Taking aim at cell lipids: shotgun lipidomics and imaging mass spectrometry push the boundaries

Statistical analysis of the processes controlling choline and ethanolamine glycerophospholipid molecular species composition

The regulation and maintenance of the cellular lipidome through biosynthetic, remodeling, and catabolic mechanisms are critical for biological homeostasis during development, health and disease. These complex mechanisms control the architectures of lipid molecular species, which have diverse yet highly regulated fatty acid chains at both the sn1 and sn2 positions. Phosphatidylcholine (PC) and phosphatidylethanolamine (PE) serve as the predominant biophysical scaffolds in membranes, acting as reservoirs for potent lipid signals and regulating numerous enzymatic processes. Here we report the first rigorous computational dissection of the mechanisms influencing PC and PE molecular architectures from high-throughput shotgun lipidomic data. Using novel statistical approaches, we have analyzed multidimensional mass spectrometry-based shotgun lipidomic data from developmental mouse heart and mature mouse heart, lung, brain, and liver tissues. We show that in PC and PE, sn1 and sn2 positions are largely independent, though for low abundance species regulatory processes may interact with both the sn1 and sn2 chain simultaneously, leading to cooperative effects. Chains with similar biochemical properties appear to be remodeled similarly. We also see that sn2 positions are more regulated than sn1, and that PC exhibits stronger cooperative effects than PE. A key aspect of our work is a novel statistically rigorous approach to determine cooperativity based on a modified Fisher's exact test using Markov Chain Monte Carlo sampling. This computational approach provides a novel tool for developing mechanistic insight into lipidomic regulation.

Multi-dimensional mass spectrometry-based shotgun lipidomics and novel strategies for lipidomic analyses

Since our last comprehensive review on multi-dimensional mass spectrometry-based shotgun lipidomics (Mass Spectrom. Rev. 24 (2005), 367), many new developments in the field of lipidomics have occurred. These developments include new strategies and refinements for shotgun lipidomic approaches that use direct infusion, including novel fragmentation strategies, identification of multiple new informative dimensions for mass spectrometric interrogation, and the development of new bioinformatic approaches for enhanced identification and quantitation of the individual molecular constituents that comprise each cell's lipidome. Concurrently, advances in liquid chromatography-based platforms and novel strategies for quantitative matrix-assisted laser desorption/ionization mass spectrometry for lipidomic analyses have been developed. Through the synergistic use of this repertoire of new mass spectrometric approaches, the power and scope of lipidomics has been greatly expanded to accelerate progress toward the comprehensive understanding of the pleiotropic roles of lipids in biological systems.

Profiling the regulatory lipids: another systemic way to unveil the biological mystery

PURPOSE OF REVIEW

The regulatory lipids are a class of bioactive lipids which regulate various important biological processes. Profiling these regulatory lipids is an attractive method to understand the role of these metabolites. This is especially true because most of these regulatory lipids are derived from several important pharmacological targets: cyclooxygenase, lipoxygenase, and cytochrome P450 enzymes. This review highlights the development of methods to profile these regulatory lipids and the recent publications employing these profiling methods.

RECENT FINDINGS

The recent development of methods for the profiling of regulatory lipids target two different directions: to expand coverage for discovery studies (fingerprinting) and to make the quantitative method more accurate, sensitive, and faster for diagnostic or more detailed studies. Recent applications of these profiling methods including assessment of in-vivo drug engagement, pathways crosstalk, and possible mechanisms for side-effects of a withdrawn anti-inflammatory drug rofecoxib are also reviewed here.

SUMMARY

The profiling of regulatory lipids is a useful tool for many investigations. The breadth of coverage, throughput limits with detection, and reproducibility of quantitation are being improved. The resulting data will assist with fundamental investigation, disease biomarker discovery, drug discovery, and drug development.

A lipid matrix model of membrane raft structure

Domains in cell membranes are created by lipid-lipid interactions and are referred to as membrane rafts. Reliable isolation methods have been developed which have shown that rafts from the same membranes have different proteins and can be sub-fractionated by immunoaffinity methods. Analysis of these raft subfractions shows that they are also comprised of different molecular species of lipids. The major lipid classes present are phospholipids, glycosphingolipids and cholesterol. Model studies show that mixtures of phospholipids, particularly sphingomyelin, and cholesterol form liquid-ordered phase with properties intermediate between a gel and fluid phase. This type of liquid-ordered phase dominates theories of domain formation and raft structure in biological membranes. Recently it has been shown that sphingolipids with long (22-26C) N-acyl fatty acids form quasi-crystalline bilayer structures with diacylphospholipids that have well-defined stoichiometries. A two tier heuristic model of membrane raft structure is proposed in which liquid-ordered phase created by a molecular complex between sphingolipids with hydrocarbon chains of approximately equal length and cholesterol acts as a primary staging area for selecting raft proteins. Tailoring of the lipid anchors of raft proteins takes place at this site. Assembly of lipid-anchored proteins on a scaffold of sphingolipids with asymmetric hydrocarbon chains and phospholipids arranged in a quasi-crystalline bilayer structure serves to concentrate and orient the proteins in a manner that couples them functionally within the membrane. Specificity is inherent in the quasi-crystalline lipid structure of liquid-ordered matrices formed by both types of complex into which protein lipid anchors are interpolated. An interaction between the sugar residues of the glycolipids and the raft proteins provides an additional level of specificity that distinguishes one raft from another.