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Rubenzucker S, Manke MC, Lehmann R, Assinger A, Borst O, Ahrends R. A Targeted, Bioinert LC-MS/MS Method for Sensitive, Comprehensive Analysis of Signaling Lipids. Anal Chem 2024; 96:9643-9652. [PMID: 38795073 PMCID: PMC11170558 DOI: 10.1021/acs.analchem.4c01388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 05/08/2024] [Accepted: 05/15/2024] [Indexed: 05/27/2024]
Abstract
Signaling lipids are key players in cellular processes. Despite their importance, no method currently allows their comprehensive monitoring in one analytical run. Challenges include a wide dynamic range, isomeric and isobaric species, and unwanted interaction along the separation path. Herein, we present a sensitive and robust targeted liquid chromatography-mass spectrometry (LC-MS/MS) approach to overcome these challenges, covering a broad panel of 17 different signaling lipid classes. It involves a simple one-phase sample extraction and lipid analysis using bioinert reversed-phase liquid chromatography coupled to targeted mass spectrometry. The workflow shows excellent sensitivity and repeatability in different biological matrices, enabling the sensitive and robust monitoring of 388 lipids in a single run of only 20 min. To benchmark our workflow, we characterized the human plasma signaling lipidome, quantifying 307 endogenous molecular lipid species. Furthermore, we investigated the signaling lipidome during platelet activation, identifying numerous regulations along important lipid signaling pathways. This highlights the potential of the presented method to investigate signaling lipids in complex biological systems, enabling unprecedentedly comprehensive analysis and direct insight into signaling pathways.
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Affiliation(s)
- Stefanie Rubenzucker
- Department
of Analytical Chemistry, University of Vienna, 1090 Vienna, Austria
- Vienna
Doctoral School in Chemistry, University
of Vienna, 1090 Vienna, Austria
| | - Mailin-Christin Manke
- DFG
Heisenberg Group Cardiovascular Thromboinflammation and Translational
Thrombocardiology, University of Tübingen, 72076 Tübingen, Germany
- Department
of Cardiology and Angiology, University
of Tübingen, 72076 Tübingen, Germany
| | - Rainer Lehmann
- Institute
for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic
Laboratory Medicine, University Hospital
Tübingen, 72076 Tübingen, Germany
| | - Alice Assinger
- Department
of Vascular Biology and Thrombosis Research, Centre of Physiology
and Pharmacology, Medical University of
Vienna, 1090 Vienna, Austria
| | - Oliver Borst
- DFG
Heisenberg Group Cardiovascular Thromboinflammation and Translational
Thrombocardiology, University of Tübingen, 72076 Tübingen, Germany
- Department
of Cardiology and Angiology, University
of Tübingen, 72076 Tübingen, Germany
| | - Robert Ahrends
- Department
of Analytical Chemistry, University of Vienna, 1090 Vienna, Austria
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2
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Xu R, Liu H, Yuan F, Kim S, Kirpich I, McClain CJ, Zhang X. Lipid Wizard: Analysis Software for Comprehensive Two-Dimensional Liquid Chromatography-Mass Spectrometry-Based Lipid Profiling. Anal Chem 2024; 96:5375-5383. [PMID: 38523323 DOI: 10.1021/acs.analchem.3c04419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
Lipids play a significant role in life activities and participate in the biological system through different pathways. Although comprehensive two-dimensional liquid chromatography-mass spectrometry (2DLC-MS) has been developed to profile lipid abundance changes, lipid identification and quantification from 2DLC-MS data remain a challenge. We created Lipid Wizard, open-source software for lipid assignment and isotopic peak stripping of the 2DLC-MS data. Lipid Wizard takes the peak list deconvoluted from the 2DLC-MS data as input and assigns each isotopic peak to the lipids recorded in the LIPID MAPS database by precursor ion m/z matching. The matched lipids are then filtered by the first-dimension retention time (1D RT), followed by the second-dimension retention time (2D RT), where the 2D RT of each lipid is predicted using an equivalent carbon number (ECN) model. The remaining assigned lipids are used for isotopic peak stripping via an iterative linear regression. The performance of Lipid Wizard was tested using a set of lipid standards and then applied to study the lipid changes in the livers of mice (fat-1) fed with alcohol.
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Affiliation(s)
- Raobo Xu
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, United States
- Alcohol Research Center, University of Louisville, Louisville, Kentucky 40292, United States
- Hepatobiology and Toxicology Center of Biomedical Research Excellence, University of Louisville, Louisville, Kentucky 40292, United States
- Center for Regulatory and Environmental Analytical Metabolomics, University of Louisville, Louisville, Kentucky 40292, United States
| | - Huan Liu
- Department of Computer Science and Engineering, University of Louisville, Louisville, Kentucky 40292, United States
| | - Fang Yuan
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, United States
- Alcohol Research Center, University of Louisville, Louisville, Kentucky 40292, United States
- Hepatobiology and Toxicology Center of Biomedical Research Excellence, University of Louisville, Louisville, Kentucky 40292, United States
- Center for Regulatory and Environmental Analytical Metabolomics, University of Louisville, Louisville, Kentucky 40292, United States
| | - Seongho Kim
- Department of Oncology, Wayne State University, Detroit, Michigan 48201, United States
- Biostatistics and Bioinformatics Core, Karmanos Cancer Institute, Wayne State University, Detroit, Michigan 48201, United States
| | - Irina Kirpich
- Alcohol Research Center, University of Louisville, Louisville, Kentucky 40292, United States
- Hepatobiology and Toxicology Center of Biomedical Research Excellence, University of Louisville, Louisville, Kentucky 40292, United States
- Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky 40292, United States
| | - Craig J McClain
- Alcohol Research Center, University of Louisville, Louisville, Kentucky 40292, United States
- Hepatobiology and Toxicology Center of Biomedical Research Excellence, University of Louisville, Louisville, Kentucky 40292, United States
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky 40292, United States
- Robley Rex Veterans Affairs Medical Center, Louisville, Kentucky 40206, United States
| | - Xiang Zhang
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, United States
- Alcohol Research Center, University of Louisville, Louisville, Kentucky 40292, United States
- Hepatobiology and Toxicology Center of Biomedical Research Excellence, University of Louisville, Louisville, Kentucky 40292, United States
- Center for Regulatory and Environmental Analytical Metabolomics, University of Louisville, Louisville, Kentucky 40292, United States
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky 40292, United States
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3
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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] [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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4
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Zhang Y, Liu F, Li XQ, Gao Y, Li KC, Zhang QH. Generic and accurate prediction of retention times in liquid chromatography by post-projection calibration. Commun Chem 2024; 7:54. [PMID: 38459241 PMCID: PMC10923921 DOI: 10.1038/s42004-024-01135-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 02/21/2024] [Indexed: 03/10/2024] Open
Abstract
Retention time predictions from molecule structures in liquid chromatography (LC) are increasingly used in MS-based targeted and untargeted analyses, providing supplementary evidence for molecule annotation and reducing experimental measurements. Nevertheless, different LC setups (e.g., differences in gradient, column, and/or mobile phase) give rise to many prediction models that can only accurately predict retention times for a specific chromatographic method (CM). Here, a generic and accurate method is present to predict retention times across different CMs, by introducing the concept of post-projection calibration. This concept builds on the direct projections of retention times between different CMs and uses 35 external calibrants to eliminate the impact of LC setups on projection accuracy. Results showed that post-projection calibration consistently achieved a median projection error below 3.2% of the elution time. The ranking results of putative candidates reached similar levels among different CMs. This work opens up broad possibilities for coordinating retention times between different laboratories and developing extensive retention databases.
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Affiliation(s)
- Yan Zhang
- Key Laboratory of Groundwater Conservation of MWR, China University of Geosciences, Beijing, 100083, People's Republic of China
- Division of Chemical Metrology and Analytical Science, National Institute of Metrology, Beijing, 100029, People's Republic of China
- Key Laboratory of Chemical Metrology and Applications on Nutrition and Health for State Market Regulation, Beijing, 100029, China
| | - Fei Liu
- Key Laboratory of Groundwater Conservation of MWR, China University of Geosciences, Beijing, 100083, People's Republic of China.
| | - Xiu Qin Li
- Division of Chemical Metrology and Analytical Science, National Institute of Metrology, Beijing, 100029, People's Republic of China
- Key Laboratory of Chemical Metrology and Applications on Nutrition and Health for State Market Regulation, Beijing, 100029, China
| | - Yan Gao
- Division of Chemical Metrology and Analytical Science, National Institute of Metrology, Beijing, 100029, People's Republic of China
- Key Laboratory of Chemical Metrology and Applications on Nutrition and Health for State Market Regulation, Beijing, 100029, China
| | - Kang Cong Li
- Division of Chemical Metrology and Analytical Science, National Institute of Metrology, Beijing, 100029, People's Republic of China
- Key Laboratory of Chemical Metrology and Applications on Nutrition and Health for State Market Regulation, Beijing, 100029, China
| | - Qing He Zhang
- Division of Chemical Metrology and Analytical Science, National Institute of Metrology, Beijing, 100029, People's Republic of China.
- Key Laboratory of Chemical Metrology and Applications on Nutrition and Health for State Market Regulation, Beijing, 100029, China.
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5
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Allwright M, Guennewig B, Hoffmann AE, Rohleder C, Jieu B, Chung LH, Jiang YC, Lemos Wimmer BF, Qi Y, Don AS, Leweke FM, Couttas TA. ReTimeML: a retention time predictor that supports the LC-MS/MS analysis of sphingolipids. Sci Rep 2024; 14:4375. [PMID: 38388524 PMCID: PMC10883992 DOI: 10.1038/s41598-024-53860-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 02/06/2024] [Indexed: 02/24/2024] Open
Abstract
The analysis of ceramide (Cer) and sphingomyelin (SM) lipid species using liquid chromatography-tandem mass spectrometry (LC-MS/MS) continues to present challenges as their precursor mass and fragmentation can correspond to multiple molecular arrangements. To address this constraint, we developed ReTimeML, a freeware that automates the expected retention times (RTs) for Cer and SM lipid profiles from complex chromatograms. ReTimeML works on the principle that LC-MS/MS experiments have pre-determined RTs from internal standards, calibrators or quality controls used throughout the analysis. Employed as reference RTs, ReTimeML subsequently extrapolates the RTs of unknowns using its machine-learned regression library of mass-to-charge (m/z) versus RT profiles, which does not require model retraining for adaptability on different LC-MS/MS pipelines. We validated ReTimeML RT estimations for various Cer and SM structures across different biologicals, tissues and LC-MS/MS setups, exhibiting a mean variance between 0.23 and 2.43% compared to user annotations. ReTimeML also aided the disambiguation of SM identities from isobar distributions in paired serum-cerebrospinal fluid from healthy volunteers, allowing us to identify a series of non-canonical SMs associated between the two biofluids comprised of a polyunsaturated structure that confers increased stability against catabolic clearance.
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Affiliation(s)
- Michael Allwright
- ForeFront, Brain and Mind Centre, The University of Sydney, Sydney, Australia
| | - Boris Guennewig
- ForeFront, Brain and Mind Centre, The University of Sydney, Sydney, Australia
| | - Anna E Hoffmann
- Translational Research Collective, Brain and Mind Centre, The University of Sydney, Sydney, NSW, 2006, Australia
- Endosane Pharmaceuticals GmbH, Berlin, Germany
| | - Cathrin Rohleder
- Translational Research Collective, Brain and Mind Centre, The University of Sydney, Sydney, NSW, 2006, Australia
- Endosane Pharmaceuticals GmbH, Berlin, Germany
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Beverly Jieu
- Translational Research Collective, Brain and Mind Centre, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Long H Chung
- Centenary Institute, The University of Sydney, Sydney, Australia
| | - Yingxin C Jiang
- Centenary Institute, The University of Sydney, Sydney, Australia
| | - Bruno F Lemos Wimmer
- Translational Research Collective, Brain and Mind Centre, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Yanfei Qi
- Centenary Institute, The University of Sydney, Sydney, Australia
| | - Anthony S Don
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
| | - F Markus Leweke
- Translational Research Collective, Brain and Mind Centre, The University of Sydney, Sydney, NSW, 2006, Australia
- Endosane Pharmaceuticals GmbH, Berlin, Germany
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Timothy A Couttas
- Translational Research Collective, Brain and Mind Centre, The University of Sydney, Sydney, NSW, 2006, Australia.
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6
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Tian Y, Zhou Y, Li L, Huang C, Lin L, Li C, Ye Y. Effect of substrate composition on physicochemical properties of the medium-long-medium structured triacylglycerol. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:942-955. [PMID: 37708388 DOI: 10.1002/jsfa.12982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 09/04/2023] [Accepted: 09/15/2023] [Indexed: 09/16/2023]
Abstract
BACKGROUND Nutritional and functional qualities and applications of structured lipids (SL) depend on the composition and molecular structure of fatty acids in the glycerol backbone of triacylglycerol (TAG). However, the relationship between the substrate composition and physicochemical qualities of SL has not been revealed. The investigation aims to disclose the effect of substrate composition on the physicochemical properties of medium-long-medium structured lipids (MLM-SLs) by enzymatic interesterification of Lipozyme TLIM/RMIM. RESULTS The medium-long-chain triacylglycerol (MLCT) yield could reach 70.32%, including 28.98% CaLCa (1,3-dioctonyl-2-linoleoyl glyceride) and 24.34% CaOCa (1,3-didecanoyl-2-oleoyl glyceride). The sn-2 unsaturated fatty acid composition mainly depended on long-chain triacylglycerol (LCT) in the substrate. The increased carbon chain length and double bond in triacylglycerol decreased its melting and crystallization temperature. The balanced substrate composition of MCT/LCT increased the size and finer crystals. Molecular docking simulation revealed that the MLCT molecule mainly interacted with the catalytic triplets of Lipozyme TLIM (Arg81-Ser83-Arg84) and the Lipozyme RMIM (Tyr183-Thr226-Arg262) by OH bond. The oxygen atom of the ester on the MLCT molecule was primarily bound to the hydrogen of hydroxyl and amino groups on the binding sites of Lipozyme TLIM/RMIM. The intermolecular interplay between MLCT and Lipozyme RMIM is more stable than Lipozyme TLIM due to the formation of lower binding affinity energy. CONCLUSION This research clarifies the interaction mechanism between MLCT molecules and lipases, and provides an in-depth understanding of the relationship between substrate composition, molecular structure and physicochemical property of MLM-SLs. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Yunong Tian
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, China
| | - Yanhui Zhou
- Hunan Singular Biological Technology Co. Ltd, Changsha, China
| | - Lu Li
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, China
| | - Chuanqing Huang
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, National Engineering Research Center for Non-Food Biorefinery, Guangxi Biomass Engineering Technology Research Center, Guangxi Academy of Sciences, Nanning, China
| | - Lin Lin
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha, China
| | - Changzhu Li
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha, China
| | - Yong Ye
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, China
- SCUT - Zhuhai Institute of Modern Industrial Innovation, Zhuhai, China
- Jiangxi Environmental Engineering Vocational College, Ganzhou, China
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7
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Zhang J, Zhou Y, Lei J, Liu X, Zhang N, Wu L, Li Y. Retention time prediction and MRM validation reinforce the biomarker identification of LC-MS based phospholipidomics. Analyst 2024; 149:515-527. [PMID: 38078496 DOI: 10.1039/d3an01735d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
Dysfunctional lipid metabolism plays a crucial role in the development and progression of various diseases. Accurate measurement of lipidomes can help uncover the complex interactions between genes, proteins, and lipids in health and diseases. The prediction of retention time (RT) has become increasingly important in both targeted and untargeted metabolomics. However, the potential impact of RT prediction on targeted LC-MS based lipidomics is still not fully understood. Herein, we propose a simplified workflow for predicting RT in phospholipidomics. Our approach involves utilizing the fatty acyl chain length or carbon-carbon double bond (DB) number in combination with multiple reaction monitoring (MRM) validation. We found that our model's predictive capacity for RT was comparable to that of a publicly accessible program (QSRR Automator). Additionally, MRM validation helped in further mitigating the interference in signal recognition. Using this developed workflow, we conducted phospholipidomics of sorafenib resistant hepatocellular carcinoma (HCC) cell lines, namely MHCC97H and Hep3B. Our findings revealed an abundance of monounsaturated fatty acyl (MUFA) or polyunsaturated fatty acyl (PUFA) phospholipids in these cell lines after developing drug resistance. In both cell lines, a total of 29 lipids were found to be co-upregulated and 5 lipids were co-downregulated. Further validation was conducted on seven of the upregulated lipids using an independent dataset, which demonstrates the potential for translation of the established workflow or the lipid biomarkers.
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Affiliation(s)
- Jiangang Zhang
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing 400030, China.
| | - Yu Zhou
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing 400030, China.
| | - Juan Lei
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing 400030, China.
| | - Xudong Liu
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing 400030, China.
| | - Nan Zhang
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing 400030, China.
| | - Lei Wu
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing 400030, China.
| | - Yongsheng Li
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing 400030, China.
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8
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Menzel JP, Young RSE, Benfield AH, Scott JS, Wongsomboon P, Cudlman L, Cvačka J, Butler LM, Henriques ST, Poad BLJ, Blanksby SJ. Ozone-enabled fatty acid discovery reveals unexpected diversity in the human lipidome. Nat Commun 2023; 14:3940. [PMID: 37402773 DOI: 10.1038/s41467-023-39617-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 06/15/2023] [Indexed: 07/06/2023] Open
Abstract
Fatty acid isomers are responsible for an under-reported lipidome diversity across all kingdoms of life. Isomers of unsaturated fatty acids are often masked in contemporary analysis by incomplete separation and the absence of sufficiently diagnostic methods for structure elucidation. Here, we introduce a comprehensive workflow, to discover unsaturated fatty acids through coupling liquid chromatography and mass spectrometry with gas-phase ozonolysis of double bonds. The workflow encompasses semi-automated data analysis and enables de novo identification in complex media including human plasma, cancer cell lines and vernix caseosa. The targeted analysis including ozonolysis enables structural assignment over a dynamic range of five orders of magnitude, even in instances of incomplete chromatographic separation. Thereby we expand the number of identified plasma fatty acids two-fold, including non-methylene-interrupted fatty acids. Detection, without prior knowledge, allows discovery of non-canonical double bond positions. Changes in relative isomer abundances reflect underlying perturbations in lipid metabolism.
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Affiliation(s)
- Jan Philipp Menzel
- School of Chemistry and Physics, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- Centre for Materials Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- Centre for Data Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- Institute of Clinical Chemistry, Inselspital, Bern University Hospital, 3010, Bern, Switzerland
| | - Reuben S E Young
- School of Chemistry and Physics, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- Centre for Materials Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- Faculty of Science, Medicine and Health, School of Chemistry and Molecular Bioscience, Wollongong, NSW, Australia
| | - Aurélie H Benfield
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Translational Research Institute, Brisbane, QLD, 4102, Australia
| | - Julia S Scott
- South Australian Immunogenomics Cancer Institute and Freemasons Centre for Male Health and Wellbeing, University of Adelaide, Adelaide, SA, Australia
- South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Puttandon Wongsomboon
- School of Chemistry and Physics, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- Centre for Materials Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Lukáš Cudlman
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 542/2, 16600, Prague, Czech Republic
- Department of Analytical Chemistry, Faculty of Science, Charles University, Prague 2, Czech Republic
| | - Josef Cvačka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 542/2, 16600, Prague, Czech Republic
- Department of Analytical Chemistry, Faculty of Science, Charles University, Prague 2, Czech Republic
| | - Lisa M Butler
- South Australian Immunogenomics Cancer Institute and Freemasons Centre for Male Health and Wellbeing, University of Adelaide, Adelaide, SA, Australia
- South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Sónia T Henriques
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Translational Research Institute, Brisbane, QLD, 4102, Australia
| | - Berwyck L J Poad
- School of Chemistry and Physics, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- Centre for Materials Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Stephen J Blanksby
- School of Chemistry and Physics, Queensland University of Technology, Brisbane, QLD, 4000, Australia.
- Centre for Materials Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia.
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9
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Zhang J, Yang S, Wang J, Xu Y, Zhao H, Lei J, Zhou Y, Chen Y, Wu L, Li Y. Equivalent carbon number based targeted odd chain fatty acyl lipidomics reveals triacylglycerol profiling in clinical colon cancer. J Lipid Res 2023:100393. [PMID: 37257561 PMCID: PMC10331287 DOI: 10.1016/j.jlr.2023.100393] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 05/15/2023] [Accepted: 05/18/2023] [Indexed: 06/02/2023] Open
Abstract
Odd chain fatty acids (OCFAs) present in very low level at nearly 1% of total fatty acids in human plasma and thus their functions were usually ignored. Recent epidemiological studies have shown that OCFAs are inversely associated with a variety of disease risks. However, the contribution of OCFAs incorporated into complex lipids remains elusive. Here, we developed a targeted odd chain fatty acyl containing lipidomics method based on equivalent carbon number and retention time prediction. The method displayed good reproducibility and robustness as shown by peak width at half height within 0.7 min and coefficient of variation (CV) under 20%. A total number of 776 lipid species with odd chain fatty acyl residues could be detected in the electrospray ionization (ESI) mode of reverse phase liquid chromatography-mass spectrometry, of which 309 lipids were further validated using multiple MRM transitiions. Using this method, we quantified odd chain fatty acyl containing lipidome in tissues from 12 colon cancer patients, revealing the remodeling of triacylglycerol (TAG). The dynamics of odd chain fatty acyl lipids were further consolidated by the association with genomic and proteomic feature of altered catabolism of branched chain amino acids and TAG endogenous synthesis in colon cancer. This lipidomics approach will be applicable for screening of dysregulated odd chain fatty acyl lipids, which enriches and improves the methods for diagnosis and prognosis evaluation of cancer using lipidomics.
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Affiliation(s)
- Jiangang Zhang
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Shuai Yang
- Department of Pathology, the 958th Hospital, Southwest Hospital, Army Medical University, Chongqing 400038, China
| | - Jingchun Wang
- Department of Gastroenterology, Xinqiao Hospital, Army Medical University, Chongqing 400037, China
| | - Yanquan Xu
- Clinical Medicine Research Center, Xinqiao Hospital, Army Medical University, Chongqing 400037, China
| | - Huakan Zhao
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Juan Lei
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Yu Zhou
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Yu Chen
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Lei Wu
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Yongsheng Li
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing 400030, China.
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Thomas D, Wu M, Nakauchi Y, Zheng M, Thompson-Peach CA, Lim K, Landberg N, Köhnke T, Robinson N, Kaur S, Kutyna M, Stafford M, Hiwase D, Reinisch A, Peltz G, Majeti R. Dysregulated Lipid Synthesis by Oncogenic IDH1 Mutation Is a Targetable Synthetic Lethal Vulnerability. Cancer Discov 2023; 13:496-515. [PMID: 36355448 PMCID: PMC9900324 DOI: 10.1158/2159-8290.cd-21-0218] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 09/18/2022] [Accepted: 11/08/2022] [Indexed: 11/12/2022]
Abstract
Isocitrate dehydrogenase 1 and 2 (IDH) are mutated in multiple cancers and drive production of (R)-2-hydroxyglutarate (2HG). We identified a lipid synthesis enzyme [acetyl CoA carboxylase 1 (ACC1)] as a synthetic lethal target in mutant IDH1 (mIDH1), but not mIDH2, cancers. Here, we analyzed the metabolome of primary acute myeloid leukemia (AML) blasts and identified an mIDH1-specific reduction in fatty acids. mIDH1 also induced a switch to b-oxidation indicating reprogramming of metabolism toward a reliance on fatty acids. Compared with mIDH2, mIDH1 AML displayed depletion of NADPH with defective reductive carboxylation that was not rescued by the mIDH1-specific inhibitor ivosidenib. In xenograft models, a lipid-free diet markedly slowed the growth of mIDH1 AML, but not healthy CD34+ hematopoietic stem/progenitor cells or mIDH2 AML. Genetic and pharmacologic targeting of ACC1 resulted in the growth inhibition of mIDH1 cancers not reversible by ivosidenib. Critically, the pharmacologic targeting of ACC1 improved the sensitivity of mIDH1 AML to venetoclax. SIGNIFICANCE Oncogenic mutations in both IDH1 and IDH2 produce 2-hydroxyglutarate and are generally considered equivalent in terms of pathogenesis and targeting. Using comprehensive metabolomic analysis, we demonstrate unexpected metabolic differences in fatty acid metabolism between mutant IDH1 and IDH2 in patient samples with targetable metabolic interventions. See related commentary by Robinson and Levine, p. 266. This article is highlighted in the In This Issue feature, p. 247.
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Affiliation(s)
- Daniel Thomas
- Department of Medicine, Division of Hematology, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Palo Alto, California
- Adelaide Medical School, University of Adelaide, South Australia and Precision Medicine, South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Manhong Wu
- Department of Anesthesiology, Pain and Perioperative Medicine, Stanford University School of Medicine, Palo Alto, California
| | - Yusuke Nakauchi
- Department of Medicine, Division of Hematology, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Palo Alto, California
| | - Ming Zheng
- Department of Anesthesiology, Pain and Perioperative Medicine, Stanford University School of Medicine, Palo Alto, California
| | - Chloe A.L. Thompson-Peach
- Adelaide Medical School, University of Adelaide, South Australia and Precision Medicine, South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Kelly Lim
- Adelaide Medical School, University of Adelaide, South Australia and Precision Medicine, South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Niklas Landberg
- Department of Medicine, Division of Hematology, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Palo Alto, California
| | - Thomas Köhnke
- Department of Medicine, Division of Hematology, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Palo Alto, California
| | - Nirmal Robinson
- Centre for Cancer Biology, University of South Australia, South Australia, Australia
| | - Satinder Kaur
- Department of Medicine, Division of Hematology, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Palo Alto, California
| | - Monika Kutyna
- Adelaide Medical School, University of Adelaide, South Australia and Precision Medicine, South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Melissa Stafford
- Department of Medicine, Division of Hematology, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Palo Alto, California
| | - Devendra Hiwase
- Adelaide Medical School, University of Adelaide, South Australia and Precision Medicine, South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Andreas Reinisch
- Department of Medicine, Division of Hematology, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Palo Alto, California
- Division of Hematology and Department of Blood Group Serology and Transfusion Medicine, Medical University of Graz, Graz, Austria
| | - Gary Peltz
- Department of Anesthesiology, Pain and Perioperative Medicine, Stanford University School of Medicine, Palo Alto, California
| | - Ravindra Majeti
- Department of Medicine, Division of Hematology, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Palo Alto, California
- Corresponding Author: Ravindra Majeti, Department of Medicine, Division of Hematology, Stanford Institute for Stem Cell Biology and Regenerative Medicine, Lokey Stem Cell Building, 265 Campus Drive, Stanford, CA 94305. Phone: 650-721-6376; Fax: 650-736-2961; E-mail:
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Wise SA. What if using certified reference materials (CRMs) was a requirement to publish in analytical/bioanalytical chemistry journals? Anal Bioanal Chem 2022; 414:7015-7022. [PMID: 35697811 DOI: 10.1007/s00216-022-04163-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/23/2022] [Accepted: 05/31/2022] [Indexed: 12/17/2022]
Abstract
Certified reference materials (CRMs) are routinely used by analytical chemists to validate new analytical methods and to demonstrate the quality of their quantitative measurements. Even though CRMs for trace element and trace organic analysis have been available and widely used for over 50 years, the majority of papers published in analytical chemistry journals do not mention the use of CRMs. What if analytical/bioanalytical chemistry journals required the use of CRMs to publish a paper? This feature article attempts to address this question by providing examples of recent papers that have made exceptional use of CRMs to validate new analytical methods and to describe novel, alternative uses of CRMs that provide new characterization of the CRM. The potential benefits of using a CRM even when it does not have certified values for the analytes of interest are presented.
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Affiliation(s)
- Stephen A Wise
- Office of Dietary Supplements, National Institutes of Health, Bethesda, MD, 20817, USA. .,Scientist Emeritus, National Institute of Standards and Technology (NIST), Gaithersburg, MD, 20899, USA.
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