The challenge of brain lipidomics

After many years backstage, lipids have made a come back in the limelight of neuroscience. This renewed excitement was sparked by a series of convergent discoveries in the fields of neural development, synaptic physiology and receptor pharmacology, which have begun to reveal the roles played by lipid messengers and their receptors in brain function. Such roles extend from the development of the neocortex to the processing of complex behaviors, encompassing a territory as vast as those traditionally assigned to growth factors, neurotransmitters and neuropeptides. Along with these basic discoveries, technical advances have simplified the identification and quantification of neural lipids, achieving a degree of sensitivity and selectivity that was unthinkable only 10 years ago. Thanks to this progress, we can now resolve complex mixtures of lipid molecules and quantify each of their components, which are often present in tissues at vanishingly low concentrations. In this review, I outline several key features of brain lipid signaling and discuss the opportunities and challenges that such features impose on future lipidomic approaches.     

The foundations and development of lipidomics

For over a century, the importance of lipid metabolism in biology was recognized but difficult to mechanistically understand due to the lack of sensitive and robust technologies for identification and quantification of lipid molecular species. The enabling technological breakthroughs emerged in the 1980s with the development of soft ionization methods (Electrospray Ionization and Matrix Assisted Laser Desorption/Ionization) that could identify and quantify intact individual lipid molecular species. These soft ionization technologies laid the foundations for what was to be later named the field of lipidomics. Further innovative advances in multistage fragmentation, dramatic improvements in resolution and mass accuracy, and multiplexed sample analysis fueled the early growth of lipidomics through the early 1990s. The field exponentially grew through the use of a variety of strategic approaches, which included direct infusion, chromatographic separation, and charge-switch derivatization, which facilitated access to the low abundance species of the lipidome. In this Thematic Review, we provide a broad perspective of the foundations, enabling advances, and predicted future directions of growth of the lipidomics field.     

Cellular lipidomics

The cellular lipidome comprises over 1000 different lipids. Most lipids look similar having a polar head and hydrophobic tails. Still, cells recognize lipids with exquisite specificity. The functionality of lipids is determined by their local concentration, which varies between organelles, between the two leaflets of the lipid bilayer and even within the lateral plane of the membrane. To incorporate function, cellular lipidomics must not only determine which lipids are present but also the concentration of each lipid at each specific intracellular location in time and the lipid's interaction partners. Moreover, cellular lipidomics must include the enzymes of lipid metabolism and transport, their specificity, localization and regulation. Finally, it requires a thorough understanding of the physical properties of lipids and membranes, especially lipid-lipid and lipid-protein interactions. In the context of a cell, the complex relationships between metabolites can only be understood by viewing them as an integrated system. Cellular lipidomics provides a framework for understanding and manipulating the vital role of lipids, especially in membrane transport and sorting and in cell signaling.     

Mediator lipidomics

Lipidomics the systematic decoding of lipid-based information in biosystems is comprised of identification and profiling of lipids and lipid-derived mediators. As practiced today, lipidomics can be subdivided into architecture/membrane-lipidomics and mediator-lipidomics. The mapping of structural components and their relation to cell activation as well as generation of potent lipid mediators and networks involves a mass spectrometry-computational approach to appreciate inter-relationships and complex mediator networks important for cell homeostasis. Cell membranes are composed of a bilayer that contains phospholipids, fatty acids, integral membrane proteins, and membrane associated proteins, sphingolipids, etc. Membrane composition of many cell types is established. However, their organization and how they affect cell function remains an area of interest and a quest for lipidomics. Membranes serve barrier functions separating the inside from outside or compartments within cells, regulating passage of nutrients, gasses, and specific ions as well as generate signals to the intracellular milieu by the membrane's ability to interact with key proteins. The nature of these interactions and decoding the structure-function information within their organization is the promise of lipidomics (A-C). Metabolism of fatty acids is also an important energy source; hence, catabolism breakdown of fatty acids, areas of metabolomics that link to the signaling pathways, and roles of lipid mediators discussed herein.     

The evolution of lipidomics through space and time

Although the foundations of mass spectrometry-based lipidomics have been practiced for over 30 years, recent technological advances in ionization modalities in conjunction with robust increases in mass accuracy and resolution have greatly accelerated the emergence, growth and importance of the field of lipidomics. Moreover, advances in the separation sciences, bioinformatic strategies and the availability of robust databases have been synergistically integrated into modern lipidomic technologies leading to unprecedented improvements in the depth, penetrance and precision of lipidomic analyses and identification of their biological and mechanistic significance. The purpose of this "opinion" article is to briefly review the evolution of lipidomics, critique the platforms that have evolved and identify areas that are likely to emerge in the years to come. Through seamlessly integrating a rich repertoire of mass spectrometric, chemical and bioinformatic strategies, the chemical identities and quantities of tens of thousands to hundreds of thousands of different lipid molecular species and their metabolic alterations during physiologic or pathophysiologic perturbations can be obtained. Thus, the field of lipidomics which already has a distinguished history of exciting new discoveries in many disease states holds unparalleled potential to identify the pleiotropic roles of lipids in health and disease at the chemical level. This article is part of a Special Issue entitled: BBALIP_Lipidomics Opinion Articles edited by Sepp Kohlwein.     

脂质组学研究进展

综述了脂质组学的研究现状和发展趋势.脂质组学是对生物体、组织或细胞中的脂质以及与其相互作用的分子进行系统分析的一门新兴学科.脂质具有多种重要的生物功能,脂质代谢异常可引发诸多人类疾病,包括糖尿病、肥胖症、癌症以及神经退行性疾病等.目前,脂质组学研究已成为一个前景广阔的热门领域,并广泛地应用到包括药物研发、分子生理学、分子病理学、功能基因组学、营养学以及环境与健康等重要领域.     

A monitor for bud emergence in the yeast morphogenesis checkpoint

Cell cycle transitions are subject to regulation by both external signals and internal checkpoints that monitor satisfactory progression of key cell cycle events. In budding yeast, the morphogenesis checkpoint arrests the cell cycle in response to perturbations that affect the actin cytoskeleton and bud formation. Herein, we identify a step in this checkpoint pathway that seems to be directly responsive to bud emergence. Activation of the kinase Hsl1p is dependent upon its recruitment to a cortical domain organized by the septins, a family of conserved filament-forming proteins. Under conditions that delayed or blocked bud emergence, Hsl1p recruitment to the septin cortex still took place, but hyperphosphorylation of Hsl1p and recruitment of the Hsl1p-binding protein Hsl7p to the septin cortex only occurred after bud emergence. At this time, the septin cortex spread to form a collar between mother and bud, and Hsl1p and Hsl7p were restricted to the bud side of the septin collar. We discuss models for translating cellular geometry (in this case, the emergence of a bud) into biochemical signals regulating cell proliferation.     

The metabolomics and lipidomics window into thyroid cancer research

Context: Thyroid carcinoma is the most common endocrine system malignancy with a fast rising incidence in the last decade for unknown reasons. Fine needle aspiration (FNA) biopsy, the gold standard in thyroid cancer (TC) screening has still its own challenges and in some cases needs a proceeding surgery.

Objective: This review highlights the role of the two most recent “omics” approaches, “metabolomics” and “lipidomics”, in the field of TC research.

Methods: All the previous studies have been extracted from the literature and major concepts were detailed in the field of TC metabolomics and lipidomics.

Results: Metabolomics and lipidomics, have potential in finding biomarkers related to thyroid carcinoma. Among the previous studies, the most important introduced altered tissue metabolites and lipids included glucose and galactose, lactate, Scyllo- and Myo inositol, hypoxanthine, citrate, cholesterol and choline.

Conclusion: Metabolomics methods have been widely used in the field of biomarker discovery in TC and attempts are still in progress to use these methods to find a reliable biomarker panel besides current diagnostic tools.     

Dynamic lipidomics of the nucleus

Once nuclear envelope membranes have been removed from isolated nuclei, around 6% of mammalian cell phospholipid is retained within the nuclear matrix, which calculations suggest may occupy 10% of the volume of this subcellular compartment. It is now acknowledged that endonuclear phospholipid, largely ignored for the past 40 years, provides substrate for lipid-mediated signaling events. However, given its abundance, it likely also has other as yet incompletely defined roles. Endonuclear phosphatidylcholine is the predominant phospholipid comprising distinct and highly saturated molecular species compared with that of the whole cell. Moreover, this unusual composition is subject to tight homeostatic maintenance even under conditions of extreme dietary manipulation, presumably reflecting a functional requirement for highly saturated endonuclear phosphatidylcholine. Recent application of new lipidomic technologies exploiting tandem electrospray ionization mass spectrometry in conjunction with deuterium stable isotope labeling have permitted us to probe not just molecular species compositions but endonuclear phospholipid acquisition and turnover with unparalleled sensitivity and specificity. What emerges is a picture of a dynamic pool of endonuclear phospholipid subject to autonomous regulation with respect to bulk cellular phospholipid metabolism. Compartmental biosynthesis de novo of endonuclear phosphatidylcholine contrasts with import of phosphatidylinositol synthesized elsewhere. However, irrespective of the precise temporal-spatial-dynamic relationships underpinning phospholipid acquisition, derangement of endonuclear lipid-mediated signaling from these parental phospholipids halts cell growth and division indicating a pivotal control point. This in turn defines the manipulation of compartmentalized endonuclear phospholipid acquisition and metabolism as intriguing potential targets for the development of future antiproliferative strategies.     

Imaging mass spectrometry for lipidomics

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is a powerful tool that enables the simultaneous detection and identification of biomolecules in analytes. MALDI-imaging mass spectrometry (MALDI-IMS) is a two-dimensional MALDI-MS technique used to visualize the spatial distribution of biomolecules without extraction, purification, separation, or labeling of biological samples. This technique can reveal the distribution of hundreds of ion signals in a single measurement and also helps in understanding the cellular profile of the biological system. MALDI-IMS has already revealed the characteristic distribution of several kinds of lipids in various tissues. The versatility of MALDI-IMS has opened a new frontier in several fields, especially in lipidomics. In this review, we describe the methodology and applications of MALDI-IMS to biological samples.     

Stable isotope analysis of dynamic lipidomics

Metabolic pathway flux is a fundamental element of biological activity, which can be quantified using a variety of mass spectrometric techniques to monitor incorporation of stable isotope-labelled substrates into metabolic products. This article contrasts developments in electrospray ionisation mass spectrometry (ESI-MS) for the measurement of lipid metabolism with more established gas chromatography mass spectrometry and isotope ratio mass spectrometry methodologies. ESI-MS combined with diagnostic tandem MS/MS scans permits the sensitive and specific analysis of stable isotope-labelled substrates into intact lipid molecular species without the requirement for lipid hydrolysis and derivatisation. Such dynamic lipidomic methodologies using non-toxic stable isotopes can be readily applied to quantify lipid metabolic fluxes in clinical and metabolic studies in vivo. However, a significant current limitation is the absence of appropriate software to generate kinetic models of substrate incorporation into multiple products in the time domain. Finally, we discuss the future potential of stable isotope-mass spectrometry imaging to quantify the location as well as the extent of lipid synthesis. This article is part of a Special Issue entitled: BBALIP_Lipidomics Opinion Articles edited by Sepp Kohlwein.     

Oxidative lipidomics of gamma-irradiation-induced intestinal injury

Although gamma-irradiation-induced tissue injury has been associated with lipid peroxidation, the individual phospholipid molecular targets have not been identified. We employed oxidative lipidomics to qualitatively and quantitatively characterize phospholipid peroxidation in a radiosensitive tissue, the small intestine, of mice exposed to total body irradiation (TBI) (10 and 15 Gy). Using electrospray ionization mass spectrometry we found that the major classes of intestine phospholipids-phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine, and phosphatidylinositol-included clusters with highly oxidizable molecular species containing docosahexaenoic fatty acid. Molecular species of cardiolipin were represented by only two major less oxidizable individual molecular species-tetralinoleoylcardiolipin and trilinoleoyl-mono-oleoylcardiolipin. Selective and robust oxidation of two anionic phospholipids-cardiolipin in mitochondria and phosphatidylserine outside of mitochondria-was observed 24 h after gamma-irradiation. MS analysis detected several TBI-induced molecular species of oxidized cardiolipin: (C(18:2))(3)(C(18:2)-OOH), (C(18:2))(2)(C(18:2)-OOH)(2), (C(18:2))(1)(C(18:2)-OOH)(3), and (C(18:2)-OOH)(4). The major molecular species involved in TBI-triggered peroxidation of phosphatidylserine included C(18:0)/C(22:6)-OOH, C(18:0)/C(22:5)-OOH, and C(18:0)/C(22:4)-OOH. More abundant phospholipids-phosphatidylcholine and phosphatidylethanolamine-did not reveal any oxidative stress responses despite the presence of highly oxidizable docosahexaenoic fatty acid residues in their molecular species. A marked activation of caspases 3/7 that was detected in the intestine of gamma-irradiated mice indicates the involvement of apoptotic cell death in the TBI injury. Given that oxidized molecular species of cardiolipin and phosphatidylserine accumulate during apoptosis of different cells in vitro we speculate that cardiolipin and phosphatidylserine oxidation products may be useful as potential biomarkers of gamma-irradiation-induced intestinal apoptosis in vivo and may represent a promising target for the discovery of new radioprotectors and radiosensitizers.     

Genomic insights into mediator lipidomics

G protein-coupled receptors (GPCR) are used ubiquitously and widely for signal transduction across the plasma membrane. The ligands for GPCRs are structurally diverse and include peptides, odorants, photon, ions and lipids. It is thought that GPCRs evolved by gene duplication and mutational events that diversified the ligand binding and signaling properties, thereby resulting in paralogues in various organisms. Genomic sequencing efforts of various organisms indicate that GPCRs evolved very early in evolution; for example, unicellular eukaryotes use GPCRs for mating, differentiation and sporulation responses and prokarotes utilize these receptors for phototransduction, as exemplified by the bacteriorhodopsin, a photon sensor. Many GPCRs fall into subfamilies, usually determined by structural similarity to their ligands. Bioactive lipids such as lysophospholipids, eicosanoids, ether lipids and endocannabinoids, which are produced widely in evolution, also signal through GPCRs. Thus, distinct subfamilies of bioactive lipid GPCRs, such as prostanoid receptors, lysophosphatidic, sphingosine 1-phosphate, leukotrienes, hydroxy fatty acids, endocannabinoids and ether lipids exist in the mammalian genome. With the increasing availability of genomic information throughout the phylogenetic tree, orthologues of bioactive lipid receptors are found in the genomes of vertebrates and chordates but not in worms, flies or other lower organisms. This is in contrast to GPCRs for biogenic amines and polypeptide growth factors, which are conserved in invertebrates as well. Thus, it appears that with the evolution of chordates, lipids may have acquired novel roles in cell-cell communication events via GPCRs. This hypothesis will be discussed using the prostanoid and lysophospholipid signaling systems. Since such bioactive lipids play critical roles in immune, vascular and nervous systems, this suggests that lipid metabolite signaling via the GPCRs co-evolved with the development of sophisticated vascular, immune and nervous systems in chordates and vertebrates.