslav E, 12. Garrett TA, Guan Z, Raetz CR (2007) Analysis of ubiqui- lipidomics. Functional Lipidomics, eds Feng L, Prestwich McAnoy A (2007) Qualitative analysis and quantita- nones, dolichols and dolichol diphosphate-oligosac- G (CRC Press/Taylor & Francis Group, London), pp 1–15. tive assessment of changes in neutral glycerol lipid charides by liquid chromatography-electrospray ion- 2. van Meer G (2005) Cellular lipidomics. EMBO J 24:3159– molecular species within cells. Methods Enzymol ization mass spectrometry. Methods Enzymol 432:117– 3165. 432:1–20. 142. 3. Wenk MR (2005) The emerging field of lipidomics. Nat 9. Ivanova P, Milne S, Byrne MO, Xiang Y, Brown HA 13. McDonald JG, Thompson B, McCrum EC, Russell DW Rev Drug Discov 4:594–610. (2007) identification and quanti- (2007) Extraction and analysis of sterols in biological 4. Schmelzer K, Fahy E, Subramaniam S, Dennis EA (2007) tation by electrospray mass spectrometry. Methods En- matrices by high-performance liquid chromatography mass spectrometry. Methods The LIPID MAPS initiative in lipidomics. Methods Enzy- zymol 432:21–57. Enzymol 432:143–168. mol 432:169–181. 10. Deems RA, Buczynski MW, Bowers-Gentry RC, 14. Moore JD, Caufield WV, Shaw W (2007) Quantitation 5. Ejsing CS, et al. (2009) Global analysis of the Harkewicz R, Dennis EA (2007) Detection and quanti- and standardization of lipid internal standards for mass yeast lipidome by quantitative shotgun mass spec- tation of eicosanoids via high performance liquid chro- spectroscopy. Methods Enzymol 432:351–367. trometry. Proc Natl Acad Sci USA 106:2136– matography/electrospray ionization mass spectrome- 15. Carman GM, Henry SA (2007) Phosphatidic acid plays a 2141. try. Methods Enzymol 432:59–82. central role in the transcriptional regulation of glyc- 6. Fahy E, et al. (2005) A comprehensive classification 11. Sullards MC, et al. (2007) Structure-specific, quantita- erophospholipid synthesis in Saccharomyces cerevisiae. system for lipids. J Lipid Res 46:839–861. tive methods for analysis of sphingolipids by liquid- J Biol Chem 282:37293–37297. 7. Fahy E, et al. (2008) Update of the LIPID MAPS compre- chromatography : ‘‘Inside- 16. Hannun YA, Obeid LM (2008) Principles of bioactive hensive classification system for lipids. J Lipid Res, out’’ sphingolipidomics. Methods Enzymol 432:83– lipid signaling: Lessons from sphingolipids. Nat Rev Mol 10.1194/jlr.R800095-JLR200. 115. Cell Biol 9:139–150.

2090 ͉ www.pnas.org͞cgi͞doi͞10.1073͞pnas.0812636106 Dennis Downloaded by guest on September 24, 2021