1
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Toward building mass spectrometry-based metabolomics and lipidomics atlases for biological and clinical research. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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2
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Oldoni E, Saunders G, Bietrix F, Garcia Bermejo ML, Niehues A, ’t Hoen PAC, Nordlund J, Hajduch M, Scherer A, Kivinen K, Pitkänen E, Mäkela TP, Gut I, Scollen S, Kozera Ł, Esteller M, Shi L, Ussi A, Andreu AL, van Gool AJ. Tackling the translational challenges of multi-omics research in the realm of European personalised medicine: A workshop report. Front Mol Biosci 2022; 9:974799. [PMID: 36310597 PMCID: PMC9608444 DOI: 10.3389/fmolb.2022.974799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/08/2022] [Indexed: 11/13/2022] Open
Abstract
Personalised medicine (PM) presents a great opportunity to improve the future of individualised healthcare. Recent advances in -omics technologies have led to unprecedented efforts characterising the biology and molecular mechanisms that underlie the development and progression of a wide array of complex human diseases, supporting further development of PM. This article reflects the outcome of the 2021 EATRIS-Plus Multi-omics Stakeholder Group workshop organised to 1) outline a global overview of common promises and challenges that key European stakeholders are facing in the field of multi-omics research, 2) assess the potential of new technologies, such as artificial intelligence (AI), and 3) establish an initial dialogue between key initiatives in this space. Our focus is on the alignment of agendas of European initiatives in multi-omics research and the centrality of patients in designing solutions that have the potential to advance PM in long-term healthcare strategies.
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Affiliation(s)
- Emanuela Oldoni
- European Infrastructure for Translational Medicine (EATRIS), Amsterdam, Netherlands
- *Correspondence: Gary Saunders, ; Emanuela Oldoni,
| | - Gary Saunders
- European Infrastructure for Translational Medicine (EATRIS), Amsterdam, Netherlands
- *Correspondence: Gary Saunders, ; Emanuela Oldoni,
| | - Florence Bietrix
- European Infrastructure for Translational Medicine (EATRIS), Amsterdam, Netherlands
| | - Maria Laura Garcia Bermejo
- Biomarkers and Therapeutic Targets Group, Ramon and Cajal Health Research Institute (IRYCIS), Madrid, Spain
| | - Anna Niehues
- Translational Metabolomic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Peter A. C. ’t Hoen
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Jessica Nordlund
- Department of Medical Sciences, Molecular Precision Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Marian Hajduch
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University and University Hospital in Olomouc, Olomouc, Czechia
| | - Andreas Scherer
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
| | - Katja Kivinen
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
- HiLIFE-Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Esa Pitkänen
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
- HiLIFE-Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Tomi Pekka Mäkela
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
- HiLIFE-Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | | | - Łukasz Kozera
- Biobanking and BioMolecular Resources Research Infrastructure-European Research Infrastructure Consortium (BBMRI-ERIC), Graz, Austria
| | - Manel Esteller
- Josep Carreras Leukemia Research Institute (IJC), Badalona, Spain
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Spain
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
| | - Anton Ussi
- European Infrastructure for Translational Medicine (EATRIS), Amsterdam, Netherlands
| | - Antonio L. Andreu
- European Infrastructure for Translational Medicine (EATRIS), Amsterdam, Netherlands
| | - Alain J. van Gool
- Translational Metabolomic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
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Muller E, Algavi YM, Borenstein E. A meta-analysis study of the robustness and universality of gut microbiome-metabolome associations. MICROBIOME 2021; 9:203. [PMID: 34641974 PMCID: PMC8507343 DOI: 10.1186/s40168-021-01149-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 08/18/2021] [Indexed: 05/15/2023]
Abstract
BACKGROUND Microbiome-metabolome studies of the human gut have been gaining popularity in recent years, mostly due to accumulating evidence of the interplay between gut microbes, metabolites, and host health. Statistical and machine learning-based methods have been widely applied to analyze such paired microbiome-metabolome data, in the hope of identifying metabolites that are governed by the composition of the microbiome. Such metabolites can be likely modulated by microbiome-based interventions, offering a route for promoting gut metabolic health. Yet, to date, it remains unclear whether findings of microbially associated metabolites in any single study carry over to other studies or cohorts, and how robust and universal are microbiome-metabolites links. RESULTS In this study, we addressed this challenge by performing a comprehensive meta-analysis to identify human gut metabolites that can be predicted based on the composition of the gut microbiome across multiple studies. We term such metabolites "robustly well-predicted". To this end, we processed data from 1733 samples from 10 independent human gut microbiome-metabolome studies, focusing initially on healthy subjects, and implemented a machine learning pipeline to predict metabolite levels in each dataset based on the composition of the microbiome. Comparing the predictability of each metabolite across datasets, we found 97 robustly well-predicted metabolites. These include metabolites involved in important microbial pathways such as bile acid transformations and polyamines metabolism. Importantly, however, other metabolites exhibited large variation in predictability across datasets, suggesting a cohort- or study-specific relationship between the microbiome and the metabolite. Comparing taxonomic contributors to different models, we found that some robustly well-predicted metabolites were predicted by markedly different sets of taxa across datasets, suggesting that some microbially associated metabolites may be governed by different members of the microbiome in different cohorts. We finally examined whether models trained on a control group of a given study successfully predicted the metabolite's level in the disease group of the same study, identifying several metabolites where the model was not transferable, indicating a shift in microbial metabolism in disease-associated dysbiosis. CONCLUSIONS Combined, our findings provide a better understanding of the link between the microbiome and metabolites and allow researchers to put identified microbially associated metabolites within the context of other studies. Video abstract.
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Affiliation(s)
- Efrat Muller
- The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Yadid M. Algavi
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Elhanan Borenstein
- The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Santa Fe Institute, Santa Fe, NM USA
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4
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A normalized signal calibration with a long-term reference improves the robustness of RPLC-MRM/MS lipidomics in plasma. Anal Bioanal Chem 2021; 413:4077-4090. [PMID: 33907864 DOI: 10.1007/s00216-021-03364-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 04/19/2021] [Indexed: 10/21/2022]
Abstract
Improving the reliability of quantification in lipidomic analyses is crucial for its successful application in the discovery of new biomarkers or in clinical practice. In this study, we propose a workflow to improve the accuracy and precision of lipidomic results issued by the laboratory. Lipid species from 11 classes were analyzed by a targeted RPLC-MRM/MS method. The peak areas of species were used to estimate concentrations by an internal standard calibration approach (IS-calibration) and by an alternative normalization signal calibration schema (NS-calibration). The latter uses a long-term reference plasma material as a matrix-matched external calibrator whose accuracy was compared to the NIST SRM-1950 mean consensus values reported by the Interlaboratory Lipidomics Comparison Exercise. The bias of lipid concentrations showed a good accuracy for 69 of 89 quantified lipids. The quantitation of species by the NS-calibration schema improved the within- and between-batch reproducibility in quality control samples, in comparison to the usual IS-calibration approach. Moreover, the NS-calibration workflow improved the robustness of the lipidomics measurements reducing the between-batch variability (relative standard deviation <10% for 95% of lipid species) in real conditions tested throughout the analysis of 120 plasma samples. In addition, we provide a free access web tool to obtain the concentration of lipid species by the two previously mentioned quantitative approaches, providing an easy follow-up of quality control tasks related to lipidomics.
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5
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Llobat L. Extracellular vesicles and domestic animal reproduction. Res Vet Sci 2021; 136:166-173. [PMID: 33647595 DOI: 10.1016/j.rvsc.2021.02.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 01/01/2021] [Accepted: 02/17/2021] [Indexed: 01/08/2023]
Abstract
Embryo implantation is a complex process in which significant changes occur continually in both the corpora lutea and in the endometrium of females and which varies depending on the embryonic, pre-implantation, or fetal stages. However, at all stages, correct maternal-embryonic communication is essential. In the last few years, a new intercellular communication tool, mediated by extracellular vesicles (EVs), has emerged. Many authors agree on the relevant role of EVs in correct communication between the mother and the embryo, as a fundamental system for the pregnancy to reach term and embryonic development to occur correctly. This review analyzes current information on known EVs, their main functions, and their role in implantation and embryonic development in domestic animals.
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Affiliation(s)
- Lola Llobat
- Grupo de Fisiopatología de la Reproducción, Departamento Producción y Sanidad Animal, Salud Pública y Ciencia y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain.
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Zoccali C, Blankestijn PJ, Bruchfeld A, Capasso G, Fliser D, Fouque D, Goumenos D, Massy Z, Rychlık I, Soler MJ, Stevens K, Spasovski G, Wanner C. The nephrology crystal ball: the medium-term future. Nephrol Dial Transplant 2020; 35:222-226. [PMID: 31598700 DOI: 10.1093/ndt/gfz199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Indexed: 12/25/2022] Open
Abstract
In January 2019, the ERA-EDTA surveyed nephrologists with questions on kidney care and kidney research designed to explore comprehension of the impact of alterations to organization of renal care and of advancements in technology and knowledge of kidney disease. Eight hundred and twenty-five ERA-EDTA members, ∼13% of the whole ERA-EDTA membership, replied to an ad hoc questionnaire. More than half of the respondents argued that kidney centres will be increasingly owned by large dialysis providers, nearly a quarter of respondents felt that many medical aspects of dialysis will be increasingly overseen by non-nephrologists and a quarter (24%) also believed that the care and long-term follow-up of kidney transplant patients will be increasingly under the responsibility of transplant physicians caring for patients with any organ transplant. Nearly half of the participants (45%, n = 367) use fully electronic clinical files integrating the clinical ward, the outpatient clinics, the haemodialysis and peritoneal dialysis units, as well as transplantation. Smartphone-based self-management programmes for the care of chronic kidney disease (CKD) patients are scarcely applied (only 11% of surveyed nephrologists), but a substantial proportion of respondents (74%) are eager to know more about the potential usefulness of these apps. Finally, European nephrologists expressed a cautious optimism about the application of omic sciences to nephrology and on wearable and implantable kidneys, but their expectations for the medium term are limited.
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Affiliation(s)
| | - Peter J Blankestijn
- Department of Nephrology, University Medical Center, Utrecht, The Netherlands
| | - Annette Bruchfeld
- Department of Renal Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Giovambattista Capasso
- Department of Traslational Medical Sciences, University Campania 'Luigi Vanvitelli', Naples, Italy
| | - Danilo Fliser
- Internal Medicine IV, Renal and Hypertensive Disease, University Medical Center, Homburg/Saar, Germany
| | - Denis Fouque
- Department of Nephrology, Dialysis, Nutrition, Centre Hospitalier Lyon Sud, Pierre Bénite Cedex, France
| | - Dimitrios Goumenos
- Department of Nephrology and Renal Transplantation, Patras University Hospital, Patras, Greece
| | - Ziad Massy
- Division of Nephrology, Ambroise Paré Hospital, Paris Ile de France West University (UVSQ), Villejuif, France
| | - Ivan Rychlık
- 1st Department of Internal Medicine, Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Maria J Soler
- Department of Nephrology, Hospital Universitari Vall d'Hebron, Nephrology Research Group, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Kate Stevens
- Glasgow Renal and Transplant Unit, Queen Elizabeth University Hospital, Glasgow, UK
| | - Goce Spasovski
- Department of Nephrology, Medical Faculty, University of Skopje, Skopje, Northern Republic of Macedonia
| | - Christoph Wanner
- Division of Nephrology, University of Würzburg, Würzburg, Germany
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7
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Jeucken A, Molenaar MR, van de Lest CHA, Jansen JWA, Helms JB, Brouwers JF. A Comprehensive Functional Characterization of Escherichia coli Lipid Genes. Cell Rep 2020; 27:1597-1606.e2. [PMID: 31042483 DOI: 10.1016/j.celrep.2019.04.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 02/25/2019] [Accepted: 04/02/2019] [Indexed: 12/14/2022] Open
Abstract
Lipid membranes are the border between living cells and their environments. The membrane's lipid composition defines fluidity, thickness, and protein activity and is controlled by the intricate actions of lipid gene-encoded enzymes. However, a comprehensive analysis of each protein's contribution to the lipidome is lacking. Here, we present such a comprehensive and functional overview of lipid genes in Escherichia coli by individual overexpression or deletion of these genes. We developed a high-throughput lipidomic platform, combining growth analysis, one-step lipid extraction, rapid LC-MS, and bioinformatic analysis into one streamlined procedure. This allowed the processing of more than 300 samples per day and revealed interesting functions of known enzymes and distinct effects of individual proteins on the phospholipidome. Our data demonstrate the plasticity of the phospholipidome and unexpected relations between lipid classes and cell growth. Modeling of lipidomic responses to short-chain alcohols provides a rationale for targeted membrane engineering.
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Affiliation(s)
- Aike Jeucken
- Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 2, 3584CM Utrecht, the Netherlands
| | - Martijn R Molenaar
- Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 2, 3584CM Utrecht, the Netherlands
| | - Chris H A van de Lest
- Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 2, 3584CM Utrecht, the Netherlands
| | - Jeroen W A Jansen
- Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 2, 3584CM Utrecht, the Netherlands
| | - J Bernd Helms
- Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 2, 3584CM Utrecht, the Netherlands
| | - Jos F Brouwers
- Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 2, 3584CM Utrecht, the Netherlands.
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8
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Goulielmos GN, Matalliotakis M, Matalliotaki C, Eliopoulos E, Matalliotakis I, Zervou MI. Endometriosis research in the -omics era. Gene 2020; 741:144545. [PMID: 32165309 DOI: 10.1016/j.gene.2020.144545] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 02/28/2020] [Accepted: 03/08/2020] [Indexed: 12/18/2022]
Abstract
Endometriosis is a pathological condition extensively studied, but its pathogenesis is not completely understood, since its pathophysiology stems from a broad spectrum of environmental influences and genetic factors. Moreover, the nature of this condition is heterogeneous and includes different anatomical entities. Scientists actively pursue discovery of novel biomarkers in the hope of better identifying susceptible individuals in early stages of the disease. High-throughput technologies have substantially revolutionized medical research and, as a first step, the advent of genotyping arrays led to large-scale genome-wide association studies (GWAS) and enabled the assessment of global transcript levels, thus giving rise to integrative genetics. In this framework, comprehensive studies have been conducted at multiple biological levels by using the "omics" platforms, thus allowing to re-examine endometriosis at a greater degree of molecular resolution. -Omics technologies can detect and analyze hundreds of markers in the same experiment and their increasing use in the field of gynecology comes from an urgent need to find new diagnostic and therapeutic tools that improve the diagnosis of endometriosis and the efficacy of assisted reproductive techniques. Proteomics and metabolomics have been introduced recently into the every day methodology of researchers collaborating with gynecologists and, importantly, multi-omics approach is advantageous to gain insight of the total information that underlies endometriosis, compared to studies of any single -omics type. In this review, we expect to present multiple studies based on the high-throughput-omics technologies and to shed light in all considerable advantages that they may confer to a proper management of endometriosis.
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Affiliation(s)
- George N Goulielmos
- Section of Molecular Pathology and Human Genetics, Department of Internal Medicine School of Medicine, University of Crete, Heraklion, Greece
| | - Michail Matalliotakis
- Section of Molecular Pathology and Human Genetics, Department of Internal Medicine School of Medicine, University of Crete, Heraklion, Greece; Third Department of Obstetrics and Gynecology, Aristotle University of Thessaloniki, Thessaloniki, Greece; Department of Obstetrics and Gynecology, Venizeleio and Pananio General Hospital of Heraklion, Heraklion, Greece
| | - Charoula Matalliotaki
- Section of Molecular Pathology and Human Genetics, Department of Internal Medicine School of Medicine, University of Crete, Heraklion, Greece; Third Department of Obstetrics and Gynecology, Aristotle University of Thessaloniki, Thessaloniki, Greece; Department of Obstetrics and Gynecology, Venizeleio and Pananio General Hospital of Heraklion, Heraklion, Greece
| | - Elias Eliopoulos
- Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Ioannis Matalliotakis
- Department of Obstetrics and Gynecology, Venizeleio and Pananio General Hospital of Heraklion, Heraklion, Greece
| | - Maria I Zervou
- Section of Molecular Pathology and Human Genetics, Department of Internal Medicine School of Medicine, University of Crete, Heraklion, Greece.
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9
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Misra BB. The Connection and Disconnection Between Microbiome and Metabolome: A Critical Appraisal in Clinical Research. Biol Res Nurs 2020; 22:561-576. [PMID: 32013533 DOI: 10.1177/1099800420903083] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Big data-driven omics research has led to a steep rise in investigations involving two of the most functional omes, the metabolome and microbiome. The former is touted as the closest to the phenotype, and the latter is implicated in general well-being and a plethora of human diseases. Although some research publications have integrated the concepts of the two domains, most focus their analyses on evidence solely originating from one or the other. With a growing interest in connecting the microbiome and metabolome in the context of disease, researchers must also appreciate the disconnect between the two domains. In the present review, drawing examples from the current literature, tools, and resources, I discuss the connections between the microbiome and metabolome and highlight challenges and opportunities in linking them together for the basic, translational, clinical, and nursing research communities.
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Affiliation(s)
- Biswapriya B Misra
- Center for Precision Medicine, Department of Internal Medicine, Section of Molecular Medicine, 12279Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC, USA
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10
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Gerl MJ, Klose C, Surma MA, Fernandez C, Melander O, Männistö S, Borodulin K, Havulinna AS, Salomaa V, Ikonen E, Cannistraci CV, Simons K. Machine learning of human plasma lipidomes for obesity estimation in a large population cohort. PLoS Biol 2019; 17:e3000443. [PMID: 31626640 PMCID: PMC6799887 DOI: 10.1371/journal.pbio.3000443] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 09/04/2019] [Indexed: 01/05/2023] Open
Abstract
Obesity is associated with changes in the plasma lipids. Although simple lipid quantification is routinely used, plasma lipids are rarely investigated at the level of individual molecules. We aimed at predicting different measures of obesity based on the plasma lipidome in a large population cohort using advanced machine learning modeling. A total of 1,061 participants of the FINRISK 2012 population cohort were randomly chosen, and the levels of 183 plasma lipid species were measured in a novel mass spectrometric shotgun approach. Multiple machine intelligence models were trained to predict obesity estimates, i.e., body mass index (BMI), waist circumference (WC), waist-hip ratio (WHR), and body fat percentage (BFP), and validated in 250 randomly chosen participants of the Malmö Diet and Cancer Cardiovascular Cohort (MDC-CC). Comparison of the different models revealed that the lipidome predicted BFP the best (R2 = 0.73), based on a Lasso model. In this model, the strongest positive and the strongest negative predictor were sphingomyelin molecules, which differ by only 1 double bond, implying the involvement of an unknown desaturase in obesity-related aberrations of lipid metabolism. Moreover, we used this regression to probe the clinically relevant information contained in the plasma lipidome and found that the plasma lipidome also contains information about body fat distribution, because WHR (R2 = 0.65) was predicted more accurately than BMI (R2 = 0.47). These modeling results required full resolution of the lipidome to lipid species level, and the predicting set of biomarkers had to be sufficiently large. The power of the lipidomics association was demonstrated by the finding that the addition of routine clinical laboratory variables, e.g., high-density lipoprotein (HDL)- or low-density lipoprotein (LDL)- cholesterol did not improve the model further. Correlation analyses of the individual lipid species, controlled for age and separated by sex, underscores the multiparametric and lipid species-specific nature of the correlation with the BFP. Lipidomic measurements in combination with machine intelligence modeling contain rich information about body fat amount and distribution beyond traditional clinical assays.
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Affiliation(s)
| | | | - Michal A. Surma
- Lipotype GmbH, Dresden, Germany
- Łukasiewicz Research Network—PORT Polish Center for Technology Development, Wroclaw, Poland
| | | | - Olle Melander
- Department of Clinical Sciences, Lund University, Malmö, Sweden
- Department of Emergency and Internal Medicine, Skåne University Hospital, Malmö, Sweden
| | - Satu Männistö
- Public Health Promotion Unit, National Institute for Health and Welfare, Helsinki, Finland
| | - Katja Borodulin
- National Institute for Health and Welfare, Helsinki, Finland
| | - Aki S. Havulinna
- National Institute for Health and Welfare, Helsinki, Finland
- Institute for Molecular Medicine Finland (FIMM-HiLife), Helsinki, Finland
| | - Veikko Salomaa
- National Institute for Health and Welfare, Helsinki, Finland
| | - Elina Ikonen
- Department of Anatomy, Faculty of Medicine, University of Helsinki, Finland
| | - Carlo V. Cannistraci
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Department of Physics, Technische Universität Dresden, Dresden, Germany
- Center for Systems Biology Dresden, Dresden, Germany
- Complex Network Intelligence Lab, Tsinghua Laboratory of Brain and Intelligence, Tsinghua University, Beijing, China
| | - Kai Simons
- Lipotype GmbH, Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
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11
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Rämö JT, Ripatti P, Tabassum R, Söderlund S, Matikainen N, Gerl MJ, Klose C, Surma MA, Stitziel NO, Havulinna AS, Pirinen M, Salomaa V, Freimer NB, Jauhiainen M, Palotie A, Taskinen MR, Simons K, Ripatti S. Coronary Artery Disease Risk and Lipidomic Profiles Are Similar in Hyperlipidemias With Family History and Population-Ascertained Hyperlipidemias. J Am Heart Assoc 2019; 8:e012415. [PMID: 31256696 PMCID: PMC6662358 DOI: 10.1161/jaha.119.012415] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Background We asked whether, after excluding familial hypercholesterolemia, individuals with high low‐density lipoprotein cholesterol (LDL‐C) or triacylglyceride levels and a family history of the same hyperlipidemia have greater coronary artery disease risk or different lipidomic profiles compared with population‐based hyperlipidemias. Methods and Results We determined incident coronary artery disease risk for 755 members of 66 hyperlipidemic families (≥2 first‐degree relatives with similar hyperlipidemia) and 19 644 Finnish FINRISK population study participants. We quantified 151 circulating lipid species from 550 members of 73 hyperlipidemic families and 897 FINRISK participants using mass spectrometric shotgun lipidomics. Familial hypercholesterolemia was excluded using functional LDL receptor testing and genotyping. Hyperlipidemias (LDL‐C or triacylglycerides >90th population percentile) associated with increased coronary artery disease risk in meta‐analysis of the hyperlipidemic families and the population cohort (high LDL‐C: hazard ratio, 1.74 [95% CI, 1.48–2.04]; high triacylglycerides: hazard ratio, 1.38 [95% CI, 1.09–1.74]). Risk estimates were similar in the family and population cohorts also after adjusting for lipid‐lowering medication. In lipidomic profiling, high LDL‐C associated with 108 lipid species, and high triacylglycerides associated with 131 lipid species in either cohort (at 5% false discovery rate; P‐value range 0.038–2.3×10−56). Lipidomic profiles were highly similar for hyperlipidemic individuals in the families and the population (LDL‐C: r=0.80; triacylglycerides: r=0.96; no lipid species deviated between the cohorts). Conclusions Hyperlipidemias with family history conferred similar coronary artery disease risk as population‐based hyperlipidemias. We identified distinct lipidomic profiles associated with high LDL‐C and triacylglycerides. Lipidomic profiles were similar between hyperlipidemias with family history and population‐ascertained hyperlipidemias, providing evidence of similar and overlapping underlying mechanisms.
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Affiliation(s)
- Joel T Rämö
- 1 Institute for Molecular Medicine Finland HiLIFE University of Helsinki Finland
| | - Pietari Ripatti
- 1 Institute for Molecular Medicine Finland HiLIFE University of Helsinki Finland
| | - Rubina Tabassum
- 1 Institute for Molecular Medicine Finland HiLIFE University of Helsinki Finland
| | - Sanni Söderlund
- 2 Research Programs Unit Clinical and Molecular Metabolism University of Helsinki Finland.,3 Endocrinology Abdominal Center Helsinki University Hospital Helsinki Finland
| | - Niina Matikainen
- 2 Research Programs Unit Clinical and Molecular Metabolism University of Helsinki Finland.,3 Endocrinology Abdominal Center Helsinki University Hospital Helsinki Finland
| | | | | | - Michal A Surma
- 4 Lipotype GmbH Dresden Germany.,5 Łukasiewicz Research Network-PORT Polish Center for Technology Development Wroclaw Poland
| | - Nathan O Stitziel
- 6 Cardiovascular Division Department of Medicine Washington University School of Medicine St. Louis MO.,7 Department of Genetics Washington University School of Medicine St. Louis MO.,8 McDonnell Genome Institute Washington University School of Medicine St. Louis MO
| | - Aki S Havulinna
- 1 Institute for Molecular Medicine Finland HiLIFE University of Helsinki Finland.,9 National Institute for Health and Welfare Helsinki Finland
| | - Matti Pirinen
- 1 Institute for Molecular Medicine Finland HiLIFE University of Helsinki Finland.,10 Department of Mathematics and Statistics Faculty of Science University of Helsinki Finland.,16 Department of Public Health Clinicum Faculty of Medicine University of Helsinki Finland
| | - Veikko Salomaa
- 9 National Institute for Health and Welfare Helsinki Finland
| | - Nelson B Freimer
- 11 Center for Neurobehavioral Genetics Semel Institute for Neuroscience and Human Behavior University of California Los Angeles CA
| | - Matti Jauhiainen
- 9 National Institute for Health and Welfare Helsinki Finland.,12 Minerva Foundation Institute for Medical Research Biomedicum Helsinki Finland
| | - Aarno Palotie
- 1 Institute for Molecular Medicine Finland HiLIFE University of Helsinki Finland.,13 Program in Medical and Population Genetics and The Stanley Center for Psychiatric Research The Broad Institute of MIT and Harvard Cambridge MA.,14 Psychiatric and Neurodevelopmental Genetics Unit Department of Psychiatry, Analytic and Translational Genetics Unit Department of Medicine, and the Department of Neurology Massachusetts General Hospital Boston MA
| | - Marja-Riitta Taskinen
- 2 Research Programs Unit Clinical and Molecular Metabolism University of Helsinki Finland
| | - Kai Simons
- 4 Lipotype GmbH Dresden Germany.,15 Max Planck Institute of Cell Biology and Genetics Dresden Germany
| | - Samuli Ripatti
- 1 Institute for Molecular Medicine Finland HiLIFE University of Helsinki Finland.,13 Program in Medical and Population Genetics and The Stanley Center for Psychiatric Research The Broad Institute of MIT and Harvard Cambridge MA.,16 Department of Public Health Clinicum Faculty of Medicine University of Helsinki Finland
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12
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Nilsen E, Smalling KL, Ahrens L, Gros M, Miglioranza KSB, Picó Y, Schoenfuss HL. Critical review: Grand challenges in assessing the adverse effects of contaminants of emerging concern on aquatic food webs. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2019; 38:46-60. [PMID: 30294805 DOI: 10.1002/etc.4290] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 09/24/2018] [Accepted: 10/03/2018] [Indexed: 05/24/2023]
Abstract
Much progress has been made in the past few decades in understanding the sources, transport, fate, and biological effects of contaminants of emerging concern (CECs) in aquatic ecosystems. Despite these advancements, significant obstacles still prevent comprehensive assessments of the environmental risks associated with the presence of CECs. Many of these obstacles center around the extrapolation of effects of single chemicals observed in the laboratory or effects found in individual organisms or species in the field to impacts of multiple stressors on aquatic food webs. In the present review, we identify 5 challenges that must be addressed to promote studies of CECs from singular exposure events to multispecies aquatic food web interactions. There needs to be: 1) more detailed information on the complexity of mixtures of CECs in the aquatic environment, 2) a greater understanding of the sublethal effects of CECs on a wide range of aquatic organisms, 3) an ascertaining of the biological consequences of variable duration CEC exposures within and across generations in aquatic species, 4) a linkage of multiple stressors with CEC exposure in aquatic systems, and 5) a documenting of the trophic consequences of CEC exposure across aquatic food webs. We examine the current literature to show how these challenges can be addressed to fill knowledge gaps. Environ Toxicol Chem 2019;38:46-60. © 2018 SETAC.
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Affiliation(s)
- Elena Nilsen
- US Geological Survey, Oregon Water Science Center, Portland, Oregon, USA
| | - Kelly L Smalling
- US Geological Survey, New Jersey Water Science Center, Lawrenceville, New Jersey, USA
| | - Lutz Ahrens
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Meritxell Gros
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Catalan Institute for Water Research, Girona, Spain
| | - Karina S B Miglioranza
- Laboratory of Ecotoxicology and Environmental Pollution, Mar del Plata University, Mar del Plata, Argentina
| | - Yolanda Picó
- Environmental and Food Safety Research Group, Center of Research on Desertification (CIDe), Faculty of Pharmacy, University of Valencia, Valencia, Spain
| | - Heiko L Schoenfuss
- Aquatic Toxicology Laboratory, St. Cloud State University, St. Cloud, Minnesota, USA
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13
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Walther A, Cannistraci CV, Simons K, Durán C, Gerl MJ, Wehrli S, Kirschbaum C. Lipidomics in Major Depressive Disorder. Front Psychiatry 2018; 9:459. [PMID: 30374314 PMCID: PMC6196281 DOI: 10.3389/fpsyt.2018.00459] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 09/04/2018] [Indexed: 01/01/2023] Open
Abstract
Omic sciences coupled with novel computational approaches such as machine intelligence offer completely new approaches to major depressive disorder (MDD) research. The complexity of MDD's pathophysiology is being integrated into studies examining MDD's biology within the omic fields. Lipidomics, as a late-comer among other omic fields, is increasingly being recognized in psychiatric research because it has allowed the investigation of global lipid perturbations in patients suffering from MDD and indicated a crucial role of specific patterns of lipid alterations in the development and progression of MDD. Combinatorial lipid-markers with high classification power are being developed in order to assist MDD diagnosis, while rodent models of depression reveal lipidome changes and thereby unveil novel treatment targets for depression. In this systematic review, we provide an overview of current breakthroughs and future trends in the field of lipidomics in MDD research and thereby paving the way for precision medicine in MDD.
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Affiliation(s)
| | - Carlo Vittorio Cannistraci
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Center for Systems Biology Dresden (CSBD), Department of Physics, TU Dresden, Dresden, Germany
- Brain Bio-Inspired Computing (BBC) Lab, IRCCS Centro Neurolesi “Bonino Pulejo”, Messina, Italy
| | | | - Claudio Durán
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Center for Systems Biology Dresden (CSBD), Department of Physics, TU Dresden, Dresden, Germany
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14
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Burla B, Arita M, Arita M, Bendt AK, Cazenave-Gassiot A, Dennis EA, Ekroos K, Han X, Ikeda K, Liebisch G, Lin MK, Loh TP, Meikle PJ, Orešič M, Quehenberger O, Shevchenko A, Torta F, Wakelam MJO, Wheelock CE, Wenk MR. MS-based lipidomics of human blood plasma: a community-initiated position paper to develop accepted guidelines. J Lipid Res 2018; 59:2001-2017. [PMID: 30115755 PMCID: PMC6168311 DOI: 10.1194/jlr.s087163] [Citation(s) in RCA: 192] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Revised: 08/11/2018] [Indexed: 12/19/2022] Open
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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Affiliation(s)
- Bo Burla
- Singapore Lipidomics Incubator (SLING), Life Sciences Institute, National University of Singapore, Singapore
| | - Makoto Arita
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Cellular and Molecular Epigenetics Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
- Division of Physiological Chemistry and Metabolism, Keio University Faculty of Pharmacy, Tokyo, Japan
| | - Masanori Arita
- National Institute of Genetics, Shizuoka, Japan and RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Anne K Bendt
- Singapore Lipidomics Incubator (SLING), Life Sciences Institute, National University of Singapore, Singapore
| | - Amaury Cazenave-Gassiot
- Department of Biochemistry, YLL School of Medicine, National University of Singapore, Singapore
| | - Edward A Dennis
- Departments of Pharmacology and Chemistry and Biochemistry, School of Medicine, University of California at San Diego, La Jolla, CA
| | - Kim Ekroos
- Lipidomics Consulting Ltd., Esbo, Finland
| | - Xianlin Han
- Barshop Institute for Longevity and Aging Studies and Department of Medicine-Diabetes, University of Texas Health Science Center at San Antonio, San Antonio, TX
| | - Kazutaka Ikeda
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Cellular and Molecular Epigenetics Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Gerhard Liebisch
- Institute of Clinical Chemistry and Laboratory Medicine, University of Regensburg, Regensburg, Germany
| | - Michelle K Lin
- Department of Biochemistry, YLL School of Medicine, National University of Singapore, Singapore
| | - Tze Ping Loh
- Department of Laboratory Medicine, National University Hospital, Singapore
| | - Peter J Meikle
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Matej Orešič
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland and School of Medical Sciences, Örebro University, Örebro, Sweden
| | - Oswald Quehenberger
- Departments of Pharmacology and Medicine, School of Medicine, University of California at San Diego, La Jolla, CA
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Federico Torta
- Department of Biochemistry, YLL School of Medicine, National University of Singapore, Singapore
| | | | - Craig E Wheelock
- Division of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Markus R Wenk
- Singapore Lipidomics Incubator (SLING), Life Sciences Institute, National University of Singapore, Singapore
- Department of Biochemistry, YLL School of Medicine, National University of Singapore, Singapore
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15
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Niu L, Xu X, Liu H, Wu X, Wang W. On the Promising Role of Enzyme Activity Assay in Interpreting Comparative Proteomic Data in Plants. Proteomics 2018; 18:e1800234. [PMID: 30179302 DOI: 10.1002/pmic.201800234] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 07/18/2018] [Indexed: 11/09/2022]
Abstract
Comparative proteomics is widely used to detect protein changes, especially differential abundance proteins (DAPs) that are involved in plant responses to development, disease, or environment. Once DAPs are identified, it is essential to validate any change in their abundance, and their role in the biological process under study. In addition to common confirmation by quantitative RT-PCR, immunoblot, and multiple reaction monitoring analysis, it has been proposed that enzyme activity assay (EAA) can be complementary to the standard proteomics results, especially regarding the elucidation of protein (enzyme) function and the mechanism of enzyme-associated biochemical or metabolic pathways. The enzymes discussed here are the DAPs identified in comparative plant proteomics. Despite the small number of enzymes in a proteome, they often make up a substantial proportion of the DAPs identified in comparative studies. Currently, only a few studies have performed EAA to complement the interpretation of proteomic data, especially activity-based protein profiling. This viewpoint aims to arouse the attention of proteomic researchers on the promising role of EAA in plant proteomics and highlights the need for high-throughput assays of enzyme activities in comparative plant proteomics.
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Affiliation(s)
- Liangjie Niu
- State Key Laboratoryy of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China.,Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xiangru Xu
- State Key Laboratoryy of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China.,Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China
| | - Hui Liu
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xiaolin Wu
- State Key Laboratoryy of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China.,Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China
| | - Wei Wang
- State Key Laboratoryy of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China.,Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China.,College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
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16
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Skotland T, Hessvik NP, Sandvig K, Llorente A. Exosomal lipid composition and the role of ether lipids and phosphoinositides in exosome biology. J Lipid Res 2018; 60:9-18. [PMID: 30076207 PMCID: PMC6314266 DOI: 10.1194/jlr.r084343] [Citation(s) in RCA: 384] [Impact Index Per Article: 64.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 07/24/2018] [Indexed: 12/11/2022] Open
Abstract
Exosomes are a type of extracellular vesicle released from cells after fusion of multivesicular bodies with the plasma membrane. These vesicles are often enriched in cholesterol, SM, glycosphingolipids, and phosphatidylserine. Lipids not only have a structural role in exosomal membranes but also are essential players in exosome formation and release to the extracellular environment. Our knowledge about the importance of lipids in exosome biology is increasing due to recent technological developments in lipidomics and a stronger focus on the biological functions of these molecules. Here, we review the available information about the lipid composition of exosomes. Special attention is given to ether lipids, a relatively unexplored type of lipids involved in membrane trafficking and abundant in some exosomes. Moreover, we discuss how the lipid composition of exosome preparations may provide useful information about their purity. Finally, we discuss the role of phosphoinositides, membrane phospholipids that help to regulate membrane dynamics, in exosome release and how this process may be linked to secretory autophagy. Knowledge about exosome lipid composition is important to understand the biology of these vesicles and to investigate possible medical applications.
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Affiliation(s)
- Tore Skotland
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital-Norwegian Radium Hospital, 0379 Oslo, Norway
| | - Nina P Hessvik
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital-Norwegian Radium Hospital, 0379 Oslo, Norway
| | - Kirsten Sandvig
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital-Norwegian Radium Hospital, 0379 Oslo, Norway.,Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Alicia Llorente
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital-Norwegian Radium Hospital, 0379 Oslo, Norway
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