Dynamic simulation of cardiolipin remodeling: greasing the wheels for an interpretative approach to lipidomics

Abstract

Lipids are critical for the regulation and control of cellular function, membrane dynamics, and signal transduction. The systematic identifi cation and analysis of all cellular lipids in a biological sample is embodied by the rapidly developing fi eld of lipidomics, which has been enabled by recent advances in mass spectrometry ( 1-3 ). A multidimensional MS-based shotgun lipidomics (MDMS-SL) approach for analysis of cellular lipidomes has been demonstrated as one of the most systematic and quantitative high-throughput platforms for global lipidomics capable of analyzing thousands of lipid molecular species directly from the lipid extracts of biological tissues ( 4, 5 ). Analysis of lipidomic data requires extensive use of bioinformatics and computational algorithms for the accurate identifi cation and quantifi cation of lipid molecular species and classes ( 5-9 ). However, most advances in bioinformatics in lipidomics have largely focused on lipid identifi cation rather than interpretation of alterations in biological function resulting in adaptive or pathologic changes in lipid metabolism ( 10 ). Thus, development of bioinformatic and systems biology approaches for the interpretation of lipidomic networks would signifi cantly advance the understanding of the roles of lipids in biological systems ( 3 ).Cardiolipin is a complex polyglycerophospholipid found almost exclusively in mitochondrial membranes of eukaryotic organisms ( 11 ). Cardiolipin is intricately involved in the effi cient production of ATP through utilizing the proton gradient as well as maintaining mitochondrial functionality ( 12-14 ). The diversity of cardiolipin molecular species varies markedly between tissues as well as among Abstract Cardiolipin is a class of mitochondrial specifi c phospholipid, which is intricately involved in mitochondrial functionality. Differences in cardiolipin species exist in a variety of tissues and diseases. It has been demonstrated that the cardiolipin profi le is a key modulator of the functions of many mitochondrial proteins. However, the chemical mechanism(s) leading to normal and/or pathological distribution of cardiolipin species remain elusive. Herein, we describe a novel approach for investigating the molecular mechanism of cardiolipin remodeling through a dynamic simulation. This approach applied data from shotgun lipidomic analyses of the heart, liver, brain, and lung mitochondrial lipidomes to model cardiolipin remodeling, including relative content, regiospecifi city, and isomeric composition of cardiolipin species. Generated cardiolipin profi les were nearly identical to those determined by shotgun lipidomics. Importantly, the simulated isomeric compositions of cardiolipin species were further substantiated through product ion analysis. Finally, unique enzymatic activities involved in cardiolipin remodeling were assessed from the parameters used in the dynamic simulation of cardiolipin profi les. Collectively, we described, verifi ed, and demonstrated a novel approach by integrating both lipidomic ana...

Simulation of triacylglycerol ion profiles: bioinformatics for interpretation of triacylglycerol biosynthesis

“…Identifi cation and quantifi cation of lipid molecular species were performed using an automated software program as previously described ( 15 ). Lipid extraction for acyl-CoA analysis, and identifi cation and quantifi cation of acyl-CoA species by matrix-assisted laser desorption/ionization time-of-fl ight mass spectrometry were performed as we previously described ( 20 ). The results are included in supplementary Table I for comparison.…”

Dysfunctional cardiac mitochondrial bioenergetic, lipidomic, and signaling in a murine model of Barth syndrome

“…Lipidomic analyses were performed as previously described, using a modifi ed Bligh and Dyer extraction protocol (26)(27)(28). Individual lipid extracts were reconstituted with 1:1 (v/v) CHCl 3 /CH 3 OH, fl ushed with nitrogen, and stored at Ϫ 20°C prior to electrospray ionization-MS using a TSQ Quantum Ultra Plus triple-quadrupole mass spectrometer (Thermo Fisher Scientific, San Jose, CA) equipped with an automated nanospray apparatus (Advion Biosciences Ltd., Ithaca, NY) and customized sequence subroutine operated under Xcalibur software.…”

Myocardial Regulation of Lipidomic Flux by Cardiolipin Synthase

“…Lipidomic analyses were performed as described previously (25,36,38). Individual lipid extracts were reconstituted with 1:1 (v/v) CHCl 3 /CH 3 OH, flushed with nitrogen, and stored at Ϫ20°C prior to electrospray ionization-MS using a TSQ Quantum Ultra Plus triple-quadrupole mass spectrometer (Thermo Fisher Scientific, San Jose, CA) equipped with an automated nanospray apparatus (Advion Biosciences Ltd., Ithaca, NY) and customized sequence subroutine operated under Xcalibur software.…”

“…Nascent CL molecular species are subsequently remodeled by the sequential actions of phospholipase to form monolysocardiolipin followed by reacylation to form mature CL molecular species by remodeling enzymes, such as tafazzin, ALCAT1, or MLCAT (22)(23)(24). Although the molecular species compositions of CL vary between tissues, the predominant mature form of CL in myocardium is tetralinoleic (18:2) CL, which has been implicated in maximizing bioenergetic efficiency (25)(26)(27)(28). Degradation of CL occurs through phospholipase A 2 -mediated hydrolysis to form monolysocardiolipin and dilysocardiolipin and through mitochondrial phospholipase D activation to form phosphatidic acid (5,29).…”