ReviewHigh-coverage lipidomics for functional lipid and pathway analyses
Graphical abstract
Introduction
Lipids, now widely-recognized as key biological molecules in vivo, execute important biochemical and/or biophysical roles in energy storage, energy mobilization, modulating membrane fluidity, membrane compartmentalization, as well as various trafficking and signaling events [[1], [2], [3]]. Aberrant lipid metabolism is implicated in the pathology of a plethora of human diseases, including diabetes, cardiovascular complications, steatohepatitis, neurodegenerative diseases and cancers [[4], [5], [6], [7]].
As reviewed elsewhere, lipid analysis has evolved tremendously over the past decades, from the application of traditional techniques such as thin layer chromatography (TLC) that only permit the detection of a rather limited set of lipid classes, to comprehensive interrogation of endogenous lipidomes at systems levels, i.e. lipidomics that covers hundreds or even thousands of individual species [8]. Lipidomics, as a relatively young member of the omics family, delivers a comprehensive snapshot of lipid profiles in a given biological context, providing vital clues for understanding the connection between lipids and phenotypes [4,9,10]. As lipidomics provides the closest readout to lipid-associated cellular phenotypes, it is being increasingly applied to study pathway perturbations in various biological and biomedical settings that implicate dysregulation in lipid metabolism [4,10,11]. Various lipids, such as ceramides, diacylglycerols, phospholipids, and oxysterols had been reported as biomarkers for a myriad of major human diseases, and a number of these discoveries were clinically translated to diagnostic tools at bedside [[12], [13], [14], [15], [16], [17]]. Mass spectrometry (MS) and nuclear magnetic resonance (NMR) represent the mainstream techniques for the characterization and quantitation of lipids. While NMR could be considered as a standalone technique, various mass spectrometers have been widely used either directly (shotgun) or coupling with different chromatographic systems, such as liquid-chromatography (LC), gas-chromatography (GC) and supercritical fluid chromatography (SFC), to allow for extensive identification and quantification of diverse lipid classes [18]. According to data collected from the Web of Science, however, research published in the field of lipidomics since the year of 2003 had largely deployed MS, which accounted for approximately 95% of the recorded research under the search term “lipidomics”, while NMR application is less common (Fig. S1). Therefore, MS is still regarded as the primary technique for lipidomics to date. It has, however, remained challenging to execute comprehensive analysis of lipidomes with accurate quantitation primarily due to a few issues, such as lack of isotopic internal standards, and the vastly different dynamic ranges of lipid classes across different biological samples, etc, as previously discussed elsewhere [8].
Although lipidomics has advanced rapidly over the past fifteen years, both in terms of quantitation and biomarker elucidation, lipid pathway analysis has experienced a considerable lag mainly due to the complexity and diversity of lipids, as well as technical constraints in achieving sufficient analytical coverage of endogenous lipids that come in immense diversity. Herein, we summarize recent progress in lipidomics, with central emphasis on the importance of achieving sufficient analytical coverage to render biological pathway analysis. We also bring up the technical constraints that impede comprehensive lipid pathway analysis, as well as the significance of considering lipid metabolic pathways from a “panoramic” perspective, instead of circumscription to conventional, two-dimensional illustration in the analysis of lipid metabolic pathways.
Section snippets
Lipidomics approaches for extending analytical coverage
As extensively reviewed elsewhere, lipid analysis at the molecular level have been largely propelled by the rapid development of key instrumentations over the past 30 years, such as the MS [8,[19], [20], [21]]. Before 1990s, GC coupling with mass spectrometry (GC-MS) was probably the fundamental technique for analysis of lipids including sterols, glycerolipids, sphingolipids, fatty acids, as well as their derivatives including prostaglandins. A major drawback in earlier studies was that lipid
The transiting role of lipidomics from phenotype validation to hypothesis generation
As lipidomics confer both identification and (relative) quantification of a myriad of lipids at molecular level, it has, for a long time, been broadly and conventionally applied to present phenotype evidence and alterations (e.g. biomarkers) in various biological and biomedical studies [[87], [88], [89], [90]]. The issue of quantification (absolute versus relative) in lipidomics has been previously reviewed in details elsewhere [8]. In terms of phenotype characterization, for example, lipidomic
High-coverage lipidomics for multi-dimensional pathway analysis
While pathway analysis is becoming an essential part in the typical lipidomics workflow, considerable challenges prevail against its wide application in various biological and biomedical settings. In most pathway analyses, a critical initial step is identifier (ID) mapping against reference database IDs or compound synonyms. Such lipid records are available in many public reference databases. Some have been developed for chemicals, like CAS and PubChem; or for biologically relevant metabolites,
High-coverage lipidomics to uncover functional lipid modules
In the foregoing lipid pathway analyses, known and reported relationships or reactions between interacting lipids are prerequisites. In a way, this requirement forbids the discovery of novel, previously unknown functional interactions between lipids in a given biological context. Co-regulated genes often display similar patterns of gene expression, which translates to intense correlations between their gene expression levels [122]. In the same light, co-regulated lipids are expected to exhibit
Concluding remarks
Advances in both front-end separation approaches and analytical technologies, together with the ever-increasing repository of knowledge pertaining to lipid biology, have allowed lipidomics to significantly aggrandize its analytical coverage and encompass an expanding repertoire of lipids in a single analytical platform. High-coverage lipidomics expedites the application of data-driven pathway and functional modules analyses that allows scientists to probe into lipid homeostasis and metabolic
CRediT authorship contribution statement
Sin Man Lam: conceived the manuscript, wrote the manuscript. Zehua Wang: wrote the manuscript. Bowen Li: conceived the manuscript, wrote the manuscript. Guanghou Shui: conceived the manuscript, wrote the manuscript.
Declaration of competing interest
The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
Acknowledgements
The authors thank Miss Xiaojie Liu for assistance with graphical illustrations. This work was financially supported by grants from the National Key R&D Program of China (2018YFA0506900, 2018YFA0800901), The Strategic Priority Research Program of the Chinese Academy of Sciences (XDA12030211), National Natural Science Foundation of China (31671226, 31871194).
Professor Guanghou Shui received his PhD degree in 2004 from the National University of Singapore (NUS). Following this, he conducted his postdoctoral research in the Department of Biochemistry in 2004–2008 and worked at a senior research fellow at NUS in 2008–2012. He joined the Institute of Genetics and Developmental Biology in 2013. The major research interests of his laboratory are (1) developing advanced lipidomics/metabolomics tools to unravel the association between lipids and onset of
References (127)
- et al.
Lipidomics as a principal tool for advancing biomedical research
J Genet Genomics
(2013) - et al.
Integration of lipidomics and metabolomics for in-depth understanding of cellular mechanism and disease progression
J Genet Genomics
(2020) - et al.
Lipidomics, en route to accurate quantitation
Biochim. Biophys. Acta Mol. Cell Biol. Lipids
(2017) - et al.
Lipidomics: a new window to biomedical frontiers
Trends Biotechnol
(2008) - et al.
Ceramides as novel disease biomarkers
Trends Mol. Med.
(2019) - et al.
Role of lipids in pathophysiology, diagnosis and therapy of hepatocellular carcinoma
Biochim. Biophys. Acta Mol. Cell Biol. Lipids
(2020) - et al.
Lipidomics: potential role in risk prediction and therapeutic monitoring for diabetes and cardiovascular disease
Pharmacol. Ther.
(2014) - et al.
Tutorial on lipidomics
Anal. Chim. Acta
(2019) - et al.
Glycerolipid and cholesterol ester analyses in biological samples by mass spectrometry
Biochim. Biophys. Acta
(2011) - et al.
Identification and quantification of neutral fecal steroids by gas-liquid chromatography and mass spectrometry: studies of human excretion during two dietary regimens
J. Lipid Res.
(1964)
Profiling of prostaglandin biosynthesis in biopsy fragments of human lung carcinomas and normal human lung by capillary gas chromatography-negative ion chemical ionization mass spectrometry
Prostaglandins
Determination of aldehydic lipid peroxidation products: malonaldehyde and 4-hydroxynonenal
Methods Enzymol
Global analyses of cellular lipidomes directly from crude extracts of biological samples by ESI mass spectrometry: a bridge to lipidomics
J. Lipid Res.
Analysis of phospholipid species in human blood using normal-phase liquid chromatography coupled with electrospray ionization ion-trap tandem mass spectrometry
J. Chromatogr. B Biomed. Sci. Appl.
Extensive characterization of human tear fluid collected using different techniques unravels the presence of novel lipid amphiphiles
J. Lipid Res.
Derivatization-independent cholesterol analysis in crude lipid extracts by liquid chromatography/mass spectrometry: applications to a rabbit model for atherosclerosis
J. Chromatogr. A
Liquid chromatography-atmospheric pressure photoionization-mass spectrometry analysis of triacylglycerol lipids--effects of mobile phases on sensitivity
J. Chromatogr. A
Comparative lipidomic analysis of mouse and human brain with Alzheimer disease
J. Biol. Chem.
An integrated method for direct interrogation of sphingolipid homeostasis in the heart and brain tissues of mice through postnatal development up to reproductive senescence
Anal. Chim. Acta
Endogenous sterol intermediates of the mevalonate pathway regulate HMGCR degradation and SREBP-2 processing
J. Lipid Res.
Lipid analysis and lipidomics by structurally selective ion mobility-mass spectrometry
Biochim. Biophys. Acta
Comprehensive lipidomic analysis of human plasma using multidimensional liquid- and gas-phase separations: two-dimensional liquid chromatography-mass spectrometry vs. liquid chromatography-trapped-ion-mobility-mass spectrometry
J. Chromatogr. A
Sensitive profiling of chemically diverse bioactive lipids
J. Lipid Res.
Off-line mixed-mode liquid chromatography coupled with reversed phase high performance liquid chromatography-high resolution mass spectrometry to improve coverage in lipidomics analysis
Anal. Chim. Acta
Sphingolipidomics: high-throughput, structure-specific, and quantitative analysis of sphingolipids by liquid chromatography tandem mass spectrometry
Methods
Quantitative analysis of sphingolipids for lipidomics using triple quadrupole and quadrupole linear ion trap mass spectrometers
J. Lipid Res.
High-throughput shotgun lipidomics by quadrupole time-of-flight mass spectrometry
J Chromatogr B Analyt Technol Biomed Life Sci
Comprehensive blood plasma lipidomics by liquid chromatography/quadrupole time-of-flight mass spectrometry
J. Chromatogr. A
Comprehensive shotgun lipidomics of human meibomian gland secretions using MS/MS(all) with successive switching between acquisition polarity modes
J. Lipid Res.
Comprehensive MS/MS profiling by UHPLC-ESI-QTOF-MS/MS using SWATH data-independent acquisition for the study of platelet lipidomes in coronary artery disease
Anal. Chim. Acta
Comprehensive lipidomics of mouse plasma using class-specific surrogate calibrants and SWATH acquisition for large-scale lipid quantification in untargeted analysis
Anal. Chim. Acta
Isolation of n-acyl phosphatidylethanolamine from pea seeds
Biochem. Biophys. Res. Commun.
Formation of N-acyl-phosphatidylethanolamines and N-acetylethanolamines: proposed role in neurotoxicity
Biochem. Pharmacol.
Occurrence and postmortem generation of anandamide and other long-chain N-acylethanolamines in mammalian brain
FEBS Lett
Anandamide and other N-acylethanolamines in mouse peritoneal macrophages
Chem. Phys. Lipids
Lipidomic analysis of endocannabinoid metabolism in biological samples
J Chromatogr B Analyt Technol Biomed Life Sci
Identification of biosynthetic precursors for the endocannabinoid anandamide in the rat brain
J. Lipid Res.
High-throughput lipidomic analysis of fatty acid derived eicosanoids and N-acylethanolamines
Biochim. Biophys. Acta
Lipid peroxidation products mediate the formation of 8-hydroxydeoxyguanosine in DNA
Free Radic. Biol. Med.
Increased levels of monohydroxy metabolites of arachidonic acid and linoleic acid in LDL and aorta from atherosclerotic rabbits
Biochim. Biophys. Acta
Sequestration of polyunsaturated fatty acids in membrane phospholipids of Caenorhabditis elegans dauer larva attenuates eicosanoid biosynthesis for prolonged survival
Redox Biol
Nitric oxide regulation of superoxide and peroxynitrite-dependent lipid peroxidation. Formation of novel nitrogen-containing oxidized lipid derivatives
J. Biol. Chem.
Methods for oxysterol analysis: past, present and future
Biochem. Pharmacol.
Endogenous cholesterol ester hydroperoxides modulate cholesterol levels and inhibit cholesterol uptake in hepatocytes and macrophages
Redox Biol
A robust, integrated platform for comprehensive analyses of acyl-coenzyme as and acyl-carnitines revealed chain length-dependent disparity in fatty acyl metabolic fates across Drosophila development
Sci. Bull.
Quantitative structural multiclass lipidomics using differential mobility: electron impact excitation of ions from organics (EIEIO) mass spectrometry
J. Lipid Res.
A comprehensive classification system for lipids
J. Lipid Res.
Update of the LIPID MAPS comprehensive classification system for lipids
J. Lipid Res.
Cellular lipidomics
EMBO J
Lipid signalling in disease
Nat. Rev. Mol. Cell Biol.
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Professor Guanghou Shui received his PhD degree in 2004 from the National University of Singapore (NUS). Following this, he conducted his postdoctoral research in the Department of Biochemistry in 2004–2008 and worked at a senior research fellow at NUS in 2008–2012. He joined the Institute of Genetics and Developmental Biology in 2013. The major research interests of his laboratory are (1) developing advanced lipidomics/metabolomics tools to unravel the association between lipids and onset of diseases; (2) lipid biology in development, metabolic disorders and associated diseases. Guanghou is the coauthor of over 150 papers resulting in an h-index of 49 based on 8500 citations.
Sin Man Lam graduated with a Ph.D. degree in Biochemistry from the National University of Singapore in 2013. She conducted postdoctoral research from 2013 to 2017 in the Institute of Genetics and Developmental Biology. She is now the chief technology officer of LipidALL Technologies and a visiting scientist at the Institute of Genetics and Developmental Biology. Her research interest lies in the translational application of omics approaches to elucidate metabolic regulation underlying biological and physiological processes, such as development and aging; as well as the use of omics-driven methodologies to interrogate metabolic dysregulation in major human diseases. She has coauthored over 60 papers in international journals.
Zehua Wang received her bachelor degree in 2014 from Lanzhou University of China. From 2014 to present, she is a PhD candidate specializing in the area of lipidomics in the Institute of Genetics and Developmental Biology. She had published three papers in international journals including Redox biology, Cell Metabolism and The Journal of Cell Biology.
Bowen Li received his master degree in 2011 from National University of Singapore. From 2008 to 2013, he worked in the Singapore Lipidomics Incubator of NUS, focusing on bioinformatics in lipidomics. Between 2013 and 2015, he studied biostatistics in School of Public Health, NUS. From 2015 to 2017 he worked in the Singapore National University Hospital as senior system analyst. He joined LipidALL Technologies in 2017. He has published over 10 articles in international journals including Diabetes Care, Metabolomics, MicrobiologyOpen, Scientific Reports, Journal of Genetics & Genomics, J. Cardiovasc. Surg, PLoS ONE, J. Anal. Test, Nat. Commun, etc.