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Lee IC, Tumanov S, Wong JW, Stocker R, Ho JW. Integrative processing of untargeted metabolomic and lipidomic data using MultiABLER. iScience 2023; 26:106881. [PMID: 37260745 PMCID: PMC10227420 DOI: 10.1016/j.isci.2023.106881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 03/13/2023] [Accepted: 05/11/2023] [Indexed: 06/02/2023] Open
Abstract
Mass spectrometry (MS)-based untargeted metabolomic and lipidomic approaches are being used increasingly in biomedical research. The adoption and integration of these data are critical to the overall multi-omic toolkit. Recently, a sample extraction method called Multi-ABLE has been developed, which enables concurrent generation of proteomic and untargeted metabolomic and lipidomic data from a small amount of tissue. The proteomics field has a well-established set of software for processing of acquired data; however, there is a lack of a unified, off-the-shelf, ready-to-use bioinformatics pipeline that can take advantage of and prepare concurrently generated metabolomic and lipidomic data for joint downstream analyses. Here we present an R pipeline called MultiABLER as a unified and simple upstream processing and analysis pipeline for both metabolomics and lipidomics datasets acquired using liquid chromatography-tandem mass spectrometry. The code is available via an open-source license at https://github.com/holab-hku/MultiABLER.
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Affiliation(s)
- Ian C.H. Lee
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Laboratory of Data Discovery for Health Limited (D4H), Hong Kong Science Park, Hong Kong SAR, China
| | - Sergey Tumanov
- Heart Research Institute, 7 Eliza Street, Newtown, NSW 2042, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jason W.H. Wong
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Centre for PanorOmic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Roland Stocker
- Heart Research Institute, 7 Eliza Street, Newtown, NSW 2042, Australia
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Joshua W.K. Ho
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Laboratory of Data Discovery for Health Limited (D4H), Hong Kong Science Park, Hong Kong SAR, China
- Centre for PanorOmic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
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De Jesus A, Pusec CM, Nguyen T, Keyhani-Nejad F, Gao P, Weinberg SE, Ardehali H. Optimized protocol to isolate primary mouse peritoneal macrophage metabolites. STAR Protoc 2022; 3:101668. [PMID: 36103306 PMCID: PMC9483642 DOI: 10.1016/j.xpro.2022.101668] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/07/2022] [Accepted: 08/04/2022] [Indexed: 01/25/2023] Open
Abstract
Peritoneal macrophages (PMs) have been shown to have higher stability compared to other macrophage subtypes. However, obtaining enough PMs from a single mouse is often a limitation for metabolomics analysis. Here, we describe a protocol to isolate metabolites from a small number of mouse primary PMs for 13C-stable glucose tracing and metabolomics. Our protocol uses X for metabolite extraction instead of methanol. Our protocol can consistently extract metabolites from low cell number samples with fewer steps than methanol-based approaches. For complete details on the use and execution of this protocol, please refer to De Jesus et al., (2022).
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Affiliation(s)
- Adam De Jesus
- Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA,Feinberg Cardiovascular Research Institute, Northwestern University, Chicago, IL 60611, USA
| | - Carolina M. Pusec
- Department of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Tivoli Nguyen
- Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA,Feinberg Cardiovascular Research Institute, Northwestern University, Chicago, IL 60611, USA
| | - Farnaz Keyhani-Nejad
- Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA,Feinberg Cardiovascular Research Institute, Northwestern University, Chicago, IL 60611, USA
| | - Peng Gao
- Robert H. Lurie Cancer Center Metabolomics Core, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Samuel E. Weinberg
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA,Corresponding author
| | - Hossein Ardehali
- Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA,Feinberg Cardiovascular Research Institute, Northwestern University, Chicago, IL 60611, USA,Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA,Corresponding author
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Endo- and Exometabolome Crosstalk in Mesenchymal Stem Cells Undergoing Osteogenic Differentiation. Cells 2022; 11:cells11081257. [PMID: 35455937 PMCID: PMC9024772 DOI: 10.3390/cells11081257] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/03/2022] [Accepted: 04/05/2022] [Indexed: 02/04/2023] Open
Abstract
This paper describes, for the first time to our knowledge, a lipidome and exometabolome characterization of osteogenic differentiation for human adipose tissue stem cells (hAMSCs) using nuclear magnetic resonance (NMR) spectroscopy. The holistic nature of NMR enabled the time-course evolution of cholesterol, mono- and polyunsaturated fatty acids (including ω-6 and ω-3 fatty acids), several phospholipids (phosphatidylcholine, phosphatidylethanolamine, sphingomyelins, and plasmalogens), and mono- and triglycerides to be followed. Lipid changes occurred almost exclusively between days 1 and 7, followed by a tendency for lipidome stabilization after day 7. On average, phospholipids and longer and more unsaturated fatty acids increased up to day 7, probably related to plasma membrane fluidity. Articulation of lipidome changes with previously reported polar endometabolome profiling and with exometabolome changes reported here in the same cells, enabled important correlations to be established during hAMSC osteogenic differentiation. Our results supported hypotheses related to the dynamics of membrane remodelling, anti-oxidative mechanisms, protein synthesis, and energy metabolism. Importantly, the observation of specific up-taken or excreted metabolites paves the way for the identification of potential osteoinductive metabolites useful for optimized osteogenic protocols.
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Chen Y, Huang W, Zhang F, Luo X, Hu B, Xie J. Metabolomic Profiling of Dongxiang Wild Rice Under Salinity Demonstrates the Significant Role of Amino Acids in Rice Salt Stress. FRONTIERS IN PLANT SCIENCE 2021; 12:729004. [PMID: 34630473 PMCID: PMC8494129 DOI: 10.3389/fpls.2021.729004] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 08/20/2021] [Indexed: 06/13/2023]
Abstract
Dongxiang common wild rice is a precious rice germplasm resource for the study and improvement of salt tolerance in rice.The metabolism profile of Dongxiang wild rice (DXWR) under salinity was determined by high performance liquid chromatography-mass spectrometry (HPLC-MS) to find differential metabolites and screen potential biomarkers for salt-tolerant rice varieties. A global untargeted metabolism analysis showed 4,878 metabolites accumulated in seedlings of Dongxiang wild rice. Principal component analysis (PCA) and orthogonal partial least squares-discriminant analysis (OPLS-DA) results provided a clear metabolism discrimination between DXWR under control and DXWR under salinity. A total of 90 metabolites were significantly changed (49 upregulated and 41 downregulated) under salinity, of which the largest increase was in DL-2-Aminoadipic acid (27.08-fold) and the largest decrease was in L-Carnitine (0.014-fold). Amino acids and nuclear glycosides were mainly upregulated, while carbohydrates and organic acids were mainly downregulated in the salt-treated group. Among the top 10 upregulated metabolites, five kinds of differential metabolites were amino acids. According to the survival rates of the seedlings under salinity, we selected three backcross inbred lines of DXWR with survival rates above 80% as salt-tolerant progenies (pro-DS) and three backcross inbred lines with survival rates below 10% as non-salt-tolerant progenies (pro-NDS) for an amino acid change analysis. This analysis found that the change in L-Asparagine (2.59-fold) was the biggest between pro-DS and pro-NDS under salinity, revealing that the contents of L-Asparagine may be one of the indices we can use to evaluate the salt tolerance of rice varieties.
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Affiliation(s)
- Yaling Chen
- Laboratory of Plant Genetic Improvement and Biotechnology, Jiangxi Normal University, Nanchang, China
| | - Wenxue Huang
- Laboratory of Plant Genetic Improvement and Biotechnology, Jiangxi Normal University, Nanchang, China
| | - Fantao Zhang
- Laboratory of Plant Genetic Improvement and Biotechnology, Jiangxi Normal University, Nanchang, China
| | - Xiangdong Luo
- Laboratory of Plant Genetic Improvement and Biotechnology, Jiangxi Normal University, Nanchang, China
| | - Biaolin Hu
- Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Rice National Engineering Laboratory, Nanchang, China
| | - Jiankun Xie
- Laboratory of Plant Genetic Improvement and Biotechnology, Jiangxi Normal University, Nanchang, China
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Campanella B, Colombaioni L, Nieri R, Benedetti E, Onor M, Bramanti E. Unraveling the Extracellular Metabolism of Immortalized Hippocampal Neurons Under Normal Growth Conditions. Front Chem 2021; 9:621548. [PMID: 33937186 PMCID: PMC8085660 DOI: 10.3389/fchem.2021.621548] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 02/16/2021] [Indexed: 01/17/2023] Open
Abstract
Metabolomic profiling of cell lines has shown many potential applications and advantages compared to animal models and human subjects, and an accurate cellular metabolite analysis is critical to understanding both the intracellular and extracellular environments in cell culture. This study provides a fast protocol to investigate in vitro metabolites of immortalized hippocampal neurons HN9.10e with minimal perturbation of the cell system using a targeted approach. HN9.10e neurons represent a reliable model of one of the most vulnerable regions of the central nervous system. Here, the assessment of their extracellular metabolic profile was performed by studying the cell culture medium before and after cell growth under standard conditions. The targeted analysis was performed by a direct, easy, high-throughput reversed-phase liquid chromatography with diode array detector (RP-HPLC-DAD) method and by headspace solid-phase microextraction-gas chromatography-mass spectrometry (HS-SPME-GC-MS) for the study of volatile organic compounds (VOCs). The analysis of six different batches of cells has allowed to investigate the metabolic reproducibility of neuronal cells and to describe the metabolic "starting" conditions that are mandatory for a well-grounded interpretation of the results of any following cellular treatment. An accurate study of the metabolic profile of the HN9.10e cell line has never been performed before, and it could represent a quality parameter before any other targeting assay or further exploration.
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Affiliation(s)
- Beatrice Campanella
- National Research Council, Institute of Chemistry of Organometallic Compounds (CNR-ICCOM), Pisa, Italy
| | - Laura Colombaioni
- National Research Council, Institute of Neuroscience (CNR-IN), Pisa, Italy
| | - Riccardo Nieri
- National Research Council, Institute of Chemistry of Organometallic Compounds (CNR-ICCOM), Pisa, Italy
| | - Edoardo Benedetti
- Hematology Unit, Department of Oncology, University of Pisa, Pisa, Italy
| | - Massimo Onor
- National Research Council, Institute of Chemistry of Organometallic Compounds (CNR-ICCOM), Pisa, Italy
| | - Emilia Bramanti
- National Research Council, Institute of Chemistry of Organometallic Compounds (CNR-ICCOM), Pisa, Italy
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Neef SK, Janssen N, Winter S, Wallisch SK, Hofmann U, Dahlke MH, Schwab M, Mürdter TE, Haag M. Metabolic Drug Response Phenotyping in Colorectal Cancer Organoids by LC-QTOF-MS. Metabolites 2020; 10:metabo10120494. [PMID: 33271860 PMCID: PMC7760698 DOI: 10.3390/metabo10120494] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/25/2020] [Accepted: 11/27/2020] [Indexed: 12/13/2022] Open
Abstract
As metabolic rewiring is crucial for cancer cell proliferation, metabolic phenotyping of patient-derived organoids is desirable to identify drug-induced changes and trace metabolic vulnerabilities of tumor subtypes. We established a novel protocol for metabolomic and lipidomic profiling of colorectal cancer organoids by liquid chromatography quadrupole time-of-flight mass spectrometry (LC-QTOF-MS) facing the challenge of capturing metabolic information from a minimal sample amount (<500 cells/injection) in the presence of an extracellular matrix (ECM). The best procedure of the tested protocols included ultrasonic metabolite extraction with acetonitrile/methanol/water (2:2:1, v/v/v) without ECM removal. To eliminate ECM-derived background signals, we implemented a data filtering procedure based on the p-value and fold change cut-offs, which retained features with signal intensities >120% compared to matrix-derived signals present in blank samples. As a proof-of-concept, the method was applied to examine the early metabolic response of colorectal cancer organoids to 5-fluorouracil treatment. Statistical analysis revealed dose-dependent changes in the metabolic profiles of treated organoids including elevated levels of 2′-deoxyuridine, 2′-O-methylcytidine, inosine and 1-methyladenosine and depletion of 2′-deoxyadenosine and specific phospholipids. In accordance with the mechanism of action of 5-fluorouracil, changed metabolites are mainly involved in purine and pyrimidine metabolism. The novel protocol provides a first basis for the assessment of metabolic drug response phenotypes in 3D organoid models.
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Affiliation(s)
- Sylvia K. Neef
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany and University of Tuebingen, 70376 Tuebingen, Germany; (S.K.N.); (N.J.); (S.W.); (S.K.W.); (U.H.); (M.H.D.); (M.S.); (T.E.M.)
| | - Nicole Janssen
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany and University of Tuebingen, 70376 Tuebingen, Germany; (S.K.N.); (N.J.); (S.W.); (S.K.W.); (U.H.); (M.H.D.); (M.S.); (T.E.M.)
| | - Stefan Winter
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany and University of Tuebingen, 70376 Tuebingen, Germany; (S.K.N.); (N.J.); (S.W.); (S.K.W.); (U.H.); (M.H.D.); (M.S.); (T.E.M.)
| | - Svenja K. Wallisch
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany and University of Tuebingen, 70376 Tuebingen, Germany; (S.K.N.); (N.J.); (S.W.); (S.K.W.); (U.H.); (M.H.D.); (M.S.); (T.E.M.)
| | - Ute Hofmann
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany and University of Tuebingen, 70376 Tuebingen, Germany; (S.K.N.); (N.J.); (S.W.); (S.K.W.); (U.H.); (M.H.D.); (M.S.); (T.E.M.)
| | - Marc H. Dahlke
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany and University of Tuebingen, 70376 Tuebingen, Germany; (S.K.N.); (N.J.); (S.W.); (S.K.W.); (U.H.); (M.H.D.); (M.S.); (T.E.M.)
- Department of Surgery, Robert-Bosch Hospital, 70376 Stuttgart, Germany
| | - Matthias Schwab
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany and University of Tuebingen, 70376 Tuebingen, Germany; (S.K.N.); (N.J.); (S.W.); (S.K.W.); (U.H.); (M.H.D.); (M.S.); (T.E.M.)
- Departments of Clinical Pharmacology, and of Pharmacy and Biochemistry, University of Tuebingen, 72074 Tuebingen, Germany
- Cluster of Excellence iFIT (EXC 2180), Image-Guided and Functionally Instructed Tumor Therapies, University of Tuebingen, 72074 Tuebingen, Germany
| | - Thomas E. Mürdter
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany and University of Tuebingen, 70376 Tuebingen, Germany; (S.K.N.); (N.J.); (S.W.); (S.K.W.); (U.H.); (M.H.D.); (M.S.); (T.E.M.)
| | - Mathias Haag
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany and University of Tuebingen, 70376 Tuebingen, Germany; (S.K.N.); (N.J.); (S.W.); (S.K.W.); (U.H.); (M.H.D.); (M.S.); (T.E.M.)
- Correspondence: ; Tel.: +49-711-8101-5429
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Addendum: An Optimised Dual Extraction Method for the Simultaneous and Accurate Analysis of Polar Metabolites and Lipids Carried out on Single Biological Samples. Metabolites 2020, 10, 338. Metabolites 2020. [PMCID: PMC7760763 DOI: 10.3390/metabo10120490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The authors wish to make the following comment to the paper [...]
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