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Wu H, Yang L, Ren D, Gu Y, Ding X, Zhao Y, Fu G, Zhang H, Yi L. Combinatory data-independent acquisition and parallel reaction monitoring method for revealing the lipid metabolism biomarkers of coronary heart disease and its comorbidities. J Sep Sci 2024; 47:e2300848. [PMID: 38682821 DOI: 10.1002/jssc.202300848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 03/11/2024] [Accepted: 03/13/2024] [Indexed: 05/01/2024]
Abstract
Disorders of lipid metabolism are a common cause of coronary heart disease (CHD) and its comorbidities. In this study, ultra-performance liquid chromatography-high-resolution mass spectrometry in data-independent acquisition (DIA) mode was applied to collect abundant tandem mass spectrometry data, which provided valuable information for lipid annotation. For the lipid isomers that could not be completely separated by chromatography, parallel reaction monitoring (PRM) mode was used for quantification. A total of 223 plasma lipid metabolites were annotated, and 116 of them were identified for their fatty acyl chain composition and location. In addition, 152 plasma lipids in patients with CHD and its comorbidities were quantitatively analyzed. Multivariate statistical analysis and metabolic pathway analysis demonstrated that glycerophospholipid and sphingolipid metabolism deserved more attention for CHD. This study proposed a method combining DIA and PRM for high-throughput characterization of plasma lipids. The results also improved our understanding of metabolic disorders of CHD and its comorbidities, which can provide valuable suggestions for medical intervention.
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Affiliation(s)
- Hao Wu
- Faculty of Chemical Engineering, Kunming University of Science and Technology, Kunming, China
- Department of Cardiology, First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
| | - Lijuan Yang
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming, China
| | - Dabing Ren
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming, China
| | - Ying Gu
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming, China
| | - Xiaoxue Ding
- Department of Cardiology, First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
- College of Medicine, Kunming University of Science and Technology, Kunming, China
| | - Yan Zhao
- Department of Cardiology, First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
- College of Medicine, Kunming University of Science and Technology, Kunming, China
| | - Guanghui Fu
- School of Science, Kunming University of Science and Technology, Kunming, China
| | - Hong Zhang
- Department of Cardiology, First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
- College of Medicine, Kunming University of Science and Technology, Kunming, China
| | - Lunzhao Yi
- Faculty of Chemical Engineering, Kunming University of Science and Technology, Kunming, China
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming, China
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2
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Gu JY, Li XB, Liao GQ, Wang TC, Wang ZS, Jia Q, Qian YZ, Zhang XL, Qiu J. Comprehensive analysis of phospholipid in milk and their biological roles as nutrients and biomarkers. Crit Rev Food Sci Nutr 2024:1-20. [PMID: 38556904 DOI: 10.1080/10408398.2024.2330696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
Phospholipids (PL) have garnered significant attention due to their physiological activities. Milk and other dairy products are important dietary sources for humans and have been extensively used to analyze the presence of PL by various analytical techniques. In this paper, the analysis techniques of PL were reviewed with the eight trigrams of phospholipidomics and a comprehensive fingerprint of 1295 PLs covering 8 subclasses in milk and other dairy products, especially. Technology is the primary productive force. Based on phospholipidomics technology, we further review the relationship between the composition of PL and factors that may be involved in processing and experimental operation, and emphasized the significance of the biological role played by PL in dietary supplements and biomarkers (production, processing and clinical research), and providing the future research directions.
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Affiliation(s)
- Jing-Yi Gu
- Institute of Quality Standards and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Agri-food Quality and Safety, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Xia-Bing Li
- Institute of Quality Standards and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Agri-food Quality and Safety, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Guang-Qin Liao
- Institute of Quality Standards and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Agri-food Quality and Safety, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Tian-Cai Wang
- Institute of Quality Standards and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Agri-food Quality and Safety, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Zi-Shuang Wang
- Institute of Quality Standards and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Agri-food Quality and Safety, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Qi Jia
- Institute of Quality Standards and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Agri-food Quality and Safety, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Yong-Zhong Qian
- Institute of Quality Standards and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Agri-food Quality and Safety, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Xing-Lian Zhang
- Institute of Quality Standards and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Agri-food Quality and Safety, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Jing Qiu
- Institute of Quality Standards and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Agri-food Quality and Safety, Ministry of Agriculture and Rural Affairs, Beijing, China
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3
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Fernández Requena B, Nadeem S, Reddy VP, Naidoo V, Glasgow JN, Steyn AJC, Barbas C, Gonzalez-Riano C. LiLA: lipid lung-based ATLAS built through a comprehensive workflow designed for an accurate lipid annotation. Commun Biol 2024; 7:45. [PMID: 38182666 PMCID: PMC10770321 DOI: 10.1038/s42003-023-05680-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 12/06/2023] [Indexed: 01/07/2024] Open
Abstract
Accurate lipid annotation is crucial for understanding the role of lipids in health and disease and identifying therapeutic targets. However, annotating the wide variety of lipid species in biological samples remains challenging in untargeted lipidomic studies. In this work, we present a lipid annotation workflow based on LC-MS and MS/MS strategies, the combination of four bioinformatic tools, and a decision tree to support the accurate annotation and semi-quantification of the lipid species present in lung tissue from control mice. The proposed workflow allowed us to generate a lipid lung-based ATLAS (LiLA), which was then employed to unveil the lipidomic signatures of the Mycobacterium tuberculosis infection at two different time points for a deeper understanding of the disease progression. This workflow, combined with manual inspection strategies of MS/MS data, can enhance the annotation process for lipidomic studies and guide the generation of sample-specific lipidome maps. LiLA serves as a freely available data resource that can be employed in future studies to address lipidomic alterations in mice lung tissue.
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Affiliation(s)
- Belén Fernández Requena
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660, Boadilla del Monte, España
| | - Sajid Nadeem
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Vineel P Reddy
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Joel N Glasgow
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Adrie J C Steyn
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
- Africa Health Research Institute, Durban, South Africa
- Centers for AIDS Research and Free Radical Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660, Boadilla del Monte, España.
| | - Carolina Gonzalez-Riano
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660, Boadilla del Monte, España.
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4
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Zafarullah M, Li J, Salemi MR, Phinney BS, Durbin-Johnson BP, Hagerman R, Hessl D, Rivera SM, Tassone F. Blood Proteome Profiling Reveals Biomarkers and Pathway Alterations in Fragile X PM at Risk for Developing FXTAS. Int J Mol Sci 2023; 24:13477. [PMID: 37686279 PMCID: PMC10488017 DOI: 10.3390/ijms241713477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/18/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023] Open
Abstract
Fragile X-associated Tremor/Ataxia Syndrome (FXTAS) is a neurodegenerative disorder associated with the FMR1 premutation. Currently, it is not possible to determine when and if individual premutation carriers will develop FXTAS. Thus, with the aim to identify biomarkers for early diagnosis, development, and progression of FXTAS, along with associated dysregulated pathways, we performed blood proteomic profiling of premutation carriers (PM) who, as part of an ongoing longitudinal study, emerged into two distinct groups: those who developed symptoms of FXTAS (converters, CON) over time (at subsequent visits) and those who did not (non-converters, NCON). We compared these groups to age-matched healthy controls (HC). We assessed CGG repeat allele size by Southern blot and PCR analysis. The proteomic profile was obtained by liquid chromatography mass spectrometry (LC-MS/MS). We identified several significantly differentiated proteins between HC and the PM groups at Visit 1 (V1), Visit 2 (V2), and between the visits. We further reported the dysregulated protein pathways, including sphingolipid and amino acid metabolism. Our findings are in agreement with previous studies showing that pathways involved in mitochondrial bioenergetics, as observed in other neurodegenerative disorders, are significantly altered and appear to contribute to the development of FXTAS. Lastly, we compared the blood proteome of the PM who developed FXTAS over time with the CSF proteome of the FXTAS patients recently reported and found eight significantly differentially expressed proteins in common. To our knowledge, this is the first report of longitudinal proteomic profiling and the identification of unique biomarkers and dysregulated protein pathways in FXTAS.
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Affiliation(s)
- Marwa Zafarullah
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California Davis, Sacramento, CA 95817, USA;
| | - Jie Li
- Genome Center, Bioinformatics Core, University of California Davis, Davis, CA 95616, USA;
| | - Michelle R. Salemi
- Genome Center, Proteomics Core, Genome and Biomedical Sciences Facility, University of California Davis, Davis, CA 95616, USA; (M.R.S.); (B.S.P.)
| | - Brett S. Phinney
- Genome Center, Proteomics Core, Genome and Biomedical Sciences Facility, University of California Davis, Davis, CA 95616, USA; (M.R.S.); (B.S.P.)
| | - Blythe P. Durbin-Johnson
- Division of Biostatistics, School of Medicine, University of California Davis, Davis, CA 95616, USA;
| | - Randi Hagerman
- MIND Institute, University of California Davis Medical Center, Sacramento, CA 95817, USA; (R.H.); (D.H.); (S.M.R.)
- Department of Pediatrics, University of California Davis Medical Center, Sacramento, CA 95817, USA
| | - David Hessl
- MIND Institute, University of California Davis Medical Center, Sacramento, CA 95817, USA; (R.H.); (D.H.); (S.M.R.)
- Department of Psychiatry and Behavioral Sciences, University of California Davis Medical Center, Sacramento, CA 95817, USA
| | - Susan M. Rivera
- MIND Institute, University of California Davis Medical Center, Sacramento, CA 95817, USA; (R.H.); (D.H.); (S.M.R.)
- Department of Psychology, University of California Davis, Davis, CA 95616, USA
- Department of Psychology, University of Maryland, College Park, MD 20742, USA
| | - Flora Tassone
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California Davis, Sacramento, CA 95817, USA;
- MIND Institute, University of California Davis Medical Center, Sacramento, CA 95817, USA; (R.H.); (D.H.); (S.M.R.)
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5
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Yeo J, Kang J, Kim H, Moon C. A Critical Overview of HPLC-MS-Based Lipidomics in Determining Triacylglycerol and Phospholipid in Foods. Foods 2023; 12:3177. [PMID: 37685110 PMCID: PMC10486615 DOI: 10.3390/foods12173177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 08/10/2023] [Accepted: 08/11/2023] [Indexed: 09/10/2023] Open
Abstract
With the current advancement in mass spectrometry (MS)-based lipidomics, the knowledge of lipidomes and their diverse roles has greatly increased, enabling a deeper understanding of the action of bioactive lipid molecules in plant- and animal-based foods. This review provides in-depth information on the practical use of MS techniques in lipidomics, including lipid extraction, adduct formation, MS analysis, data processing, statistical analysis, and bioinformatics. Moreover, this contribution demonstrates the effectiveness of MS-based lipidomics for identifying and quantifying diverse lipid species, especially triacylglycerols and phospholipids, in foods. Further, it summarizes the wide applications of MS-based lipidomics in food science, such as for assessing food processing methods, detecting food adulteration, and measuring lipid oxidation in foods. Thus, MS-based lipidomics may be a useful method for identifying the action of individual lipid species in foods.
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Affiliation(s)
- JuDong Yeo
- Department of Food Science and Biotechnology of Animal Resources, Konkuk University, Seoul 05029, Republic of Korea; (J.K.); (H.K.); (C.M.)
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6
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Xue L, Liu K, Yan C, Dun J, Xu Y, Wu L, Yang H, Liu H, Xie L, Wang G, Liang Y. Schisandra lignans ameliorate nonalcoholic steatohepatitis by regulating aberrant metabolism of phosphatidylethanolamines. Acta Pharm Sin B 2023; 13:3545-3560. [PMID: 37655337 PMCID: PMC10465965 DOI: 10.1016/j.apsb.2023.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 03/16/2023] [Accepted: 04/19/2023] [Indexed: 09/02/2023] Open
Abstract
Nonalcoholic steatohepatitis (NASH) is a spectrum of chronic liver disease characterized by hepatic lipid metabolism disorder. Recent reports emphasized the contribution of triglyceride and diglyceride accumulation to NASH, while the other lipids associated with the NASH pathogenesis remained unexplored. The specific purpose of our study was to explore a novel pathogenesis and treatment strategy of NASH via profiling the metabolic characteristics of lipids. Herein, multi-omics techniques based on LC-Q-TOF/MS, LC-MS/MS and MS imaging were developed and used to screen the action targets related to NASH progress and treatment. A methionine and choline deficient (MCD) diet-induced mouse model of NASH was then constructed, and Schisandra lignans extract (SLE) was applied to alleviate hepatic damage by regulating the lipid metabolism-related enzymes CES2A and CYP4A14. Hepatic lipidomics indicated that MCD-diet led to aberrant accumulation of phosphatidylethanolamines (PEs), and SLE could significantly reduce the accumulation of intrahepatic PEs. Notably, exogenous PE (18:0/18:1) was proved to significantly aggravate the mitochondrial damage and hepatocyte apoptosis. Supplementing PE (18:0/18:1) also deteriorated the NASH progress by up regulating intrahepatic proinflammatory and fibrotic factors, while PE synthase inhibitor exerted a prominent hepatoprotective role. The current work provides new insights into the relationship between PE metabolism and the pathogenesis of NASH.
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Affiliation(s)
- Lijuan Xue
- Key Lab of Drug Metabolism & Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Keanqi Liu
- Key Lab of Drug Metabolism & Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Caixia Yan
- Zhejiang Provincial Key Laboratory for Drug Evaluation and Clinical Research, Department of Clinical Pharmacy, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Junling Dun
- Analytical Applications Center, Shimadzu (China) Co., Ltd., Shanghai 200233, China
| | - Yexin Xu
- Key Lab of Drug Metabolism & Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Linlin Wu
- Key Lab of Drug Metabolism & Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Huizhu Yang
- Key Lab of Drug Metabolism & Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Huafang Liu
- Key Lab of Drug Metabolism & Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Lin Xie
- Key Lab of Drug Metabolism & Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Guangji Wang
- Key Lab of Drug Metabolism & Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Yan Liang
- Key Lab of Drug Metabolism & Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
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Bellot PENR, Braga ES, Omage FB, da Silva Nunes FL, Lima SCVC, Lyra CO, Marchioni DML, Pedrosa LFC, Barbosa F, Tasic L, Sena-Evangelista KCM. Plasma lipid metabolites as potential biomarkers for identifying individuals at risk of obesity-induced metabolic complications. Sci Rep 2023; 13:11729. [PMID: 37474543 PMCID: PMC10359283 DOI: 10.1038/s41598-023-38703-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 07/13/2023] [Indexed: 07/22/2023] Open
Abstract
Lipidomics studies have indicated an association between obesity and lipid metabolism dysfunction. This study aimed to evaluate and compare cardiometabolic risk factors, and the lipidomic profile in adults and older people. A cross-sectional study was conducted with 72 individuals, divided into two sex and age-matched groups: obese (body mass index-BMI ≥ 30 kg/m2; n = 36) and non-obese (BMI < 30 kg/m2; n = 36). The lipidomic profiles were evaluated in plasma using 1H nuclear magnetic resonance (1H-NMR) spectroscopy. Obese individuals had higher waist circumference (p < 0.001), visceral adiposity index (p = 0.029), homeostatic model assessment insulin resistance (HOMA-IR) (p = 0.010), and triacylglycerols (TAG) levels (p = 0.018). 1H-NMR analysis identified higher amounts of saturated lipid metabolite fragments, lower levels of unsaturated lipids, and some phosphatidylcholine species in the obese group. Two powerful machine learning (ML) models-k-nearest neighbors (kNN) and XGBoost (XGB) were employed to characterize the lipidomic profile of obese individuals. The results revealed metabolic alterations associated with obesity in the NMR signals. The models achieved high accuracy of 86% and 81%, respectively. The feature importance analysis identified signal at 1.50-1.60 ppm (-CO-CH2-CH2-, Cholesterol and fatty acid in TAG, Phospholipids) to have the highest importance in the two models.
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Affiliation(s)
- Paula Emília Nunes Ribeiro Bellot
- Postgraduate Program in Nutrition, Center for Health Sciences, Federal University of Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Erik Sobrinho Braga
- Biological Chemistry Laboratory, Department of Organic Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Folorunsho Bright Omage
- Biological Chemistry Laboratory, Department of Organic Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
- Computational Biology Research Group, Embrapa Agricultural Informatics, Campinas, São Paulo, Brazil
| | - Francisca Leide da Silva Nunes
- Postgraduate Program in Nutrition, Center for Health Sciences, Federal University of Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | | | - Clélia Oliveira Lyra
- Department of Nutrition, Federal University of Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Dirce Maria Lobo Marchioni
- Department of Nutrition, School of Public Health, University of São Paulo, São Paulo Campus, São Paulo, SP, Brazil
| | | | - Fernando Barbosa
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto of the University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Ljubica Tasic
- Biological Chemistry Laboratory, Department of Organic Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
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Tomaiuolo M, Nardelli V, Mentana A, Campaniello M, Zianni R, Iammarino M. Untargeted Lipidomics and Chemometric Tools for the Characterization and Discrimination of Irradiated Camembert Cheese Analyzed by UHPLC-Q-Orbitrap-MS. Foods 2023; 12:foods12112198. [PMID: 37297444 DOI: 10.3390/foods12112198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/22/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
In this work, an investigation using UHPLC-Q-Orbitrap-MS and multivariate statistics was conducted to obtain the lipid fingerprint of Camembert cheese and to explore its correlated variation with respect to X-ray irradiation treatment. A total of 479 lipids, categorized into 16 different lipid subclasses, were measured. Furthermore, the identification of oxidized lipids was carried out to better understand the possible phenomena of lipid oxidation related to this technological process. The results confirm that the lipidomic approach adopted is effective in implementing the knowledge of the effects of X-ray irradiation on food and evaluating its safety aspects. Furthermore, Partial Least Squares-Discriminant Analysis (PLS-DA) and Linear Discriminant Analysis (LDA) were applied showing high discriminating ability with excellent values of accuracy, specificity and sensitivity. Through the PLS-DA and LDA models, it was possible to select 40 and 24 lipids, respectively, including 3 ceramides (Cer), 1 hexosyl ceramide (HexCer), 1 lysophosphatidylcholine (LPC), 1 lysophosphatidylethanolamine (LPE), 3 phosphatidic acids (PA), 4 phosphatidylcholines (PC), 10 phosphatidylethanolamines (PE), 5 phosphatidylinositols (PI), 2 phosphatidylserines (PS), 3 diacylglycerols (DG) and 9 oxidized triacylglycerols (OxTG) as potential markers of treatment useful in food safety control plans.
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Affiliation(s)
- Michele Tomaiuolo
- Laboratorio Nazionale di Riferimento per il Trattamento degli Alimenti e dei loro Ingredienti con Radiazioni Ionizzanti, Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia, 20-71121 Foggia, Italy
| | - Valeria Nardelli
- Laboratorio Nazionale di Riferimento per il Trattamento degli Alimenti e dei loro Ingredienti con Radiazioni Ionizzanti, Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia, 20-71121 Foggia, Italy
| | - Annalisa Mentana
- Laboratorio Nazionale di Riferimento per il Trattamento degli Alimenti e dei loro Ingredienti con Radiazioni Ionizzanti, Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia, 20-71121 Foggia, Italy
| | - Maria Campaniello
- Laboratorio Nazionale di Riferimento per il Trattamento degli Alimenti e dei loro Ingredienti con Radiazioni Ionizzanti, Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia, 20-71121 Foggia, Italy
| | - Rosalia Zianni
- Laboratorio Nazionale di Riferimento per il Trattamento degli Alimenti e dei loro Ingredienti con Radiazioni Ionizzanti, Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia, 20-71121 Foggia, Italy
| | - Marco Iammarino
- Laboratorio Nazionale di Riferimento per il Trattamento degli Alimenti e dei loro Ingredienti con Radiazioni Ionizzanti, Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia, 20-71121 Foggia, Italy
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9
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Acunha T, Rocha BA, Nardini V, Barbosa F, Faccioli LH. Lipidomic profiling of the Brazilian yellow scorpion venom: new insights into inflammatory responses following Tityus serrulatus envenomation. J Toxicol Environ Health A 2023; 86:283-295. [PMID: 36895096 DOI: 10.1080/15287394.2023.2188896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Due to the high prevalence and clinical relevance, scorpionism is a critical public health issue in several Brazilian regions. Tityus serrulatus, commonly known as the Brazilian yellow scorpion, is the most venomous genus found in Brazilian fauna and associated with severe clinical manifestations such as localized pain, hypertension, sweating, tachycardia and complex hyperinflammatory responses. In general, T. serrulatus venom contains a complex mixture of active compounds, including proteins, peptides, and amino acids. Although knowledge of the protein fractions of scorpion venom is available, venom lipid components are not yet comprehensively known. The aim of the present study was to determine and characterize the lipid constituents/profile of the T. serratus venom utilizing liquid chromatography coupled with high-resolution mass spectrometry. Lipid species (164 in total) belonging to 3 different lipid categories, glycerophospholipids, sphingolipids, and glycerolipids, were identified. A further search on MetaCore/MetaDrug platform, which is based upon a manually curated database of molecular interactions, molecular pathways, gene-disease associations, chemical metabolism, and toxicity information, exhibited several metabolic pathways for 24 of previously identified lipid species, including activation of nuclear factor kappa B and oxidative stress pathways. Further several bioactive compounds, such as plasmalogens, lyso-platelet-activating factors, and sphingomyelins, associated with systemic responses triggered by T. serrulatus envenomation were detected. Finally, lipidomic data presented provide advanced and valuable information to better comprehend the mechanisms underlying the complex pathophysiology induced by T. serrulatus envenomation.
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Affiliation(s)
| | | | | | - Fernando Barbosa
- Departamento de Análise Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Lúcia Helena Faccioli
- Departamento de Análise Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
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10
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Lara ML, Carvalho MG, de Souza FF, Schmith RA, Codognoto VM, De Vita B, Freitas Dell'Aqua CDP, Landim FDC, Alvarenga MLE. Influence of culture conditions on the secretome of mesenchymal stem cells derived from feline adipose tissue: Proteomics approach. Biochimie 2023; 211:78-86. [PMID: 36931338 DOI: 10.1016/j.biochi.2023.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 03/08/2023] [Accepted: 03/13/2023] [Indexed: 03/18/2023]
Abstract
This study aimed to describe the secretome of mesenchymal stem cells derived from feline adipose tissue (AD-MSCs) and compare the effects of different culture conditions on AD-MSC proteomics using a shotgun approach. Adipose tissue was collected from 5 female cats and prepared to culture. Conditioned media was collected at third passage, in which the cells were cultured under 4 conditions, normoxia with fetal bovine serum (N + FBS), hypoxia with FBS (H + FBS), normoxia without FBS (N - FBS), and hypoxia without FBS (H - FBS). Then, the secretome was concentrated and prepared for proteomic approaches. Secretomes cultured with FBS-free medium had more than twice identified proteins in comparison with the secretomes cultured with FBS. In contrast, hypoxic conditions did not increase protein amount and affected only a small proteome fraction. Relevant proteins were related to the extracellular matrix promoting environmental modulation, influencing cell signaling pathways, and providing a suitable environment for cell proliferation and maintenance. Moreover, other proteins were also related to cell adhesion, migration and morphogenesis. Culture conditions can influence protein abundance in AD-MSC secretome, and can give also more specificity to cell and cell-free treatments for different diseases.
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Affiliation(s)
- Maria Laura Lara
- Department of Veterinary Surgery and Animal Reproduction, School of Veterinary Medicine and Animal Science, São Paulo State University - UNESP, Botucatu, São Paulo, Brazil
| | - Marcos Gomides Carvalho
- Department of Veterinary Surgery and Animal Reproduction, School of Veterinary Medicine and Animal Science, São Paulo State University - UNESP, Botucatu, São Paulo, Brazil
| | - Fabiana Ferreira de Souza
- Department of Veterinary Surgery and Animal Reproduction, School of Veterinary Medicine and Animal Science, São Paulo State University - UNESP, Botucatu, São Paulo, Brazil.
| | - Rubia Alves Schmith
- Department of Veterinary Surgery and Animal Reproduction, School of Veterinary Medicine and Animal Science, São Paulo State University - UNESP, Botucatu, São Paulo, Brazil
| | - Viviane Maria Codognoto
- Department of Veterinary Surgery and Animal Reproduction, School of Veterinary Medicine and Animal Science, São Paulo State University - UNESP, Botucatu, São Paulo, Brazil
| | - Bruna De Vita
- Department of Veterinary Surgery and Animal Reproduction, School of Veterinary Medicine and Animal Science, São Paulo State University - UNESP, Botucatu, São Paulo, Brazil; International Product Marketing Manager - PROCARE HEALTH, Universitat de Barcelona, Barcelona, Catalunha, Spain
| | - Camila de Paula Freitas Dell'Aqua
- Department of Veterinary Surgery and Animal Reproduction, School of Veterinary Medicine and Animal Science, São Paulo State University - UNESP, Botucatu, São Paulo, Brazil
| | - Fernada da Cruz Landim
- Department of Veterinary Surgery and Animal Reproduction, School of Veterinary Medicine and Animal Science, São Paulo State University - UNESP, Botucatu, São Paulo, Brazil
| | - Marina Landim E Alvarenga
- Department of Veterinary Surgery and Animal Reproduction, School of Veterinary Medicine and Animal Science, São Paulo State University - UNESP, Botucatu, São Paulo, Brazil; Omics Animal Biotechnology, Botucatu, São Paulo, Brazil
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11
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Khodadadi Karimvand S, Mohammad Jafari J, Vali Zade S, Abdollahi H. Practical and comparative application of efficient data reduction - Multivariate curve resolution. Anal Chim Acta 2023; 1243:340824. [PMID: 36697179 DOI: 10.1016/j.aca.2023.340824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 01/11/2023] [Accepted: 01/11/2023] [Indexed: 01/13/2023]
Abstract
The term 'Big Data' has recently attracted much attention in science. Working with big data sets can be both challenging and rewarding. The complexity and big data sets make the analysis difficult to deal with, and the increasing volume of data sets requires the development of new practical methods for their handling. In this contribution, we explored the efficient data reduction-multivariate curve resolution (EDR-MCR) strategy based on the convex hull theory for quantitative and qualitative analysis of large chemical data sets. For the quantitative example, the potential of the EDR-MCR method for selecting a representative calibration set was investigated, and the results were compared with the widely used Kennard-Stone (KS) algorithm. The EDR-MCR strategy strongly limits the number of calibration samples with a high potency of prediction performance. The priority of EDR-MCR over KS is its ability to find informative variables and eliminate redundant features. Moreover, the EDR-MCR strategy was also applied for the qualitative analysis of a large-scale metabolomic data set. The comparable analysis results of EDR-MCR with the region of interest (ROI) method confirmed the ability of this method for quantitative analysis of big mass spectrophotometer data sets.
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Affiliation(s)
| | - Jamile Mohammad Jafari
- Department of Chemistry, Institute for Advanced Studies in Basic Sciences, P.O. Box 45195-1159, Zanjan, Iran
| | - Somaye Vali Zade
- Halal Research Center of IRI, Food and Drug Administration, Ministry of Health and Medical Education, Tehran, Iran
| | - Hamid Abdollahi
- Department of Chemistry, Institute for Advanced Studies in Basic Sciences, P.O. Box 45195-1159, Zanjan, Iran.
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12
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Ni Z, Wölk M, Jukes G, Mendivelso Espinosa K, Ahrends R, Aimo L, Alvarez-Jarreta J, Andrews S, Andrews R, Bridge A, Clair GC, Conroy MJ, Fahy E, Gaud C, Goracci L, Hartler J, Hoffmann N, Kopczyinki D, Korf A, Lopez-Clavijo AF, Malik A, Ackerman JM, Molenaar MR, O'Donovan C, Pluskal T, Shevchenko A, Slenter D, Siuzdak G, Kutmon M, Tsugawa H, Willighagen EL, Xia J, O'Donnell VB, Fedorova M. Guiding the choice of informatics software and tools for lipidomics research applications. Nat Methods 2023; 20:193-204. [PMID: 36543939 PMCID: PMC10263382 DOI: 10.1038/s41592-022-01710-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 11/02/2022] [Indexed: 12/24/2022]
Abstract
Progress in mass spectrometry lipidomics has led to a rapid proliferation of studies across biology and biomedicine. These generate extremely large raw datasets requiring sophisticated solutions to support automated data processing. To address this, numerous software tools have been developed and tailored for specific tasks. However, for researchers, deciding which approach best suits their application relies on ad hoc testing, which is inefficient and time consuming. Here we first review the data processing pipeline, summarizing the scope of available tools. Next, to support researchers, LIPID MAPS provides an interactive online portal listing open-access tools with a graphical user interface. This guides users towards appropriate solutions within major areas in data processing, including (1) lipid-oriented databases, (2) mass spectrometry data repositories, (3) analysis of targeted lipidomics datasets, (4) lipid identification and (5) quantification from untargeted lipidomics datasets, (6) statistical analysis and visualization, and (7) data integration solutions. Detailed descriptions of functions and requirements are provided to guide customized data analysis workflows.
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Affiliation(s)
- Zhixu Ni
- Center of Membrane Biochemistry and Lipid Research, Faculty of Medicine Carl Gustav Carus of TU Dresden, Dresden, Germany
| | - Michele Wölk
- Center of Membrane Biochemistry and Lipid Research, Faculty of Medicine Carl Gustav Carus of TU Dresden, Dresden, Germany
| | - Geoff Jukes
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, UK
| | | | - Robert Ahrends
- Department of Analytical Chemistry, University of Vienna, Vienna, Austria
| | - Lucila Aimo
- Swiss-Prot group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Geneva, Switzerland
| | - Jorge Alvarez-Jarreta
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Simon Andrews
- Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - Robert Andrews
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, UK
| | - Alan Bridge
- Swiss-Prot group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Geneva, Switzerland
| | - Geremy C Clair
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Matthew J Conroy
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, UK
| | - Eoin Fahy
- Department of Bioengineering, University of California, San Diego, CA, USA
| | - Caroline Gaud
- Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - Laura Goracci
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Jürgen Hartler
- Institute of Pharmaceutical Sciences, University of Graz, Graz, Austria
- Field of Excellence BioHealthe-University of Graz, Graz, Austria
| | - Nils Hoffmann
- Center for Biotechnology, University of Bielefeld, Bielefeld, Germany
| | - Dominik Kopczyinki
- Department of Analytical Chemistry, University of Vienna, Vienna, Austria
| | - Ansgar Korf
- Bruker Daltonics GmbH & Co. KG, Bremen, Germany
| | | | - Adnan Malik
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Martijn R Molenaar
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Claire O'Donovan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Tomáš Pluskal
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Denise Slenter
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands
| | - Gary Siuzdak
- Scripps Center for Metabolomics and Mass Spectrometry, The Scripps Research Institute, La Jolla, CA, USA
| | - Martina Kutmon
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands
- Maastricht Centre for Systems Biology, Maastricht University, Maastricht, The Netherlands
| | - Hiroshi Tsugawa
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Egon L Willighagen
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands
| | - Jianguo Xia
- Institute of Parasitology, McGill University, Montreal, Canada
| | - Valerie B O'Donnell
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, UK.
| | - Maria Fedorova
- Center of Membrane Biochemistry and Lipid Research, Faculty of Medicine Carl Gustav Carus of TU Dresden, Dresden, Germany.
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13
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Zhang J, Zhang Q, Fan J, Yu J, Li K, Bai J. Lipidomics reveals alterations of lipid composition and molecular nutrition in irradiated marble beef. Food Chem X 2023; 17:100617. [PMID: 36974174 PMCID: PMC10039263 DOI: 10.1016/j.fochx.2023.100617] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 02/07/2023] [Accepted: 02/23/2023] [Indexed: 02/27/2023] Open
Abstract
Electron beam irradiation can effectively inhibit microbial growth, but the changes of lipid during irradiation have not been comprehensively analyzed in marble beef. Here, UHPLC-MS/MS was used to detect lipids changes of irradiated marble beef. A total of 1032 lipids were identified and classified into 3 lipid classes and 8 subclasses in irradiated marble beef. 9 lipid biomarkers were screened with increasing irradiation dose. 122 differential lipids were generated and involved in 4 metabolic pathways included Glycerophospholipid metabolism, Linoleic acid metabolism, alpha-Linolenic acid metabolism and Arachidonic acid metabolism though PC(18:0/14:0), PE(16:0/16:0) and PE(18:0/16:0) in irradiated. Our results showed that irradiation had effect on the lipid of marbled beef, but the increase of irradiation dose from 2.5 kGy to 4.5 kGy had little effect on lipids. These results help us to understand the dynamic changes of irradiated meat lipids and lay a foundation for the application of irradiation in meat preservation.
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14
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Calderón C, Lämmerhofer M. Nutritional lipidomics for the characterization of lipids in food. Advances in Food and Nutrition Research 2023. [PMID: 37516469 DOI: 10.1016/bs.afnr.2022.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Lipids represent one out of three major macronutrient classes in the human diet. It is estimated to account for about 15-20% of the total dietary intake. Triacylglycerides comprise the majority of them, estimated 90-95%. Other lipid classes include free fatty acids, phospholipids, cholesterol, and plant sterols as minor components. Various methods are used for the characterization of nutritional lipids, however, lipidomics approaches become increasingly attractive for this purpose due to their wide coverage, comprehensiveness and holistic view on composition. In this chapter, analytical methodologies and workflows utilized for lipidomics profiling of food samples are outlined with focus on mass spectrometry-based assays. The chapter describes common lipid extraction protocols, the distinct instrumental mass-spectrometry based analytical platforms for data acquisition, chromatographic and ion-mobility spectrometry methods for lipid separation, briefly mentions alternative methods such as gas chromatography for fatty acid profiling and mass spectrometry imaging. Critical issues of important steps of lipidomics workflows such as structural annotation and identification, quantification and quality assurance are discussed as well. Applications reported over the period of the last 5years are summarized covering the discovery of new lipids in foodstuff, differential profiling approaches for comparing samples from different origin, species, varieties, cultivars and breeds, and for food processing quality control. Lipidomics as a powerful tool for personalized nutrition and nutritional intervention studies is briefly discussed as well. It is expected that this field is significantly growing in the near future and this chapter gives a short insight into the power of nutritional lipidomics approaches.
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15
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Albert M, Vázquez J, Falcón-Pérez JM, Balboa MA, Liesa M, Balsinde J, Guerra S. ISG15 Is a Novel Regulator of Lipid Metabolism during Vaccinia Virus Infection. Microbiol Spectr 2022; 10:e0389322. [PMID: 36453897 PMCID: PMC9769738 DOI: 10.1128/spectrum.03893-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 11/10/2022] [Indexed: 12/03/2022] Open
Abstract
Interferon-stimulated gene 15 (ISG15) is a 15-kDa ubiquitin-like modifier that binds to target proteins in a process termed ISGylation. ISG15, first described as an antiviral molecule against many viruses, participates in numerous cellular processes, from immune modulation to the regulation of genome stability. Interestingly, the role of ISG15 as a regulator of cell metabolism has recently gained strength. We previously described ISG15 as a regulator of mitochondrial functions in bone marrow-derived macrophages (BMDMs) in the context of Vaccinia virus (VACV) infection. Here, we demonstrate that ISG15 regulates lipid metabolism in BMDMs and that ISG15 is necessary to modulate the impact of VACV infection on lipid metabolism. We show that Isg15-/- BMDMs demonstrate alterations in the levels of several key proteins of lipid metabolism that result in differences in the lipid profile compared with Isg15+/+ (wild-type [WT]) BMDMs. Specifically, Isg15-/- BMDMs present reduced levels of neutral lipids, reflected by decreased lipid droplet number. These alterations are linked to increased levels of lipases and are independent of enhanced fatty acid oxidation (FAO). Moreover, we demonstrate that VACV causes a dysregulation in the proteomes of BMDMs and alterations in the lipid content of these cells, which appear exacerbated in Isg15-/- BMDMs. Such metabolic changes are likely caused by increased expression of the metabolic regulators peroxisome proliferator-activated receptor-γ (PPARγ) and PPARγ coactivator-1α (PGC-1α). In summary, our results highlight that ISG15 controls BMDM lipid metabolism during viral infections, suggesting that ISG15 is an important host factor to restrain VACV impact on cell metabolism. IMPORTANCE The functions of ISG15 are continuously expanding, and growing evidence supports its role as a relevant modulator of cell metabolism. In this work, we highlight how the absence of ISG15 impacts macrophage lipid metabolism in the context of viral infections and how poxviruses modulate metabolism to ensure successful replication. Our results open the door to new advances in the comprehension of macrophage immunometabolism and the interaction between VACV and the host.
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Affiliation(s)
- Manuel Albert
- Department of Preventive Medicine, Public Health and Microbiology, Universidad Autónoma de Madrid, Madrid, Spain
| | - Jesús Vázquez
- Centro Nacional de Investigaciones Cardiovasculares (CNIC-ISCIII), Madrid, Spain
| | | | - María A. Balboa
- Consejo Superior de Investigaciones Científicas (CSIC), Instituto de Biología y Genética Molecular, Valladolid, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain
| | - Marc Liesa
- Department of Medicine, Endocrinology, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
- Institut de Biologia Molecular de Barcelona, IBMB, CSIC, Barcelona, Spain
| | - Jesús Balsinde
- Consejo Superior de Investigaciones Científicas (CSIC), Instituto de Biología y Genética Molecular, Valladolid, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain
| | - Susana Guerra
- Department of Preventive Medicine, Public Health and Microbiology, Universidad Autónoma de Madrid, Madrid, Spain
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16
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Ganeshalingam M, Enstad S, Sen S, Cheema S, Esposito F, Thomas R. Role of lipidomics in assessing the functional lipid composition in breast milk. Front Nutr 2022; 9:899401. [PMID: 36118752 PMCID: PMC9478754 DOI: 10.3389/fnut.2022.899401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 08/02/2022] [Indexed: 11/13/2022] Open
Abstract
Breast milk is the ideal source of nutrients for infants in early life. Lipids represent 2–5% of the total breast milk composition and are a major energy source providing 50% of an infant’s energy intake. Functional lipids are an emerging class of lipids in breast milk mediating several different biological functions, health, and developmental outcome. Lipidomics is an emerging field that studies the structure and function of lipidome. It provides the ability to identify new signaling molecules, mechanisms underlying physiological activities, and possible biomarkers for early diagnosis and prognosis of diseases, thus laying the foundation for individualized, targeted, and precise nutritional management strategies. This emerging technique can be useful to study the major role of functional lipids in breast milk in several dimensions. Functional lipids are consumed with daily food intake; however, they have physiological benefits reported to reduce the risk of disease. Functional lipids are a new area of interest in lipidomics, but very little is known of the functional lipidome in human breast milk. In this review, we focus on the role of lipidomics in assessing functional lipid composition in breast milk and how lipid bioinformatics, a newly emerging branch in this field, can help to determine the mechanisms by which breast milk affects newborn health.
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Affiliation(s)
- Moganatharsa Ganeshalingam
- School of Science and the Environment/Boreal Ecosystems Research Initiative, Memorial University of Newfoundland, Corner Brook, NL, Canada
- *Correspondence: Moganatharsa Ganeshalingam,
| | - Samantha Enstad
- Neonatal Intensive Care Unit, Orlando Health Winne Palmer Hospital for Women and Babies, Orlando, FL, United States
| | - Sarbattama Sen
- Department of Pediatric Newborn Medicine, Brigham and Women’s Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Sukhinder Cheema
- Department of Biochemistry, Memorial University of Newfoundland, St. John’s, NL, Canada
| | - Flavia Esposito
- Department of Mathematics, University of Bari Aldo Moro, Bari, Italy
| | - Raymond Thomas
- School of Science and the Environment/Boreal Ecosystems Research Initiative, Memorial University of Newfoundland, Corner Brook, NL, Canada
- Raymond Thomas,
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17
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Marques NFS, Codognoto VM, de Souza FF, Scott C, Janini LCZ, Brochine S, Tironi SMT, de Camargo LS, Alvarez MVN, Oba E. Proteomics of follicular fluid from buffaloes (Bubalus bubalis): unraveling the secrets of follicular development. Livest Sci 2022. [DOI: 10.1016/j.livsci.2022.104947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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18
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Zhou F, Ren J, Liu Y, Li X, Wang W, Wu C. Interep: An R Package for High-Dimensional Interaction Analysis of the Repeated Measurement Data. Genes (Basel) 2022; 13:genes13030544. [PMID: 35328097 PMCID: PMC8950762 DOI: 10.3390/genes13030544] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/12/2022] [Accepted: 03/13/2022] [Indexed: 02/05/2023] Open
Abstract
We introduce interep, an R package for interaction analysis of repeated measurement data with high-dimensional main and interaction effects. In G × E interaction studies, the forms of environmental factors play a critical role in determining how structured sparsity should be imposed in the high-dimensional scenario to identify important effects. Zhou et al. (2019) (PMID: 31816972) proposed a longitudinal penalization method to select main and interaction effects corresponding to the individual and group structure, respectively, which requires a mixture of individual and group level penalties. The R package interep implements generalized estimating equation (GEE)-based penalization methods with this sparsity assumption. Moreover, alternative methods have also been implemented in the package. These alternative methods merely select effects on an individual level and ignore the group-level interaction structure. In this software article, we first introduce the statistical methodology corresponding to the penalized GEE methods implemented in the package. Next, we present the usage of the core and supporting functions, which is followed by a simulation example with R codes and annotations. The R package interep is available at The Comprehensive R Archive Network (CRAN).
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Affiliation(s)
- Fei Zhou
- Department of Statistics, Kansas State University, Manhattan, KS 66506, USA; (F.Z.); (Y.L.); (X.L.)
| | - Jie Ren
- Department of Biostatistics and Health Data Sciences, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
| | - Yuwen Liu
- Department of Statistics, Kansas State University, Manhattan, KS 66506, USA; (F.Z.); (Y.L.); (X.L.)
| | - Xiaoxi Li
- Department of Statistics, Kansas State University, Manhattan, KS 66506, USA; (F.Z.); (Y.L.); (X.L.)
| | - Weiqun Wang
- Department of Food, Nutrition, Dietetics and Health, Kansas State University, Manhattan, KS 66506, USA;
| | - Cen Wu
- Department of Statistics, Kansas State University, Manhattan, KS 66506, USA; (F.Z.); (Y.L.); (X.L.)
- Correspondence: ; Tel.: +1-7855322231
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19
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Li B, Stuart DD, Shanta PV, Pike CD, Cheng Q. Probing Herbicide Toxicity to Algae ( Selenastrum capricornutum) by Lipid Profiling with Machine Learning and Microchip/MALDI-TOF Mass Spectrometry. Chem Res Toxicol 2022; 35:606-615. [PMID: 35289601 DOI: 10.1021/acs.chemrestox.1c00397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS)-based lipid profiling is a powerful method to study the cytotoxicity of chemical exposure to microorganisms at the single cell level. We report here a combined approach of machine learning (ML) and microchip-based MALDI-time of flight (TOF) mass spectrometry to investigate the cytotoxic effect of herbicides on algae through single cell lipid profiling. Algal species Selenastrum capricornutum was chosen as the target system, and its exposure to different doses of common chemical herbicides and the resulting cytotoxic behaviors under various stress conditions were characterized. A lipid library for S. capricornutum has been established with 63 identified lipids that include glycosyldiacylglycerols and triacylglycerols. We demonstrated that major alternations occurred for lipids with functional groups of digalactosyldiacylglycerol (DGDG), triacylglycerol (TAG), and monogalactosyldiacylglycerol (MGDG). DGDG was shown to decrease upon exposure to herbicides of norflurazon and atrazine, while some MGDG and TAG lipids would increase for norflurazon. Compared to other algae, S. capricornutum was more strongly impacted by norflurazon than atrazine while the latter was observed to have a greater effect on C. reinhardtii. Machine learning algorithms have been applied to improve the classification of herbicide impact and help identify lipid species affected by the chemical exposure. A total of 69 machine learning models were trained and tested for the identification of ideal algorithms in the classification process, in which flexible discriminant analysis and support vector machine model were found to be the most accurate and consistent. The ML algorithms accurately differentiated herbicide impact and have identified cytotoxic differences that were previously hidden. The results suggest that herbicides express toxicity among different algae likely on the basis of metabolic differences. The ML-assisted method proves to be highly effective and can provide an advanced technological platform for probing cytotoxicity for bacterial species and in metabolic pathway analysis.
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20
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Cabezas R, Martin-Jiménez C, Zuluaga M, Pinzón A, Barreto GE, González J. Integrated Metabolomics and Lipidomics Reveal High Accumulation of Glycerophospholipids in Human Astrocytes under the Lipotoxic Effect of Palmitic Acid and Tibolone Protection. Int J Mol Sci 2022; 23:ijms23052474. [PMID: 35269616 PMCID: PMC8910245 DOI: 10.3390/ijms23052474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/05/2022] [Accepted: 02/07/2022] [Indexed: 12/03/2022] Open
Abstract
Lipotoxicity is a metabolic condition resulting from the accumulation of free fatty acids in non-adipose tissues which involves a series of pathological responses triggered after chronic exposure to high levels of fatty acids, severely detrimental to cellular homeostasis and viability. In brain, lipotoxicity affects both neurons and other cell types, notably astrocytes, leading to neurodegenerative processes, such as Alzheimer (AD) and Parkinson diseases (PD). In this study, we performed for the first time, a whole lipidomic characterization of Normal Human Astrocytes cultures exposed to toxic concentrations of palmitic acid and the protective compound tibolone, to establish and identify the set of potential metabolites that are modulated under these experimental treatments. The study covered 3843 features involved in the exo- and endo-metabolome extracts obtained from astrocytes with the mentioned treatments. Through multivariate statistical analysis such as PCA (principal component analysis), partial least squares (PLS-DA), clustering analysis, and machine learning enrichment analysis, it was possible to determine the specific metabolites that were affected by palmitic acid insult, such as phosphoethanolamines, phosphoserines phosphocholines and glycerophosphocholines, with their respective metabolic pathways impact. Moreover, our results suggest the importance of tibolone in the generation of neuroprotective metabolites by astrocytes and may be relevant to the development of neurodegenerative processes.
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Affiliation(s)
- Ricardo Cabezas
- Grupo de Investigación en Ciencias Biomédicas GRINCIBIO, Facultad de Medicina, Universidad Antonio Nariño, Bogota 110231, Colombia
- Correspondence: (R.C.); (J.G.); Tel.: +571-3159273304 (J.G.)
| | - Cynthia Martin-Jiménez
- Division of Neuropharmacology and Neurologic Diseases, Yerkes National Primate Research Center, Atlanta, GA 30301, USA;
| | - Martha Zuluaga
- Escuela de Ciencias Básicas Tecnologías e Ingenierías, Universidad Nacional Abierta y a Distancia, Bogota 111511, Colombia;
- Grupo de Investigación en Cromatografía y Técnicas Afines, Universidad de Caldas, Manizales 170002, Colombia
| | - Andrés Pinzón
- Laboratorio de Bioinformática y Biología de Sistemas, Universidad Nacional de Colombia-Bogotá, Bogota 111321, Colombia;
| | - George E. Barreto
- Department of Biological Sciences, University of Limerick, V94 T9PX Limerick, Ireland;
- Health Research Institute, University of Limerick, V94 T9PX Limerick, Ireland
| | - Janneth González
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana Bogotá, Bogota 110231, Colombia
- Correspondence: (R.C.); (J.G.); Tel.: +571-3159273304 (J.G.)
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21
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Sun J, Hu P, Lyu C, Tian J, Meng X, Tan H, Dong W. Targeted Lipidomics Analysis of Oxylipids in Hazelnut Oil during Storage by Liquid Chromatography Coupled to Tandem Mass Spectrometry. J Agric Food Chem 2022; 70:1715-1723. [PMID: 35084847 DOI: 10.1021/acs.jafc.1c06811] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Hazelnut oil is a high-grade edible oil with high nutritional value and unique taste. However, it is prone to oxidative degradation during storage. Herein, we used liquid chromatography coupled to tandem mass spectrometry to carry out a lipidomics analysis of the storage process of hazelnut oil. A total of 41 triacylglycerols and 12 oxylipids were determined. The contents of all oxylipids increased significantly after storage (p < 0.05). The oxylipid accumulation of hazelnut oil during storage was clarified for the first time. Nine significantly different oxylipids were further screened out. It was considered that the 15th day of storage is the dividing point. In addition, the lipoxygenase-catalyzed oxidation may be the major contributor to lipid oxidation of hazelnut oil. This study provides a new insight and theoretical basis to explore the storage oxidation mechanism of hazelnut oil and take quality control measures.
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Affiliation(s)
- Jiayang Sun
- College of Food Science, Shenyang Agricultural University, Dongling Road, Shenhe District, Shenyang, Liaoning 110866, People's Republic of China
| | - Pengpeng Hu
- College of Foreign Language Teaching Development, Shenyang Agricultural University, Dongling Road, Shenhe District, Shenyang, Liaoning 110866, People's Republic of China
| | - Chunmao Lyu
- College of Food Science, Shenyang Agricultural University, Dongling Road, Shenhe District, Shenyang, Liaoning 110866, People's Republic of China
| | - Jinlong Tian
- College of Food Science, Shenyang Agricultural University, Dongling Road, Shenhe District, Shenyang, Liaoning 110866, People's Republic of China
| | - Xianjun Meng
- College of Food Science, Shenyang Agricultural University, Dongling Road, Shenhe District, Shenyang, Liaoning 110866, People's Republic of China
| | - Hui Tan
- College of Food Science, Shenyang Agricultural University, Dongling Road, Shenhe District, Shenyang, Liaoning 110866, People's Republic of China
| | - Wenxuan Dong
- College of Horticulture, Shenyang Agricultural University, Dongling Road, Shenhe District, Shenyang, Liaoning 110866, People's Republic of China
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22
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Araujo MS, de Oliveira Henriques Paulo OL, Scott C, Paranzini CS, Codognoto VM, de Paula Freitas Dell'Aqua C, Papa FO, de Souza FF. Insights into the influence of canine breed on proteomics of the spermatozoa and seminal plasma. J Proteomics 2022; 257:104508. [DOI: 10.1016/j.jprot.2022.104508] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 01/17/2022] [Accepted: 01/30/2022] [Indexed: 11/28/2022]
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23
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Vieweg I, Bender ML, Semenchuk PR, Hop H, Nahrgang J. Effects of chronic crude oil exposure on the fitness of polar cod (Boreogadus saida) through changes in growth, energy reserves and survival. Mar Environ Res 2022; 174:105545. [PMID: 34999412 DOI: 10.1016/j.marenvres.2021.105545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 12/04/2021] [Accepted: 12/17/2021] [Indexed: 06/14/2023]
Abstract
Climate models predict extended periods with sea-ice free Arctic waters during the next decade, which will allow more shipping activity and easier access to petroleum resources. Increased industrial activities raise concerns about the biological effects of accidental petroleum release on key species of the Arctic marine ecosystem, such as the polar cod (Boreogadus saida). This study examines effects on physiological traits related to the fitness of adult polar cod, such as growth, survival, and lipid parameters. Fish were exposed to environmentally-relevant crude oil doses through their diet over an 8-month period, concurrent with reproductive development. In liver tissue, lipid class composition differed between treatments while in gonad tissue, lipid class composition varied between sexes, but not treatments. Crude oil did not affect growth and survival, which indicated that polar cod were relatively robust to dietary crude oil exposure at doses tested (0.11-1.14 μg crude oil/g fish/day) in this study.
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Affiliation(s)
- Ireen Vieweg
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT the Arctic University of Norway, N-9037, Tromsø, Norway.
| | - Morgan Lizabeth Bender
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT the Arctic University of Norway, N-9037, Tromsø, Norway
| | - Philipp Robert Semenchuk
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT the Arctic University of Norway, N-9037, Tromsø, Norway; Division of Conservation Biology, Vegetation Ecology and Landscape Ecology, Department of Botany and Biodiversity Research, Rennweg 14, 1030, Vienna, Australia
| | - Haakon Hop
- Norwegian Polar Institute, Fram Centre, N-9296, Tromsø, Norway
| | - Jasmine Nahrgang
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT the Arctic University of Norway, N-9037, Tromsø, Norway
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24
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Song Y, Cai C, Song Y, Sun X, Liu B, Xue P, Zhu M, Chai W, Wang Y, Wang C, Li M. A Comprehensive Review of Lipidomics and Its Application to Assess Food Obtained from Farm Animals. Food Sci Anim Resour 2022; 42:1-17. [PMID: 35028570 PMCID: PMC8728500 DOI: 10.5851/kosfa.2021.e59] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/10/2021] [Accepted: 10/13/2021] [Indexed: 12/04/2022] Open
Abstract
Lipids are one of the major macronutrients essential for adequate growth and
maintenance of human health. Their structure is not only complex but also
diverse, which makes systematic and holistic analyses challenging; consequently,
little is known regarding the relationship between phenotype and mechanism of
action. In recent years, rapid advancements have been made in the fields of
lipidomics and bioinformatics. In comparison with traditional approaches, mass
spectrometry-based lipidomics can rapidly identify as well as quantify
>1,000 lipid species at the same time, facilitating comprehensive, robust
analyses of lipids in tissues, cells, and body fluids. Accordingly, lipidomics
is now being widely applied in various fields, particularly food and nutrition
science. In this review, we discuss lipid classification, extraction techniques,
and detection and analysis using lipidomics. We also cover how lipidomics is
being used to assess food obtained from livestock and poultry. The information
included herein should serve as a reference to determine how to characterize
lipids in animal food samples, enhancing our understanding of the application of
lipidomics in the field in animal husbandry.
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Affiliation(s)
- Yinghua Song
- College of Agronomy, Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng 252059, China
| | - Changyun Cai
- College of Agronomy, Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng 252059, China
| | - Yingzi Song
- College of Agronomy, Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng 252059, China
| | - Xue Sun
- College of Agronomy, Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng 252059, China
| | - Baoxiu Liu
- College of Agronomy, Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng 252059, China
| | - Peng Xue
- College of Agronomy, Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng 252059, China
| | - Mingxia Zhu
- College of Agronomy, Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng 252059, China
| | - Wenqiong Chai
- College of Agronomy, Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng 252059, China
| | - Yonghui Wang
- College of Agronomy, Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng 252059, China
| | - Changfa Wang
- College of Agronomy, Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng 252059, China
| | - Mengmeng Li
- College of Agronomy, Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng 252059, China
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25
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Olund Villumsen S, Benfeitas R, Knudsen AD, Gelpi M, Høgh J, Thomsen MT, Murray D, Ullum H, Neogi U, Nielsen SD. Integrative Lipidomics and Metabolomics for System-Level Understanding of the Metabolic Syndrome in Long-Term Treated HIV-Infected Individuals. Front Immunol 2022; 12:742736. [PMID: 35095835 PMCID: PMC8791652 DOI: 10.3389/fimmu.2021.742736] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 12/22/2021] [Indexed: 11/23/2022] Open
Abstract
People living with HIV (PLWH) require life-long anti-retroviral treatment and often present with comorbidities such as metabolic syndrome (MetS). Systematic lipidomic characterization and its association with the metabolism are currently missing. We included 100 PLWH with MetS and 100 without MetS from the Copenhagen Comorbidity in HIV Infection (COCOMO) cohort to examine whether and how lipidome profiles are associated with MetS in PLWH. We combined several standard biostatistical, machine learning, and network analysis techniques to investigate the lipidome systematically and comprehensively and its association with clinical parameters. Additionally, we generated weighted lipid-metabolite networks to understand the relationship between lipidomic profiles with those metabolites associated with MetS in PLWH. The lipidomic dataset consisted of 917 lipid species including 602 glycerolipids, 228 glycerophospholipids, 61 sphingolipids, and 26 steroids. With a consensus approach using four different statistical and machine learning methods, we observed 13 differentially abundant lipids between PLWH without MetS and PLWH with MetS, which mainly belongs to diacylglyceride (DAG, n = 2) and triacylglyceride (TAG, n = 11). The comprehensive network integration of the lipidomics and metabolomics data suggested interactions between specific glycerolipids' structural composition patterns and key metabolites involved in glutamate metabolism. Further integration of the clinical data with metabolomics and lipidomics resulted in the association of visceral adipose tissue (VAT) and exposure to earlier generations of antiretroviral therapy (ART). Our integrative omics data indicated disruption of glutamate and fatty acid metabolism, suggesting their involvement in the pathogenesis of PLWH with MetS. Alterations in the lipid homeostasis and glutaminolysis need clinical interventions to prevent accelerated aging in PLWH with MetS.
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Affiliation(s)
- Sofie Olund Villumsen
- Department of Infectious Diseases, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Rui Benfeitas
- National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Andreas Dehlbæk Knudsen
- Department of Infectious Diseases, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Marco Gelpi
- Department of Infectious Diseases, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Julie Høgh
- Department of Infectious Diseases, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Magda Teresa Thomsen
- Department of Infectious Diseases, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Daniel Murray
- Personalized Medicine of Infectious Complications in Immune Deficiency (PERSIMUNE), Rigshospitalet, Copenhagen, Denmark
| | - Henrik Ullum
- Department of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Ujjwal Neogi
- The Systems Virology Lab, Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, ANA Futura, Stockholm, Sweden
- Manipal Institute of Virology (MIV), Manipal Academy of Higher Education, Manipal, India
| | - Susanne Dam Nielsen
- Department of Infectious Diseases, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
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26
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Menéndez-Pedriza A, Jaumot J, Bedia C. Lipidomic analysis of single and combined effects of polyethylene microplastics and polychlorinated biphenyls on human hepatoma cells. J Hazard Mater 2022; 421:126777. [PMID: 34364209 DOI: 10.1016/j.jhazmat.2021.126777] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 07/27/2021] [Accepted: 07/27/2021] [Indexed: 06/13/2023]
Abstract
Microplastics are an emerging environmental issue as a result of their ubiquity, persistence, and intrinsic toxic potential. In addition, their ability to sorb and transport a wide variety of environmental pollutants (i.e. "Trojan Horse" effect) exerts significant adverse impacts upon ecosystems. The toxicological evaluation of the single and combined effects produced by polyethylene microplastics and two polychlorinated biphenyl congeners was performed on the human hepatoma cell line HepG2 by cell viability assessment and an untargeted lipidomic study. The cell lethality evaluation evinced that MPs did not induce relevant cell lethality at any of the concentration range tested, while both PCBs presented a hormetic behavior. The lipidomic analysis suggested that both single PCB exposures induced significant lipidomic changes, especially for glycerophospholipids and glycerolipids. In contrast, for MPs single exposure, the most remarkable change was the substantial enhancement of triglyceride content. Regarding combined exposures, results showed that MPs could induce even more harmful effects than those produced intrinsically as a result of desorbing previously sorbed toxic pollutants. To the best of our knowledge, this is the first study assessing the toxicity of microplastics and their possible "Trojan Horse" effect by applying an untargeted lipidomic methodology.
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Affiliation(s)
- Albert Menéndez-Pedriza
- Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Joaquim Jaumot
- Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Carmen Bedia
- Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain.
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27
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Zhang H, Wang J, Zhao J, Sun C, Wang J, Wang Q, Qu F, Yun X, Feng Z. Integrated Lipidomic and Transcriptomic Analysis Reveals Lipid Metabolism in Foxtail Millet ( Setaria italica). Front Genet 2021; 12:758003. [PMID: 34868233 PMCID: PMC8635157 DOI: 10.3389/fgene.2021.758003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 10/27/2021] [Indexed: 11/28/2022] Open
Abstract
Foxtail millet (Setaria italica) as the main traditional crop in China, is rich in many kinds of high quality fatty acids (FAs). In this study, Ultra-high performance liquid chromatography-time-of-flight-tandem mass spectrometer (UHPLC-Q-TOF-MS/MS) was used to determine the lipids of JG35 and JG39. A total of 2,633 lipid molecules and 31 lipid subclasses were identified, mainly including thirteen kinds of glycerophospholipids (GP), eleven kinds of glycerolipids (GL), four kinds of sphingolipids (SP), two kinds of fatty acyls (FA) and one kind of sterol (ST). Among them JG35 had higher contents of diacylglycerols (DG) and ceramides (Cer), while triacylglycerols, phosphatidyl ethanolamine, phosphatidic acid, sterol, fatty acyls and pardiolipin (TG, PE, PA, ST, FA and CL) were higher in JG39. Meantime, the correlation analysis of lipidomics and transcriptomics was used to map the main differential lipid metabolism pathways of foxtail millet. The results shown that a differentially expressed genes (DEGs) of FATA/B for the synthesis of FA was highly expressed in JG35, and the related genes for the synthesis DG (ACCase, KAS, HAD, KCS, LACS and GAPT), TG (DGAT and PDAT) and CL (CLS) were highly expressed in JG39. The results of this study will provide a theoretical basis for the future study of lipidomics, improvement of lipid quality directionally and breeding of idiosyncratic quality varieties in foxtail millet.
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Affiliation(s)
- Haiying Zhang
- College of Agriculture, Shanxi Agricultural University, Taigu, China
| | - Junyou Wang
- College of Agriculture, Shanxi Agricultural University, Taigu, China
| | - Jing Zhao
- College of Agriculture, Shanxi Agricultural University, Taigu, China
| | - Changqing Sun
- College of Agriculture, Shanxi Agricultural University, Taigu, China
| | - Jin Wang
- College of Agriculture, Shanxi Agricultural University, Taigu, China
| | - Qian Wang
- Hebei Zhihai Technology Co., Ltd., Xingtai, China
| | - Fei Qu
- College of Agriculture, Shanxi Agricultural University, Taigu, China
| | - Xiaodong Yun
- College of Agriculture, Shanxi Agricultural University, Taigu, China
| | - Zhiwei Feng
- Shanxi Institute of Organic Dryland Farming, Shanxi Agricultural University, Taiyuan, China
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28
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Malkusch S, Hahnefeld L, Gurke R, Lötsch J. Visually guided preprocessing of bioanalytical laboratory data using an interactive R notebook (pguIMP). CPT Pharmacometrics Syst Pharmacol 2021; 10:1371-1381. [PMID: 34598320 PMCID: PMC8592507 DOI: 10.1002/psp4.12704] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 07/06/2021] [Accepted: 08/10/2021] [Indexed: 01/05/2023]
Abstract
The evaluation of pharmacological data using machine learning requires high data quality. Therefore, data preprocessing, that is, cleaning analytical laboratory errors, replacing missing values or outliers, and transforming data adequately before actual data analysis, is crucial. Because current tools available for this purpose often require programming skills, preprocessing tools with graphical user interfaces that can be used interactively are needed. In collaboration between data scientists and experts in bioanalytical diagnostics, a graphical software package for data preprocessing called pguIMP is proposed, which contains a fixed sequence of preprocessing steps to enable reproducible interactive data preprocessing. As an R-based package, it also allows direct integration into this data science environment without requiring any programming knowledge. The implementation of contemporary data processing methods, including machine-learning-based imputation techniques, ensures the generation of corrected and cleaned bioanalytical data sets that preserve data structures such as clusters better than is possible with classical methods. This was evaluated on bioanalytical data sets from lipidomics and drug research using k-nearest-neighbors-based imputation followed by k-means clustering and density-based spatial clustering of applications with noise. The R package provides a Shiny-based web interface designed to be easy to use for non-data analysis experts. It is demonstrated that the spectrum of methods provided is suitable as a standard pipeline for preprocessing bioanalytical data in biomedical research domains. The R package pguIMP is freely available at the comprehensive R archive network (https://cran.r-project.org/web/packages/pguIMP/index.html).
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Affiliation(s)
- Sebastian Malkusch
- Institute of Clinical Pharmacology, Goethe-University, Frankfurt am Main, Germany
| | - Lisa Hahnefeld
- Institute of Clinical Pharmacology, Goethe-University, Frankfurt am Main, Germany
| | - Robert Gurke
- Institute of Clinical Pharmacology, Goethe-University, Frankfurt am Main, Germany.,Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Frankfurt am Main, Germany
| | - Jörn Lötsch
- Institute of Clinical Pharmacology, Goethe-University, Frankfurt am Main, Germany.,Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Frankfurt am Main, Germany
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29
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Madeira C, Madeira D, Ladd N, Schubert CJ, Diniz MS, Vinagre C, Leal MC. Conserved fatty acid profiles and lipid metabolic pathways in a tropical reef fish exposed to ocean warming - An adaptation mechanism of tolerant species? Sci Total Environ 2021; 782:146738. [PMID: 33836377 DOI: 10.1016/j.scitotenv.2021.146738] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 03/15/2021] [Accepted: 03/21/2021] [Indexed: 06/12/2023]
Abstract
Climate warming is causing rapid spatial expansion of ocean warm pools from equatorial latitudes towards the subtropics. Sedentary coral reef inhabitants in affected areas will thus be trapped in high temperature regimes, which may become the "new normal". In this study, we used clownfish Amphiprion ocellaris as model organism to study reef fish mechanisms of thermal adaptation and determine how high temperature affects multiple lipid aspects that influence physiology and thermal tolerance. We exposed juvenile fish to two different experimental conditions, implemented over 28 days: average tropical water temperatures (26 °C, control) or average warm pool temperatures (30 °C). We then performed several analyses on fish muscle and liver tissues: i) total lipid content (%), ii) lipid peroxides, iii) fatty acid profiles, iv) lipid metabolic pathways, and v) weight as body condition metric. Results showed that lipid storage capacity in A. ocellaris was not affected by elevated temperature, even in the presence of lipid peroxides in both tissues assessed. Additionally, fatty acid profiles were unresponsive to elevated temperature, and lipid metabolic networks were consequently well conserved. Consistent with these results, we did not observe changes in fish weight at elevated temperature. There were, however, differences in fatty acid profiles between tissue types and over time. Liver showed enhanced α-linolenic and linoleic acid metabolism, which is an important pathway in stress response signaling and modulation on environmental changes. Temporal oscillations in fatty acid profiles are most likely related to intrinsic factors such as growth, which leads to the mobilization of energetic reserves between different tissues throughout time according to organism needs. Based on these results, we propose that the stability of fatty acid profiles and lipid metabolic pathways may be an important thermal adaptation feature of fish exposed to warming environments.
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Affiliation(s)
- Carolina Madeira
- UCIBIO - Applied Molecular Biosciences Unit, NOVA School of Science and Technology, 2829-516 Caparica, Portugal; MARE - Marine and Environmental Sciences Centre, University of Lisbon, Campo Grande, 1749-016 Lisboa, Portugal.
| | - Diana Madeira
- UCIBIO - Applied Molecular Biosciences Unit, NOVA School of Science and Technology, 2829-516 Caparica, Portugal; CESAM - Centre for Environmental and Marine Studies, University of Aveiro, Edifício ECOMARE, Estrada do Porto de Pesca Costeira, 3830-565 Gafanha da Nazaré, Portugal
| | - Nemiah Ladd
- Centre for Ecology, Evolution and Biogeochemistry, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Seestrasse 79, 6047 Kastanienbaum, Switzerland; Ecosystem Physiology, University of Freiburg, 53/54 Georges-Köhler Allee, 79119 Freiburg, Germany
| | - Carsten J Schubert
- Centre for Ecology, Evolution and Biogeochemistry, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Seestrasse 79, 6047 Kastanienbaum, Switzerland
| | - Mário S Diniz
- UCIBIO - Applied Molecular Biosciences Unit, NOVA School of Science and Technology, 2829-516 Caparica, Portugal
| | - Catarina Vinagre
- MARE - Marine and Environmental Sciences Centre, University of Lisbon, Campo Grande, 1749-016 Lisboa, Portugal; CCMAR - Centre of Marine Sciences, University of Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Miguel C Leal
- CESAM - Centre for Environmental and Marine Studies, University of Aveiro, Edifício ECOMARE, Estrada do Porto de Pesca Costeira, 3830-565 Gafanha da Nazaré, Portugal; Centre for Ecology, Evolution and Biogeochemistry, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Seestrasse 79, 6047 Kastanienbaum, Switzerland
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30
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Shanta PV, Li B, Stuart DD, Cheng Q. Lipidomic Profiling of Algae with Microarray MALDI-MS toward Ecotoxicological Monitoring of Herbicide Exposure. Environ Sci Technol 2021; 55:10558-10568. [PMID: 34286960 DOI: 10.1021/acs.est.1c01138] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Misuse of agrochemicals has a long-lasting negative impact on aquatic systems. Mismanagement of herbicides in agri-food sectors is often linked to a simultaneous decline in the health of downstream waterways. However, monitoring the herbicide levels in these areas is a laborious task, and modern analytical approaches, such as solid-phase extraction-liquid chromatography-mass spectrometry (SPE-LC-MS) and enzyme-linked immunosorbent assay, are low-throughput and require significant sample preparation. We report here the use of microchip technology in combination with matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) for the assessment of the ecotoxicological effect of agrochemicals on aquatic species at the single-cell level. This approach quantifies the fluctuations in lipid content in sentinel organisms and targets the microalga, Chlamydomonas reinhardtii (C. reinhardtii), as the model system. Specifically, we investigated the cytotoxicity of three herbicides (atrazine, clomazone, and norflurazon) on C. reinhardtii by analyzing the lipid component variation upon assorted herbicide exposure. Lipidomic profiling reveals a significantly altered lipid content at >EC50 in atrazine-exposed cells. The response for norflurazon showed similar trends but diminished in magnitude, while the result for clomazone was near muted. At lower herbicide concentrations, digalactosyldiacylglycerols showed a rapid decrease in abundance, while several other lipids displayed a moderate increase. The microchip-based MALDI technique demonstrates the ability to achieve lipidomic profiling of aquatic species exposed to different stressors, proving effective for high-throughput screening and single-cell analysis in ecotoxicity studies.
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Affiliation(s)
- Peter V Shanta
- Environmental Toxicology, University of California, Riverside, California 92521, United States
| | - Bochao Li
- Environmental Toxicology, University of California, Riverside, California 92521, United States
| | - Daniel D Stuart
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Quan Cheng
- Environmental Toxicology, University of California, Riverside, California 92521, United States
- Department of Chemistry, University of California, Riverside, California 92521, United States
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31
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Moraes JGN, Behura SK, Geary TW, Spencer TE. Analysis of the uterine lumen in fertility-classified heifers: I. Glucose, prostaglandins, and lipids†. Biol Reprod 2021; 102:456-474. [PMID: 31616913 DOI: 10.1093/biolre/ioz191] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 08/27/2019] [Accepted: 10/01/2019] [Indexed: 12/18/2022] Open
Abstract
Survival and growth of the bovine conceptus (embryo and associated extraembryonic membranes) are dependent on endometrial secretions or histotroph found in the uterine lumen. Previously, serial embryo transfer was used to classify heifers as high fertile (HF), subfertile (SF), or infertile (IF). Here, we investigated specific histotroph components [glucose, prostaglandins (PGs), and lipids] in the uterine lumen of day 17 pregnant and open fertility-classified heifers. Concentrations of glucose in the uterine lumen were increased by pregnancy but did not differ among fertility-classified heifers. Differences in expression of genes encoding glucose transporters and involved with glycolysis and gluconeogenesis were observed between conceptuses collected from HF and SF heifers. In the uterine lumen, PGE2 and PGF2α were increased by pregnancy, and HF heifers had higher concentrations of PGE2, PGF2α, and 6-keto-PFG1α than SF heifers. Differences were found in expression of genes regulating PG signaling, arachidonic acid metabolism, and peroxisome proliferator-activated receptor signaling among conceptuses and endometrium from fertility-classified heifers. Lipidomics was conducted exclusively in samples from HF heifers, and phosphatidylcholine was the main lipid class that increased in the uterine lumen by pregnancy. Expression of several lipid metabolism genes differed between HF and SF conceptuses, and a number of fatty acids were differentially abundant in the uterine lumen of pregnant HF and SF heifers. These results support the ideas that uterine luminal histotroph impacts conceptus survival and programs its development and is a facet of dysregulated conceptus-endometrial interactions that result in loss of the conceptus in SF cattle during the implantation period of pregnancy establishment.
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Affiliation(s)
- Joao G N Moraes
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, USA
| | - Susanta K Behura
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, USA
| | - Thomas W Geary
- USDA-ARS, Fort Keogh Livestock and Range Research Laboratory, Miles City, Montana, USA
| | - Thomas E Spencer
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, USA
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Pérez-Cova M, Jaumot J, Tauler R. Untangling comprehensive two-dimensional liquid chromatography data sets using regions of interest and multivariate curve resolution approaches. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116207] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Carvalho MG, Silva KM, Aristizabal VHV, Ortiz PEO, Paranzini CS, Melchert A, Amaro JL, Souza FF. Effects of Obesity and Diabetes on Sperm Cell Proteomics in Rats. J Proteome Res 2021; 20:2628-2642. [PMID: 33705140 DOI: 10.1021/acs.jproteome.0c01044] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Infertility caused by male factors is potentially associated with metabolic disorders such as obesity and/or diabetes. This experimental study was conducted in a male rodent model to assess the effects of different diseases on semen quality and sperm proteomics. Ten Wistar rats were used for each treatment. Rats were fed commercial food provided controllably to the control group and the diabetic group, and a hypercaloric diet supplemented with 5% sucrose in water was provided ad libitum to the obese group for 38 weeks. Diabetes was induced with 35 mg/kg streptozotocin. After euthanasia, testicles, spermatozoa, fat, and blood (serum) samples were collected. Spermatozoa were evaluated for quality and subjected to proteomics analyses. Histology and cytology of the testis, and serum leptin, adiponectin, interleukin 8 (IL-8), blood glucose, and testosterone levels, were also assessed. Body weight, retroperitoneal and testicular fat, and the Lee index were also measured. Obesity and diabetes were induced. The diabetic group showed noticeable changes in spermatogenesis and sperm quality. The mass spectrometry proteomics data have been deposited in Mendeley Data (doi: 10.17632/rfp7kfjcsd.5). Fifteen proteins varied in abundance between groups, especially proteins related to energy production and structural function of the spermatozoa, suggesting disturbances in energy production with a subsequent alteration in sperm motility in both groups, but with a compensatory response in the obese group.
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Affiliation(s)
- Marcos G Carvalho
- Department of Veterinary Surgery and Animal Reproduction, School of Veterinary Medicine and Animal Science, São Paulo State University "Júlio de Mesquita Filho"-UNESP, Rua Prof. Dr. Walter Maurício Correa, s/n, Rubião Junior, 18681-681 Botucatu, São Paulo, Brazil
| | - Kelry M Silva
- Department of Veterinary Surgery and Animal Reproduction, School of Veterinary Medicine and Animal Science, São Paulo State University "Júlio de Mesquita Filho"-UNESP, Rua Prof. Dr. Walter Maurício Correa, s/n, Rubião Junior, 18681-681 Botucatu, São Paulo, Brazil
| | - Viviana H V Aristizabal
- Department of Veterinary Surgery and Animal Reproduction, School of Veterinary Medicine and Animal Science, São Paulo State University "Júlio de Mesquita Filho"-UNESP, Rua Prof. Dr. Walter Maurício Correa, s/n, Rubião Junior, 18681-681 Botucatu, São Paulo, Brazil
| | - Pablo E O Ortiz
- Department of Veterinary Surgery and Animal Reproduction, School of Veterinary Medicine and Animal Science, São Paulo State University "Júlio de Mesquita Filho"-UNESP, Rua Prof. Dr. Walter Maurício Correa, s/n, Rubião Junior, 18681-681 Botucatu, São Paulo, Brazil
| | - Cristiane S Paranzini
- Department of Veterinary Surgery and Animal Reproduction, School of Veterinary Medicine and Animal Science, São Paulo State University "Júlio de Mesquita Filho"-UNESP, Rua Prof. Dr. Walter Maurício Correa, s/n, Rubião Junior, 18681-681 Botucatu, São Paulo, Brazil.,Envol Biomedical, Immokalee, Florida 34143, United States
| | - Alessandra Melchert
- Department of Veterinary Clinical, School of Veterinary Medicine and Animal Science, São Paulo State University "Júlio de Mesquita Filho"-UNESP, 18618-681 Botucatu, São Paulo, Brazil
| | - João L Amaro
- Department of Surgical Specialties and Anesthesiology, Urology, School of Medicine, São Paulo State University ̈Júlio de Mesquita Filho"-UNESP, 18618-687 Botucatu, São Paulo, Brazil
| | - Fabiana F Souza
- Department of Veterinary Surgery and Animal Reproduction, School of Veterinary Medicine and Animal Science, São Paulo State University "Júlio de Mesquita Filho"-UNESP, Rua Prof. Dr. Walter Maurício Correa, s/n, Rubião Junior, 18681-681 Botucatu, São Paulo, Brazil
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Phan Q, Tomasino E. Untargeted lipidomic approach in studying pinot noir wine lipids and predicting wine origin. Food Chem 2021; 355:129409. [PMID: 33799257 DOI: 10.1016/j.foodchem.2021.129409] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 02/15/2021] [Accepted: 02/16/2021] [Indexed: 12/21/2022]
Abstract
An untargeted lipidomic profiling approach based on ultra - performance liquid chromatography - time-of-flight tandem mass spectrometry (UPLC-TOF-MS/MS) was successfully used to study the origin of commercial Pinot noir wines. The total wine lipids were extracted using a modified Bligh-Dyer method. In all wine samples, the total lipids were less than 0.1% (w/w) of wine. The wines analyzed consisted of 222 lipids from 11 different classes. 48 commercial Pinot noir wine samples were collected from producers in Burgundy, California, Oregon, and New Zealand. Lipidomic data was studied using advanced multivariate analysis methods, random forest, k-nearest neighbor (k-NN), and linear discriminant analysis. The overall classification accuracy was 97.5% for random forest and 90% for k-NN. Wine lipids showed a strong potential for classifying wines by origin, with the top 58 lipids contributing to the discrimination. This information could potentially be used for further study of the impacts of lipids on wine characteristics and authenticity.
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Affiliation(s)
- Quynh Phan
- Department of Food Science and Technology, Oregon State University, 100 Wiegand Hall, Corvallis, OR 97331, United States
| | - Elizabeth Tomasino
- Department of Food Science and Technology, Oregon State University, 100 Wiegand Hall, Corvallis, OR 97331, United States.
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Lainetti PF, Leis-Filho AF, Kobayashi PE, de Camargo LS, Laufer-Amorim R, Fonseca-Alves CE, Souza FF. Proteomics Approach of Rapamycin Anti-Tumoral Effect on Primary and Metastatic Canine Mammary Tumor Cells In Vitro. Molecules 2021; 26:molecules26051213. [PMID: 33668689 PMCID: PMC7956669 DOI: 10.3390/molecules26051213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/22/2020] [Accepted: 12/28/2020] [Indexed: 12/05/2022] Open
Abstract
Rapamycin is an antifungal drug with antitumor activity and acts inhibiting the mTOR complex. Due to drug antitumor potential, the aim of this study was to evaluate its effect on a preclinical model of primary mammary gland tumors and their metastases from female dogs. Four cell lines from our cell bank, two from primary canine mammary tumors (UNESP-CM1, UNESP-CM60) and two metastases (UNESP-MM1, and UNESP-MM4) were cultured in vitro and investigated for rapamycin IC50. Then, cell lines were treated with rapamycin IC50 dose and mRNA and protein were extracted in treated and non-treated cells to perform AKT, mTOR, PTEN and 4EBP1 gene expression and global proteomics by mass spectrometry. MTT assay demonstrated rapamycin IC50 dose for all different tumor cells between 2 and 10 μM. RT-qPCR from cultured cells, control versus treated group and primary tumor cells versus metastatic tumor cells, did not shown statistical differences. In proteomics were found 273 proteins in all groups, and after data normalization 49 and 92 proteins were used for statistical analysis for comparisons between control versus rapamycin treatment groups, and metastasis versus primary tumor versus metastasis rapamycin versus primary tumor rapamycin, respectively. Considering the two statistical analysis, four proteins, phosphoglycerate mutase, malate dehydrogenase, l-lactate dehydrogenase and nucleolin were found in decreased abundance in the rapamycin group and they are related with cellular metabolic processes and enhanced tumor malignant behavior. Two proteins, dihydrolipoamide dehydrogenase and superoxide dismutase, also related with metabolic processes, were found in higher abundance in rapamycin group and are associated with apoptosis. The results suggested that rapamycin was able to inhibit cell growth of mammary gland tumor and metastatic tumors cells in vitro, however, concentrations needed to reach the IC50 were higher when compared to other studies.
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Affiliation(s)
- Patrícia F. Lainetti
- Department of Veterinary Surgery and Animal Reproduction, School of Veterinary Medicine and Animal Science, São Paulo State University—UNESP, Botucatu 18618-681, Brazil; (P.F.L.); (L.S.d.C.); (C.E.F.-A.)
| | - Antonio F. Leis-Filho
- Department of Veterinary Clinic, School of Veterinary Medicine and Animal Science, São Paulo State University—UNESP, Botucatu 18618-681, Brazil; (A.F.L.-F.); (P.E.K.); (R.L.-A.)
| | - Priscila E. Kobayashi
- Department of Veterinary Clinic, School of Veterinary Medicine and Animal Science, São Paulo State University—UNESP, Botucatu 18618-681, Brazil; (A.F.L.-F.); (P.E.K.); (R.L.-A.)
| | - Laíza S. de Camargo
- Department of Veterinary Surgery and Animal Reproduction, School of Veterinary Medicine and Animal Science, São Paulo State University—UNESP, Botucatu 18618-681, Brazil; (P.F.L.); (L.S.d.C.); (C.E.F.-A.)
| | - Renee Laufer-Amorim
- Department of Veterinary Clinic, School of Veterinary Medicine and Animal Science, São Paulo State University—UNESP, Botucatu 18618-681, Brazil; (A.F.L.-F.); (P.E.K.); (R.L.-A.)
| | - Carlos E. Fonseca-Alves
- Department of Veterinary Surgery and Animal Reproduction, School of Veterinary Medicine and Animal Science, São Paulo State University—UNESP, Botucatu 18618-681, Brazil; (P.F.L.); (L.S.d.C.); (C.E.F.-A.)
- Institute of Health Sciences, Universidade Paulista—UNIP, Bauru 17048-290, Brazil
| | - Fabiana F. Souza
- Department of Veterinary Surgery and Animal Reproduction, School of Veterinary Medicine and Animal Science, São Paulo State University—UNESP, Botucatu 18618-681, Brazil; (P.F.L.); (L.S.d.C.); (C.E.F.-A.)
- Correspondence: ; Tel.: +55-14-38802237
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Dreier DA, Nouri MZ, Denslow ND, Martyniuk CJ. Lipidomics reveals multiple stressor effects (temperature × mitochondrial toxicant) in the zebrafish embryo toxicity test. Chemosphere 2021; 264:128472. [PMID: 33039916 DOI: 10.1016/j.chemosphere.2020.128472] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 09/25/2020] [Accepted: 09/26/2020] [Indexed: 05/27/2023]
Abstract
Aquatic organisms are exposed to multiple stressors in the environment, including contaminants and rising temperatures due to climate change. The objective of this study was to characterize the effect of increased temperature on chemical-induced toxicity and lipid profiles during embryonic development and hatch in fish. This is important because temperature and many environmental chemicals modulate cellular metabolism and lipids, both of which play integral roles for normal embryonic development. As such, we employed the zebrafish embryo toxicity test for multiple stressor exposures, using the mitochondrial toxicant 2,4-Dinitrophenol (DNP; 6-30 μM) in conjunction with different temperature treatments (28 °C and 33 °C). We found a positive relationship between temperature and lethality at lower DNP concentrations, suggesting temperature stress can increase toxicant sensitivity. Next, we used LC-MS/MS for lipidomics following exposure to sublethal stressor combinations. It was determined that temperature stress at 33 °C augmented DNP-induced effects on the lipidome, including the upregulation of bioactive lipids involved in apoptosis (e.g., ceramides). These data reveal potential implications for climate change and sensitivity to environmental pollution and demonstrate the utility of lipidomics to characterize metabolic pathways underlying toxicity. Data such as these are expected to advance adverse outcome pathways by establishing multiple stressor networks that include intermediate lipid responses.
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Affiliation(s)
- David A Dreier
- Center for Environmental & Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Mohammad-Zaman Nouri
- Center for Environmental & Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Nancy D Denslow
- Center for Environmental & Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Christopher J Martyniuk
- Center for Environmental & Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA.
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Abstract
Shotgun lipidomics is an analytical approach for large-scale and systematic analysis of the composition, structure, and quantity of cellular lipids directly from lipid extracts of biological samples by mass spectrometry. This approach possesses advantages of high throughput and quantitative accuracy, especially in absolute quantification. As cancer research deepens at the level of quantitative biology and metabolomics, the demand for lipidomics approaches such as shotgun lipidomics is becoming greater. In this chapter, the principles, approaches, and some applications of shotgun lipidomics for cancer research are overviewed.
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Affiliation(s)
- Jianing Wang
- Barshop Institute for Longevity and Aging Studies, San Antonio, TX, USA
| | - Chunyan Wang
- Barshop Institute for Longevity and Aging Studies, San Antonio, TX, USA
| | - Xianlin Han
- Barshop Institute for Longevity and Aging Studies, San Antonio, TX, USA.
- Department of Medicine - Diabetes, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.
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Wu B, Wei F, Xu S, Xie Y, Lv X, Chen H, Huang F. Mass spectrometry-based lipidomics as a powerful platform in foodomics research. Trends Food Sci Technol 2021; 107:358-76. [DOI: 10.1016/j.tifs.2020.10.045] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Alves MA, Lamichhane S, Dickens A, McGlinchey A, Ribeiro HC, Sen P, Wei F, Hyötyläinen T, Orešič M. Systems biology approaches to study lipidomes in health and disease. Biochim Biophys Acta Mol Cell Biol Lipids 2020; 1866:158857. [PMID: 33278596 DOI: 10.1016/j.bbalip.2020.158857] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/13/2020] [Accepted: 11/27/2020] [Indexed: 12/15/2022]
Abstract
Lipids have many important biological roles, such as energy storage sources, structural components of plasma membranes and as intermediates in metabolic and signaling pathways. Lipid metabolism is under tight homeostatic control, exhibiting spatial and dynamic complexity at multiple levels. Consequently, lipid-related disturbances play important roles in the pathogenesis of most of the common diseases. Lipidomics, defined as the study of lipidomes in biological systems, has emerged as a rapidly-growing field. Due to the chemical and functional diversity of lipids, the application of a systems biology approach is essential if one is to address lipid functionality at different physiological levels. In parallel with analytical advances to measure lipids in biological matrices, the field of computational lipidomics has been rapidly advancing, enabling modeling of lipidomes in their pathway, spatial and dynamic contexts. This review focuses on recent progress in systems biology approaches to study lipids in health and disease, with specific emphasis on methodological advances and biomedical applications.
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Affiliation(s)
- Marina Amaral Alves
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
| | - Santosh Lamichhane
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
| | - Alex Dickens
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
| | - Aidan McGlinchey
- School of Medical Sciences, Örebro University, 702 81 Örebro, Sweden
| | | | - Partho Sen
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland; School of Medical Sciences, Örebro University, 702 81 Örebro, Sweden
| | - Fang Wei
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, PR China
| | | | - Matej Orešič
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland; School of Medical Sciences, Örebro University, 702 81 Örebro, Sweden.
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Sun T, Wang X, Cong P, Xu J, Xue C. Mass spectrometry-based lipidomics in food science and nutritional health: A comprehensive review. Compr Rev Food Sci Food Saf 2020; 19:2530-2558. [PMID: 33336980 DOI: 10.1111/1541-4337.12603] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 05/14/2020] [Accepted: 06/10/2020] [Indexed: 12/16/2022]
Abstract
With the advance in science and technology as well as the improvement of living standards, the function of food is no longer just to meet the needs of survival. Food science and its associated nutritional health issues have been increasingly debated. Lipids, as complex metabolites, play a key role both in food and human health. Taking advantages of mass spectrometry (MS) by combining its high sensitivity and accuracy with extensive selective determination of all lipid classes, MS-based lipidomics has been employed to resolve the conundrum of addressing both qualitative and quantitative aspects of high-abundance and low-abundance lipids in complex food matrices. In this review, we systematically summarize current applications of MS-based lipidomics in food field. First, common MS-based lipidomics procedures are described. Second, the applications of MS-based lipidomics in food science, including lipid composition characterization, adulteration, traceability, and other issues, are discussed. Third, the application of MS-based lipidomics for nutritional health covering the influence of food on health and disease is introduced. Finally, future research trends and challenges are proposed. MS-based lipidomics plays an important role in the field of food science, promoting continuous development of food science and integration of food knowledge with other disciplines. New methods of MS-based lipidomics have been developed to improve accuracy and sensitivity of lipid analysis in food samples. These developments offer the possibility to fully characterize lipids in food samples, identify novel functional lipids, and better understand the role of food in promoting healt.
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Affiliation(s)
- Tong Sun
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Xincen Wang
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Peixu Cong
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Jie Xu
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Changhu Xue
- College of Food Science and Engineering, Ocean University of China, Qingdao, China.,Qingdao National Laboratory for Marine Science and Technology, Laboratory of Marine Drugs & Biological Products, Qingdao, China
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Ventura G, Bianco M, Calvano CD, Losito I, Cataldi TRI. HILIC-ESI-FTMS with All Ion Fragmentation (AIF) Scans as a Tool for Fast Lipidome Investigations. Molecules 2020; 25:molecules25102310. [PMID: 32423109 PMCID: PMC7287777 DOI: 10.3390/molecules25102310] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/06/2020] [Accepted: 05/13/2020] [Indexed: 01/17/2023] Open
Abstract
Lipidomics suffers from the lack of fast and reproducible tools to obtain both structural information on intact phospholipids (PL) and fatty acyl chain composition. Hydrophilic interaction liquid chromatography with electrospray ionization coupled to an orbital-trap Fourier-transform analyzer operating using all ion fragmentation mode (HILIC-ESI-FTMS-AIF MS) is seemingly a valuable resource in this respect. Here, accurate m/z values, HILIC retention times and AIF MS scan data were combined for PL assignment in standard mixtures or real lipid extracts. AIF scans in both positive and negative ESI mode, achieved using collisional induced dissociation for fragmentation, were applied to identify both the head-group of each PL class and the fatty acyl chains, respectively. An advantage of the AIF approach was the concurrent collection of tandem MS-like data, enabling the identification of linked fatty acyl chains of precursor phospholipids through the corresponding carboxylate anions. To illustrate the ability of AIF in the field of lipidomics, two different types of real samples, i.e., the lipid extracts obtained from human plasma and dermal fibroblasts, were examined. Using AIF scans, a total of 253 intact lipid species and 18 fatty acids across 4 lipid classes were recognized in plasma samples, while FA C20:3 was confirmed as the fatty acyl chain belonging to phosphatidylinositol, PI 38:3, which was found to be down-regulated in fibroblast samples of Parkinson's disease patients.
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Affiliation(s)
- Giovanni Ventura
- Department of Chemistry, University of Bari Aldo Moro, via Orabona 4, 70126 Bari, Italy; (G.V.); (M.B.); (I.L.)
| | - Mariachiara Bianco
- Department of Chemistry, University of Bari Aldo Moro, via Orabona 4, 70126 Bari, Italy; (G.V.); (M.B.); (I.L.)
| | - Cosima Damiana Calvano
- SMART Inter-Departmental Research Center, 70126 Bari, Italy
- Department of Pharmacy-Drug Sciences, University of Bari “Aldo Moro”, via Orabona 4, 70126 Bari, Italy
- Correspondence: (C.D.C.); (T.R.I.C.)
| | - Ilario Losito
- Department of Chemistry, University of Bari Aldo Moro, via Orabona 4, 70126 Bari, Italy; (G.V.); (M.B.); (I.L.)
- SMART Inter-Departmental Research Center, 70126 Bari, Italy
| | - Tommaso R. I. Cataldi
- Department of Chemistry, University of Bari Aldo Moro, via Orabona 4, 70126 Bari, Italy; (G.V.); (M.B.); (I.L.)
- SMART Inter-Departmental Research Center, 70126 Bari, Italy
- Correspondence: (C.D.C.); (T.R.I.C.)
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Custódio M, Maciel E, Domingues MR, Lillebø AI, Calado R. Nutrient availability affects the polar lipidome of Halimione portulacoides leaves cultured in hydroponics. Sci Rep 2020; 10:6583. [PMID: 32313165 PMCID: PMC7171145 DOI: 10.1038/s41598-020-63551-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 03/27/2020] [Indexed: 12/02/2022] Open
Abstract
Halophytes are increasingly regarded as suitable extractive species and co-products for coastal Integrated Multi-Trophic Aquaculture (IMTA) and studying their lipidome is a valid means towards their economic valorization. Halimione portulacoides (L.) Aellen edible leaves are rich in functional lipids with nutraceutical and pharmaceutical relevance and the present study aimed to investigate the extent to which its lipidome remains unchanged under a range of dissolved inorganic nitrogen (N) and phosphorus (P) concentrations typical of aquaculture effluents. Lipidomics analysis, done by hydrophilic interaction liquid chromatography coupled to high resolution mass spectrometry, identified 175 lipid species in the lipid extract of leaves: 140 phospholipids (PLs) and 35 glycolipids (GLs). Plants irrigated with a saline solution with 20-100 mg DIN-N L-1 and 3-15.5 mg DIP-P L-1 under a 1-week hydraulic retention time displayed a relatively stable lipidome. At lower concentrations (6 mg DIN-N L-1 and 0.8 mg DIP-P L-1), plants exhibited less PLs and GLs per unit of leaves dry weight and the GLs fraction of the lipidome changed significantly. This study reveals the importance of analyzing the lipidomic profile of halophytes under different nutritional regimens in order to establish nutrient-limitation thresholds and assure production conditions that deliver a final product with a consistent lipid profile.
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Affiliation(s)
- Marco Custódio
- ECOMARE, Centre for Environmental and Marine Studies (CESAM), Department of Biology, University of Aveiro, Santiago University Campus, 3810-193, Aveiro, Portugal.
| | - Elisabete Maciel
- ECOMARE, Centre for Environmental and Marine Studies (CESAM), Department of Biology, University of Aveiro, Santiago University Campus, 3810-193, Aveiro, Portugal
- ECOMARE, Centre for Environmental and Marine Studies (CESAM), Department of Chemistry, University of Aveiro, Santiago University Campus, 3810-193, Aveiro, Portugal
- Mass Spectrometry Center, Department of Chemistry & QOPNA & LAQV - Requinte, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Maria Rosário Domingues
- ECOMARE, Centre for Environmental and Marine Studies (CESAM), Department of Chemistry, University of Aveiro, Santiago University Campus, 3810-193, Aveiro, Portugal
- Mass Spectrometry Center, Department of Chemistry & QOPNA & LAQV - Requinte, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Ana Isabel Lillebø
- ECOMARE, Centre for Environmental and Marine Studies (CESAM), Department of Biology, University of Aveiro, Santiago University Campus, 3810-193, Aveiro, Portugal
| | - Ricardo Calado
- ECOMARE, Centre for Environmental and Marine Studies (CESAM), Department of Biology, University of Aveiro, Santiago University Campus, 3810-193, Aveiro, Portugal.
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Pérez-Albaladejo E, Lacorte S, Porte C. Differential Toxicity of Alkylphenols in JEG-3 Human Placental Cells: Alteration of P450 Aromatase and Cell Lipid Composition. Toxicol Sci 2020; 167:336-346. [PMID: 30247713 DOI: 10.1093/toxsci/kfy243] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Alkylphenols (APs) are a diverse class of chemicals that can cross the placental barrier and interfere with embryonic and fetal development. This work investigates the comparative toxicity, ability to inhibit aromatase activity, and to alter the lipid composition of 10 alkylphenols in the human placenta choriocarcinoma cell line JEG-3. Among the selected APs, 4-dodecylphenol (DP), 4-heptylphenol (HP), and 4-cumylphenol (CP) showed the highest cytotoxicity (EC50: 18-65 µM). Aromatase inhibition was closely related to the hydrophobicity of APs. HP significantly induced the generation of reactive oxygen species (ROS) (43-fold), inhibited placental aromatase activity (IC50: 41 µM), and induced a general dose-dependent depletion of polyunsaturated lipids (10-20 µM), which were attributed to high levels of oxidative stress. In contrast, 2,4,6-tri-tert-butylphenol (TTBP) significantly induced the intracellular accumulation of triacylglycerides (TGs), whereas DP increased the synthesis of phosphatidylcholines (PCs) and TGs at the expense of diacylglycerides (DGs). Overall, this study evidences the different modes of action of alkylphenols in human placental JEG-3 cells, describes differential lipidomic fingerprints, and highlights DP, HP, CP, and TTBP as the ones that caused the most harmful effects.
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Affiliation(s)
| | - Silvia Lacorte
- Environmental Chemistry Department, IDAEA-CSIC, C/Jordi Girona 18-26, Barcelona 08034, Spain
| | - Cinta Porte
- Environmental Chemistry Department, IDAEA-CSIC, C/Jordi Girona 18-26, Barcelona 08034, Spain
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Wu Z, Bagarolo GI, Thoröe-Boveleth S, Jankowski J. "Lipidomics": Mass spectrometric and chemometric analyses of lipids. Adv Drug Deliv Rev 2020; 159:294-307. [PMID: 32553782 DOI: 10.1016/j.addr.2020.06.009] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 06/03/2020] [Accepted: 06/06/2020] [Indexed: 01/01/2023]
Abstract
Lipids are ubiquitous in the human organism and play essential roles as components of cell membranes and hormones, for energy storage or as mediators of cell signaling pathways. As crucial mediators of the human metabolism, lipids are also involved in metabolic diseases, cardiovascular and renal diseases, cancer and/or hepatological and neurological disorders. With rapidly growing evidence supporting the impact of lipids on both the genesis and progression of these diseases as well as patient wellbeing, the characterization of the human lipidome has gained high interest and importance in life sciences and clinical diagnostics within the last 15 years. This is mostly due to technically advanced molecular identification and quantification methods, mainly based on mass spectrometry. Mass spectrometry has become one of the most powerful tools for the identification of lipids. New lipidic mediators or biomarkers of diseases can be analysed by state-of-the art mass spectrometry techniques supported by sophisticated bioinformatics and biostatistics. The lipidomic approach has developed dramatically in the realm of life sciences and clinical diagnostics due to the available mass spectrometric methods and in particular due to the adaptation of biostatistical methods in recent years. Therefore, the current knowledge of lipid extraction methods, mass-spectrometric approaches, biostatistical data analysis, including workflows for the interpretation of lipidomic high-throughput data, are reviewed in this manuscript.
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Affiliation(s)
- Zhuojun Wu
- Institute for Molecular Cardiovascular Research, University Hospital RWTH Aachen, Aachen, Pauwelsstraße 30, 52074 Aachen, Germany
| | - Giulia Ilaria Bagarolo
- Institute for Molecular Cardiovascular Research, University Hospital RWTH Aachen, Aachen, Pauwelsstraße 30, 52074 Aachen, Germany
| | - Sven Thoröe-Boveleth
- Institute for Molecular Cardiovascular Research, University Hospital RWTH Aachen, Aachen, Pauwelsstraße 30, 52074 Aachen, Germany
| | - Joachim Jankowski
- Institute for Molecular Cardiovascular Research, University Hospital RWTH Aachen, Aachen, Pauwelsstraße 30, 52074 Aachen, Germany; School for Cardiovascular Diseases, Maastricht University, Universiteitssingel 50, Maastricht, The Netherlands.
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Zhou F, Ren J, Li G, Jiang Y, Li X, Wang W, Wu C. Penalized Variable Selection for Lipid-Environment Interactions in a Longitudinal Lipidomics Study. Genes (Basel) 2019; 10:E1002. [PMID: 31816972 DOI: 10.3390/genes10121002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 11/26/2019] [Indexed: 12/20/2022] Open
Abstract
Lipid species are critical components of eukaryotic membranes. They play key roles in many biological processes such as signal transduction, cell homeostasis, and energy storage. Investigations of lipid-environment interactions, in addition to the lipid and environment main effects, have important implications in understanding the lipid metabolism and related changes in phenotype. In this study, we developed a novel penalized variable selection method to identify important lipid-environment interactions in a longitudinal lipidomics study. An efficient Newton-Raphson based algorithm was proposed within the generalized estimating equation (GEE) framework. We conducted extensive simulation studies to demonstrate the superior performance of our method over alternatives, in terms of both identification accuracy and prediction performance. As weight control via dietary calorie restriction and exercise has been demonstrated to prevent cancer in a variety of studies, analysis of the high-dimensional lipid datasets collected using 60 mice from the skin cancer prevention study identified meaningful markers that provide fresh insight into the underlying mechanism of cancer preventive effects.
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Codognoto VM, Yamada PH, Schmith RA, Rydygier de Ruediger F, de Paula Freitas-Dell'Aqua C, de Souza FF, Brochine S, do Carmo LM, Vieira AF, Oba E. Cross comparison of seminal plasma proteins from cattle and buffalo (Bubalus bubalis). Reprod Domest Anim 2019; 55:81-92. [PMID: 31733131 DOI: 10.1111/rda.13589] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 10/25/2019] [Accepted: 11/13/2019] [Indexed: 11/27/2022]
Abstract
The objective of this study was to evaluate seminal plasma proteins from cattle and buffalo (Bubalus bubalis), to identify differences between related species. Sixteen buffaloes and 16 cattle between 30 and 60 months of age were used. Semen collection was performed by electroejaculation, followed by macroscopic and microscopic subjective analyses. After analysis, the samples were centrifuged at 800 g for 10 min, and the supernatant (seminal plasma) was recentrifuged at 10,000 g for 30 min at 4°C. The total protein concentration was determined by the Bradford method, and the proteins were digested in solution for mass spectrometry (nLC-MS/MS). Multivariate statistical analysis was used to evaluate the proteomics results by non-hierarchical clustering the considering exponentially modified protein abundance index (emPAI). Principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA) were used for clustering. Proteomics identified 78 proteins, and multivariate analysis showed 4 that were over-expressed in buffaloes (cystatin C, prosaposin, peptide YY and keratin type II cytoskeletal 5) and 9 in cattle (spermadhesin-1, seminal plasma protein PDC-109, ribonuclease 4, metalloproteinase inhibitor 2, acrosin inhibitor 1, seminal ribonuclease, C-type natriuretic peptide, angiogenin-1 and osteopontin). Among the proteins identified in seminal plasma, the C-type natriuretic peptide and metalloproteinase inhibitors were described for the first time in buffaloes. Some protease inhibitors were found over-expressed in buffaloes, and important proteins in seminal plasma of cattle were not identified or were found at lower expression levels in buffaloes, which can contribute to reproductive performance in this species.
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Affiliation(s)
- Viviane Maria Codognoto
- Department of Animal Reproduction and Veterinary Radiology, School of Veterinary Medicine and Animal Science (FMVZ), São Paulo State University (UNESP), Botucatu, Brazil
| | - Paulo Henrique Yamada
- Department of Animal Reproduction and Veterinary Radiology, School of Veterinary Medicine and Animal Science (FMVZ), São Paulo State University (UNESP), Botucatu, Brazil
| | - Rúbia Alves Schmith
- Department of Animal Reproduction and Veterinary Radiology, School of Veterinary Medicine and Animal Science (FMVZ), São Paulo State University (UNESP), Botucatu, Brazil
| | - Felipe Rydygier de Ruediger
- Department of Animal Reproduction and Veterinary Radiology, School of Veterinary Medicine and Animal Science (FMVZ), São Paulo State University (UNESP), Botucatu, Brazil
| | - Camila de Paula Freitas-Dell'Aqua
- Department of Animal Reproduction and Veterinary Radiology, School of Veterinary Medicine and Animal Science (FMVZ), São Paulo State University (UNESP), Botucatu, Brazil
| | - Fabiana Ferreira de Souza
- Department of Animal Reproduction and Veterinary Radiology, School of Veterinary Medicine and Animal Science (FMVZ), São Paulo State University (UNESP), Botucatu, Brazil
| | - Suzane Brochine
- Department of Animal Reproduction and Veterinary Radiology, School of Veterinary Medicine and Animal Science (FMVZ), São Paulo State University (UNESP), Botucatu, Brazil
| | - Lucas Monteiro do Carmo
- Department of Animal Reproduction and Veterinary Radiology, School of Veterinary Medicine and Animal Science (FMVZ), São Paulo State University (UNESP), Botucatu, Brazil
| | - Andressa Filaz Vieira
- Department of Animal Reproduction and Veterinary Radiology, School of Veterinary Medicine and Animal Science (FMVZ), São Paulo State University (UNESP), Botucatu, Brazil
| | - Eunice Oba
- Department of Animal Reproduction and Veterinary Radiology, School of Veterinary Medicine and Animal Science (FMVZ), São Paulo State University (UNESP), Botucatu, Brazil
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Portarena S, Leonardi L, Scartazza A, Lauteri M, Baldacchini C, Farinelli D, Famiani F, Ciolfi M, Brugnoli E. Combining analysis of fatty acid composition and δ13C in extra-virgin olive oils as affected by harvest period and cultivar: Possible use in traceability studies. Food Control 2019; 105:151-8. [DOI: 10.1016/j.foodcont.2019.05.029] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Deng Y, Pan M, Nie H, Zheng C, Tang K, Zhang Y, Yang Q. Lipidomic Analysis of the Protective Effects of Shenling Baizhu San on Non-Alcoholic Fatty Liver Disease in Rats. Molecules 2019; 24:E3943. [PMID: 31683679 DOI: 10.3390/molecules24213943] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/28/2019] [Accepted: 10/30/2019] [Indexed: 12/13/2022] Open
Abstract
Shenling Baizhu San (SLBZS), a famous traditional Chinese medicine, has been demonstrated to exert protective effects against non-alcoholic fatty liver disease (NAFLD), but its exact mechanisms have not been well understood. The aim of this study was to investigate the mechanisms underlying the protective effects of SLBZS in a rat model of NAFLD using lipidomics and to evaluate the role of Sirtuin 1 (SIRT1) in the mechanism of SLBZS against NAFLD. The rat model of NAFLD was induced by high-fat feeding. An ultra-performance liquid chromatography-mass spectrometry (UHPLC-MS)-based untargeted lipidomics approach was applied to analyze hepatic lipid alterations, and the SIRT1-selective inhibitor EX 527 was used to inhibit SIRT expression in the liver. The results of body and biochemical parameters, as well as histological changes, indicated that SLBZS administration exerted protective effects against NAFLD. Lipidomic analysis showed that 30 lipid species were effectively regulated by SLBZS administration in rats fed a high-fat diet. Pathway analysis indicated that glycerophospholipid metabolism and glycerolipid metabolism were potential target pathways closely involved in the mechanism of SLBZS against NAFLD. Moreover, the beneficial effects of SLBZS on hepatic steatosis, some biochemical parameters and hepatic lipid species were partly diminished by SIRT1 inhibition. In conclusion, our results suggested that SLBZS administration could effectively alter some hepatic lipid species in rats fed a high-fat diet, which was mainly associated with the regulation of glycerophospholipid and glycerolipid metabolism. Furthermore, the beneficial effects of SLBZS on hepatic lipid metabolism may be at least partly attributed to SIRT1 activation in the liver.
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Izumi Y, Matsuda F, Hirayama A, Ikeda K, Kita Y, Horie K, Saigusa D, Saito K, Sawada Y, Nakanishi H, Okahashi N, Takahashi M, Nakao M, Hata K, Hoshi Y, Morihara M, Tanabe K, Bamba T, Oda Y. Inter-Laboratory Comparison of Metabolite Measurements for Metabolomics Data Integration. Metabolites 2019; 9:E257. [PMID: 31683650 PMCID: PMC6918145 DOI: 10.3390/metabo9110257] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 10/26/2019] [Accepted: 10/28/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND One of the current problems in the field of metabolomics is the difficulty in integrating data collected using different equipment at different facilities, because many metabolomic methods have been developed independently and are unique to each laboratory. METHODS In this study, we examined whether different analytical methods among 12 different laboratories provided comparable relative quantification data for certain metabolites. Identical samples extracted from two cell lines (HT-29 and AsPc-1) were distributed to each facility, and hydrophilic and hydrophobic metabolite analyses were performed using the daily routine protocols of each laboratory. RESULTS The results indicate that there was no difference in the relative quantitative data (HT-29/AsPc-1) for about half of the measured metabolites among the laboratories and assay methods. Data review also revealed that errors in relative quantification were derived from issues such as erroneous peak identification, insufficient peak separation, a difference in detection sensitivity, derivatization reactions, and extraction solvent interference. CONCLUSION The results indicated that relative quantification data obtained at different facilities and at different times would be integrated and compared by using a reference materials shared for data normalization.
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Affiliation(s)
- Yoshihiro Izumi
- Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.
| | - Fumio Matsuda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Akiyoshi Hirayama
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan.
| | - Kazutaka Ikeda
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-Ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Yoshihiro Kita
- Department of Lipidomics, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Kanta Horie
- Translational Science, Neurology Business Group, Eisai Co., Ltd., 5-1-3 Tokodai, Tsukuba, Ibaraki 300-2635, Japan.
| | - Daisuke Saigusa
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.
| | - Kosuke Saito
- Division of Medical Safety Science, National Institute of Health Science, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa 210-9501, Japan.
| | - Yuji Sawada
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Hiroki Nakanishi
- Research Center for Biosignal, Akita University, 1-1-1 Hondo, Akita-city, Akita 010-8543, Japan.
| | - Nobuyuki Okahashi
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Masatomo Takahashi
- Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.
| | - Motonao Nakao
- Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.
| | - Kosuke Hata
- Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.
| | - Yutaro Hoshi
- Pharmacokinetic Research Laboratories, Ono Pharmaceutical Co., Ltd., 17-2 Wadai, Tsukuba, Ibaraki 300-4247, Japan.
| | - Motohiko Morihara
- Translational Research Laboratories, Ono Pharmaceutical Co., Ltd., 3-1-1 Sakurai Shimamoto-cho, Mishima-gun, Osaka 618-8585, Japan.
| | - Kazuhiro Tanabe
- Medical Solution Promotion Department, Medical Solution Segment, LSI Medience Corporation, 3-30-1, Shimura, Itabashi-ku, Tokyo 174-8555, Japan.
| | - Takeshi Bamba
- Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.
| | - Yoshiya Oda
- Department of Lipidomics, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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