As an emerging field, lipidomics still encounters methodological challenges. Indeed, as it is an –omics field, analysis of data is time and labour intensive, if the necessary and appropriate bioinformatics tools are not existent. Here I present two programs I developed to address the challenges of peak identification and peak annotation and filtering for a targeted lipidomics approach, which is not supported by available software. The first program, Lipid Identification Tool (LIT), consists of a stand-alone offline search engine, which provides a robust in silico database generated by linear equations based on lipid structures, containing information lacking on presently available online databases. The second program, Lipid Identification for Targeted Lipidomics (LITL), allows the annotation of HPLC-ESI-MS/MS MRM acquired spectral data in text-based format, comparing them to a library of identities, via retention time and mass-over-charge of detected ions, and to easily export the results to a statistical analysis software. // La lipidomique est un jeune domaine encore proie à des défis quant à sa méthodologie. En effet, l’analyse de données en lipidomique demeurera longue et ardue, tant que des outils bioinformatiques appropriés ne sont pas créés. Je décris ici deux de mes programmes développés pour remédier aux défis d’identification de pics et d’annotations et de sélection de pics provenant d’une approche lipidomique dénommée ciblée, données présentement incompatibles avec d’autres programmes. Lipid Identification Tool (LIT) est un moteur de recherche hors-ligne possédant une robuste base de données in silico générée mathématiquement, et contenant des informations sur des espèces lipidiques non décrites dans les bases de données disponibles. Lipid Identification for Targeted Lipidomics (LITL) permet l’annotation de données provenant de méthodes HPLC-ESI-MS/MS MRM, en comparant leur temps de rétention ainsi que leur rapport masse-sur-charge à une bibliothèque d’identités lipidiques, et permet de les exporter facilement vers un logiciel d’analyse statistique.

Preeclampsia (PE), a life threatening pregnancy-related disorder, is characterized mainly by new onset of hypertension and proteinuria after 20 weeks of gestation. Currently, PE cannot be predicted prior to onset of symptoms and there is no cure for the disease. There is a clear value in having biomarkers able, early in a pregnancy, to identify women at risk for PE so that proper treatment therapies could be developed. Although a number of serum candidate markers have been proposed to be altered in PE patients, their use is limited due to poor sensitivity and specificity. Therefore, there is ongoing need for better set of novel biomarkers predicting PE. Consequently, for my first project, we used a serum proteomic approach involving reversed phase capillary-liquid chromatography-electrospray ionization-quadrupole-time of flight mass spectrometry (cLC-ESI-QTOF). Our approach focuses on the less abundant (nM or lower), lower molecular weight peptides and lipids predicting PE. We got previously collected sera from pregnant women at 12–14 weeks gestation. There were 24 controls, having term uncomplicated pregnancies and 24 cases, which developed PE later in the same pregnancy. Many statistically significant serum PE biomarker candidates were found comparing cases and controls. In addition, multimarker combinations having high detection sensitivity and specificity (AUC >0.9) were developed using logistic regression analysis. For my second project, serum lipidomic analysis of sera from pregnant women was undertaken to determine if useful PE lipid biomarkers exist. A discovery study involving a shotgun lipidomic approach was performed using sera collected at 12-14 weeks of pregnancy from 27 controls with uncomplicated pregnancies and 29 cases that later developed PE. Lipids were extracted using organic solvent and analyzed by direct infusion into a time-of-flight mass spectrometer. Statistically significant lipid markers were found and reevaluated in a second confirmatory study having 43 controls and 37 PE cases. The initial study detected 45 potential PE markers. Of these, 23 markers continued to be statistically significant in the second confirmatory set. Several multi-marker panels with AUC >0.85 and high predictive values were developed from these markers. My third project also involved the above mentioned approach for detection of novel lipid biomarkers for Alzheimer's disease. Alzheimer's disease (AD) is a progressive neurodegenerative disorder and the most common cause of age-related dementia. Currently, there are no methods to detect Alzheimer's at an early stage when treatment therapies could be applied. Therefore, there is need for detection of panel of biomarkers for detecting patients at risk to AD at an early stage. In the initial discovery set, sera from 29 different stage AD cases and 32 controls were analyzed using direct infusion mass spectrometry (ESI-TOF). This study yielded 89 potential lipid biomarkers which were evaluated in another confirmation study. Of these, 35 markers continued to be statistically significant in the second confirmatory set. Using the confirmed markers, several multi-marker panels with AUC > 0.87 were developed for any stage AD cases vs controls. Multi-marker panels with AUCs > 0.90 were developed for each specific CDR vs controls, including the earliest stage of AD. These lipidomic biomarkers are likely to distinguish AD cases regardless of the stage from controls. In conclusion, we successfully detected, validated and identified low molecular weight novel biomarkers for PE and lipid biomarkers for AD.

N-Acylphosphatidylethanolamine (NAPE) and its hydrolysis product, N-acylethanolamine (NAE), are minor but ubiquitous lipids in multicellular eukaryotes. Various physiological processes are severely affected by altering the expression of fatty acid amide hydrolase (FAAH), an NAE-hydrolyzing enzyme. To determine the effect of altered FAAH activity on NAPE molecular species composition, NAE metabolism, and general membrane lipid metabolism, quantitative profiles of NAPEs, NAEs, galactolipids, and major and minor phospholipids for FAAH mutants of Arabidopsis were determined. The NAPE molecular species content was dramatically affected by reduced FAAH activity and elevated NAE content in faah knockouts, increasing by as much as 36-fold, far more than the NAE content, suggesting negative feedback regulation of phospholipase D-mediated NAPE hydrolysis by NAE. The N-acyl composition of NAPE remained similar to that of NAE, suggesting that the NAPE precursor pool largely determines NAE composition. Exogenous NAE 12:0 treatment elevated endogenous polyunsaturated NAE and NAPE levels in seedlings; NAE levels were increased more in faah knockouts than in wild-type or FAAH overexpressors. Treated seedlings with elevated NAE and NAPE levels showed impaired growth and reduced galactolipid synthesis by the “prokaryotic” (i.e., plastidic), but not the “eukaryotic” (i.e., extraplastidic), pathway. Overall, our data provide new insights into the regulation of NAPE–NAE metabolism and coordination of membrane lipid metabolism and seedling development.

The main treatment for myocardial infarction is early reperfusion of ischemic tissue. Ischemia and reperfusion (IR) produces reactive oxygen species that oxidize membrane phospholipids. The production of oxidized lipids and their role on cell death in cardiac IR injury is unknown. Using in vitro model of IR, our goal was to identify oxidized phosphatidylcholines (OxPC) from cardiomyocytes, to determine their bioactivity on cardiomyocyte viability and mitochondrial permeability, and using an OxPC specific EO6 antibody inhibit OxPC activity on cardiomyocytes. Rat cardiomyocytes were exposed to IR and lipid extracts underwent lipidomic analysis with HPLC-MS/MS to quantitate 82 novel OxPC species. Cell viability and mitochondrial permeability were determined in vehicle control, non-oxidized control PC, and fragmented OxPC molecules. EO6 antibody was applied and cell viability was assessed. Cardiomyocytes under IR demonstrated increased relevant OxPCs particularly fragmented species. OxPC treatment resulted in loss of cardiomyocyte viability, increased mitochondrial permeability when compared to control. EO6 antibody blocked the loss of cardiomyocyte viability. We have shown for the first time that OxPCs are generated cardiomyocytes during IR and they have detrimental effects on cardiomyocyte viability. Additionally the EO6 antibody inhibits the bioactivity of the OxPCs on cardiomyocytes and could be part of a future treatment regimen.

Stroke is a devastating and debilitating condition resulting from a blockage or hemorrhage in the vasculature of the brain. Despite extensive research, the etiology and pathophysiology of the disease at the level of the cell membrane are poorly understood, and effective treatment has been elusive. Though much research has shown marked increases in lipid metabolism following stroke, the impact of these changes have often been overlooked given the technical challenges associated with identifying regionally specific changes in degenerating tissue. The advent of lipidomics – a systems biology approach to the large-scale profiling of individual lipid species in tissues – has renewed interest in understanding the role of membrane lipids and their metabolites in the cell and in ischemic injury. In this thesis, I have used an unbiased LC-ESI-MS-based lipidomic approach to profile the small molecular weight glycerophosphocholine second messenger lipidome in anterior and posterior regions of cortex and striatum in the forebrain of wild-type and platelet activating factor receptor (PAFR) null-mutant mice before and after middle cerebral artery occlusion (MCAO). From these profiles, I have outlined the potential use of lipid second messenger distribution as topographic landmarks to identify functional subdomains within neural tissue. Further, I have demonstrated that ischemia does not simply disrupt lipid second messenger metabolism globally but produces regionally specific changes in discrete species and that these changes are altered by the loss of lipid regulatory effectors (i.e., PAFR null mutation). Based on the lipid species identified in this profile of healthy and ischemic tissue, I proposed that tight regulation of PC(O-22:6/2:0) homeostasis by PAFR-expressing microglia is ii required for proper dopaminergic signaling in prefrontal cortex. Finally, I have outlined a model whereby increased PAF synthesis following ischemia contributes the inflammatory response by promoting blood-brain barrier permeability, microglial activation and immune cell infiltration in a PAFR-dependent manner.

Mass spectrometry has increasingly become the method of choice for the analysis of complex biological samples, including proteins and lipids. This thesis describes the development of MS-based analytical methodologies for the analysis of complex proteomic and lipidomic samples. Chapter 3 describes the development of microfluidic proteomic reactors, in the formats of SCX reactor, SCX 96-well plate reactor, and SAX reactor, for the enzymatic digestion of complex proteomic samples for subsequent LC-MS/MS analysis. These microfluidic proteomic reactors greatly simplified the enzymatic digestion of complex proteomic samples by combining multiple processing steps, such as rapid extraction and enrichment of proteins. Furthermore, chemical and enzymatic treatments of proteins were all performed in a few nanoliters effective volume, resulting in an increased protein digestion efficacy. After the protein digestion process, the resulting peptides were eluted in buffers that were compatible with HPLC-MS/MS analysis. In chapter 4, a methodology based on nano-HPLC-ESI-MS/MS for the analysis of PAF and LPC lipid species is described. In this method, lipid extracts from biological samples were separated by nano-flow HPLC prior to being introduced into a Q-TRAP 2000 mass spectrometer, where the lipid species of interest were detected using a precursor ion scan at m/z 184. Absolute quantitation of PAF family lipid species were performed with standard addition method, where 5 standard solutions containing 0.2-1 ng each of C16:0, C18:0 PAF and C16:0, C18:0 lyso-PAF were used in the experiment. Further, the spiking of identical amount of non-endogenous C13:0 LPC at time of extraction allow the relative comparisons of other LPC lipid species of interest between different samples. The developed methods were employed to analyze the changes of PAF and LPC lipid species in NGFdifferentiated PC12 cells, in the posterior/entorhinal cortex of AD patients and TgCRND8 transgenic mice, and over the course of 24 hour exposure of human hNT neurons to Aβ42 treatment, respectively, in comparison to controls. iii Chapter 5 describes the development of a novel shotgun lipidomic methodology for the determination of stereospecificity of diacyl glycerophospholipids including glycerophosphatidic acids (PA), glycerophosphoserines (PS), glycerophosphoglycerols (PG), glycerophosphoinositols(PI), and glycerophosphoethanolamines (PE), which can be conventionally ionized under negative ion mode. The stereospecificity of diacyl glycerophospholipids was determined based on the relative abundance of the lyso-form fragment ions, attributed to the neutral loss of fatty acyl moieties. The fragmentation patterns of a variety of diacyl glycerophospholipid standards were first fully examined over a wide range of collision energy. We observed that lyso-form fragment ions corresponding to the neutral loss of fatty acyl moieties attached to the sn2 position as free fatty acids ([M-Sn2]-) and as ketenes ([M-(Sn2-H2O)]-) exhibited consistently higher intensity than their counter part ions due to the neutral loss of fatty acyl moieties attached to the sn1 position ([M-Sn1]- and [M-(Sn1-H2O)]-). We then examined the product ion spectra of diacyl glycerophospholipids recorded from lipid extracts of rat hepatoma cells, where the stereospecific information of these lipids was conclusively determined.

Lipidomics and metabolomics are powerful tools for the examination of cellular metabolism and physiology. Methods for lipid analysis need to be developed that begin with small samples and do not overly dilute or disperse the sample in the separation process. Microchips provide a platform for interfacing lysis of small cell populations with on-chip solid phase extraction for isolating lipid samples to generate high quality mass spectra from very small samples. Chapter 1 of this dissertation presents a novel method for small scale lipidomics of bacterial cells by microchip based extraction coupled with untargeted profiling of glycerophospholipids using nanoelectrospray ionization mass spectrometry. Chapter 2 and 3 focus on the development of LC-MS/MS methods to study biological pathways. In Chapter 2, I describe a method for analysis of the phospholipids metabolite, GroPIns, in the medium of the pathogenic yeast Candida albicans. This method was applied to aid in the characterization of the GroPIns transport protein, Git1, in C. albicans. Chapter 3 extends the studies of part two and describes an efficient method based on HILIC-MS/MS for the separation and quantification of five lipid-related extracellular metabolites in yeast Saccharomyces cerevisiae. This newly developed methodology was successfully applied to determine the extracellualr levels of glycerophosphoinositol, glycerophosphocholine, glycerol 3-phosphate, inositol and choline in wild type and mutant strains. / Bayer School of Natural and Environmental Sciences / Chemistry and Biochemistry / PhD / Dissertation

Doctor of Philosophy / Department of Human Nutrition / Weiqun Wang / Body weight control via increasing exercise and/or decreasing calorie intake has been linked to a reduced cancer risk in animal models. However, the underlying mechanisms are not clear. This study assessed the impact of exercise with or without limited dietary calorie intake on the overview profiling of phospholipids and gene expression in the skin tissues of weight controlled-mice. Mice were randomly assigned to three groups: ad libitum-fed sedentary control, ad libitum-fed treadmill exercise at 13.4 m/min for 60 min/d, 5 d/wk (Ex+AL), and exercise but pair-fed with the sedentary control (Ex+PF). After 10 wks, Ex+PF but not Ex+AL mice demonstrated a significant decrease in both body weight and percentage of body fat when compared to the sedentary controls. Among 338 phospholipids measured in the skin samples by electrospray ionization mass spectrometry, most classes of phosphatidylinositol (PI), phosphatidylcholine-containing lipids with ether linkage (ePC), and some lysophosphatidylcholine (lysoPC) significantly decreased in Ex+PF mice when compared to the controls. Furthermore, some species of phosphatidylcholine (PC) and phosphatidylethanolamine (PE) containing omega-3 18:0-22:6 fatty acyl combinations increased significantly in Ex+PF mice. A total of 25 significantly-changed phospholipids were distinguishable between diet and exercise treatments by discriminant analysis. The reduced PI in Ex+PF mice was observed concomitantly with a significant reduction of PI3K protein expression. Among the 45,101 probe sets tested in skin tissues, expression of 839 genes was significantly changed by exercise with or without limited dietary calorie intake. The genes with impacted expression were involved in oxidative stress, inflammatory response, lipolysis, protein synthesis, and signaling pathway. Up-regulated expression of genes involved in elongation of long chain fatty acids in Ex+PF but not Ex+AL mice appears to partially account for increased level of 18:0-22:5PC/PE and 18:0-22:6 PC/PE. Taken together, these data indicate that controlling body weight via exercise with limited dietary calorie intake rather than exercise alone significantly modified phospholipid and gene expression profiles. The altered profiles may be associated with cancer preventive mechanisms; in particular, reduced PI and PI-related PI3K expression and altered expression of genes involved in protein kinase activity and lipid metabolism may prevent cancer.

En plus de leurs propriétés structurales comme constituants majeurs des membranes biologiques des cellules, les lipides jouent de nombreux rôles dans la signalisation cellulaire, le stockage d’énergie et le transport de protéines. Leurs importances biologiques ont mené à une augmentation accrue des méthodes analytiques pour la caractérisation d’espèces moléculaires uniques. De récents progrès en spectrométrie de masse ont amené à la caractérisation et à la quantification des espèces moléculaires des lipides dans des extraits lipidiques bruts (Han and Gross, 2005; Murphy et al., 2001). Par exemple, les espèces moléculaires de phospholipides peuvent être identifiées spécifiquement par leur tête polaire, la nature de leurs chaînes d’acide gras et leur positionnement au niveau du squelette glycérol. / In addition to their structural properties as main constituents of biological membranes, lipids play a multitude of roles such as in cell signalling, energy storage, and protein transport. Their biological importance has led to an increasing focus on analytical methods for the characterisation of their individual molecular species. Improvements in mass spectrometric technology has provided a great advantage for the characterisation and quantification of molecular lipid species in total lipid extracts (Han and Gross, 2005; Murphy et al., 2001). For instance, phospholipid molecular species can be identified on the basis of a characteristic fragment of the lipid class, the nature of the acyl chains and their positions on the glycerol backbone.A method allowing the quantitative profiling of the yeast lipidome was developed in a recent study using automated shotgun infusion strategy (Ejsing et al., 2009). We applied this method to characterise several lysophospholipid acyltransferase yeast mutants produced using reverse-genetics. These enzymes are involved in essential biological processes like de novo synthesis or remodelling of the phospholipid membrane component (Testet et al., 2005; Le Guedard et al., 2009). The comparative analysis of phospholipid molecular species from the wild-type strain and the corresponding deletion mutants has allowed us to identify lipid compositional changes, and has given us significant indications about the in vivo function of the encoded lysophospholipid acyltransferases.

Stroke is a devastating and debilitating condition resulting from a blockage or hemorrhage in the vasculature of the brain. Despite extensive research, the etiology and pathophysiology of the disease at the level of the cell membrane are poorly understood, and effective treatment has been elusive. Though much research has shown marked increases in lipid metabolism following stroke, the impact of these changes have often been overlooked given the technical challenges associated with identifying regionally specific changes in degenerating tissue. The advent of lipidomics – a systems biology approach to the large-scale profiling of individual lipid species in tissues – has renewed interest in understanding the role of membrane lipids and their metabolites in the cell and in ischemic injury. In this thesis, I have used an unbiased LC-ESI-MS-based lipidomic approach to profile the small molecular weight glycerophosphocholine second messenger lipidome in anterior and posterior regions of cortex and striatum in the forebrain of wild-type and platelet activating factor receptor (PAFR) null-mutant mice before and after middle cerebral artery occlusion (MCAO). From these profiles, I have outlined the potential use of lipid second messenger distribution as topographic landmarks to identify functional subdomains within neural tissue. Further, I have demonstrated that ischemia does not simply disrupt lipid second messenger metabolism globally but produces regionally specific changes in discrete species and that these changes are altered by the loss of lipid regulatory effectors (i.e., PAFR null mutation). Based on the lipid species identified in this profile of healthy and ischemic tissue, I proposed that tight regulation of PC(O-22:6/2:0) homeostasis by PAFR-expressing microglia is ii required for proper dopaminergic signaling in prefrontal cortex. Finally, I have outlined a model whereby increased PAF synthesis following ischemia contributes the inflammatory response by promoting blood-brain barrier permeability, microglial activation and immune cell infiltration in a PAFR-dependent manner.