152 results on '"Ekroos K"'
Search Results
2. Clinical lipidomics-A community-driven roadmap to translate research into clinical applications
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Vvedenskaya, O, Holcapek, M, Vogeser, M, Ekroos, K, Meikle, PJ, Bendt, AK, Vvedenskaya, O, Holcapek, M, Vogeser, M, Ekroos, K, Meikle, PJ, and Bendt, AK
- Abstract
Lipid metabolites, beyond triglycerides and cholesterol, have been shown to have vast potential for applications in clinical applications, with substantial societal and economical value. To successfully evolve from the current research-grade methods to assays suitable for routine clinical applications, a harmonization - if not standardization - of these mass spectrometry-based workflows is necessary. Input on clinical needs and technological capabilities must be obtained from all relevant stakeholders, including wet lab scientists, informaticians and data scientists, manufacturers, and medical professionals. In order to build bridges between this diverse group of professionals, the International Lipidomics Society and its Clinical Lipidomics Interest Group were created. This opinion article is intended to provide an overview of international efforts to tackle the issues of workflow harmonization, and to serve as an open invitation for others to join this growing community.
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- 2022
3. Multi-Omic analyses characterize the ceramide/sphingomyelin pathway as a therapeutic target in Alzheimer's disease
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Baloni, P, Arnold, M, Buitrago, L, Nho, K, Moreno, H, Huynh, K, Brauner, B, Louie, G, Kueider-Paisley, A, Suhre, K, Saykin, AJ, Ekroos, K, Meikle, PJ, Hood, L, Price, ND, Doraiswamy, PM, Funk, CC, Hernandez, AI, Kastenmueller, G, Baillie, R, Han, X, Kaddurah-Daouk, R, Baloni, P, Arnold, M, Buitrago, L, Nho, K, Moreno, H, Huynh, K, Brauner, B, Louie, G, Kueider-Paisley, A, Suhre, K, Saykin, AJ, Ekroos, K, Meikle, PJ, Hood, L, Price, ND, Doraiswamy, PM, Funk, CC, Hernandez, AI, Kastenmueller, G, Baillie, R, Han, X, and Kaddurah-Daouk, R
- Abstract
Dysregulation of sphingomyelin and ceramide metabolism have been implicated in Alzheimer's disease. Genome-wide and transcriptome-wide association studies have identified various genes and genetic variants in lipid metabolism that are associated with Alzheimer's disease. However, the molecular mechanisms of sphingomyelin and ceramide disruption remain to be determined. We focus on the sphingolipid pathway and carry out multi-omics analyses to identify central and peripheral metabolic changes in Alzheimer's patients, correlating them to imaging features. Our multi-omics approach is based on (a) 2114 human post-mortem brain transcriptomics to identify differentially expressed genes; (b) in silico metabolic flux analysis on context-specific metabolic networks identified differential reaction fluxes; (c) multimodal neuroimaging analysis on 1576 participants to associate genetic variants in sphingomyelin pathway with Alzheimer's disease pathogenesis; (d) plasma metabolomic and lipidomic analysis to identify associations of lipid species with dysregulation in Alzheimer's; and (e) metabolite genome-wide association studies to define receptors within the pathway as a potential drug target. We validate our hypothesis in amyloidogenic APP/PS1 mice and show prolonged exposure to fingolimod alleviated synaptic plasticity and cognitive impairment in mice. Our integrative multi-omics approach identifies potential targets in the sphingomyelin pathway and suggests modulators of S1P metabolism as possible candidates for Alzheimer's disease treatment.
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- 2022
4. Clinical dyslipidaemia is associated with changes in the lipid composition and inflammatory properties of apolipoprotein-B-containing lipoproteins from women with type 2 diabetes
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Ståhlman, M., Pham, H. T., Adiels, M., Mitchell, T. W., Blanksby, S. J., Fagerberg, B., Ekroos, K., and Borén, J.
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- 2012
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5. Muscle ceramide content in man is higher in type I than type II fibers and not influenced by glycogen content
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Nordby, P., Prats, C., Kristensen, D., Ekroos, K., Forsberg, G., Andersen, J. L., Ploug, T., Dela, F., Storlien, L., and Helge, J. W.
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- 2010
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6. Serum saturated fatty acids containing triacylglycerols are better markers of insulin resistance than total serum triacylglycerol concentrations
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Kotronen, A., Velagapudi, V. R., Yetukuri, L., Westerbacka, J., Bergholm, R., Ekroos, K., Makkonen, J., Taskinen, M.-R., Orešič, M., and Yki-Järvinen, H.
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- 2009
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7. Lipidomics in health & disease: I33
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Ekroos, K.
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- 2010
8. MS-based lipidomics of human blood plasma: a community-initiated position paper to develop accepted guidelines
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Burla, B, Arita, M, Bendt, AK, Cazenave-Gassiot, A, Dennis, EA, Ekroos, K, Han, X, Ikeda, K, Liebisch, G, Lin, MK, Loh, TP, Meikle, PJ, Oresic, M, Quehenberger, O, Shevchenko, A, Torta, F, Wakelam, MJO, Wheelock, CE, Wenk, MR, Burla, B, Arita, M, Bendt, AK, Cazenave-Gassiot, A, Dennis, EA, Ekroos, K, Han, X, Ikeda, K, Liebisch, G, Lin, MK, Loh, TP, Meikle, PJ, Oresic, M, Quehenberger, O, Shevchenko, A, Torta, F, Wakelam, MJO, Wheelock, CE, and Wenk, MR
- Abstract
Human blood is a self-regenerating lipid-rich biological fluid that is routinely collected in hospital settings. The inventory of lipid molecules found in blood plasma (plasma lipidome) offers insights into individual metabolism and physiology in health and disease. Disturbances in the plasma lipidome also occur in conditions that are not directly linked to lipid metabolism; therefore, plasma lipidomics based on MS is an emerging tool in an array of clinical diagnostics and disease management. However, challenges exist in the translation of such lipidomic data to clinical applications. These relate to the reproducibility, accuracy, and precision of lipid quantitation, study design, sample handling, and data sharing. This position paper emerged from a workshop that initiated a community-led process to elaborate and define a set of generally accepted guidelines for quantitative MS-based lipidomics of blood plasma or serum, with harmonization of data acquired on different instrumentation platforms across independent laboratories as an ultimate goal. We hope that other fields may benefit from and follow such a precedent.
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- 2018
9. Plasma ceramides identify residual cardiovascular risk in statin treated coronary artery disease patients
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Laaksonen, R., primary, Ekroos, K., additional, Sysi-Aho, M., additional, Vihervaara, T., additional, Kauhanen, D., additional, Hilvo, M., additional, Hurme, R., additional, Pedersen, E. Ringdal, additional, Tell, G., additional, and Nygård, O., additional
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- 2016
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10. Lipidomics of plasma, liver and aorta of Pcsk9-KO mice
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Chiesa, G., primary, Busnelli, M., additional, Parolini, C., additional, Manzini, S., additional, Ganzetti, G.S., additional, Dellera, F., additional, Suoniemi, M., additional, Hilvo, M., additional, Hurme, R., additional, Ekroos, K., additional, Sirtori, C.R., additional, and Laaksonen, R., additional
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- 2016
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11. Hepatocyte-specific PPAP2B ablation increases plasma levels of several minor pro-atherogenic lipid species and worsens atherosclerosis in apoE -/- MICE
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Busnelli, M., primary, Manzini, S., additional, Hilvo, M., additional, Parolini, C., additional, Ganzetti, G.S., additional, Dellera, F., additional, Ekroos, K., additional, Jänis, M., additional, Sirtori, C.R., additional, Laaksonen, R., additional, and Chiesa, G., additional
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- 2016
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12. Impact of dietary treatments on the lipidomic profile of plasma, aorta and liver from ldlr-ko and pcsk9-ko mice
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Busnelli, M., primary, Parolini, C., additional, Manzini, S., additional, Ganzetti, G.S., additional, Dellera, F., additional, Katainen, R., additional, Suoniemi, M., additional, Tarasov, K., additional, Hurme, R., additional, Ekroos, K., additional, Sirtori, C.R., additional, Laaksonen, R., additional, and Chiesa, G., additional
- Published
- 2014
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13. Structural lipidomics
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Ekroos, K, Mitchell, Todd, Brown, Simon, Blanksby, Stephen, Ekroos, K, Mitchell, Todd, Brown, Simon, and Blanksby, Stephen
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- 2012
14. Long- and medium-chain Fatty acids induce insulin resistance to a similar extent in humans despite marked differences in muscle fat accumulation.
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Hoeks, J., Hoeks, J., Mensink, M.R., Hesselink, M.K.C., Ekroos, K., Schrauwen, P., Hoeks, J., Hoeks, J., Mensink, M.R., Hesselink, M.K.C., Ekroos, K., and Schrauwen, P.
- Abstract
Context:Animal studies revealed that medium-chain fatty acids (MCFA), due to their metabolic characteristics, are not stored in skeletal muscle and may therefore not give rise to potentially hazardous lipid species impeding insulin signaling.Objective:We here hypothesized that infusion of medium-chain triacylglycerols (MCT) in healthy lean subjects does not lead to ectopic fat accumulation and hence does not result in lipid-induced insulin resistance.Design and Methods:Nine healthy lean male subjects underwent a 6-h hyperinsulinemic-euglycemic clamp with simultaneous infusion of 1) a 100% long-chain triacylglycerols (LCT) emulsion, 2) a 50/50% MCT/LCT emulsion, or 3) glycerol in a randomized crossover design. Muscle biopsies were taken before and after each clamp.Results:MCT/LCT infusion raised plasma free fatty acid levels to a similar level compared with LCT infusion alone. Despite elevated free fatty acid levels, intramyocellular triacylglycerol (IMTG) levels were not affected by the MCT/LCT emulsion, whereas LCT infusion resulted in an approximately 1.6-fold increase in IMTG. These differences in muscle fat accumulation did not result in significant differences in lipid-induced insulin resistance between LCT (-28%, P = 0.003) and MCT/LCT (-20%, P < 0.001). Total skeletal muscle ceramide content as well as lactosyl- and glucosylceramide levels were not affected by any of the interventions. In addition, the distribution pattern of all ceramide species remained unaltered.Conclusions:Although we confirm that MCFA do not lead to ceramide and IMTG accumulation in skeletal muscle tissue in humans, they do induce insulin resistance. These results indicate that, in humans, MCFA may not be beneficial in preventing peripheral insulin resistance.
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- 2012
15. Clinical dyslipidaemia is associated with changes in the lipid composition and inflammatory properties of apolipoprotein-B-containing lipoproteins from women with type 2 diabetes
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Stahlman, M, Pham, Huong, Adiels, M, Mitchell, Todd, Blanksby, Stephen, Fagerberg, B, Ekroos, K, Boren, J, Stahlman, M, Pham, Huong, Adiels, M, Mitchell, Todd, Blanksby, Stephen, Fagerberg, B, Ekroos, K, and Boren, J
- Abstract
Free to read at publisher The aim of this study was to use lipidomics to determine if the lipid composition of apolipoprotein-B-containing lipoproteins is modified by dyslipidaemia in type 2 diabetes and if any of the identified changes potentially have biological relevance in the pathophysiology of type 2 diabetes. VLDL and LDL from normolipidaemic and dyslipidaemic type 2 diabetic women and controls were isolated and quantified with HPLC and mass spectrometry. A detailed molecular characterisation of VLDL triacylglycerols (TAG) was also performed using the novel ozone-induced dissociation method, which allowed us to distinguish vaccenic acid (C18:1 n-7) from oleic acid (C18:1 n-9) in specific TAG species. Lipid class composition was very similar in VLDL and LDL from normolipidaemic type 2 diabetic and control participants. By contrast, dyslipidaemia was associated with significant changes in both lipid classes (e.g. increased diacylglycerols) and lipid species (e.g. increased C16:1 and C20:3 in phosphatidylcholine and cholesteryl ester and increased C16:0 [palmitic acid] and vaccenic acid in TAG). Levels of palmitic acid in VLDL and LDL TAG correlated with insulin resistance, and VLDL TAG enriched in palmitic acid promoted increased secretion of proinflammatory mediators from human smooth muscle cells. We showed that dyslipidaemia is associated with major changes in both lipid class and lipid species composition in VLDL and LDL from women with type 2 diabetes. In addition, we identified specific molecular lipid species that both correlate with clinical variables and are proinflammatory. Our study thus shows the potential of advanced lipidomic methods to further understand the pathophysiology of type 2 diabetes.
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- 2012
16. Muscle ceramide content in man is higher in type I than type II fibers and not influenced by glycogen content
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Nordby, P, Prats, C, Kristensen, D, Ekroos, K, Forsberg, G, Andersen, J L, Ploug, T, Dela, F, Storlien, L, Helge, J W, Nordby, P, Prats, C, Kristensen, D, Ekroos, K, Forsberg, G, Andersen, J L, Ploug, T, Dela, F, Storlien, L, and Helge, J W
- Abstract
Human muscle is studied during glycogen depletion and repletion to understand the influence of exercise and muscle glycogen on total ceramide content. In addition, fiber-type-specific ceramide storage is investigated. Ten healthy males (26.4 +/- 0.9 years, BMI 24.4 +/- 0.7 kg m(-2) and VO2max 57 +/- 2 mL O2 min(-1) kg(-1)) participated in the study. On the first day, one leg was glycogen-depleted (DL) by exhaustive intermittent exercise followed by low carbohydrate diet. Next day, in the overnight fasted condition, muscle biopsies were excised from vastus lateralis before and after exhaustive exercise from both DL and control leg (CL). Muscle glycogen was analyzed biochemically and total muscle ceramide content by 2D quantitative lipidomic approach. Furthermore, fiber-type ceramide content was determined by fluorescence immunohistochemistry. Basal muscle glycogen was decreased (P < 0.05) with 50 +/- 6% in DL versus CL. After exhaustive exercise, muscle glycogen was similar in CL and DL 139 +/- 38 and 110 +/- 31 mmol kg(-1), respectively. Total muscle ceramide 58 +/- 1 pmol mg(-1) was not influenced by glycogen or exercise. Ceramide content was consistently higher (P < 0.001) in type I than in type II muscle fibers. In conclusion, human skeletal muscle, ceramide content is higher in type I than in type II. Despite rather large changes in muscle glycogen induced by prior depletion, exercise to exhaustion and repletion, total muscle ceramide concentration remained unchanged.
- Published
- 2010
17. Differences in membrane acyl phospholipid composition between an endothermic mammal and an ectothermic reptile are not limited to any phospholipid class
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Mitchell, Todd, Ekroos, K, Blanksby, Stephen, Hulbert, Anthony, Else, Paul, Mitchell, Todd, Ekroos, K, Blanksby, Stephen, Hulbert, Anthony, and Else, Paul
- Abstract
This study examined questions concerning differences in the acyl composition of membrane phospholipids that have been linked to the faster rates of metabolic processes in endotherms versus ectotherms. In liver, kidney, heart and brain of the ectothermic reptile, Trachydosaurus rugosus, and the endothermic mammal, Rattus norvegicus, previous findings of fewer unsaturates but a greater unsaturation index (UI) in membranes of the mammal versus those of the reptile were confirmed. Moreover, the study showed that the distribution of phospholipid head-group classes was similar in the same tissues of the reptile and mammal and that the differences in acyl composition were present in all phospholipid classes analysed, suggesting a role for the physical over the chemical properties of membranes in determining the faster rates of metabolic processes in endotherms. The most common phosphatidylcholine (PC) molecules present in all tissues (except brain) of the reptile were 16:0/18:1, 16:0/18:2, 18:0/18:2, 18:1/18:1 and 18:1/18:2, whereas arachidonic acid (20:4), containing PCs 16:0/ 20: 4, 18: 0/ 20: 4, were the common molecules in the mammal. The most abundant phosphatidylethanolamines ( PE) used in the tissue of the reptile were 18:0/18:2, 18:0/20:4, 18:1/18:1, 18:1/18:2 and 18:1/20:4, compared to 16: 0/ 18: 2, 16: 0/ 20: 4, 16: 0/ 22: 6, 18: 0/ 20: 4, 18: 0/ 22: 6 and 18:1/20: 4 in the mammal. UI differences were primarily due to arachidonic acid found in both PC and PEs, whereas docosahexaenoic acid (22:6) was a lesser contributor mainly within PEs and essentially absent in the kidney. The phospholipid composition of brain was more similar in the reptile and mammal compared to those of other tissues.
- Published
- 2007
18. Differences in membrane acyl phospholipid composition between an endothermic mammal and an ectothermic reptile are not limited to any phospholipid class
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Blanksby, Stephen J, Mitchell, Todd W, Hulbert, Anthony J, Else, Paul, Ekroos, K, Blanksby, Stephen J, Mitchell, Todd W, Hulbert, Anthony J, Else, Paul, and Ekroos, K
- Abstract
This study examined questions concerning differences in the acyl composition of membrane phospholipids that have been linked to the faster rates of metabolic processes in endotherms versus ectotherms. In liver, kidney, heart and brain of the ectothermic reptile, Trachydosaurus rugosus, and the endothermic mammal, Rattus norvegicus, previous findings of fewer unsaturates but a greater unsaturation index (UI) in membranes of the mammal versus those of the reptile were confirmed. Moreover, the study showed that the distribution of phospholipid head-group classes was similar in the same tissues of the reptile and mammal and that the differences in acyl composition were present in all phospholipid classes analysed, suggesting a role for the physical over the chemical properties of membranes in determining the faster rates of metabolic processes in endotherms. The most common phosphatidylcholine (PC) molecules present in all tissues (except brain) of the reptile were 16:0/18:1, 16:0/18:2, 18:0/18:2, 18:1/18:1 and 18:1/18:2, whereas arachidonic acid (20:4), containing PCs 16:0/20:4, 18:0/20:4, were the common molecules in the mammal. The most abundant phosphatidylethanolamines (PE) used in the tissue of the reptile were 18:0/18:2, 18:0/20:4, 18:1/18:1, 18:1/18:2 and 18:1/20:4, compared to 16:0/18:2, 16:0/20:4, 16:0/22:6, 18:0/20:4, 18:0/22:6 and 18:1/20:4 in the mammal. UI differences were primarily due to arachidonic acid found in both PC and PEs, whereas docosahexaenoic acid (22:6) was a lesser contributor mainly within PEs and essentially absent in the kidney. The phospholipid composition of brain was more similar in the reptile and mammal compared to those of other tissues.
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- 2007
19. 188 DIABETIC DYSLIPIDEMIA IS RESPONSIBLE FOR QUALITATIVE AND QUANTITATIVE CHANGES IN HDL LIPID COMPOSITION
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Ståhlman, M., primary, Kontush, A., additional, Fagerberg, B., additional, Ekroos, K., additional, Chapman, J., additional, and Borén, J., additional
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- 2011
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20. 24 SENSITIVE BIOMARKER FOR STATIN-INDUCED MYOTOXICITY
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Laaksonen, R., primary, Tarasov, K., additional, Kauhanen, D., additional, Sylvänne, T., additional, Jänis, M., additional, Hurme, R., additional, Ekroos, K., additional, Mombelli, G., additional, Sirtori, C., additional, and Tardif, J.-C., additional
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- 2011
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21. 488 EFFICACY BIOMARKER FOR PCSK9 INHIBITORS
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Laaksonen, R., primary, Koistinen, K., additional, Huuhilo, R., additional, Tarasov, K., additional, Hurme, R., additional, Ekroos, K., additional, Prat, A., additional, Seidah, N., additional, and Jänis, M., additional
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- 2011
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22. 128 ARAP2-INDUCED CHANGES IN SPHINGOLIPID BIOSYNTHESIS PROMOTE LIPID DROPLET FORMATION BY INCREASING GLUT1 LEVELS IN THE PLASMA MEMBRANE
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Li, L., primary, Mobini, R., additional, Lu, E., additional, Rutberg, M., additional, Ståhlman, M., additional, Håversen, L., additional, Liu, B., additional, Larsson, T., additional, Perkins, R., additional, Andersson, L., additional, Koistinen, K., additional, Ekroos, K., additional, Borén, J., additional, and Olofsson, S.-O., additional
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- 2011
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23. W27 LIPID LOWERING THERAPY INDUCES A SIGNIFICANT UPREGULATION OF THE PLASMA LIPIDOME IN FH PATIENTS
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Laaksonen, R., primary, Jänis, M., additional, Tarasov, K., additional, Hurme, R., additional, Marais, D., additional, and Ekroos, K., additional
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- 2010
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24. Abstract: 585 LIPIDOMICS CAN BE USED IN PERSONALIZING CHOLESTEROL SYNTHESIS AND ABSORPTION INHIBITOR TREATMENTS
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Laaksonen, R, primary, Gouni-Berthold, I, additional, Gylling, H, additional, Berthold, H, additional, Verma, A, additional, Tarasov, K, additional, Hurme, R, additional, and Ekroos, K, additional
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- 2009
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25. Abstract: 70 CHANGES IN LIPOPROTEIN COMPOSITION IN DIABETIC DYSLIPIEMIA
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Ståhlman, M, primary, Hiukka, A, additional, Taskinen, M-R, additional, Ekroos, K, additional, and Boren, J, additional
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- 2009
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26. Abstract: 105 INCREASED PLASMA CERAMIDES FOLLOW STATIN-INDUCED MUSCLE TOXICITY
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Laaksonen, R, primary, Mombelli, G, additional, Tarasov, K, additional, Kauhanen, D, additional, Koistinen, K, additional, Hurme, R, additional, Sirtori, C, additional, and Ekroos, K, additional
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- 2009
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27. Abstract: P1164 EZETIMIBE RESULTS IN INCREASED HDL LIPID CONTENT AND PARTICLE SIZE
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Ekroos, K, primary, Ståhlman, M, additional, Verma, A, additional, Sylvänne, T, additional, Hurme, R, additional, Berthold, H, additional, Gouni-Berthold, I, additional, Boren, J, additional, and Laaksonen, R, additional
- Published
- 2009
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28. Concordant inter-laboratory derived concentrations of ceramides in human plasma reference materials via authentic standards.
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Torta F, Hoffmann N, Burla B, Alecu I, Arita M, Bamba T, Bennett SAL, Bertrand-Michel J, Brügger B, Cala MP, Camacho-Muñoz D, Checa A, Chen M, Chocholoušková M, Cinel M, Chu-Van E, Colsch B, Coman C, Connell L, Sousa BC, Dickens AM, Fedorova M, Eiríksson FF, Gallart-Ayala H, Ghorasaini M, Giera M, Guan XL, Haid M, Hankemeier T, Harms A, Höring M, Holčapek M, Hornemann T, Hu C, Hülsmeier AJ, Huynh K, Jones CM, Ivanisevic J, Izumi Y, Köfeler HC, Lam SM, Lange M, Lee JC, Liebisch G, Lippa K, Lopez-Clavijo AF, Manzi M, Martinefski MR, Math RGH, Mayor S, Meikle PJ, Monge ME, Moon MH, Muralidharan S, Nicolaou A, Nguyen-Tran T, O'Donnell VB, Orešič M, Ramanathan A, Riols F, Saigusa D, Schock TB, Schwartz-Zimmermann H, Shui G, Singh M, Takahashi M, Thorsteinsdóttir M, Tomiyasu N, Tournadre A, Tsugawa H, Tyrrell VJ, van der Gugten G, Wakelam MO, Wheelock CE, Wolrab D, Xu G, Xu T, Bowden JA, Ekroos K, Ahrends R, and Wenk MR
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- Humans, Calibration, Mass Spectrometry methods, Lipidomics methods, Reproducibility of Results, Ceramides blood, Reference Standards, Laboratories standards
- Abstract
In this community effort, we compare measurements between 34 laboratories from 19 countries, utilizing mixtures of labelled authentic synthetic standards, to quantify by mass spectrometry four clinically used ceramide species in the NIST (National Institute of Standards and Technology) human blood plasma Standard Reference Material (SRM) 1950, as well as a set of candidate plasma reference materials (RM 8231). Participants either utilized a provided validated method and/or their method of choice. Mean concentration values, and intra- and inter-laboratory coefficients of variation (CV) were calculated using single-point and multi-point calibrations, respectively. These results are the most precise (intra-laboratory CVs ≤ 4.2%) and concordant (inter-laboratory CVs < 14%) community-derived absolute concentration values reported to date for four clinically used ceramides in the commonly analyzed SRM 1950. We demonstrate that calibration using authentic labelled standards dramatically reduces data variability. Furthermore, we show how the use of shared RM can correct systematic quantitative biases and help in harmonizing lipidomics. Collectively, the results from the present study provide a significant knowledge base for translation of lipidomic technologies to future clinical applications that might require the determination of reference intervals (RIs) in various human populations or might need to estimate reference change values (RCV), when analytical variability is a key factor for recall during multiple testing of individuals., (© 2024. The Author(s).)
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- 2024
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29. Pitfalls in lipid mass spectrometry of mammalian samples - a brief guide for biologists.
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Skotland T, Ekroos K, McDonald J, Ahrends R, Liebisch G, and Sandvig K
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- Animals, Humans, Lipid Metabolism, Lipids analysis, Lipids chemistry, Mass Spectrometry methods, Mammals
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- 2024
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30. The lipidomics reporting checklist a framework for transparency of lipidomic experiments and repurposing resource data.
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Kopczynski D, Ejsing CS, McDonald JG, Bamba T, Baker ES, Bertrand-Michel J, Brügger B, Coman C, Ellis SR, Garrett TJ, Griffiths WJ, Guan XL, Han X, Höring M, Holčapek M, Hoffmann N, Huynh K, Lehmann R, Jones JW, Kaddurah-Daouk R, Köfeler HC, Meikle PJ, Metz TO, O'Donnell VB, Saigusa D, Schwudke D, Shevchenko A, Torta F, Vizcaíno JA, Welti R, Wenk MR, Wolrab D, Xia Y, Ekroos K, Ahrends R, and Liebisch G
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- Humans, Lipids analysis, Lipids chemistry, Lipidomics methods, Lipidomics standards, Checklist
- Abstract
The rapid increase in lipidomic studies has led to a collaborative effort within the community to establish standards and criteria for producing, documenting, and disseminating data. Creating a dynamic easy-to-use checklist that condenses key information about lipidomic experiments into common terminology will enhance the field's consistency, comparability, and repeatability. Here, we describe the structure and rationale of the established Lipidomics Minimal Reporting Checklist to increase transparency in lipidomics research., Competing Interests: Conflict of interests Kaddurah-Daouk is an inventor on key patents in the field of metabolomics and hold equity in Metabolon, a biotech company in North Carolina. In addition, she holds patents licensed to Chymia LLC and PsyProtix with royalties and ownership. Kim Ekroos is the owner of Lipidomics Consulting Ltd., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)
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- 2024
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31. Toward Omics-Scale Quantitative Mass Spectrometry Imaging of Lipids in Brain Tissue Using a Multiclass Internal Standard Mixture.
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Vandenbosch M, Mutuku SM, Mantas MJQ, Patterson NH, Hallmark T, Claesen M, Heeren RMA, Hatcher NG, Verbeeck N, Ekroos K, and Ellis SR
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- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization methods, Lipids analysis, Brain metabolism, Diagnostic Imaging, Lipidomics
- Abstract
Mass spectrometry imaging (MSI) has accelerated our understanding of lipid metabolism and spatial distribution in tissues and cells. However, few MSI studies have approached lipid imaging quantitatively and those that have focused on a single lipid class. We overcome this limitation by using a multiclass internal standard (IS) mixture sprayed homogeneously over the tissue surface with concentrations that reflect those of endogenous lipids. This enabled quantitative MSI (Q-MSI) of 13 lipid classes and subclasses representing almost 200 sum-composition lipid species using both MALDI (negative ion mode) and MALDI-2 (positive ion mode) and pixel-wise normalization of each lipid species in a manner analogous to that widely used in shotgun lipidomics. The Q-MSI approach covered 3 orders of magnitude in dynamic range (lipid concentrations reported in pmol/mm
2 ) and revealed subtle changes in distribution compared to data without normalization. The robustness of the method was evaluated by repeating experiments in two laboratories using both timsTOF and Orbitrap mass spectrometers with an ∼4-fold difference in mass resolution power. There was a strong overall correlation in the Q-MSI results obtained by using the two approaches. Outliers were mostly rationalized by isobaric interferences or the higher sensitivity of one instrument for a particular lipid species. These data provide insight into how the mass resolving power can affect Q-MSI data. This approach opens up the possibility of performing large-scale Q-MSI studies across numerous lipid classes and subclasses and revealing how absolute lipid concentrations vary throughout and between biological tissues.- Published
- 2023
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32. LipidSpace: Simple Exploration, Reanalysis, and Quality Control of Large-Scale Lipidomics Studies.
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Kopczynski D, Hoffmann N, Troppmair N, Coman C, Ekroos K, Kreutz MR, Liebisch G, Schwudke D, and Ahrends R
- Subjects
- Lipidomics, Lipids analysis
- Abstract
Lipid analysis gained significant importance due to the enormous range of lipid functions, e.g., energy storage, signaling, or structural components. Whole lipidomes can be quantitatively studied in-depth thanks to recent analytical advancements. However, the systematic comparison of thousands of distinct lipidomes remains challenging. We introduce LipidSpace, a standalone tool for analyzing lipidomes by assessing their structural and quantitative differences. A graph-based comparison of lipid structures is the basis for calculating structural space models and subsequently computing lipidome similarities. When adding study variables such as body weight or health condition, LipidSpace can determine lipid subsets across all lipidomes that describe these study variables well by utilizing machine-learning approaches. The user-friendly GUI offers four built-in tutorials and interactive visual interfaces with pdf export. Many supported data formats allow an efficient (re)analysis of data sets from different sources. An integrated interactive workflow guides the user through the quality control steps. We used this suite to reanalyze and combine already published data sets (e.g., one with about 2500 samples and 576 lipids in one run) and made additional discoveries to the published conclusions with the potential to fill gaps in the current lipid biology understanding. LipidSpace is available for Windows or Linux (https://lifs-tools.org).
- Published
- 2023
- Full Text
- View/download PDF
33. Investigating Performance of the SLIM-Based High Resolution Ion Mobility Platform for Separation of Isomeric Phosphatidylcholine Species.
- Author
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Kedia K, Harris R, Ekroos K, Moser KW, DeBord D, Tiberi P, Goracci L, Zhang NR, Wang W, Spellman DS, and Bateman K
- Abstract
Lipids are structurally diverse molecules that play a pivotal role in a plethora of biological processes. However, deciphering the biological roles of the specific lipids is challenging due to the existence of numerous isomers. This high chemical complexity of the lipidome is one of the major challenges in lipidomics research, as the traditional liquid chromatography-mass spectrometry (LC-MS) based approaches are often not powerful enough to resolve these isomeric and isobaric nuances within complex samples. Thus, lipids are uniquely suited to the benefits provided by multidimensional liquid chromatography-ion mobility-mass spectrometry (LC-IM-MS) analysis. However, many forms of lipid isomerism, including double-bond positional isomers and regioisomers, are structurally similar such that their collision cross section (CCS) differences are unresolvable via conventional IM approaches. Here we evaluate the performance of a high resolution ion mobility (HRIM) system based on structures for lossless ion manipulation (SLIM) technology interfaced to a high resolution quadrupole time-of-flight (QTOF) analyzer to address the noted lipidomic isomerism challenge. SLIM implements the traveling wave ion mobility technique along an ∼13 m ion path, providing longer path lengths to enable improved separation of isomeric features. We demonstrate the power of HRIM-MS to dissect isomeric PC standards differing only in double bond (DB) and stereospecific number (SN) positions. The partial separation of protonated DB isomers is significantly enhanced when they are analyzed as metal adducts. For sodium adducts, we achieve close to baseline separation of three different PC 18:1/18:1 isomers with different cis -double bond locations. Similarly, PC 18:1/18:1 ( cis -9) can be resolved from the corresponding PC 18:1/18:1 ( trans -9) form. The separation capacity is further enhanced when using silver ion doping, enabling the baseline separation of regioisomers that cannot be resolved when measured as sodium adducts. The sensitivity and reproducibility of the approach were assessed, and the performance for more complex mixtures was benchmarked by identifying PC isomers in total brain and liver lipid extracts.
- Published
- 2023
- Full Text
- View/download PDF
34. Ex vivo instability of lipids in whole blood: preanalytical recommendations for clinical lipidomics studies.
- Author
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Wang Q, Hoene M, Hu C, Fritsche L, Ahrends R, Liebisch G, Ekroos K, Fritsche A, Birkenfeld AL, Liu X, Zhao X, Li Q, Su B, Peter A, Xu G, and Lehmann R
- Subjects
- Edetic Acid, Reproducibility of Results, Mass Spectrometry methods, Lipidomics methods, Lipids chemistry
- Abstract
Reliability, robustness, and interlaboratory comparability of quantitative measurements is critical for clinical lipidomics studies. Lipids' different ex vivo stability in blood bears the risk of misinterpretation of data. Clear recommendations for the process of blood sample collection are required. We studied by UHPLC-high resolution mass spectrometry, as part of the "Preanalytics interest group" of the International Lipidomics Society, the stability of 417 lipid species in EDTA whole blood after exposure to either 4°C, 21°C, or 30°C at six different time points (0.5 h-24 h) to cover common daily routine conditions in clinical settings. In total, >800 samples were analyzed. 325 and 288 robust lipid species resisted 24 h exposure of EDTA whole blood to 21°C or 30°C, respectively. Most significant instabilities were detected for FA, LPE, and LPC. Based on our data, we recommend cooling whole blood at once and permanent. Plasma should be separated within 4 h, unless the focus is solely on robust lipids. Lists are provided to check the ex vivo (in)stability of distinct lipids and potential biomarkers of interest in whole blood. To conclude, our results contribute to the international efforts towards reliable and comparable clinical lipidomics data paving the way to the proper diagnostic application of distinct lipid patterns or lipid profiles in the future., Competing Interests: Conflict of interest The authors declare that they have no conflicts of interest with the contents of this article., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)
- Published
- 2023
- Full Text
- View/download PDF
35. Multi-Omic analyses characterize the ceramide/sphingomyelin pathway as a therapeutic target in Alzheimer's disease.
- Author
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Baloni P, Arnold M, Buitrago L, Nho K, Moreno H, Huynh K, Brauner B, Louie G, Kueider-Paisley A, Suhre K, Saykin AJ, Ekroos K, Meikle PJ, Hood L, Price ND, Doraiswamy PM, Funk CC, Hernández AI, Kastenmüller G, Baillie R, Han X, and Kaddurah-Daouk R
- Subjects
- Animals, Ceramides, Fingolimod Hydrochloride, Genome-Wide Association Study, Humans, Mice, Sphingolipids metabolism, Sphingolipids therapeutic use, Sphingomyelins therapeutic use, Alzheimer Disease drug therapy, Alzheimer Disease genetics, Alzheimer Disease metabolism
- Abstract
Dysregulation of sphingomyelin and ceramide metabolism have been implicated in Alzheimer's disease. Genome-wide and transcriptome-wide association studies have identified various genes and genetic variants in lipid metabolism that are associated with Alzheimer's disease. However, the molecular mechanisms of sphingomyelin and ceramide disruption remain to be determined. We focus on the sphingolipid pathway and carry out multi-omics analyses to identify central and peripheral metabolic changes in Alzheimer's patients, correlating them to imaging features. Our multi-omics approach is based on (a) 2114 human post-mortem brain transcriptomics to identify differentially expressed genes; (b) in silico metabolic flux analysis on context-specific metabolic networks identified differential reaction fluxes; (c) multimodal neuroimaging analysis on 1576 participants to associate genetic variants in sphingomyelin pathway with Alzheimer's disease pathogenesis; (d) plasma metabolomic and lipidomic analysis to identify associations of lipid species with dysregulation in Alzheimer's; and (e) metabolite genome-wide association studies to define receptors within the pathway as a potential drug target. We validate our hypothesis in amyloidogenic APP/PS1 mice and show prolonged exposure to fingolimod alleviated synaptic plasticity and cognitive impairment in mice. Our integrative multi-omics approach identifies potential targets in the sphingomyelin pathway and suggests modulators of S1P metabolism as possible candidates for Alzheimer's disease treatment., (© 2022. The Author(s).)
- Published
- 2022
- Full Text
- View/download PDF
36. Benchmarking One-Phase Lipid Extractions for Plasma Lipidomics.
- Author
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Höring M, Stieglmeier C, Schnabel K, Hallmark T, Ekroos K, Burkhardt R, and Liebisch G
- Subjects
- Humans, Mass Spectrometry methods, Methanol chemistry, Phospholipids, Solvents chemistry, Triglycerides, Benchmarking, Lipidomics
- Abstract
A key element of successful lipidomics analysis is a sufficient extraction of lipid molecules typically by two-phase systems such as chloroform-based Bligh and Dyer (B&D). However, numerous metabolomics and lipidomics studies today apply easy to use one-phase extractions. In this work, quantitative flow injection analysis high-resolution mass spectrometry was applied to benchmark the lipid recovery of popular one-phase extraction methods for human plasma samples. The following organic solvents were investigated: methanol (MeOH), ethanol (EtOH), 2-propanol (IPA), 1-butanol (BuOH), acetonitrile (ACN) and the solvent mixtures BuOH/MeOH (3:1) and MeOH/ACN (1:1). The recovery of polar lysophospholipids was sufficient for all tested solvents. However, nonpolar lipid classes such as triglycerides (TG) and cholesteryl esters (CE) revealed extraction efficiencies less than 5% due to precipitation in polar solvents EtOH, MeOH, MeOH/ACN, and ACN. Sample pellets also contained a substantial amount of phospholipids, for example, more than 75% of total phosphatidylcholine and sphingomyelin for ACN. The loss of lipids by precipitation was directly related to the polarity of solvents and lipid classes. Although, lipid recovery increased with the volume of organic solvent, recovery in polar MeOH remains incomplete also for less polar lipid classes such as ceramides. Addition of stable isotope-labeled internal standards prior to lipid extraction could compensate for insufficient lipid recovery for polar lipid classes including lysolipids and phospholipids but not for nonpolar CE and TG. In summary, application of one-phase extractions should be limited to polar lipid classes unless sufficient recovery/solubility of nonpolar lipids has been demonstrated. The presented data reveal that appropriate lipid extraction efficiency is fundamental to achieve accurate lipid quantification.
- Published
- 2022
- Full Text
- View/download PDF
37. Introducing the Lipidomics Minimal Reporting Checklist.
- Author
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McDonald JG, Ejsing CS, Kopczynski D, Holčapek M, Aoki J, Arita M, Arita M, Baker ES, Bertrand-Michel J, Bowden JA, Brügger B, Ellis SR, Fedorova M, Griffiths WJ, Han X, Hartler J, Hoffmann N, Koelmel JP, Köfeler HC, Mitchell TW, O'Donnell VB, Saigusa D, Schwudke D, Shevchenko A, Ulmer CZ, Wenk MR, Witting M, Wolrab D, Xia Y, Ahrends R, Liebisch G, and Ekroos K
- Subjects
- Lipid Metabolism, Mass Spectrometry, Checklist, Lipidomics
- Published
- 2022
- Full Text
- View/download PDF
38. Validation of a multiplexed and targeted lipidomics assay for accurate quantification of lipidomes.
- Author
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Zhang NR, Hatcher NG, Ekroos K, Kedia K, Kandebo M, Marcus JN, Smith SM, Bateman KP, and Spellman DS
- Subjects
- Animals, Chromatography, Liquid, Lipids, Mice, Reproducibility of Results, Lipidomics, Tandem Mass Spectrometry methods
- Abstract
A major challenge of lipidomics is to determine and quantify the precise content of complex lipidomes to the exact lipid molecular species. Often, multiple methods are needed to achieve sufficient lipidomic coverage to make these determinations. Multiplexed targeted assays offer a practical alternative to enable quantitative lipidomics amenable to quality control standards within a scalable platform. Herein, we developed a multiplexed normal phase liquid chromatography-hydrophilic interaction chromatography multiple reaction monitoring method that quantifies lipid molecular species across over 20 lipid classes spanning wide polarities in a single 20-min run. Analytical challenges such as in-source fragmentation, isomer separations, and concentration dynamics were addressed to ensure confidence in selectivity, quantification, and reproducibility. Utilizing multiple MS/MS product ions per lipid species not only improved the confidence of lipid identification but also enabled the determination of relative abundances of positional isomers in samples. Lipid class-based calibration curves were applied to interpolate lipid concentrations and guide sample dilution. Analytical validation was performed following FDA Bioanalytical Method Validation Guidance for Industry. We report repeatable and robust quantitation of 900 lipid species measured in NIST-SRM-1950 plasma, with over 700 lipids achieving inter-assay variability below 25%. To demonstrate proof of concept for biomarker discovery, we analyzed plasma from mice treated with a glucosylceramide synthase inhibitor, benzoxazole 1. We observed expected reductions in glucosylceramide levels in treated animals but, more notably, identified novel lipid biomarker candidates from the plasma lipidome. These data highlight the utility of this qualified lipidomic platform for enabling biological discovery., Competing Interests: Conflicts of interest The authors declare that they have no competing interests on every aspect of the work., (Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved.)
- Published
- 2022
- Full Text
- View/download PDF
39. Clinical lipidomics - A community-driven roadmap to translate research into clinical applications.
- Author
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Vvedenskaya O, Holčapek M, Vogeser M, Ekroos K, Meikle PJ, and Bendt AK
- Abstract
Lipid metabolites, beyond triglycerides and cholesterol, have been shown to have vast potential for applications in clinical applications, with substantial societal and economical value. To successfully evolve from the current research-grade methods to assays suitable for routine clinical applications, a harmonization - if not standardization - of these mass spectrometry-based workflows is necessary. Input on clinical needs and technological capabilities must be obtained from all relevant stakeholders, including wet lab scientists, informaticians and data scientists, manufacturers, and medical professionals. In order to build bridges between this diverse group of professionals, the International Lipidomics Society and its Clinical Lipidomics Interest Group were created. This opinion article is intended to provide an overview of international efforts to tackle the issues of workflow harmonization, and to serve as an open invitation for others to join this growing community., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2022 THE AUTHORS. Publishing services by ELSEVIER B.V. on behalf of MSACL.)
- Published
- 2022
- Full Text
- View/download PDF
40. Comparison of Kit-Based Metabolomics with Other Methodologies in a Large Cohort, towards Establishing Reference Values.
- Author
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Saigusa D, Hishinuma E, Matsukawa N, Takahashi M, Inoue J, Tadaka S, Motoike IN, Hozawa A, Izumi Y, Bamba T, Kinoshita K, Ekroos K, Koshiba S, and Yamamoto M
- Abstract
Metabolic profiling is an omics approach that can be used to observe phenotypic changes, making it particularly attractive for biomarker discovery. Although several candidate metabolites biomarkers for disease expression have been identified in recent clinical studies, the reference values of healthy subjects have not been established. In particular, the accuracy of concentrations measured by mass spectrometry (MS) is unclear. Therefore, comprehensive metabolic profiling in large-scale cohorts by MS to create a database with reference ranges is essential for evaluating the quality of the discovered biomarkers. In this study, we tested 8700 plasma samples by commercial kit-based metabolomics and separated them into two groups of 6159 and 2541 analyses based on the different ultra-high-performance tandem mass spectrometry (UHPLC-MS/MS) systems. We evaluated the quality of the quantified values of the detected metabolites from the reference materials in the group of 2541 compared with the quantified values from other platforms, such as nuclear magnetic resonance (NMR), supercritical fluid chromatography tandem mass spectrometry (SFC-MS/MS) and UHPLC-Fourier transform mass spectrometry (FTMS). The values of the amino acids were highly correlated with the NMR results, and lipid species such as phosphatidylcholines and ceramides showed good correlation, while the values of triglycerides and cholesterol esters correlated less to the lipidomics analyses performed using SFC-MS/MS and UHPLC-FTMS. The evaluation of the quantified values by MS-based techniques is essential for metabolic profiling in a large-scale cohort.
- Published
- 2021
- Full Text
- View/download PDF
41. Quality control requirements for the correct annotation of lipidomics data.
- Author
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Köfeler HC, Eichmann TO, Ahrends R, Bowden JA, Danne-Rasche N, Dennis EA, Fedorova M, Griffiths WJ, Han X, Hartler J, Holčapek M, Jirásko R, Koelmel JP, Ejsing CS, Liebisch G, Ni Z, O'Donnell VB, Quehenberger O, Schwudke D, Shevchenko A, Wakelam MJO, Wenk MR, Wolrab D, and Ekroos K
- Subjects
- Humans, Quality Control, Lipidomics, Metabolomics
- Published
- 2021
- Full Text
- View/download PDF
42. Development of an On-Tissue Derivatization Method for MALDI Mass Spectrometry Imaging of Bioactive Lipids Containing Phosphate Monoester Using Phos-tag.
- Author
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Iwama T, Kano K, Saigusa D, Ekroos K, van Echten-Deckert G, Vogt J, and Aoki J
- Subjects
- Animals, Mice, Pyridines, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Lipids, Phosphates
- Abstract
Matrix-assisted laser desorption ionization-mass spectrometry imaging (MALDI-MSI) is an emerging label-free method for mapping the distribution of diverse molecular species in tissue sections. Despite recent progress in MALDI-MSI analyses of lipids, it is still difficult to visualize minor bioactive lipids including lysophosphatidic acid (LPA) and sphingosine-1-phosphate (S1P). Here, we have developed a novel on-tissue derivatization method using Phos-tag, a zinc complex that specifically binds to a phosphate monoester group. MALDI-MSI with Phos-tag derivatization made it possible to image LPA and S1P in the murine brain. Furthermore, we were able to visualize other low-abundance lipids containing phosphate monoester, such as phosphatidic acid and ceramide-1-phosphate. Compared with conventional MALDI-MS, this derivatization produced LPA images with high spatial accuracy discriminating LPA artificially produced during MALDI-MS analysis. In mice with deficiencies in enzymes that degrade LPA and S1P, we observed marked S1P and/or LPA accumulation in specific regions of the brain. Thus, the present study provides a simple and optimal way to reveal the spatial localization of potent bioactive lipid phosphates such as LPA and S1P in tissues.
- Published
- 2021
- Full Text
- View/download PDF
43. High-defined quantitative snapshots of the ganglioside lipidome using high resolution ion mobility SLIM assisted shotgun lipidomics.
- Author
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Wormwood Moser KL, Van Aken G, DeBord D, Hatcher NG, Maxon L, Sherman M, Yao L, and Ekroos K
- Subjects
- Animals, Humans, Ions, Isomerism, Mass Spectrometry, Mice, Gangliosides, Lipidomics
- Abstract
Defects in sphingolipid metabolism have emerged as a common link across neurodegenerative disorders, and a deeper understanding of the lipid content in preclinical models and patient specimens offers opportunities for development of new therapeutic targets and biomarkers. Sphingolipid metabolic pathways include the formation of glycosphingolipid species that branch into staggeringly complex structural heterogeneity within the globoside and ganglioside sub-lipidomes. Characterization of these sub-lipidomes has typically relied on liquid chromatography-mass spectrometry-based (LC-MS) approaches, but such assays are challenging and resource intensive due to the close structural heterogeneity, the presence of isobaric and isomeric species, and broad dynamic range of endogenous glycosphingolipids. Here, we apply Structures for Lossless Ion Manipulations (SLIM)-based High Resolution Ion Mobility (HRIM)-MS to enable rapid, repeatable, quantitative assays with deep structural information sufficient to resolve endogenous brain gangliosides at the level of individual molecular species. Analyses were performed using a prototype SLIM-MS instrument equipped with a 13-m serpentine path which enabled resolution of closely related isomeric analytes such as GD1a d36:1 and GD1b d36:1 based on recorded mass-to-charge (m/z) and arrival times. To demonstrate the power of our methodology, brain extracts derived from wild-type mice hemi-brains were analyzed by HRIM-MS using flow injection analyses (FIA) without the need for additional separation by liquid chromatography. Endogenous ganglioside species were readily resolved, identified, and quantified by FIA-SLIM-MS analyses within 2 min per sample. Thus, the FIA-SLIM-MS platform enables robust quantification across a broad range of lipid species in biological specimens in a standardized assay format that is readily scalable to support studies with large sample numbers., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier B.V. All rights reserved.)
- Published
- 2021
- Full Text
- View/download PDF
44. Recommendations for good practice in MS-based lipidomics.
- Author
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Köfeler HC, Ahrends R, Baker ES, Ekroos K, Han X, Hoffmann N, Holčapek M, Wenk MR, and Liebisch G
- Subjects
- Humans, Mass Spectrometry, Lipidomics standards, Lipids analysis
- Abstract
In the last 2 decades, lipidomics has become one of the fastest expanding scientific disciplines in biomedical research. With an increasing number of new research groups to the field, it is even more important to design guidelines for assuring high standards of data quality. The Lipidomics Standards Initiative is a community-based endeavor for the coordination of development of these best practice guidelines in lipidomics and is embedded within the International Lipidomics Society. It is the intention of this review to highlight the most quality-relevant aspects of the lipidomics workflow, including preanalytics, sample preparation, MS, and lipid species identification and quantitation. Furthermore, this review just does not only highlights examples of best practice but also sheds light on strengths, drawbacks, and pitfalls in the lipidomic analysis workflow. While this review is neither designed to be a step-by-step protocol by itself nor dedicated to a specific application of lipidomics, it should nevertheless provide the interested reader with links and original publications to obtain a comprehensive overview concerning the state-of-the-art practices in the field., Competing Interests: Conflict of interest The authors declare that they have no conflicts of interest with the contents of this article., (Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved.)
- Published
- 2021
- Full Text
- View/download PDF
45. Ceramide ratios are affected by cigarette smoke but not heat-not-burn or e-vapor aerosols across four independent mouse studies.
- Author
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Lavrynenko O, Titz B, Dijon S, Santos DD, Nury C, Schneider T, Guedj E, Szostak J, Kondylis A, Phillips B, Ekroos K, Martin F, Peitsch MC, Hoeng J, and Ivanov NV
- Subjects
- Aerosols adverse effects, Animals, Ceramides analysis, Chromatography, Liquid methods, Female, Humans, Mice, Mice, Inbred C57BL, Mice, Knockout, Proteomics, Risk Factors, Tandem Mass Spectrometry methods, Time Factors, Apolipoproteins E genetics, Ceramides metabolism, E-Cigarette Vapor adverse effects, Lung metabolism, Smoke adverse effects
- Abstract
Aims: Smoking is an important risk factor for the development of chronic obstructive pulmonary disease and cardiovascular diseases. This study aimed to further elucidate the role of ceramides, as a key lipid class dysregulated in disease states., Main Methods: In this article we developed and validated LC-MS/MS method for ceramides (Cer(d18:1/16:0), Cer(d18:1/18:0), Cer(d18:1/24:0) and Cer(d18:1/24:1(15Z)) for the absolute quantification. We deployed it together with proteomics and transcriptomic analysis to assess the effects of cigarette smoke (CS) from the reference cigarette as well as aerosols from heat-not-burn (HnB) tobacco and e-vapor products in apolipoprotein E-deficient (ApoE
-/- ) mice over several time points., Key Findings: In the lungs, CS exposure substantially elevated the ratios of Cer(d18:1/24:0) and Cer(d18:1/24:1) to Cer(d18:1/18:0) in two independent ApoE-/- mouse inhalation studies. Data from previous studies, in both ApoE-/- and wild-type mice, further confirmed the reproducibility of this finding. Elevation of these ceramide ratios was also observed in plasma/serum, the liver, and-for the Cer(d18:1/24:1(15Z)) to Cer(d18:1/18:0) ratio-the abdominal aorta. Also, the levels of acid ceramidase (Asah1) and glucocerebrosidase (Gba)-lysosomal enzymes involved in the hydrolysis of glucosylceramides-were consistently elevated in the lungs after CS exposure. In contrast, exposure to HnB tobacco product and e-vapor aerosols did not induce significant changes in the ceramide profiles or associated enzymes., Significance: Our work in mice contributes to the accumulating evidence on the importance of ceramide ratios as biologically relevant markers for respiratory disorders, adding to their already demonstrated role in cardiovascular disease risk assessment in humans., (Copyright © 2020 The Authors. Published by Elsevier Inc. All rights reserved.)- Published
- 2020
- Full Text
- View/download PDF
46. Impact of ion suppression by sample cap liners in lipidomics.
- Author
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Benke PI, Burla B, Ekroos K, Wenk MR, and Torta F
- Subjects
- Chromatography, Liquid, Humans, Lipids, Mass Spectrometry, Lipidomics, Metabolomics
- Abstract
Contamination from the polymeric material released by vial caps used for sample introduction in liquid chromatography can significantly affect the signal of the analyte of interest. In particular, repeated injections from the same sample vial can enhance this suppressing effect. Multiple injections of the same sample are often used in metabolomics and lipidomics during routine analyses. Here we demonstrate how the presence of contaminant polymers, originating from the vial closures, significantly influences the estimation of the relative amount of endogenous lipids in human plasma. Furthermore, this can negatively impact other operations in mass spectrometric analysis, such as instrument equilibration and tuning or the common use of technical replicates to improve confidence in data interpretation. Our observations provide critical information on how to improve future analyses through the use of appropriate vial caps, solvents, chromatographic separations and equipment., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. Acknowledgements Work in our laboratory is supported by grants from the National University of Singapore via the Life Sciences Institute (LSI), the National Research Foundation (NRF, NRFI2015-05 and NRFSBP-P4), the NRF and A∗STAR IAF-ICP I1901E0040, NUS iHealthtech Precision Medicine and Personalised Therapeutics., (Copyright © 2020 Elsevier B.V. All rights reserved.)
- Published
- 2020
- Full Text
- View/download PDF
47. Correction of Isobaric Overlap Resulting from Sodiated Ions in Lipidomics.
- Author
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Höring M, Ekroos K, Baker PRS, Connell L, Stadler SC, Burkhardt R, and Liebisch G
- Subjects
- Algorithms, Humans, Lipidomics statistics & numerical data, Lipids chemistry, Sodium chemistry, Spectrometry, Mass, Electrospray Ionization methods, Spectrometry, Mass, Electrospray Ionization statistics & numerical data, Lipidomics methods, Lipids blood
- Abstract
Lipidomic analyses aim for absolute quantification of lipid species profiles in biological samples. In past years, mass spectrometry (MS) methods based on high resolution accurate masses (HRAM) have increasingly been applied to identify and quantify lipid species on the MS level. This strategy requires consideration of isobaric overlaps which may also result from various adduct ions. Generally applied solvent additives favor the formation of protonated and ammoniated ions in positive ion mode, yet sodiated ions are also frequently observed. These sodiated ions interfere with protonated ions of the species of the same lipid class with two additional CH
2 and three double bonds (Δ m / z = 0.0025) and the first isotopic peak overlaps with ammoniated ions of a species with one additional CH2 and four double bonds (Δ m / z = 0.0057). In this work, we present an algorithm based on the sodiated to protonated/ammoniated adduct ion ratios of applied internal standards to correct for these interferences. We could demonstrate that these ratios differ significantly between lipid classes but are affected by neither chain length nor number of double bonds within a lipid class. Finally, the algorithm is demonstrated for correcting human serum samples analyzed by Fourier-transform mass spectrometry (FTMS). Here, the application of sodium correction significantly reduced overestimations and misidentifications.- Published
- 2020
- Full Text
- View/download PDF
48. Lipid-based biomarkers for CVD, COPD, and aging - A translational perspective.
- Author
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Ekroos K, Lavrynenko O, Titz B, Pater C, Hoeng J, and Ivanov NV
- Subjects
- Cardiovascular Diseases diagnosis, Humans, Pulmonary Disease, Chronic Obstructive diagnosis, Risk Assessment, Aging metabolism, Biomarkers analysis, Biomarkers metabolism, Cardiovascular Diseases metabolism, Lipids analysis, Pulmonary Disease, Chronic Obstructive metabolism
- Abstract
For many diseases, there is an unmet need for new or better biomarkers for improved disease risk assessment and monitoring, as available markers lack sufficient specificity. Lipids are drawing major interest as potential candidates for filling these gaps. This has recently been demonstrated by the identification of selective ceramides for prediction of cardiovascular mortality, enabling improved risk assessment of cardiovascular disease compared with conventional clinical markers. In this review, we discuss current lipid biomarker findings and the possible connection between cardiovascular disease, chronic obstructive pulmonary disease, and aging. Moreover, we discuss how to overcome the current roadblocks facing lipid biomarker research. We stress the need for improved quantification, standardization of methodologies, and establishment of initial reference values to allow for an efficient transfer path of research findings into the clinical landscape, and, ultimately, to put newly identified biomarkers into practical use., Competing Interests: Declaration of Competing Interest KE is the founder and CEO of Lipidomics Consulting Ltd. OL, BT, PC, JH, and NVI are employees of Philip Morris International., (Copyright © 2020 The Authors. Published by Elsevier Ltd.. All rights reserved.)
- Published
- 2020
- Full Text
- View/download PDF
49. Lipidomic analysis.
- Author
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Holčapek M, Liebisch G, and Ekroos K
- Published
- 2020
- Full Text
- View/download PDF
50. Lipidomics: Current state of the art in a fast moving field.
- Author
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O'Donnell VB, Ekroos K, Liebisch G, and Wakelam M
- Subjects
- Animals, Biomarkers analysis, Biomarkers metabolism, Biomedical Research, Humans, Lipid Metabolism, Lipids analysis, Mass Spectrometry, Precision Medicine, Lipidomics
- Abstract
Lipids are essential for all facets of life. They play three major roles: energy metabolism, structural, and signaling. They are dynamic molecules strongly influenced by endogenous and exogenous factors including genetics, diet, age, lifestyle, drugs, disease and inflammation. As precision medicine starts to become mainstream, there is a huge burgeoning interest in lipids and their potential to act as unique biomarkers or prognostic indicators. Lipids comprise a large component of all metabolites (around one-third), and our expanding knowledge about their dynamic behavior is fueling the hope that mapping their regulatory biochemical pathways on a systems level will revolutionize our ability to prevent, diagnose, and stratify major human diseases. Up to now, clinical lipid measurements have consisted primarily of total cholesterol or triglycerides, as a measure for cardiovascular risk and response to lipid lowering drugs. Nowadays, we are able to measure thousands of individual lipids that make up the lipidome. nuclear magnetic resonance spectrometry (NMR) metabolomics is also being increasingly used in large cohort studies where it can report on total levels of selected lipid classes, and relative levels of fatty acid saturation. To support the application of lipidomics research, LIPID MAPS was established in 2003, and since then has gone on to become the go-to resource for several lipid databases, lipid drawing tools, data deposition, and more recently lipidomics informatics tools, and a lipid biochemistry encyclopedia, LipidWeb. Alongside this, the recently established Lipidomics Standards Initiative plays a key role in standardization of lipidomics methodologies. This article is categorized under: Laboratory Methods and Technologies > Metabolomics Analytical and Computational Methods > Analytical Methods., (© 2019 Wiley Periodicals, Inc.)
- Published
- 2020
- Full Text
- View/download PDF
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