Advances in high performance liquid chromatography-electrospray ionization-mass spectrometry made in proteomics and now applied to the emerging field of lipidomics has enabled the identification of lipid composition at the molecular level. These improvements have given fresh impetus to lipid research. Modulating lipid compositions has been suggested to represent a novel therapeutic target for intervention in Alzheimer’s disease. A better understanding of how metabolic alterations in the lipid landscape alter Alzheimer’s disease prognosis is required to realize this promise. To achieve this goal, further methodological improvement in lipidomic data acquisition and analysis are required as are comprehensive comparative analyses of lipid metabolism at the systems level in clinical samples and mouse models of human neurodegenerative disease. In this thesis, I present two new lipidomic bioinformatic tools Retention Time Standardization and Registration (RTStaR) and Visualization and Phospholipid Identification (VaLID) designed to facilitate analysis of high performance liquid chromatography-electrospray ionization-mass spectrometry lipidomic data. Using these tools and methodologies, I then comparatively profiled the glycerophosphocholine lipidome in the plasma of young adults, cognitively normal elderly with vascular impairment, mild cognitive impairment and late-onset Alzheimer’s disease patients and the entorhinal-hippocampal circuit of late-onset Alzheimer’s disease patients, TgCRND8 human amyloid beta precursor protein transgenic mice (Alzheimer’s disease mouse model), and across the lifespan of NonTg female littermates. Systems-level analyses identified aberrant glycerophosphocholine metabolic pathways systemically perturbed by age, disease, and amyloid beta biogenesis resulting in the regionally-specific accumulation of critical platelet-activating factor and, to a lesser extent, the lysoglycerophosphocholine, metabolites in brain that could be, in part, predicted by changes in plasma. Finally, using proteomic approaches I identified additional changes in lipid metabolic pathways associated with phenoconversion in the TgCRND8 mouse model of Alzheimer’s disease.

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<div> <div> <div> <p>Flaviviruses is a genus within the family Flaviviridae. The genus consists of more than 70 viruses, including important threatening human pathogens such as dengue virus (DENV), West Nile virus (WNV), and Zika virus (ZIKV). These viruses are causative agents for a range of mild to lethal diseases and there are currently no US- licensed therapeutic treatments for infection. The virus genome is a positive-sense, single-stranded RNA, encoding ten viral proteins. Of the ten flavivirus proteins, Non- Structural protein 1 (NS1) remains the most elusive in terms of its functions. To date NS1 has been linked to disease pathology and progression and plays roles in virus replication and assembly. However, little is understood how NS1 orchestrates these functions and how NS1 from different viruses function distinctively from one another. Moreover, flavivirus NS1 has a peculiar ability to associate with lipid membranes. During the life cycle of NS1, the protein travels through the classical secretory path- way, similar to infectious virus particles, and is secreted into the extracellular space as mostly hexameric oligomers containing a lipid core. How the protein binds to lipids and whether such lipid binding is important for NS1 functions and overall flavivirus pathology remain unknown. Using structure-based mutagenesis, we found a group of mutants on WNV NS1, which particularly altered the viral specific infectivity but maintained wild-type level of virus replication. Purified mutated virus particles revealed that the specific infectivity alteration was not because of the particle but interaction of the virus particles and NS1 mutated proteins. Here we demonstrated that specific residues on NS1 were responsible for distinctly roles in NS1 functions and the virus specific infectivity was regulated by NS1 protein. In other structure-base study, we focused on the membrane association ability of NS1. All structure-predicted regions on NS1 were examined for its contribution for the membrane/lipid binding function. This interaction was required for NS1 biology activities including intracel- lular trafficking, oligomerization, and endocytosis. The lipidomes from deletion of each membrane association region revealed differences in lipid classes binding to each region and the composition flexiblity of the lipid cargo of NS1 hexamer. </p> </div> </div> </div>

Lipidomics is a rapidly expanding research field that has captured extensive attention worldwide in the past few years due to the increasing awareness of the crucial roles of lipids in biological systems. The aim of lipidomics is to comprehensively analyze all lipids, to study their structure, biological function within the cell as well as interactions of lipids with other molecules. A combination of advanced analytical techniques, such as extraction, chromatography and mass spectrometry, is an effective tool for studying all aspects of lipidomics. This dissertation thesis is based on two journal publications and presents application of analytical strategies based on chromatography and mass spectrometry for investigation and characterization of new lipid classes of vernix caseosa. Firstly, the applicability of nonaqueous reversed-phase liquid chromatography atmospheric pressure ionization tandem mass spectrometry (LC- APCI-MS2 ) for structural characterization of cholesteryl esters of ω-(O-acyl)-hydroxy fatty acids (Chl-ωOAHFAs) in vernix caseosa was investigated. For this purpose, a TLC chromatography method for the isolation of neutral Chl-ωOAHFAs from vernix caseosa was developed. Their general structure was established using multi-step mass spectrometric approach requiring transesterification...

The capability to characterize disease states by way of determining novel biomarkers has led to a high demand of single cell and organelle analytical methodologies due to the unexpected heterogeneity present in cells of the same type. Lipids are of particular interest in the search for biomarkers due to their active roles in cellular metabolism and energy storage. Analyzing localized lipid chemistry from individual cells and organelles is challenging however, due to low analyte volume, limited discriminate instrumentation, and common requirements of separation procedures and expenditure of cell sample. Using nanomanipulation in combination with mass spectrometry, individual cells and organelles can be extracted from tissues and cultures in vitro to determine if heterogeneity at the cellular level is present. The discriminate extraction of a single cell or organelle allows the remainder of cell culture or tissue to remain intact, while the high sensitivity and chemical specificity of mass spectrometry provides structural information for limited volumes without the need for chromatographic separation. Mass analysis of lipids extracted from individual cells can be carried out in multiple mass spectrometry platforms through direct-inject mass spectrometry using nanoelectrospray-ionization and through matrix-assisted laser/desorption ionization.

付記する学位プログラム名: 充実した健康長寿社会を築く総合医療開発リーダー育成プログラム / 京都大学 / 0048 / 新制・課程博士 / 博士(工学) / 甲第21794号 / 工博第4611号 / 新制||工||1718(附属図書館) / 京都大学大学院工学研究科合成・生物化学専攻 / (主査)教授 梅田 眞郷, 教授 跡見 晴幸, 教授 秋吉 一成 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DGAM

Zusammenfassung Die menschliche Hautoberfläche enthält beträchtliche Mengen unterschiedlicher Lipide. Sie werden entweder in tieferen Hautschichten synthetisiert und wandern im Zuge der Hautdifferenzierung/Desquamation nach oben (stratum corneum lipide), oder entstehen im Inneren von Talgdrüsen und werden auf der Hautoberfläche ausgeschieden. Zusammen kann die Gesamtheit aller Hautoberflächenlipide als Hautlipidom bezeichnet werden. Ein besseres Verständnis der Variabilität von Hautoberflächenlipiden ist aus zweierlei Gründen das Ziel dieser Arbeit. Die erste Motivation ist ein besseres Verständnis der Hautbiologie an sich. Als wichtiger Bestandteil der Epidermis definieren Hautoberflächenlipide bestimmte Aspekte der Hautmikroanatomie und –physiologie und determinieren zentrale Hautparameter. Die zweite Motivation ist die Erlangung der Fähigkeit ein krankes Hautlipidom erkennen zu können. Dazu muss man wissen wie ein gesundes Hautlipidom variieren kann. Die Zusammensetzung des Hautlipidomes unterliegt erheblichen Schwankungen. Lipide sind das Produkt mehrerer komplexer, miteinander verbundener Synthesewege des Stoffwechesl. Als solche können ihre Mengen auf Prozesse im menschlichen Körper reagieren. Lipidschwankungen können besonders ausgeprägt sein, wenn sie im Zuge einer Hautkrankheit, als ethologischer Faktor oder als Folge auftreten, und damit Barriereeigenschaften der Haut beeinflussen. Aber mutmaßlich gibt es auch einen Schwankungsbereich, der als physiologisch einzuordnen wäre. Zur Vermessung der Hautlipidomzusammensetzung und –variabilität haben wir eine Technologie entwickelt und validiert, die der quantitativen, Hochdurchsatz-Shotgun-Massenspektrometire von Tape-stripping Oberhautproben basiert. Sie ermöglicht die Quantifizierung von 16 Lipidklassen bis runter auf Mengen individueller molekularer Lipidspezies, und ist dabei reproduzierbar und hochdurchsatzfähig. Mit dieser Technologie haben wir die bis heute umfangreichste Hautlipidom-Studie unter Einbeziehung von 268 menschlicher Oberhautproben durchgeführt. Wir haben den Zusammenhang zwischen Tiefe der Probenentnahme und der Zusammensetzung der Hautlipide, die Lipidomvariabilität an 14 unterschiedlichen anatomischen Loci, sowie die Populationsvariabilität des Hautlipidoms innerhalb von 104 Probanden untersucht.:The physiological lipidome of human epidermis Contents Abbreviations III Introduction 1 Architecture of the human shell 4 Measuring skin lipid composition 6 Skin sampling 6 Lipid extraction 9 Lipid identification 10 Lipid quantification 14 The design of this study 16 Material and methods 18 Method development and validation 18 Sampling development 18 Establishment of sample extraction and robotic handling 19 Establishment of mass spectrometric lipid identification 20 Establishment of lipid quantification 21 Skin lipidomic study 22 Sampling preparation 22 Standard sampling via tape stripping 23 Sampling via sequential tape-stripping 25 Lipid extraction 25 MS data acquisition 26 Lipid identification and data processing 27 Results 29 Method development and validation 29 Skin sampling via tape-stripping 29 Lipid extraction 31 Lipid identification 31 Lipid quantification 36 Skin lipidomic study results 38 Vertical skin surface lipid profile 38 Anatomical skin surface lipid variability 43 Inter-individual skin surface lipid variability 46 Discussion 50 Method development and validation 50 Skin sampling via tape-stripping 50 Lipid extraction 52 Lipid identification 53 Lipid quantification 55 Physiological lipid composition and variability 56 Lipidome variability vs sampling depth 56 Intra-individual lipidome variability 58 Inter-individual lipidome variability 59 General discussion 61 Conclusions 63 Abstract 66 Zusammenfassung 67 Literature 68 Acknowledgments 81 Anlage 1: Erklärungen zur Eröffnung des Promotionsverfahrens 83 Anlage 2: Gesetzliche Vorgaben 84 / The human skin surface contains considerable amounts of different lipids, both synthesized in deeper skin layers and migrating upwards (stratum corneum lipids), or generated in sebaceous glands and secreted on the skin surface (sebaceous lipids). Jointly the entirety of all skin surface lipids (SSLs) can be referred to as the skin lipidome. The composition of the skin lipidome is known to vary considerably. Lipids are product of several complex synthesis pathways, interconnected with the body’s metabolism. As such, lipid amounts may vary in response to what is happening inside of us. Lipid variations can be most pronounced when occurring in skin disorders, either as etiological cause or as effect, causing altered skin barrier properties. But certainly there is a range of variation in SSL amount which could be described as physiological. Attaining better knowledge of the physiological skin surface lipid variability is the purpose of this work for two main reasons. The first fundamental reason is to better understand skin biology. As major epidermis constituent, SSL composition and variability defines certain aspects of skin microanatomy, physiology and determines crucial skin properties. The second motivation is to acquire the ability to recognize what characterizes a sick skin lipidome. To this end, one must know how much a healthy skin lipidome can vary. To assess skin lipidome composition and variability, we developed and validated a quantitative high-throughput shotgun mass spectrometry-based platform for lipid analysis of tape-stripped stratum corneum (SC) skin samples. It features coverage of 16 lipid classes; total quantification to the level of individual lipid molecules; high reproducibility and high-throughput capabilities. With this method, we conducted the hitherto largest lipidomic survey of 268 human SC samples, where we investigated the relationship between sampling depth and lipid composition, lipidome variability in samples from 14 different sampling sites on the human body and finally, we assessed the impact of age and sex on lipidome variability in 104 healthy subjects.:The physiological lipidome of human epidermis Contents Abbreviations III Introduction 1 Architecture of the human shell 4 Measuring skin lipid composition 6 Skin sampling 6 Lipid extraction 9 Lipid identification 10 Lipid quantification 14 The design of this study 16 Material and methods 18 Method development and validation 18 Sampling development 18 Establishment of sample extraction and robotic handling 19 Establishment of mass spectrometric lipid identification 20 Establishment of lipid quantification 21 Skin lipidomic study 22 Sampling preparation 22 Standard sampling via tape stripping 23 Sampling via sequential tape-stripping 25 Lipid extraction 25 MS data acquisition 26 Lipid identification and data processing 27 Results 29 Method development and validation 29 Skin sampling via tape-stripping 29 Lipid extraction 31 Lipid identification 31 Lipid quantification 36 Skin lipidomic study results 38 Vertical skin surface lipid profile 38 Anatomical skin surface lipid variability 43 Inter-individual skin surface lipid variability 46 Discussion 50 Method development and validation 50 Skin sampling via tape-stripping 50 Lipid extraction 52 Lipid identification 53 Lipid quantification 55 Physiological lipid composition and variability 56 Lipidome variability vs sampling depth 56 Intra-individual lipidome variability 58 Inter-individual lipidome variability 59 General discussion 61 Conclusions 63 Abstract 66 Zusammenfassung 67 Literature 68 Acknowledgments 81 Anlage 1: Erklärungen zur Eröffnung des Promotionsverfahrens 83 Anlage 2: Gesetzliche Vorgaben 84

京都大学 / 新制・課程博士 / 博士(医学) / 甲第24795号 / 医博第4987号 / 新制||医||1066(附属図書館) / 京都大学大学院医学研究科医学専攻 / (主査)教授 小林 恭, 教授 波多野 悦朗, 教授 羽賀 博典 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

Lipids are increasingly recognized as bioactive mediators of extracellular vesicle (EV) functions. However, while EV proteins and nucleic acids are well described, EV lipids are insufficiently understood due to lack of adequate quantitative methods. We adapted an established targeted and quantitative mass spectrometry (LC-MS/MS) method originally developed for analysis of 94 eicosanoids and seven polyunsaturated fatty acids (PUFA) in human plasma. Additionally, the influence of freeze–thaw (FT) cycles, injection volume, and extraction solvent were investigated. The modified protocol was applied to lipidomic analysis of differently polarized macrophage-derived EVs. We successfully quantified three PUFAs and eight eicosanoids within EVs. Lipid extraction showed reproducible PUFA and eicosanoid patterns. We found a particularly high impact of FT cycles on EV lipid profiles, with significant reductions of up to 70%. Thus, repeated FT will markedly influence analytical results and may alter EV functions, emphasizing the importance of a standardized sample pretreatment protocol for the analysis of bioactive lipids in EVs. EV lipid profiles differed largely depending on the polarization of the originating macrophages. Particularly, we observed major changes in the arachidonic acid pathway. We emphasize the importance of a standardized sample pretreatment protocol for the analysis of bioactive lipids in EVs.

Biological research has benefitted greatly from the advent of omic methods. For many biomolecules, mass spectrometry (MS) methods are most widely employed due to the sensitivity which allows low quantities of sample and the speed which allows analysis of complex samples. Improvements in instrument and sample preparation techniques create opportunities for large scale experimentation. The complexity and volume of data produced by modern MS-omic instrumentation challenges biological interpretation, while the complexity of the instrumentation, sample noise, and complexity of data analysis present difficulties in maintaining and ensuring data quality, validity, and relevance. We present a corpus of tools which improves quality assurance capabilities of instruments, provides comparison abilities for evaluating data analysis tool performance, distills ideas pertinent in MS analysis into a consistent nomenclature, enhances all lipid analysis by automatic structural classification, implements a rigorous and chemically derived lipid fragmentation prediction tool, introduces custom structural analysis approaches and validation techniques, simplifies protein analysis form SDS-PAGE sample excisions, and implements a robust peak detection algorithm. These contributions provide improved identification of biomolecules, improved quantitation, and improve data quality and algorithm clarity to the MS-omic field.