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1.  Eicosanoid Storm in Infection and Inflammation 
Nature reviews. Immunology  2015;15(8):511-523.
Controlled immune responses to infection and injury involve complex molecular signaling networks with coordinated and often opposing actions. Eicosanoids and related bioactive lipid mediators derived from polyunsaturated fatty acids constitute a major bioactive lipid network, which is among the most complex and challenging pathways to map in a physiological context. Eicosanoid signaling, similar to cytokine signaling and inflammasome formation, has been viewed as primarily a pro-inflammatory component of the innate immune response; however, recent advances in lipidomics have helped to elucidate unique eicosanoids and related docosanoids with anti-inflammatory and pro-resolution functions. This has advanced our overall understanding of the inflammatory response and its therapeutic implications. The induction of a pro- and anti-inflammatory eicosanoid storm through the activation of inflammatory receptors by infectious agents is reviewed.
doi:10.1038/nri3859
PMCID: PMC4606863  PMID: 26139350
2.  Release and Capture of Bioactive Oxidized Phospholipids and Oxidized Cholesteryl Esters During Percutaneous Coronary and Peripheral Arterial Interventions in Humans 
Objective
To assess whether oxidized lipids are released downstream from obstructive plaques following percutaneous coronary and peripheral interventions using distal protection devices.
Background
Oxidation of lipoproteins generates multiple bioactive oxidized lipids that affect atherothrombosis and endothelial function. Direct evidence of their role during therapeutic procedures, which may result in no-reflow phenomenon, myocardial infarction and stroke, is lacking.
Methods
The presence of specific oxidized lipids was assessed in embolized material captured by distal protection filter devices during uncomplicated saphenous vein graft, carotid, renal, and superficial femoral artery interventions. The presence of oxidized phospholipids (OxPL) and oxidized cholesteryl esters (OxCE) was evaluated in 24 filters using liquid chromatography, tandem mass spectrometry, enzyme-linked immunosorbent assays (ELISA) and immunostaining.
Results
Phosphatidylcholine (PC)-containing OxPL (PC-OxPL), including PONPC [1-palmitoyl-2-(9-oxononanayl) PC], representing a major PC-OxPL molecule quantitated within plaque material, POVPC [1-palmitoyl-2-(5-oxovaleroyl)-sn-glycero-3-phosphocholine] and PGPC (1-palmitoyl-2-glutaroyl-sn -glycero-3-phosphocholine) were identified in the extracted lipid portion from all vascular beds. Several species of OxCE, such as keto, hydroperoxide, hydroxy, and epoxy cholesterol ester derivatives from cholesteryl linoleate and cholesteryl arachidonate were also present. The presence of OxPL was confirmed using enzyme linked immunoassays and immunohistochemistry of captured material.
Conclusion
This study documents the direct release and capture of OxPL and OxCE during percutaneous interventions from multiple arterial beds in humans. Entrance of bioactive oxidized lipids into the microcirculation may mediate adverse clinical outcomes during therapeutic procedures.
doi:10.1016/j.jacc.2014.01.055
PMCID: PMC4629781  PMID: 24613321
oxidized phospholipids; oxidized cholesterol esters; lipoproteins; angioplasty
3.  Targeted Deletion and Lipidomic Analysis Identify Epithelial Cell COX-2 as a Major Driver of Chemically-induced Skin Cancer 
Molecular cancer research : MCR  2014;12(11):1677-1688.
Pharmacologic and global gene deletion studies demonstrate that cyclooxygenase-2 (PTGS2/COX2) plays a critical role in DMBA/TPA-induced skin tumor induction. While many cell types in the tumor microenvironment express COX-2, the cell types in which COX-2 expression is required for tumor promotion are not clearly established. Here, cell-type specific Cox-2 gene deletion reveals a vital role for skin epithelial cell COX-2 expression in DMBA/TPA tumor induction. In contrast, myeloid Cox-2 gene deletion has no effect on DMBA/TPA tumorigenesis. The infrequent, small tumors that develop on mice with an epithelial cell-specific Cox-2 gene deletion have decreased proliferation and increased cell differentiation properties. Blood vessel density is reduced in tumors with an epithelial cell-specific Cox-2 gene deletion, compared to littermate control tumors, suggesting a reciprocal relationship in tumor progression between COX-2 expressing tumor epithelial cells and microenvironment endothelial cells. Lipidomics analysis of skin and tumors from DMBA/TPA-treated mice suggests that the prostaglandins PGE2 and PGF2α are likely candidates for the epithelial cell COX-2-dependent eicosanoids that mediate tumor progression. This study both illustrates the value of cell-type specific gene deletions in understanding the cellular roles of signal-generating pathways in complex microenvironments and emphasizes the benefit of a systems-based lipidomic analysis approach to identify candidate lipid mediators of biological responses.
doi:10.1158/1541-7786.MCR-14-0397-T
PMCID: PMC4233191  PMID: 25063587
COX-2; cyclooxygenase; DMBA/TPA-induced skin cancer; lipidomics
4.  Comprehensive Ultra Performance Liquid Chromatographic Separation and Mass Spectrometric Analysis of Eicosanoid Metabolites Suitable for Human Materials 
Journal of chromatography. A  2014;1359:60-69.
Over the past decade, the number of known eicosanoids has expanded immensely and we have now developed an ultra-performance liquid chromatography - electrospray ionization triple quadrupole mass spectrometric (UPLC-QTRAP/MS/MS) method to monitor and quantify numerous eicosanoids. The UPLC-QTRAP/MS/MS approach utilizes scheduled multiple reaction monitoring (MRM) to optimize sensitivity, number of metabolites that can be analyzed and the time requirement of the analysis. A total of 184 eicosanoids including 26 deuterated internal standards can be separated and monitored in a single 5 min UPLC run. To demonstrate a practical application, human plasma samples were analyzed following solid-phase extraction (SPE) and the recovery rate and matrix effects were determined for the 26 deuterated internal standards added to the plasma. The method was validated and shown to be sensitive with the limit of quantitation at pg levels for most compounds, accurate with recovery rates of 70-120%, and precise with a CV<30 for all compounds. Also, the method showed a linear response over a range spanning several orders of magnitude. In a QC human plasma sample, we identified and rigorously quantified over 120 eicosanoids.
doi:10.1016/j.chroma.2014.07.006
PMCID: PMC4592635  PMID: 25074422
Eicosanoids; Ultra-performance liquid chromatography; Tandem mass spectrometry; Plasma; Lipidomics
5.  Cell-type-specific roles for COX-2 in UVB-induced skin cancer 
Carcinogenesis  2014;35(6):1310-1319.
In human tumors, and in mouse models, cyclooxygenase-2 (COX-2) levels are frequently correlated with tumor development/burden. In addition to intrinsic tumor cell expression, COX-2 is often present in fibroblasts, myofibroblasts and endothelial cells of the tumor microenvironment, and in infiltrating immune cells. Intrinsic cancer cell COX-2 expression is postulated as only one of many sources for prostanoids required for tumor promotion/progression. Although both COX-2 inhibition and global Cox-2 gene deletion ameliorate ultraviolet B (UVB)-induced SKH-1 mouse skin tumorigenesis, neither manipulation can elucidate the cell type(s) in which COX-2 expression is required for tumorigenesis; both eliminate COX-2 activity in all cells. To address this question, we created Cox-2 flox/flox mice, in which the Cox-2 gene can be eliminated in a cell-type-specific fashion by targeted Cre recombinase expression. Cox-2 deletion in skin epithelial cells of SKH-1 Cox-2 flox/flox;K14Cre + mice resulted, following UVB irradiation, in reduced skin hyperplasia and increased apoptosis. Targeted epithelial cell Cox-2 deletion also resulted in reduced tumor incidence, frequency, size and proliferation rate, altered tumor cell differentiation and reduced tumor vascularization. Moreover, Cox-2 flox/flox;K14Cre + papillomas did not progress to squamous cell carcinomas. In contrast, Cox-2 deletion in SKH-1 Cox-2 flox/flox; LysMCre + myeloid cells had no effect on UVB tumor induction. We conclude that (i) intrinsic epithelial COX-2 activity plays a major role in UVB-induced skin cancer, (ii) macrophage/myeloid COX-2 plays no role in UVB-induced skin cancer and (iii) either there may be another COX-2-dependent prostanoid source(s) that drives UVB skin tumor induction or there may exist a COX-2-independent pathway(s) to UVB-induced skin cancer.
doi:10.1093/carcin/bgu020
PMCID: PMC4043244  PMID: 24469308
6.  A Lipidomic Perspective on Inflammatory Macrophage Eicosanoid Signaling 
Macrophages are central to essential physiological processes including the regulation of innate and adaptive immunity, but they are also central to a number of inflammatory disease states. These immune cells also possess remarkable plasticity and display various shades of functionalities based on changes in the surrounding molecular environment. Macrophage biology has defined various phenotypes and roles in inflammation based primarily on cytokine and chemokine profiles of cells in different activation states. Importantly, macrophages are elite producers of eicosanoids and other related lipid mediators during inflammation, but specific roles of these molecules have not generally been incorporated into the larger context of macrophage biology. In this review, we discuss the current classification of macrophage types and their roles in inflammation and disease, along with the practical challenges of studying biologically relevant phenotypes ex vivo. Using the latest advances in eicosanoid lipidomics, we highlight several key studies from our laboratory that provide a comprehensive understanding of how eicosanoid metabolism differs between macrophage phenotypes, along with how this metabolism is altered by changes in membrane fatty acid distribution and varied durations of Toll-like receptor (TLR) priming. In conclusion, we summarize several examples of the benefit of macrophage plasticity to develop accurate cellular mechanisms of lipid metabolism, and insights from lipidomic analyses about the differences in eicosanoid pathway enzyme activity in vitro vs. ex vivo cell studies. Examples of new techniques to further understand the role of macrophage eicosanoid signaling in vivo are also discussed.
doi:10.1016/j.jbior.2013.09.009
PMCID: PMC3946543  PMID: 24113376
7.  NCoR REPRESSION OF LXRs RESTRICTS MACROPHAGE BIOSYNTHESIS OF INSULIN-SENSITIZING OMEGA 3 FATTY ACIDS 
Cell  2013;155(1):200-214.
Macrophage-mediated inflammation is a major contributor to obesity-associated insulin resistance. The co-repressor NCoR interacts with inflammatory pathway genes in macrophages, suggesting that its removal would result in increased activity of inflammatory responses. Surprisingly, we find that macrophage-specific deletion of NCoR instead results in an anti-inflammatory phenotype along with robust systemic insulin sensitization in obese mice. We present evidence that de-repression of LXRs contributes to this paradoxical anti-inflammatory phenotype by causing increased expression of genes that direct biosynthesis of palmitoleic acid and ω3 fatty acids. Remarkably, the increased ω3 fatty acid levels primarily inhibit NF-κB-dependent inflammatory responses by uncoupling NF-κB binding and enhancer/promoter histone acetylation from subsequent steps required for pro-inflammatory gene activation. This provides a mechanism for the in vivo anti-inflammatory insulin sensitive phenotype observed in mice with macrophage-specific deletion of NCoR. Therapeutic methods to harness this mechanism could lead to a new approach to insulin sensitizing therapies.
doi:10.1016/j.cell.2013.08.054
PMCID: PMC4131699  PMID: 24074869
nuclear co-repressor; insulin resistance; obesity; macrophage; inflammation
8.  New potent and selective polyfluoroalkyl ketone inhibitors of GVIA calcium-independent phospholipase A2 
Bioorganic & medicinal chemistry  2013;21(18):10.1016/j.bmc.2013.07.010.
Group VIA calcium-independent phospholipase A2 (GVIA iPLA2) has recently emerged as an important pharmaceutical target. Selective and potent GVIA iPLA2 inhibitors can be used to study its role in various neurological disorders. In the current work, we explore the significance of the introduction of a substituent in previously reported potent GVIA iPLA2 inhibitors. 1,1,1,2,2-Pentafluoro-7-(4-methoxyphenyl)heptan-3-one (GK187) is the most potent and selective GVIA iPLA2 inhibitor ever reported with a XI(50) value of 0.0001, and with no significant inhibition against GIVA cPLA2 or GV sPLA2. We also compare the inhibition of two difluoromethyl ketones on GVIA iPLA2, GIVA cPLA2, and GV sPLA2.
doi:10.1016/j.bmc.2013.07.010
PMCID: PMC3883354  PMID: 23916152
Phospholipase A2; Inhibitor; GVIA iPLA2; Polyfluoroalkyl ketone; Pentafluoroethyl ketones
9.  Lipidomics Technologies at the End of the First Decade and the Beginning of the Next123 
Advances in Nutrition  2013;4(5):565-567.
The lipidome is composed of all of the biomolecules defined as lipids, which encompass compounds of amazing structural diversity and complexity. It has been ∼1 decade since the study of “lipidomics” was begun in earnest, and the technologies and tools for data analysis have advanced considerably over this period. This workshop summarized the scope of the lipidome and technologies for its analysis, lipidomics databases and other online tools, and examples of the application of lipidomics to nutritional research. The slides from the workshop, online lipidomics tools, and databases are available at http://www.lipidmaps.org.
doi:10.3945/an.113.004333
PMCID: PMC3771151  PMID: 24038259
10.  Lipidomic Profiling of Influenza Infection Identifies Mediators that Induce and Resolve Inflammation 
Cell  2013;154(1):213-227.
Summary
Bioactive lipid mediators play a crucial role in the induction and resolution of inflammation. To elucidate their involvement during influenza infection, LC/MS lipidomic profiling of 141 lipid species was performed on a mouse influenza model using two viruses of significantly different pathogenicity. Infection by the low pathogenicity strain, X31/H3N2, induced a pro-inflammatory response followed by a distinct anti-inflammatory response; infection by the high pathogenicity strain, PR8/H1N1, resulted in overlapping pro- and anti-inflammatory states. Integration of the large-scale lipid measurements with targeted gene expression data demonstrated that 5 lipoxygenase metabolites correlated with the pathogenic phase of the infection whereas 12/15-lipoxygenase metabolites were associated with the resolution phase. Hydroxylated linoleic acid, specifically the ratio of 13- to 9-HODE, was identified as a potential biomarker for immune status during an active infection. Importantly, some of the findings from the animal model were recapitulated in studies of human nasopharyngeal lavages obtained during the 2009–2011 influenza seasons.
doi:10.1016/j.cell.2013.05.052
PMCID: PMC3753192  PMID: 23827684
11.  Inflammatory hyperalgesia induces essential bioactive lipid production in the spinal cord 
Journal of neurochemistry  2010;114(4):981-993.
Lipid molecules play an important role in regulating the sensitivity of sensory neurons and enhancing pain perception, and growing evidence indicates that the effect occurs both at the site of injury and in the spinal cord. Using high-throughput mass spectrometry methodology, we sought to determine the contribution of spinal bioactive lipid species to inflammation-induced hyperalgesia in rats. Quantitative analysis of cerebrospinal fluid (CSF) and spinal cord tissue for eicosanoids, ethanolamides and fatty acids revealed the presence of 102 distinct lipid species. After induction of peripheral inflammation by intraplantar injection of carrageenan to the ipsilateral hind paw, lipid changes in cyclooxygenase (COX) and 12-lipoxygenase (12-LOX) signaling pathways peaked at 4 hours in the CSF. In contrast, changes occurred in a temporally disparate manner in the spinal cord with LOX-derived hepoxilins (HX) followed by COX-derived prostaglandin (PG) E2, and subsequently the ethanolamine anandamide (AEA). Systemic treatment with the mu opioid agonist morphine, the COX inhibitor ketorolac, or the LOX inhibitor NDGA significantly reduced tactile allodynia, while their effects on the lipid metabolites were different. Morphine did not alter the lipid profile in the presence or absence of carrageenan inflammation. Ketorolac caused a global reduction in eicosanoid metabolism in naïve animals that remained suppressed following injection of carrageenan. NDGA-treated animals also displayed reduced basal levels of COX and 12-LOX metabolites, but only 12-LOX metabolites remained decreased after carrageenan treatment. These findings suggest that both COX and 12-LOX play an important role in the induction of carrageenan-mediated hyperalgesia through these pathways.
doi:10.1111/j.1471-4159.2010.06815.x
PMCID: PMC3994888  PMID: 20492349
12.  LIPID MAPS-Nature Lipidomics Gateway: An Online Resource for Students and Educators Interested in Lipids 
Journal of chemical education  2011;89(2):291-292.
The LIPID MAPS-Nature Lipidomics Gateway is a free, comprehensive online resource providing tutorials and instructional material, experimental data for lipids and genes along with protocols and standards, databases of lipid structures and lipid-associated genes or proteins, and a variety of lipidomics tools.
doi:10.1021/ed200088u
PMCID: PMC3995124  PMID: 24764601
Graduate Education/Research; Upper-Division Undergraduate; Biochemistry; Interdisciplinary/Multidisciplinary; Computer-Based Learning; Internet/Web-Based Learning; Lipids; Mass Spectrometry
13.  Polyoxygenated Cholesterol Ester Hydroperoxide Activates TLR4 and SYK Dependent Signaling in Macrophages 
PLoS ONE  2013;8(12):e83145.
Oxidation of low-density lipoprotein (LDL) is one of the major causative mechanisms in the development of atherosclerosis. In previous studies, we showed that minimally oxidized LDL (mmLDL) induced inflammatory responses in macrophages, macropinocytosis and intracellular lipid accumulation and that oxidized cholesterol esters (OxCEs) were biologically active components of mmLDL. Here we identified a specific OxCE molecule responsible for the biological activity of mmLDL and characterized signaling pathways in macrophages in response to this OxCE. Using liquid chromatography – tandem mass spectrometry and biological assays, we identified an oxidized cholesteryl arachidonate with bicyclic endoperoxide and hydroperoxide groups (BEP-CE) as a specific OxCE that activates macrophages in a TLR4/MD-2-dependent manner. BEP-CE induced TLR4/MD-2 binding and TLR4 dimerization, phosphorylation of SYK, ERK1/2, JNK and c-Jun, cell spreading and uptake of dextran and native LDL by macrophages. The enhanced macropinocytosis resulted in intracellular lipid accumulation and macrophage foam cell formation. Bone marrow-derived macrophages isolated from TLR4 and SYK knockout mice did not respond to BEP-CE. The presence of BEP-CE was demonstrated in human plasma and in the human plaque material captured in distal protection devices during percutaneous intervention. Our results suggest that BEP-CE is an endogenous ligand that activates the TLR4/SYK signaling pathway. Because BEP-CE is present in human plasma and human atherosclerotic lesions, BEP-CE-induced and TLR4/SYK-mediated macrophage responses may contribute to chronic inflammation in human atherosclerosis.
doi:10.1371/journal.pone.0083145
PMCID: PMC3871536  PMID: 24376657
14.  Regulated accumulation of desmosterol integrates macrophage lipid metabolism and inflammatory responses 
Cell  2012;151(1):138-152.
Summary
Inflammation and macrophage foam cells are characteristic features of atherosclerotic lesions, but the mechanisms linking cholesterol accumulation to inflammation and LXR-dependent response pathways are poorly understood. To investigate this relationship, we utilized lipidomic and transcriptomic methods to evaluate the effect of diet and LDL receptor genotype on macrophage foam cell formation within the peritoneal cavities of mice. Foam cell formation was associated with significant changes in hundreds of lipid species and unexpected suppression, rather than activation, of inflammatory gene expression. We provide evidence that regulated accumulation of desmosterol underlies many of the homeostatic responses observed in macrophage foam cells, including activation of LXR target genes, inhibition of SREBP target genes, selective reprogramming of fatty acid metabolism and suppression of inflammatory response genes. These observations suggest that macrophage activation in atherosclerotic lesions results from extrinsic, pro-inflammatory signals generated within the artery wall that suppress homeostatic and anti-inflammatory functions of desmosterol.
doi:10.1016/j.cell.2012.06.054
PMCID: PMC3464914  PMID: 23021221
15.  Insertion of the Ca2+-Independent Phospholipase A2 into a Phospholipid Bilayer via Coarse-Grained and Atomistic Molecular Dynamics Simulations 
PLoS Computational Biology  2013;9(7):e1003156.
Group VI Ca2+-independent phospholipase A2 (iPLA2) is a water-soluble enzyme that is active when associated with phospholipid membranes. Despite its clear pharmaceutical relevance, no X-ray or NMR structural information is currently available for the iPLA2 or its membrane complex. In this paper, we combine homology modeling with coarse-grained (CG) and all-atom (AA) molecular dynamics (MD) simulations to build structural models of iPLA2 in association with a phospholipid bilayer. CG-MD simulations of the membrane insertion process were employed to provide a starting point for an atomistic description. Six AA-MD simulations were then conducted for 60 ns, starting from different initial CG structures, to refine the membrane complex. The resulting structures are shown to be consistent with each other and with deuterium exchange mass spectrometry (DXMS) experiments, suggesting that our approach is suitable for the modeling of iPLA2 at the membrane surface. The models show that an anchoring region (residues 710–724) forms an amphipathic helix that is stabilized by the membrane. In future studies, the proposed iPLA2 models should provide a structural basis for understanding the mechanisms of lipid extraction and drug-inhibition. In addition, the dual-resolution approach discussed here should provide the means for the future exploration of the impact of lipid diversity and sequence mutations on the activity of iPLA2 and related enzymes.
Author Summary
The Ca2+-independent phospholipase A2 (iPLA2) enzyme is a potential target for the development of medicinal agents against heart and neurological diseases, multiple sclerosis, arthritis, and cancer. However, no structural information is currently available for the iPLA2. The binding of the enzyme to human membranes is driven by favorable electrostatic and non-polar interactions, but the detailed influence of these factors is not well understood. In this paper, we have combined coarse-grained and all-atom simulations of a homology model of the iPLA2. The coarse-grained description allows highly efficient simulations of the protein insertion into a lipid bilayer, while the all-atom simulations are used to refine the structures of the protein–membrane complexes. Finally, the resulting structures are validated experimentally with deuterium exchange experiments. In future works, this approach could be used to build models of other PLA2s. The iPLA2 models presented here open the door to the computational design of new inhibitors with improved potency and selectivity.
doi:10.1371/journal.pcbi.1003156
PMCID: PMC3723492  PMID: 23935474
16.  Correction: Assessing Phospholipase A2 Activity toward Cardiolipin by Mass Spectrometry 
PLoS ONE  2013;8(6):10.1371/annotation/47607b18-ed69-4a08-8619-60c39bd83a13.
doi:10.1371/annotation/47607b18-ed69-4a08-8619-60c39bd83a13
PMCID: PMC3741025
18.  Assessing Phospholipase A2 Activity toward Cardiolipin by Mass Spectrometry 
PLoS ONE  2013;8(3):e59267.
Cardiolipin, a major component of mitochondria, is critical for mitochondrial functioning including the regulation of cytochrome c release during apoptosis and proper electron transport. Mitochondrial cardiolipin with its unique bulky amphipathic structure is a potential substrate for phospholipase A2 (PLA2) in vivo. We have developed mass spectrometric methodology for analyzing PLA2 activity toward various cardiolipin forms and demonstrate that cardiolipin is a substrate for sPLA2, cPLA2 and iPLA2, but not for Lp-PLA2. Our results also show that none of these PLA2s have significant PLA1 activities toward dilyso-cardiolipin. To understand the mechanism of cardiolipin hydrolysis by PLA2, we also quantified the release of monolyso-cardiolipin and dilyso-cardiolipin in the PLA2 assays. The sPLA2s caused an accumulation of dilyso-cardiolipin, in contrast to iPLA2 which caused an accumulation of monolyso-cardiolipin. Moreover, cardiolipin inhibits iPLA2 and cPLA2, and activates sPLA2 at low mol fractions in mixed micelles of Triton X-100 with the substrate 1-palmitoyl-2-arachidonyl-sn-phosphtidylcholine. Thus, cardiolipin functions as both a substrate and a regulator of PLA2 activity and the ability to assay the various forms of PLA2 is important in understanding its function.
doi:10.1371/journal.pone.0059267
PMCID: PMC3606342  PMID: 23533611
19.  Binding Conformation of 2-Oxoamide Inhibitors to Group IVA Cytosolic Phospholipase A2 Determined by Molecular Docking Combined with Molecular Dynamics 
The Group IVA cytosolic phospholipase A2 (GIVA cPLA2) plays a central role in inflammation. Long chain 2-oxoamides constitute a class of potent GIVA cPLA2 inhibitors that exhibit potent in vivo anti-inflammatory and analgesic activity. We have now gained insight into the binding of 2-oxoamide inhibitors in the GIVA cPLA2 active site through a combination of molecular docking calculations and molecular dynamics simulations. Recently, the location of the 2-oxoamide inhibitor AX007 within the active site of the GIVA cPLA2 was determined using a combination of deuterium exchange mass spectrometry followed by molecular dynamics simulations. After the optimization of the AX007-GIVA cPLA2 complex using the docking algorithm Surflex-Dock, a series of additional 2-oxoamide inhibitors have been docked in the enzyme active site. The calculated binding affinity presents a good statistical correlation with the experimental inhibitory activity (r2 = 0.76, N = 11). A molecular dynamics simulation of the docking complex of the most active compound has revealed persistent interactions of the inhibitor with the enzyme active site and proves the stability of the docking complex and the validity of the binding suggested by the docking calculations. The combination of molecular docking calculations and molecular dynamics simulations is useful in defining the binding of small-molecule inhibitors and provides a valuable tool for the design of new compounds with improved inhibitory activity against GIVA cPLA2.
doi:10.1021/ci2005093
PMCID: PMC3265118  PMID: 22196172
20.  Spinal TLR4 mediates the transition to a persistent mechanical hypersensitivity after the resolution of inflammation in serum-transferred arthritis 
Pain  2011;152(12):2881-2891.
Persistent pain after resolution of clinically appreciable signs of arthritis poses a therapeutic challenge and immunosuppressive therapies do not meet this medical need. To investigate this conversion to persistent pain, we utilized the K/BxN serum transfer arthritis model, which has persistent mechanical hypersensitivity despite the resolution of visible inflammation. Toll-like receptor (TLR) 4 has been implicated as a potential therapeutic target in neuropathic and other pain models. We compared the relative courses of serum transfer arthritis and mechanical hypersensitivity in wild type (WT) and Tlr4−/− mice. K/BxN serum transfer induced similar joint swelling and inflammation from days 4–22 in WT and Tlr4−/− mice. Unlike WT mice, Tlr4−/− mice displayed a significant reversal in mechanical hypersensitivity and diminished appearance of glial activation markers after resolution of peripheral inflammation. Intrathecal (IT) delivery of a TLR4 antagonist, LPS-RS (10μg), on days 6, 9, and 12 abrogated the transition to persistent mechanical hypersensitivity in WT arthritic mice, while later administration had no impact. We utilized a lipodomics LC/MS/MS methodology to determine spinal cord profiles of bioactive lipid species following early LPS-RS treatment compared to vehicle treated controls. WT arthritic mice had reduced spinal levels of the anti-inflammatory prostaglandin 15d-PGJ2 on day 6, compared to IT LPS-RS treated mice. Direct IT application of 15d-PGJ2 (0.5μg) on day 6 improved mechanical hypersensitivity in arthritic mice within 15 minutes. Hence, TLR4 signaling altered spinal bioactive lipid profiles in the serum transfer model and played a critical role in the transition from acute to chronic post-inflammatory mechanical hypersensitivity.
doi:10.1016/j.pain.2011.09.020
PMCID: PMC3347973  PMID: 22019135
arthritis; allodynia; astrocytes; microglia; inflammation; Toll-like receptor 4 (TLR4)
21.  The Human Plasma Lipidome 
The New England journal of medicine  2011;365(19):1812-1823.
doi:10.1056/NEJMra1104901
PMCID: PMC3412394  PMID: 22070478
22.  High Sensitivity Quantitative Lipidomics Analysis of Fatty Acids in Biological Samples by Gas Chromatography-Mass Spectrometry 
Biochimica et biophysica acta  2011;1811(11):648-656.
Historically considered to be simple membrane components serving as structural elements and energy storing entities, fatty acids are now increasingly recognized as potent signaling molecules involved in many metabolic processes. Quantitative determination of fatty acids and exploration of fatty acid profiles have become common place in lipid analysis. We present here a reliable and sensitive method for comprehensive analysis of free fatty acids and fatty acid composition of complex lipids in biological material. The separation and quantitation of fatty acids is achieved by capillary gas chromatography. The analytical method uses pentafluorobenzyl bromide derivatization and negative chemical ionization gas chromatography-mass spectrometry. The chromatographic procedure provides base line separation between saturated and unsaturated fatty acids of different chain lengths as well as between most positional isomers. Fatty acids are extracted in the presence of isotope-labeled internal standards for high quantitation accuracy. Mass spectrometer conditions are optimized for broad detection capacity and sensitivity capable of measuring trace amounts of fatty acids in complex biological samples.
doi:10.1016/j.bbalip.2011.07.006
PMCID: PMC3205314  PMID: 21787881
25.  Applications of Mass Spectrometry to Lipids and Membranes 
Annual review of biochemistry  2011;80:301-325.
Lipidomics, a major part of metabolomics, constitutes the detailed analysis and global characterization, both spatial and temporal, of the structure and function of lipids (the lipidome) within a living system. As with proteomics, mass spectrometry has earned a central analytical role in lipidomics, and this role will continue to grow with technological developments. Currently, there exist two mass spectrometry-based lipidomics approaches, one based on a division of lipids into categories and classes prior to analysis, the “comprehensive lipidomics analysis by separation simplification” (CLASS), and the other in which all lipid species are analyzed together without prior separation, shotgun. In exploring the lipidome of various living systems, novel lipids are being discovered, and mass spectrometry is helping characterize their chemical structure. Deuterium exchange mass spectrometry (DXMS) is being used to investigate the association of lipids and membranes with proteins and enzymes, and imaging mass spectrometry (IMS) is being applied to the in situ analysis of lipids in tissues.
doi:10.1146/annurev-biochem-060409-092612
PMCID: PMC3410560  PMID: 21469951
CLASS; DXMS; imaging mass spectrometry; lipidomics; novel lipids; shotgun

Results 1-25 (52)