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House RRJ, Soper-Hopper MT, Vincent MP, Ellis AE, Capan CD, Madaj ZB, Wolfrum E, Isaguirre CN, Castello CD, Johnson AB, Escobar Galvis ML, Williams KS, Lee H, Sheldon RD. A diverse proteome is present and enzymatically active in metabolite extracts. Nat Commun 2024; 15:5796. [PMID: 38987243 PMCID: PMC11237058 DOI: 10.1038/s41467-024-50128-z] [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: 01/26/2024] [Accepted: 07/02/2024] [Indexed: 07/12/2024] Open
Abstract
Metabolite extraction is the critical first-step in metabolomics experiments, where it is generally regarded to inactivate and remove proteins. Here, arising from efforts to improve extraction conditions for polar metabolomics, we discover a proteomic landscape of over 1000 proteins within metabolite extracts. This is a ubiquitous feature across several common extraction and sample types. By combining post-resuspension stable isotope addition and enzyme inhibitors, we demonstrate in-extract metabolite interconversions due to residual transaminase activity. We extend these findings with untargeted metabolomics where we observe extensive protein-mediated metabolite changes, including in-extract formation of glutamate dipeptide and depletion of total glutathione. Finally, we present a simple extraction workflow that integrates 3 kDa filtration for protein removal as a superior method for polar metabolomics. In this work, we uncover a previously unrecognized, protein-mediated source of observer effects in metabolomics experiments with broad-reaching implications across all research fields using metabolomics and molecular metabolism.
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Affiliation(s)
- Rachel Rae J House
- Department of Cell Biology, Van Andel Institute, Grand Rapids, MI, USA
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
- Mass Spectrometry Core, Van Andel Institute, Grand Rapids, MI, USA
| | | | | | - Abigail E Ellis
- Mass Spectrometry Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Colt D Capan
- Mass Spectrometry Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Zachary B Madaj
- Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Emily Wolfrum
- Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, MI, USA
| | | | | | - Amy B Johnson
- Mass Spectrometry Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Martha L Escobar Galvis
- Office of the Cores, Core Technologies and Services, Van Andel Institute, Grand Rapids, MI, USA
| | - Kelsey S Williams
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
| | - Hyoungjoo Lee
- Mass Spectrometry Core, Van Andel Institute, Grand Rapids, MI, USA
| | - Ryan D Sheldon
- Mass Spectrometry Core, Van Andel Institute, Grand Rapids, MI, USA.
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He Y, Yu Q, Ma X, Lv D, Wang H, Qiu W, Chen XF, Jiao Y, Liu Y. A metabolomics approach reveals metabolic disturbance of human cholangiocarcinoma cells after parthenolide treatment. JOURNAL OF ETHNOPHARMACOLOGY 2024; 328:118075. [PMID: 38513779 DOI: 10.1016/j.jep.2024.118075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 03/09/2024] [Accepted: 03/18/2024] [Indexed: 03/23/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Tanacetum parthenium (L.) Schultz-Bip, commonly known as feverfew, has been traditionally used to treat fever, migraines, rheumatoid arthritis, and cancer. Parthenolide (PTL), the main bioactive ingredient isolated from the shoots of feverfew, is a sesquiterpene lactone with anti-inflammatory and antitumor properties. Previous studies showed that PTL exerts anticancer activity in various cancers, including hepatoma, cholangiocarcinoma, acute myeloid leukemia, breast, prostate, and colorectal cancer. However, the metabolic mechanism underlying the anticancer effect of PTL remains poorly understood. AIM OF THE STUDY To explore the anticancer activity and underlying mechanism of PTL in human cholangiocarcinoma cells. MATERIAL AND METHODS In this investigation, the effects and mechanisms of PTL on human cholangiocarcinoma cells were investigated via a liquid chromatography/mass spectrometry (LC/MS)-based metabolomics approach. First, cell proliferation and apoptosis were evaluated using cell counting kit-8 (CCK-8), flow cytometry analysis, and western blotting. Then, LC/MS-based metabolic profiling along with orthogonal partial least-squares discriminant analysis (OPLS-DA) has been constructed to distinguish the metabolic changes between the negative control group and the PTL-treated group in TFK1 cells. Next, enzyme-linked immunosorbent assay (ELISA) was applied to investigate the changes of metabolic enzymes associated with significantly alerted metabolites. Finally, the metabolic network related to key metabolic enzymes, metabolites, and metabolic pathways was established using MetaboAnalyst 5.0 and Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway Database. RESULTS PTL treatment could induce the proliferation inhibition and apoptosis of TFK1 in a concentration-dependent manner. Forty-three potential biomarkers associated with the antitumor effect of PTL were identified, which primarily related to glutamine and glutamate metabolism, alanine, aspartate and glutamate metabolism, phenylalanine, tyrosine and tryptophan biosynthesis, phenylalanine metabolism, arginine biosynthesis, arginine and proline metabolism, glutathione metabolism, nicotinate and nicotinamide metabolism, pyrimidine metabolism, fatty acid metabolism, phospholipid catabolism, and sphingolipid metabolism. Pathway analysis of upstream and downstream metabolites, we found three key metabolic enzymes, including glutaminase (GLS), γ-glutamyl transpeptidase (GGT), and carnitine palmitoyltransferase 1 (CPT1), which mainly involved in glutamine and glutamate metabolism, glutathione metabolism, and fatty acid metabolism. The changes of metabolic enzymes associated with significantly alerted metabolites were consistent with the levels of metabolites, and the metabolic network related to key metabolic enzymes, metabolites, and metabolic pathways was established. PTL may exert its antitumor effect against cholangiocarcinoma by disturbing metabolic pathways. Furthermore, we selected two positive control agents that are considered as first-line chemotherapy standards in cholangiocarcinoma therapy to verify the reliability and accuracy of our metabolomic study on PTL. CONCLUSION This research enhanced our comprehension of the metabolic profiling and mechanism of PTL treatment on cholangiocarcinoma cells, which provided some references for further research into the anti-cancer mechanisms of other drugs.
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Affiliation(s)
- Yongping He
- School of Pharmacy, Guangxi Medical University, Guangxi, Nanning, 530021, China; School of Pharmacy, Naval Medical University (Second Military Medical University), Shanghai, 200433, China; Department of Pharmacy, The People's Hospital of Chongzuo, Guangxi, Chongzuo, 532200, China
| | - Qianxue Yu
- School of Pharmacy, Naval Medical University (Second Military Medical University), Shanghai, 200433, China
| | - Xiaoyu Ma
- School of Pharmacy, Naval Medical University (Second Military Medical University), Shanghai, 200433, China
| | - Diya Lv
- School of Pharmacy, Naval Medical University (Second Military Medical University), Shanghai, 200433, China
| | - Hui Wang
- School of Pharmacy, Naval Medical University (Second Military Medical University), Shanghai, 200433, China
| | - Weian Qiu
- School of Pharmacy, Guangxi Medical University, Guangxi, Nanning, 530021, China
| | - Xiao Fei Chen
- School of Pharmacy, Naval Medical University (Second Military Medical University), Shanghai, 200433, China; Shanghai Key Laboratory for Pharmaceutical Metabolite Research, Shanghai, 200433, China
| | - Yang Jiao
- School of Pharmacy, Guangxi Medical University, Guangxi, Nanning, 530021, China.
| | - Yue Liu
- School of Pharmacy, Naval Medical University (Second Military Medical University), Shanghai, 200433, China; Shanghai Key Laboratory for Pharmaceutical Metabolite Research, Shanghai, 200433, China.
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Nováková S, Baranovičová E, Hatoková Z, Beke G, Pálešová J, Záhumenská R, Baďurová B, Janíčková M, Strnádel J, Halašová E, Škovierová H. Comparison of Various Extraction Approaches for Optimized Preparation of Intracellular Metabolites from Human Mesenchymal Stem Cells and Fibroblasts for NMR-Based Study. Metabolites 2024; 14:268. [PMID: 38786745 PMCID: PMC11122815 DOI: 10.3390/metabo14050268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/02/2024] [Accepted: 05/03/2024] [Indexed: 05/25/2024] Open
Abstract
Metabolomics has proven to be a sensitive tool for monitoring biochemical processes in cell culture. It enables multi-analysis, clarifying the correlation between numerous metabolic pathways. Together with other analysis, it thus provides a global view of a cell's physiological state. A comprehensive analysis of molecular changes is also required in the case of mesenchymal stem cells (MSCs), which currently represent an essential portion of cells used in regenerative medicine. Reproducibility and correct measurement are closely connected to careful metabolite extraction, and sample preparation is always a critical point. Our study aimed to compare the efficiencies of four harvesting and six extraction methods. Several organic reagents (methanol, ethanol, acetonitrile, methanol-chloroform, MTBE) and harvesting approaches (trypsinization vs. scraping) were tested. We used untargeted nuclear magnetic resonance spectroscopy (NMR) to determine the most efficient method for the extraction of metabolites from human adherent cells, specifically human dermal fibroblasts adult (HDFa) and dental pulp stem cells (DPSCs). A comprehensive dataset of 29 identified and quantified metabolites were determined to possess statistically significant differences in the abundances of several metabolites when the cells were detached mechanically to organic solvent compared to when applying enzymes mainly in the classes of amino acids and peptides for both types of cells. Direct scraping to organic solvent is a method that yields higher abundances of determined metabolites. Extraction with the use of different polar reagents, 50% and 80% methanol, or acetonitrile, mostly showed the same quality. For both HDFa and DPSC cells, the MTBE method, methanol-chloroform, and 80% ethanol extractions showed higher extraction efficiency for the most identified and quantified metabolites Thus, preparation procedures provided a cell sample processing protocol that focuses on maximizing extraction yield. Our approach may be useful for large-scale comparative metabolomic studies of human mesenchymal stem cell samples.
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Affiliation(s)
- Slavomíra Nováková
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava (JFM CU), Malá Hora 4C, 036 01 Martin, Slovakia; (S.N.); (Z.H.); (J.P.); (R.Z.); (J.S.); (E.H.); (H.Š.)
| | - Eva Baranovičová
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava (JFM CU), Malá Hora 4C, 036 01 Martin, Slovakia; (S.N.); (Z.H.); (J.P.); (R.Z.); (J.S.); (E.H.); (H.Š.)
| | - Zuzana Hatoková
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava (JFM CU), Malá Hora 4C, 036 01 Martin, Slovakia; (S.N.); (Z.H.); (J.P.); (R.Z.); (J.S.); (E.H.); (H.Š.)
| | - Gábor Beke
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51 Bratislava, Slovakia;
| | - Janka Pálešová
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava (JFM CU), Malá Hora 4C, 036 01 Martin, Slovakia; (S.N.); (Z.H.); (J.P.); (R.Z.); (J.S.); (E.H.); (H.Š.)
| | - Romana Záhumenská
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava (JFM CU), Malá Hora 4C, 036 01 Martin, Slovakia; (S.N.); (Z.H.); (J.P.); (R.Z.); (J.S.); (E.H.); (H.Š.)
| | - Bibiána Baďurová
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava (JFM CU), Malá Hora 4C, 036 01 Martin, Slovakia; (S.N.); (Z.H.); (J.P.); (R.Z.); (J.S.); (E.H.); (H.Š.)
| | - Mária Janíčková
- Department of Stomatology and Maxillofacial Surgery, University Hospital in Martin and JFM CU, Kollárova 2, 036 01 Martin, Slovakia;
| | - Ján Strnádel
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava (JFM CU), Malá Hora 4C, 036 01 Martin, Slovakia; (S.N.); (Z.H.); (J.P.); (R.Z.); (J.S.); (E.H.); (H.Š.)
| | - Erika Halašová
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava (JFM CU), Malá Hora 4C, 036 01 Martin, Slovakia; (S.N.); (Z.H.); (J.P.); (R.Z.); (J.S.); (E.H.); (H.Š.)
| | - Henrieta Škovierová
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava (JFM CU), Malá Hora 4C, 036 01 Martin, Slovakia; (S.N.); (Z.H.); (J.P.); (R.Z.); (J.S.); (E.H.); (H.Š.)
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Luo X, Li L. Effects of Solvent Evaporation Methods and Short-Term Room Temperature Storage on High-Coverage Cellular Metabolome Analysis. Metabolites 2023; 13:1052. [PMID: 37887377 PMCID: PMC10609186 DOI: 10.3390/metabo13101052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 09/25/2023] [Accepted: 10/02/2023] [Indexed: 10/28/2023] Open
Abstract
Cellular metabolomics provides insights into the metabolic processes occurring within cells and can help researchers understand how these processes are regulated and how they relate to cellular function, health, and disease. In this technical note, we investigated the effects of solvent evaporation equipment and storage condition on high-coverage cellular metabolomics. We previously introduced a robust CIL LC-MS-based cellular metabolomics workflow that encompasses various steps, including cell harvest, metabolic quenching, cell lysis, metabolite extraction, differential chemical isotope labeling, and LC-MS analysis. This workflow has consistently served as the cornerstone of our collaborative research and service projects. As a core facility catering to users with diverse research needs and financial resources, we have encountered scenarios requiring short-term sample storage. For example, the need often arises to transport samples at room temperature from user sites to our core facility. Herein, we present a study in which we compared different solvent evaporation methods (specifically, the nitrogen blowdown evaporator, SpeedVac concentrator, and lyophilizer) and diverse storage conditions (including dried samples stored in a freezer, samples stored in a freezer with methanol, dried samples stored at room temperature, and samples stored at room temperature with methanol). Our findings indicate that the choice of solvent evaporation equipment did not significantly impact the cellular metabolome. However, we observed a noteworthy change in the metabolome after 7 days of storage when cells were stored with methanol, regardless of whether they were kept at -80 °C or room temperature, in contrast to cells that were dried and frozen. Importantly, we detected no significant alterations in cells that were dried and stored at room temperature. In conclusion, to ensure the production of high-quality CIL LC-MS metabolomics results, we strongly recommend that, in situations where low-temperature storage is not feasible, cell samples should be thoroughly dried before storage or shipment at room temperature.
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Affiliation(s)
- Xian Luo
- The Metabolomics Innovation Centre, Edmonton, AB T6G 2G2, Canada;
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Liang Li
- The Metabolomics Innovation Centre, Edmonton, AB T6G 2G2, Canada;
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
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Suresh MV, Aktay S, Yalamanchili G, Solanki S, Sathyarajan DT, Arnipalli MS, Pennathur S, Raghavendran K. Role of succinate in airway epithelial cell regulation following traumatic lung injury. JCI Insight 2023; 8:e166860. [PMID: 37737265 PMCID: PMC10561732 DOI: 10.1172/jci.insight.166860] [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: 11/07/2022] [Accepted: 08/17/2023] [Indexed: 09/23/2023] Open
Abstract
Lung contusion and gastric aspiration (LC and GA) are major risk factors for developing acute respiratory distress following trauma. Hypoxia from lung injury is mainly regulated by hypoxia-inducible factor 1α (HIF-1α). Published data from our group indicate that HIF-1α regulation in airway epithelial cells (AEC) drives the acute inflammatory response following LC and GA. Metabolomic profiling and metabolic flux of Type II AEC following LC revealed marked increases in glycolytic and TCA intermediates in vivo and in vitro that were HIF-1α dependent. GLUT-1/4 expression was also increased in HIF-1α+/+ mice, suggesting that increased glucose entry may contribute to increased intermediates. Importantly, lactate incubation in vitro on Type II cells did not significantly increase the inflammatory byproduct IL-1β. Contrastingly, succinate had a direct proinflammatory effect on human small AEC by IL-1β generation in vitro. This effect was reversed by dimethylmalonate, suggesting an important role for succinate dehydrogenase in mediating HIF-1α effects. We confirmed the presence of the only known receptor for succinate binding, SUCNR1, on Type II AEC. These results support the hypothesis that succinate drives HIF-1α-mediated airway inflammation following LC. This is the first report to our knowledge of direct proinflammatory activation of succinate in nonimmune cells such as Type II AEC in direct lung injury models.
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Su AL, Harris SM, Elkin ER, Karnovsky A, Colacino J, Loch-Caruso RK. Trichloroethylene Metabolite S-(1,2-Dichlorovinyl)-l-cysteine Stimulates Changes in Energy Metabolites and Amino Acids in the BeWo Human Placental Trophoblast Model during Syncytialization. Chem Res Toxicol 2023; 36:882-899. [PMID: 37162359 PMCID: PMC10499396 DOI: 10.1021/acs.chemrestox.3c00007] [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: 05/11/2023]
Abstract
Syncytialization, the fusion of cytotrophoblasts into an epithelial barrier that constitutes the maternal-fetal interface, is a crucial event of placentation. This process is characterized by distinct changes to amino acid and energy metabolism. A metabolite of the industrial solvent trichloroethylene (TCE), S-(1,2-dichlorovinyl)-l-cysteine (DCVC), modifies energy metabolism and amino acid abundance in HTR-8/SVneo extravillous trophoblasts. In the current study, we investigated DCVC-induced changes to energy metabolism and amino acids during forskolin-stimulated syncytialization in BeWo cells, a human villous trophoblastic cell line that models syncytialization in vitro. BeWo cells were exposed to forskolin at 100 μM for 48 h to stimulate syncytialization. During syncytialization, BeWo cells were also treated with DCVC at 0 (control), 10, or 20 μM. Following treatment, the targeted metabolomics platform, "Tricarboxylic Acid Plus", was used to identify changes in energy metabolism and amino acids. DCVC treatment during syncytialization decreased oleic acid, aspartate, proline, uridine diphosphate (UDP), UDP-d-glucose, uridine monophosphate, and cytidine monophosphate relative to forskolin-only treatment controls, but did not increase any measured metabolite. Notable changes stimulated by syncytialization in the absence of DCVC included increased adenosine monophosphate and guanosine monophosphate, as well as decreased aspartate and glutamate. Pathway analysis revealed multiple pathways in amino acid and sugar metabolisms that were altered with forskolin-stimulated syncytialization alone and DCVC treatment during syncytialization. Analysis of ratios of metabolites within the pathways revealed that DCVC exposure during syncytialization changed metabolite ratios in the same or different direction compared to syncytialization alone. Building off our oleic acid findings, we found that extracellular matrix metalloproteinase-2, which is downstream in oleic acid signaling, underwent the same changes as oleic acid. Together, the metabolic changes stimulated by DCVC treatment during syncytialization suggest changes in energy metabolism and amino acid abundance as potential mechanisms by which DCVC could impact syncytialization and pregnancy.
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Affiliation(s)
- Anthony L. Su
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, Michigan 48109
| | - Sean M. Harris
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, Michigan 48109
| | - Elana R. Elkin
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, Michigan 48109
| | - Alla Karnovsky
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Justin Colacino
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, Michigan 48109
- Department of Nutritional Sciences, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Rita Karen Loch-Caruso
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, Michigan 48109
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Wang T, Wang X, Zhuang Y, Wang G. A systematic evaluation of quenching and extraction procedures for quantitative metabolome profiling of HeLa carcinoma cell under 2D and 3D cell culture conditions. Biotechnol J 2023; 18:e2200444. [PMID: 36796787 DOI: 10.1002/biot.202200444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 01/13/2023] [Accepted: 02/10/2023] [Indexed: 02/18/2023]
Abstract
Metabolic reprogramming has been coined as a hallmark of cancer, accompanied by which the alterations in metabolite levels have profound effects on gene expression, cellular differentiation, and the tumor environment. Yet a systematic evaluation of quenching and extraction procedures for quantitative metabolome profiling of tumor cells is currently lacking. To achieve this, this study is aimed at establishing an unbiased and leakage-free metabolome preparation protocol for HeLa carcinoma cell. We evaluated 12 combinations of quenching and extraction methods from three quenchers (liquid nitrogen, -40°C 50% methanol, 0.5°C normal saline) and four extractants (-80°C 80% methanol, 0.5°C methanol/chloroform/water [1:1:1 v/v/v], 0.5°C 50% acetonitrile, 75°C 70% ethanol) for global metabolite profiling of adherent HeLa carcinoma cells. Based on the isotope dilution mass spectrometry (IDMS) method, gas/liquid chromatography in tandem with mass spectrometry was used to quantitatively determine 43 metabolites including sugar phosphates, organic acids, amino acids (AAs), adenosine nucleotides, and coenzymes involved in central carbon metabolism. The results showed that the total amount of the intracellular metabolites in cell extracts obtained using different sample preparation procedures with the IDMS method ranged from 21.51 to 295.33 nmol per million cells. Among 12 combinations, cells that washed twice with phosphate buffered saline (PBS), quenched with liquid nitrogen, and then extracted with 50% acetonitrile were found to be the most optimal method to acquire intracellular metabolites with high efficiency of metabolic arrest and minimal loss during sample preparation. In addition, the same conclusion was drawn as these 12 combinations were applied to obtain quantitative metabolome data from three-dimensional (3D) tumor spheroids. Furthermore, a case study was carried out to evaluate the effect of doxorubicin (DOX) on both adherent cells and 3D tumor spheroids using quantitative metabolite profiling. Pathway enrichment analysis using targeted metabolomics data showed that DOX exposure would significantly affect AA metabolism-related pathways, which might be related to the mitigation of redox stress. Strikingly, our data suggested that compared to two-dimensional (2D) cells the increased intracellular glutamine level in 3D cells benefited replenishing the tricarboxylic acid (TCA) cycle when the glycolysis was limited after dosing with DOX. Taken together, this study provides a well-established quenching and extraction protocol for quantitative metabolome profiling of HeLa carcinoma cell under 2D and 3D cell culture conditions. Based on this, quantitative time-resolved metabolite data can serve to the generation of hypotheses on metabolic reprogramming to reveal its important role in tumor development and treatment.
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Affiliation(s)
- Tong Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology (ECUST), Shanghai, People's Republic of China
| | - Xueting Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology (ECUST), Shanghai, People's Republic of China
| | - Yingping Zhuang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology (ECUST), Shanghai, People's Republic of China.,Qingdao Innovation Institute of East China University of Science and Technology, Shanghai, People's Republic of China
| | - Guan Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology (ECUST), Shanghai, People's Republic of China.,Qingdao Innovation Institute of East China University of Science and Technology, Shanghai, People's Republic of China
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Bala N, Yu L, Liu LP, Shelton L, Xu Y, Ghayee HK, Alli AA. Metabolic Characterization and Glyceraldehyde-3-Phosphate Dehydrogenase-Dependent Regulation of Epithelial Sodium Channels in hPheo1 Wild-type and SDHB Knockdown Cells. Endocrinology 2023; 164:7034155. [PMID: 36763043 DOI: 10.1210/endocr/bqad026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 01/26/2023] [Accepted: 01/30/2023] [Indexed: 02/11/2023]
Abstract
Pheochromocytomas (PCC) and paragangliomas (PGL) are rare neuroendocrine tumors with limited curative treatment options outside of surgical resection. Patients with mutations in succinate dehydrogenase subunit B (SDHB) are at an increased risk of malignant and aggressive disease. As cation channels are associated with tumorigenesis, we studied the expression and activity of cation channels from the Degenerin superfamily in a progenitor cell line derived from a human PCC. hPheo1 wild-type (WT) and SDHB knockdown (KD) cells were studied to investigate whether epithelial sodium channels (ENaC) and acid-sensing ion channels (ASIC) are regulated by the activity of glyceraldehyde-3-phosphate dehydrogenase (GAPDH). First, we performed targeted metabolomic studies and quantified changes in glycolysis pathway intermediates and citric acid cycle intermediates using hPheo1 WT cells and SDHB KD cells. Next, we performed protein biochemistry and electrophysiology studies to characterize the protein expression and activity, respectively, of these ion channels. Our western blot experiments show both ENaC alpha and ASIC1/2 are expressed in both hPheo1 WT and SDHB KD cells, with lower levels of a cleaved 60 kDa form of ENaC in SDHB KD cells. Single-channel patch clamp studies corroborate these results and further indicate channel activity is decreased in SDHB KD cells. Additional experiments showed a more significant decreased membrane potential in SDHB KD cells, which were sensitive to amiloride compared to WT cells. We provide evidence for the differential expression and activity of ENaC and ASIC hybrid channels in hPheo1 WT and SDHB KD cells, providing an important area of investigation in understanding SDHB-related disease.
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Affiliation(s)
- Niharika Bala
- Department of Physiology and Aging, University of Florida College of Medicine, Gainesville, FL, USA
| | - Ling Yu
- Department of Physiology and Aging, University of Florida College of Medicine, Gainesville, FL, USA
| | - Lauren P Liu
- Department of Physiology and Aging, University of Florida College of Medicine, Gainesville, FL, USA
| | | | - Yiling Xu
- Department of Medicine, Division of Endocrinology & Metabolism, University of Florida College of Medicine, Gainesville, FL, USA
| | - Hans K Ghayee
- Department of Medicine, Division of Endocrinology & Metabolism, University of Florida College of Medicine, Gainesville, FL, USA
- Malcom Randall VA Medical Center, Gainesville, FL, USA
| | - Abdel A Alli
- Department of Physiology and Aging, University of Florida College of Medicine, Gainesville, FL, USA
- Department of Medicine Division of Nephrology, Hypertension, and Renal Transplantation, University of Florida College of Medicine, Gainesville, FL, USA
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Muehlbauer LK, Jen A, Zhu Y, He Y, Shishkova E, Overmyer KA, Coon JJ. Rapid Multi-Omics Sample Preparation for Mass Spectrometry. Anal Chem 2023; 95:659-667. [PMID: 36594155 PMCID: PMC10026941 DOI: 10.1021/acs.analchem.2c02042] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Multi-omics analysis is a powerful and increasingly utilized approach to gain insight into complex biological systems. One major hindrance with multi-omics, however, is the lengthy and wasteful sample preparation process. Preparing samples for mass spectrometry (MS)-based multi-omics involves extraction of metabolites and lipids with organic solvents, precipitation of proteins, and overnight digestion of proteins. These existing workflows are disparate and laborious. Here, we present a simple, efficient, and unified approach to prepare lipids, metabolites, and proteins for MS analysis. Our approach, termed the Bead-enabled Accelerated Monophasic Multi-omics (BAMM) method, combines an n-butanol-based monophasic extraction with unmodified magnetic beads and accelerated protein digestion. We demonstrate that the BAMM method affords comparable depth, quantitative reproducibility, and recovery of biomolecules as state-of-the-art multi-omics methods (e.g., Matyash extraction and overnight protein digestion). However, the BAMM method only requires about 3 h to perform, which saves 11 steps and 19 h on average compared to published multi-omics methods. Furthermore, we validate the BAMM method for multiple sample types and formats (biofluid, culture plate, and pellet) and show that in all cases, it produces high biomolecular coverage and data quality.
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Affiliation(s)
- Laura K. Muehlbauer
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Annie Jen
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Yunyun Zhu
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Yuchen He
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Evgenia Shishkova
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- National Center for Quantitative Biology of Complex Systems, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Katherine A. Overmyer
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- National Center for Quantitative Biology of Complex Systems, University of Wisconsin-Madison, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Joshua J. Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- National Center for Quantitative Biology of Complex Systems, University of Wisconsin-Madison, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53715, USA
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Hissong R, Evans KR, Evans CR. Compound Identification Strategies in Mass Spectrometry-Based Metabolomics and Pharmacometabolomics. Handb Exp Pharmacol 2023; 277:43-71. [PMID: 36409330 DOI: 10.1007/164_2022_617] [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] [Indexed: 11/23/2022]
Abstract
The metabolome is composed of a vast array of molecules, including endogenous metabolites and lipids, diet- and microbiome-derived substances, pharmaceuticals and supplements, and exposome chemicals. Correct identification of compounds from this diversity of classes is essential to derive biologically relevant insights from metabolomics data. In this chapter, we aim to provide a practical overview of compound identification strategies for mass spectrometry-based metabolomics, with a particular eye toward pharmacologically-relevant studies. First, we describe routine compound identification strategies applicable to targeted metabolomics. Next, we discuss both experimental (data acquisition-focused) and computational (software-focused) strategies used to identify unknown compounds in untargeted metabolomics data. We then discuss the importance of, and methods for, assessing and reporting the level of confidence of compound identifications. Throughout the chapter, we discuss how these steps can be implemented using today's technology, but also highlight research underway to further improve accuracy and certainty of compound identification. For readers interested in interpreting metabolomics data already collected, this chapter will supply important context regarding the origin of the metabolite names assigned to features in the data and help them assess the certainty of the identifications. For those planning new data acquisition, the chapter supplies guidance for designing experiments and selecting analysis methods to enable accurate compound identification, and it will point the reader toward best-practice data analysis and reporting strategies to allow sound biological and pharmacological interpretation.
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11
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Guo S, Li B, Wang D, Li L, Chen Y, Menghe B. Metabolomic analysis of cooperative adaptation between Co-cultured Lacticaseibacillus casei Zhang and Lactiplantibacillus plantarum P8. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.114105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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12
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Tong Y, Sun M, Chen L, Wang Y, Li Y, Li L, Zhang X, Cai Y, Qie J, Pang Y, Xu Z, Zhao J, Zhang X, Liu Y, Tian S, Qin Z, Feng J, Zhang F, Zhu J, Xu Y, Lou W, Ji Y, Zhao J, He F, Hou Y, Ding C. Proteogenomic insights into the biology and treatment of pancreatic ductal adenocarcinoma. J Hematol Oncol 2022; 15:168. [PMID: 36434634 PMCID: PMC9701038 DOI: 10.1186/s13045-022-01384-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 11/02/2022] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Pancreatic ductal adenocarcinoma (PDAC) is a devastating disease with poor prognosis. Proteogenomic characterization and integrative proteomic analysis provide a functional context to annotate genomic abnormalities with prognostic value. METHODS We performed an integrated multi-omics analysis, including whole-exome sequencing, RNA-seq, proteomic, and phosphoproteomic analysis of 217 PDAC tumors with paired non-tumor adjacent tissues. In vivo functional experiments were performed to further illustrate the biological events related to PDAC tumorigenesis and progression. RESULTS A comprehensive proteogenomic landscape revealed that TP53 mutations upregulated the CDK4-mediated cell proliferation process and led to poor prognosis in younger patients. Integrative multi-omics analysis illustrated the proteomic and phosphoproteomic alteration led by genomic alterations such as KRAS mutations and ADAM9 amplification of PDAC tumorigenesis. Proteogenomic analysis combined with in vivo experiments revealed that the higher amplification frequency of ADAM9 (8p11.22) could drive PDAC metastasis, though downregulating adhesion junction and upregulating WNT signaling pathway. Proteome-based stratification of PDAC revealed three subtypes (S-I, S-II, and S-III) related to different clinical and molecular features. Immune clustering defined a metabolic tumor subset that harbored FH amplicons led to better prognosis. Functional experiments revealed the role of FH in altering tumor glycolysis and in impacting PDAC tumor microenvironments. Experiments utilizing both in vivo and in vitro assay proved that loss of HOGA1 promoted the tumor growth via activating LARP7-CDK1 pathway. CONCLUSIONS This proteogenomic dataset provided a valuable resource for researchers and clinicians seeking for better understanding and treatment of PDAC.
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Affiliation(s)
- Yexin Tong
- grid.8547.e0000 0001 0125 2443Institute of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433 China
| | - Mingjun Sun
- grid.8547.e0000 0001 0125 2443Institute of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433 China
| | - Lingli Chen
- grid.8547.e0000 0001 0125 2443Institute of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433 China
| | - Yunzhi Wang
- grid.8547.e0000 0001 0125 2443Institute of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433 China
| | - Yan Li
- grid.8547.e0000 0001 0125 2443Institute of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433 China
| | - Lingling Li
- grid.8547.e0000 0001 0125 2443Institute of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433 China
| | - Xuan Zhang
- grid.8547.e0000 0001 0125 2443Institute of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433 China
| | - Yumeng Cai
- grid.8547.e0000 0001 0125 2443Institute of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433 China
| | - Jingbo Qie
- grid.8547.e0000 0001 0125 2443Institute of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433 China
| | - Yanrui Pang
- grid.8547.e0000 0001 0125 2443Institute of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433 China
| | - Ziyan Xu
- grid.8547.e0000 0001 0125 2443Institute of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433 China
| | - Jiangyan Zhao
- grid.8547.e0000 0001 0125 2443Institute of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433 China
| | - Xiaolei Zhang
- grid.8547.e0000 0001 0125 2443Institute of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433 China
| | - Yang Liu
- grid.8547.e0000 0001 0125 2443Institute of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433 China
| | - Sha Tian
- grid.8547.e0000 0001 0125 2443Institute of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433 China
| | - Zhaoyu Qin
- grid.8547.e0000 0001 0125 2443Institute of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433 China
| | - Jinwen Feng
- grid.8547.e0000 0001 0125 2443Institute of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433 China
| | - Fan Zhang
- grid.8547.e0000 0001 0125 2443Institute of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433 China
| | - Jiajun Zhu
- grid.8547.e0000 0001 0125 2443Institute of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433 China
| | - Yifan Xu
- grid.8547.e0000 0001 0125 2443Institute of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433 China
| | - Wenhui Lou
- grid.8547.e0000 0001 0125 2443Institute of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433 China
| | - Yuan Ji
- grid.8547.e0000 0001 0125 2443Institute of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433 China
| | - Jianyuan Zhao
- grid.16821.3c0000 0004 0368 8293Institute for Development and Regenerative Cardiovascular Medicine, MOE-Shanghai Key Laboratory of Children’s Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092 China ,grid.207374.50000 0001 2189 3846Department of Anatomy and Neuroscience Research Institute, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001 China
| | - Fuchu He
- grid.8547.e0000 0001 0125 2443Institute of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433 China ,grid.419611.a0000 0004 0457 9072State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing, 102206 China ,grid.506261.60000 0001 0706 7839Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Beijing, 102206 China
| | - Yingyong Hou
- grid.8547.e0000 0001 0125 2443Institute of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433 China
| | - Chen Ding
- grid.8547.e0000 0001 0125 2443Institute of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200433 China
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Mishra V, Prajapati G, Baranwal V, Mishra RK. NMR-Based Metabolomic Imprinting Elucidates Macrophage Polarization of THP-1 Cell Lines Stimulated by Zinc Oxide Nanoparticles. ACS APPLIED BIO MATERIALS 2022; 5:4873-4885. [PMID: 36126340 DOI: 10.1021/acsabm.2c00603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Zinc oxide (ZnO) nanoparticles (NPs) have been widely used in industry, cosmetics, drugs, bioimaging, and drug delivery. ZnO NPs have been found to interact and interfere with cellular physiology via macrophages, thereby resulting in macrophage polarization. The functional reprogramming of the cells is synchronized through cellular metabolic adaptations. The current study, therefore, aims to establish crosstalk between ZnO-NP-induced metabolic alterations and macrophage polarization in PMA-activated THP-1 cell lines. We observed moderate to heightened cytotoxic response in terms of cell viability and proliferation. The results also revealed increased Th1-type cytokine and chemokine expression. In order to characterize the changes in metabolite concentration in treatment groups, we employed multivariate data analysis (principal component analysis and partial least-squares discriminant analysis) of 1H NMR spectra. The results revealed biologically relevant patterns and alterations in many metabolic pathways. These alterations and patterns were found to be in line across the immune-cytotoxic axis. Furthermore, the results also implicate the role of carbon metabolism toward the classical activation of macrophage polarization. The omics approach could identify the markers involved in NP-induced toxicity, thus elaborating our vision of cytotoxicity that is currently limited to end-point and cytokine assays. Also, it could be emphasized that metabolic reconfiguration upon NP stimulation could direct macrophage polarization toward classical activation.
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Affiliation(s)
- Vani Mishra
- Nanotechnology Application Centre (NAC), University of Allahabad, Prayagraj 211002, India
| | - Gurudayal Prajapati
- NMR Centre SAIF Laboratory, CSIR-Central Drug Research Institute (CDRI), Lucknow 226031, India
| | - Vikas Baranwal
- Graphene Research Labs Pvt. Ltd., 135 Road 10, KIADB IT Park, Bengaluru 562149, India
| | - Rohit Kumar Mishra
- Centre of Science and Society, Institute of Interdisciplinary Sciences (IIDS), University of Allahabad, Prayagraj 211002, India
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mTORC1 and mTORC2 Complexes Regulate the Untargeted Metabolomics and Amino Acid Metabolites Profile through Mitochondrial Bioenergetic Functions in Pancreatic Beta Cells. Nutrients 2022; 14:nu14153022. [PMID: 35893876 PMCID: PMC9332257 DOI: 10.3390/nu14153022] [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: 06/19/2022] [Revised: 07/15/2022] [Accepted: 07/18/2022] [Indexed: 02/04/2023] Open
Abstract
Background: Pancreatic beta cells regulate bioenergetics efficiency and secret insulin in response to glucose and nutrient availability. The mechanistic Target of Rapamycin (mTOR) network orchestrates pancreatic progenitor cell growth and metabolism by nucleating two complexes, mTORC1 and mTORC2. Objective: To determine the impact of mTORC1/mTORC2 inhibition on amino acid metabolism in mouse pancreatic beta cells (Beta-TC-6 cells, ATCC-CRL-11506) using high-resolution metabolomics (HRM) and live-mitochondrial functions. Methods: Pancreatic beta TC-6 cells were incubated for 24 h with either: RapaLink-1 (RL); Torin-2 (T); rapamycin (R); metformin (M); a combination of RapaLink-1 and metformin (RLM); Torin-2 and metformin (TM); compared to the control. We applied high-resolution mass spectrometry (HRMS) LC-MS/MS untargeted metabolomics to compare the twenty natural amino acid profiles to the control. In addition, we quantified the bioenergetics dynamics and cellular metabolism by live-cell imaging and the MitoStress Test XF24 (Agilent, Seahorse). The real-time, live-cell approach simultaneously measures the oxygen consumption rate (OCR) and extracellular acidification rate (ECAR) to determine cellular respiration and metabolism. Statistical significance was assessed using ANOVA on Ranks and post-hoc Welch t-Tests. Results: RapaLink-1, Torin-2, and rapamycin decreased L-aspartate levels compared to the control (p = 0.006). Metformin alone did not affect L-aspartate levels. However, L-asparagine levels decreased with all treatment groups compared to the control (p = 0.03). On the contrary, L-glutamate and glycine levels were reduced only by mTORC1/mTORC2 inhibitors RapaLink-1 and Torin-2, but not by rapamycin or metformin. The metabolic activity network model predicted that L-aspartate and AMP interact within the same activity network. Live-cell bioenergetics revealed that ATP production was significantly reduced in RapaLink-1 (122.23 ± 33.19), Torin-2 (72.37 ± 17.33) treated cells, compared to rapamycin (250.45 ± 9.41) and the vehicle control (274.23 ± 38.17), p < 0.01. However, non-mitochondrial oxygen consumption was not statistically different between RapaLink-1 (67.17 ± 3.52), Torin-2 (55.93 ± 8.76), or rapamycin (80.01 ± 4.36, p = 0.006). Conclusions: Dual mTORC1/mTORC2 inhibition by RapaLink-1 and Torin-2 differentially altered the amino acid profile and decreased mitochondrial respiration compared to rapamycin treatment which only blocks the FRB domain on mTOR. Third-generation mTOR inhibitors may alter the mitochondrial dynamics and reveal a bioenergetics profile that could be targeted to reduce mitochondrial stress.
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15
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The CXCL12/CXCR4/ACKR3 Signaling Axis Regulates PKM2 and Glycolysis. Cells 2022; 11:cells11111775. [PMID: 35681470 PMCID: PMC9179862 DOI: 10.3390/cells11111775] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/13/2022] [Accepted: 05/24/2022] [Indexed: 02/06/2023] Open
Abstract
In response to CXCL12, CXCR4 and ACKR3 both recruit β-arrestin 2, regulating the assembly of interacting proteins that drive signaling and contribute to the functions of both receptors in cancer and multiple other diseases. A prior proteomics study revealed that β-arrestin 2 scaffolds pyruvate kinase M2 (PKM2), an enzyme implicated in shifting cells to glycolytic metabolism and poor prognosis in cancer. We hypothesized that CXCL12 signaling regulates PKM2 protein interactions, oligomerization, and glucose metabolism. We used luciferase complementation in cell-based assays and a tumor xenograft model of breast cancer in NSG mice to quantify how CXCR4 and ACKR3 change protein interactions in the β-arrestin-ERK-PKM2 pathway. We also used mass spectrometry to analyze the effects of CXCL12 on glucose metabolism. CXCL12 signaling through CXCR4 and ACKR3 stimulated protein interactions among β-arrestin 2, PKM2, ERK2, and each receptor, leading to the dissociation of PKM2 from β-arrestin 2. The activation of both receptors reduced the oligomerization of PKM2, reflecting a shift from tetramers to dimers or monomers with low enzymatic activity. Mass spectrometry with isotopically labeled glucose showed that CXCL12 signaling increased intermediate metabolites in glycolysis and the pentose phosphate pathway, with ACKR3 mediating greater effects. These data establish how CXCL12 signaling regulates PKM2 and reprograms cellular metabolism.
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16
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Fritsche-Guenther R, Gloaguen Y, Eisenberger A, Kirwan JA. Analysis of adherent cell culture lysates with low metabolite concentrations using the Biocrates AbsoluteIDQ p400 HR kit. Sci Rep 2022; 12:7933. [PMID: 35562573 PMCID: PMC9106690 DOI: 10.1038/s41598-022-11118-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 03/07/2022] [Indexed: 11/09/2022] Open
Abstract
The AbsoluteIDQ p400 HR kit is a commercial product for targeted metabolomics. While the kit has been validated for human plasma and serum, adherent cell lysates have not yet been evaluated. We have optimized the detection of polar and lipid metabolites in cell lysates using the kit to enable robust and repeatable analysis of the detected metabolites. Parameters optimized include total cell mass, loading volume and extraction solvent. We present a cell preparation and analytical method and report on the performance of the kit with regard to detectability of the targeted metabolites and their repeatability. The kit can be successfully used for a relative quantification analysis of cell lysates from adherent cells although validated only for human plasma and serum. Most metabolites are below the limit of the Biocrates' set quantification limits and we confirmed that this relative quantification can be used for further statistical analysis. Using this approach, up to 45% of the total metabolites in the kit can be detected with a reasonable analytical performance (lowest median RSD 9% and 13% for LC and FIA, respectively) dependent on the method used. We recommend using ethanol as the extraction solvent for cell lysates of osteosarcoma cell lines for the broadest metabolite coverage and 25 mg of cell mass with a loading volume of 20 µL per sample.
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Affiliation(s)
- Raphaela Fritsche-Guenther
- Berlin Institute of Health (BIH) @ Charité, BIH Metabolomics Platform, Anna-Louisa-Karsch-Str. 2, 10178, Berlin, Germany
| | - Yoann Gloaguen
- Berlin Institute of Health (BIH) @ Charité, BIH Metabolomics Platform, Anna-Louisa-Karsch-Str. 2, 10178, Berlin, Germany.,Core Unit Bioinformatics, Berlin Institute of Health (BIH) @ Charité, Chariteplatz 1, 10117, Berlin, Germany
| | - Alina Eisenberger
- Berlin Institute of Health (BIH) @ Charité, BIH Metabolomics Platform, Anna-Louisa-Karsch-Str. 2, 10178, Berlin, Germany
| | - Jennifer A Kirwan
- Berlin Institute of Health (BIH) @ Charité, BIH Metabolomics Platform, Anna-Louisa-Karsch-Str. 2, 10178, Berlin, Germany.
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Development of a non-target metabolomics-based screening method for elucidating metabolic and probiotic potential of bifidobacteria. INNOV FOOD SCI EMERG 2022. [DOI: 10.1016/j.ifset.2022.102971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Tikunov AP, Tipton JD, Garrett TJ, Shinde SV, Kim HJ, Gerber DA, Herring LE, Graves LM, Macdonald JM. Green Chemistry Preservation and Extraction of Biospecimens for Multi-omic Analyses. Methods Mol Biol 2022; 2394:267-298. [PMID: 35094334 DOI: 10.1007/978-1-0716-1811-0_17] [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] [Indexed: 05/16/2023]
Abstract
The Environmental Protection Agency's definition of "Green Chemistry" is "the design of chemical products and processes that reduces or eliminates the use or generation of hazardous substances. Green chemistry applies across the life cycle of a chemical product, including its design, manufacture, use, and ultimate disposal." Conventional omic tissue extraction procedures use solvents that are toxic and carcinogenic, such as chloroform and methyl-tert-butyl ether for lipidomics, or caustic chaotropic solutions for genomics and transcriptomics, such as guanidine or urea. A common preservation solution for pathology is formaldehyde, which is a carcinogen. Use of acetonitrile as a universal biospecimen preservation and extraction solvent will reduce these hazardous wastes, because it is less toxic and more environmentally friendly than the conventional solvents used in biorepository and biospecimen research. A new extraction method never applied to multi-omic, system biology research, called cold-induced phase separation (CIPS), uses freezing point temperatures to induce a phase separation of acetonitrile-water mixtures. Also, the CO2 exposure during CIPS will acidify the water precipitating DNA out of aqueous phase. The resulting phase separation brings hydrophobic lipids to the top acetonitrile fraction that is easily decanted from the bottom aqueous fraction, especially when the water is frozen. This CIPS acetonitrile extract contains the lipidome (lipids), the bottom aqueous fraction is sampled to obtain the transcriptome (RNA) fraction, and the remaining water and pellet is extracted with 60% acetonitrile to isolate the metabolome (<1 kD polar molecules). Finally, steps 4 and 5 use a TRIzol™ liquid-liquid extraction SOP of the pellet to isolate the genome (DNA) and proteome (proteins). This chapter details the multi-omic sequential extraction SOP and potential problems associated with each of the 5 steps, with steps 2, 4, and 5 still requiring validation. The metabolomic and lipidomic extraction efficiencies using the CIPS SOP is compared to conventional solvent extraction SOPs and is analyzed by nuclear magnetic resonance (NMR) spectroscopy and liquid chromatography-mass spectrometry (LC-MS), respectively. Acetonitrile biospecimen preservation combined with the CIPS multi-omic extraction SOP is green chemistry technology that will eliminate the generation of the hazardous substances associated with biospecimen processing and permits separation and safe disposal of acetonitrile avoiding environmental contamination.
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Affiliation(s)
- Andrey P Tikunov
- Departments of Biomedical Engineering, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Jeremiah D Tipton
- Departments of Biomedical Engineering, University of North Carolina School of Medicine, Chapel Hill, NC, USA
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, College of Medicine, Gainesville, FL, USA
| | - Timothy J Garrett
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, College of Medicine, Gainesville, FL, USA
| | - Sachi V Shinde
- Departments of Biomedical Engineering, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Hong Jin Kim
- Departments of Surgery, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - David A Gerber
- Departments of Surgery, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Laura E Herring
- Departments of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Lee M Graves
- Departments of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Jeffrey M Macdonald
- Departments of Biomedical Engineering, University of North Carolina School of Medicine, Chapel Hill, NC, USA.
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Coprocessing Corn Germ Meal for Oil Recovery and Ethanol Production: A Process Model for Lipid-Producing Energy Crops. Processes (Basel) 2022. [DOI: 10.3390/pr10040661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Efforts to engineer high-productivity crops to accumulate oils in their vegetative tissue present the possibility of expanding biodiesel production. However, processing the new crops for lipid recovery and ethanol production from cell wall saccharides is challenging and expensive. In a previous study using corn germ meal as a model substrate, we reported that liquid hot water (LHW) pretreatment enriched the lipid concentration by 2.2 to 4.2 fold. This study investigated combining oil recovery with ethanol production by extracting oil following LHW and simultaneous saccharification and co-fermentation (SSCF) of the biomass. Corn germ meal was again used to model the oil-bearing energy crops. Pretreated germ meal hydrolysate or solids (160 and 180 °C for 10 min) were fermented, and lipids were extracted from both the spent fermentation whole broth and fermentation solids, which were recovered by centrifugation and convective drying. Lipid contents in spent fermentation solids increased 3.7 to 5.7 fold compared to the beginning germ meal. The highest lipid yield achieved after fermentation was 36.0 mg lipid g−1 raw biomass; the maximum relative amount of triacylglycerol (TAG) was 50.9% of extracted oil. Although the fermentation step increased the lipid concentration of the recovered solids, it did not improve the lipid yields of pretreated biomass and detrimentally affected oil compositions by increasing the relative concentrations of free fatty acids.
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Su AL, Harris SM, Elkin ER, Karnovsky A, Colacino JA, Loch-Caruso R. Trichloroethylene modifies energy metabolites in the amniotic fluid of Wistar rats. Reprod Toxicol 2022; 109:80-92. [PMID: 35301063 PMCID: PMC9000924 DOI: 10.1016/j.reprotox.2022.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 03/05/2022] [Accepted: 03/11/2022] [Indexed: 10/18/2022]
Abstract
Exposure to trichloroethylene (TCE), an industrial solvent, is associated with several adverse pregnancy outcomes in humans and decreased fetal weight in rats. However, effects of TCE on energy metabolites in amniotic fluid, which have associations with pregnancy outcomes, has not been published previously. In the current exploratory study, timed-pregnant Wistar rats were exposed to 480 mg TCE/kg/day via vanilla wafer or to vehicle (wafer) alone from gestational day (GD) 6-16. Amniotic fluid collected on GD 16 was analyzed for metabolites important in energy metabolism using short chain fatty acid and tricarboxylic acid plus platforms (N = 4 samples/sex/treatment). TCE decreased concentrations of the following metabolites in amniotic fluid for both fetal sexes: 6-phosphogluconate, guanosine diphosphate, adenosine diphosphate, adenosine triphosphate, and flavin adenine dinucleotide. TCE decreased fructose 1,6-bisphosphate and guanosine triphosphate concentrations in amniotic fluid of male but not female fetuses. Moreover, TCE decreased uridine diphosphate-D-glucuronate concentrations, and increased arginine and phosphocreatine concentrations, in amniotic fluid of female fetuses only. No metabolites were increased in amniotic fluid of male fetuses. Pathway analysis suggested that TCE altered folate biosynthesis and pentose phosphate pathway in both sexes. Using metabolite ratios to investigate changes within specific pathways, some ratio alterations, including those in arginine metabolism and phenylalanine metabolism, were detected in females only. Ratio analysis also suggested enzymes, including gluconokinase, as potential TCE targets. Together, results from this exploratory study suggest that TCE differentially modified energy metabolites in amniotic fluid based on sex. These findings may inform future studies of TCE reproductive toxicity.
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Affiliation(s)
- Anthony L Su
- Department of Environmental Health Sciences, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109, USA.
| | - Sean M Harris
- Department of Environmental Health Sciences, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109, USA.
| | - Elana R Elkin
- Department of Environmental Health Sciences, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109, USA.
| | - Alla Karnovsky
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Palmer Commons, 100 Washtenaw Ave #2017, Ann Arbor, MI 48109, USA.
| | - Justin A Colacino
- Department of Environmental Health Sciences, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109, USA; Department of Nutritional Sciences, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109, USA.
| | - Rita Loch-Caruso
- Department of Environmental Health Sciences, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109, USA.
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21
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Comparison of Lysis and Detachment Sample Preparation Methods for Cultured Triple-Negative Breast Cancer Cells Using UHPLC–HRMS-Based Metabolomics. Metabolites 2022; 12:metabo12020168. [PMID: 35208242 PMCID: PMC8879193 DOI: 10.3390/metabo12020168] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/03/2022] [Accepted: 02/07/2022] [Indexed: 12/12/2022] Open
Abstract
Dysregulation of cellular metabolism is now a well-recognized hallmark of cancer. Studies investigating the metabolic features of cancer cells have shed new light onto processes in cancer cell biology and have identified many potential novel treatment options. The advancement of mass spectrometry-based metabolomics has improved the ability to monitor multiple metabolic pathways simultaneously in various experimental settings. However, questions still remain as to how certain steps in the metabolite extraction process affect the metabolic profiles of cancer cells. Here, we use ultra-high-performance liquid chromatography–high-resolution mass spectrometry (UHPLC–HRMS) untargeted metabolomics to investigate the effects of different detachment and lysis methods on the types and abundances of metabolites extracted from MDA-MB-231 cells through the use of in-house standards libraries and pathway analysis software. Results indicate that detachment methods (trypsinization vs. scraping) had the greatest effect on metabolic profiles whereas lysis methods (homogenizer beads vs. freeze–thaw cycling) had a lesser, though still significant, effect. No singular method was clearly superior over others, with certain metabolite classes giving higher abundances or lower variation for each detachment–lysis combination. These results indicate the importance of carefully selecting sample preparation methods for cell-based metabolomics to optimize the extraction performance for certain compound classes.
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22
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Mitchell J, Kim SJ, Howe C, Lee S, Her JY, Patel M, Kim G, Lee J, Im E, Rhee SH. Chronic Intestinal Inflammation Suppresses Brain Activity by Inducing Neuroinflammation in Mice. THE AMERICAN JOURNAL OF PATHOLOGY 2022; 192:72-86. [PMID: 34619134 PMCID: PMC8759038 DOI: 10.1016/j.ajpath.2021.09.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 09/08/2021] [Accepted: 09/22/2021] [Indexed: 01/03/2023]
Abstract
Chronic gut inflammation such as inflammatory bowel disease is believed to be associated with neurodegenerative diseases in humans. However, the direct evidence for and the underlying mechanism of this brain-gut interaction remain elusive. In this study, manganese-enhanced magnetic resonance imaging was used to assess functional brain activity from awake and freely moving mice with chronic colitis. Manganese ion uptake (indicative of Ca2+ influx into neuronal cells) and accumulation were reduced in the hippocampus of chronic colitis mice compared with control mice. Long-term memory declined and neuroinflammatory signals, including IL-1β production and activation of caspase-1, caspase-11, and gasdermin, were induced. High-mobility group box 1 (HMGB1) levels were elevated both in the serum and in the hippocampus; however, lipopolysaccharide (LPS) levels remained at low levels without significant changes in these samples. The blood-brain barrier permeability was increased in chronic colitis mice. In the presence of LPS, HMGB1 treatment induced the activation of caspase-11 and gasdermin in the mouse microglial cell line SIM-A9. These findings suggest that HMGB1 released from the inflamed intestine may move to the brain through the blood circulatory system; in conjunction with a low level of endogenous LPS, elevated HMGB1 can subsequently activate caspase-mediated inflammatory responses in the brain.
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Affiliation(s)
- Jonathon Mitchell
- Department of Biological Sciences, Oakland University, Rochester, Michigan
| | - Su Jin Kim
- Department of Biological Sciences, Oakland University, Rochester, Michigan; College of Pharmacy, Pusan National University, Busan, Republic of Korea
| | - Cody Howe
- Department of Biological Sciences, Oakland University, Rochester, Michigan
| | - Seulah Lee
- College of Pharmacy, Pusan National University, Busan, Republic of Korea
| | - Ji Yun Her
- College of Pharmacy, Pusan National University, Busan, Republic of Korea
| | - Marisa Patel
- Department of Biological Sciences, Oakland University, Rochester, Michigan
| | - Gayoung Kim
- Department of Biological Sciences, Oakland University, Rochester, Michigan
| | - Jaewon Lee
- College of Pharmacy, Pusan National University, Busan, Republic of Korea
| | - Eunok Im
- College of Pharmacy, Pusan National University, Busan, Republic of Korea.
| | - Sang Hoon Rhee
- Department of Biological Sciences, Oakland University, Rochester, Michigan.
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23
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Li Y, Li H, Xie Y, Chen S, Qin R, Dong H, Yu Y, Wang J, Qian X, Qin W. An Integrated Strategy for Mass Spectrometry-Based Multiomics Analysis of Single Cells. Anal Chem 2021; 93:14059-14067. [PMID: 34643370 DOI: 10.1021/acs.analchem.0c05209] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Single-cell-based genomics and transcriptomics analysis have revealed substantial cellular heterogeneity among seemingly identical cells. Knowledge of the cellular heterogeneity at multiomics levels is vital for a better understanding of tumor metastasis and drug resistance, stem cell differentiation, and embryonic development. However, unlike genomics and transcriptomics studies, single-cell characterization of metabolites, proteins, and post-translational modifications at the omics level remains challenging due to the lack of amplification methods and the wide diversity of these biomolecules. Therefore, new tools that are capable of investigating these unamplifiable "omes" from the same single cells are in high demand. In this work, a microwell chip was prepared and the internal surface was modified for hydrophilic interaction liquid chromatography-based tandem extraction of metabolites and proteins and subsequent protein digestion. Next, direct electrospray ionization mass spectrometry was adopted for single-cell metabolome identification, and a data-independent acquisition-mass spectrometry approach was established for simultaneous proteome profiling and phosphoproteome analysis without phosphopeptide enrichment. This integrated strategy resulted in 132 putatively annotated compounds, more than 1200 proteins, and the first large-scale phosphorylation data set from single-cell analysis. Application of this strategy in chemical perturbation studies provides a multiomics view of cellular changes, demonstrating its capability for more comprehensive investigation of cellular heterogeneity.
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Affiliation(s)
- Yuanyuan Li
- Research Center for Analytical Sciences, College of Sciences, Northeastern University, Shenyang 110819, P. R. China
| | - Hang Li
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, P. R. China
| | - Yuping Xie
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, P. R. China
| | - Shuo Chen
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, P. R. China
| | - Ritian Qin
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, P. R. China
| | - Hangyan Dong
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, P. R. China
| | - Yongliang Yu
- Research Center for Analytical Sciences, College of Sciences, Northeastern University, Shenyang 110819, P. R. China
| | - Jianhua Wang
- Research Center for Analytical Sciences, College of Sciences, Northeastern University, Shenyang 110819, P. R. China
| | - Xiaohong Qian
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, P. R. China
| | - Weijie Qin
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, P. R. China.,College of Basic Medicine, Anhui Medical University, Hefei 230032, P. R. China
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24
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Giner MP, Christen S, Bartova S, Makarov MV, Migaud ME, Canto C, Moco S. A Method to Monitor the NAD + Metabolome-From Mechanistic to Clinical Applications. Int J Mol Sci 2021; 22:10598. [PMID: 34638936 PMCID: PMC8508997 DOI: 10.3390/ijms221910598] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 01/07/2023] Open
Abstract
Nicotinamide adenine dinucleotide (NAD+) and its reduced form (NADH) are coenzymes employed in hundreds of metabolic reactions. NAD+ also serves as a substrate for enzymes such as sirtuins, poly(ADP-ribose) polymerases (PARPs) and ADP-ribosyl cyclases. Given the pivotal role of NAD(H) in health and disease, studying NAD+ metabolism has become essential to monitor genetic- and/or drug-induced perturbations related to metabolic status and diseases (such as ageing, cancer or obesity), and its possible therapies. Here, we present a strategy based on liquid chromatography-tandem mass spectrometry (LC-MS/MS), for the analysis of the NAD+ metabolome in biological samples. In this method, hydrophilic interaction chromatography (HILIC) was used to separate a total of 18 metabolites belonging to pathways leading to NAD+ biosynthesis, including precursors, intermediates and catabolites. As redox cofactors are known for their instability, a sample preparation procedure was developed to handle a variety of biological matrices: cell models, rodent tissues and biofluids, as well as human biofluids (urine, plasma, serum, whole blood). For clinical applications, quantitative LC-MS/MS for a subset of metabolites was demonstrated for the analysis of the human whole blood of nine volunteers. Using this developed workflow, our methodology allows studying NAD+ biology from mechanistic to clinical applications.
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Affiliation(s)
- Maria Pilar Giner
- Nestle Research, EPFL Innovation Park, H, 1015 Lausanne, Switzerland; (M.P.G.); (S.C.); (S.B.); (C.C.)
| | - Stefan Christen
- Nestle Research, EPFL Innovation Park, H, 1015 Lausanne, Switzerland; (M.P.G.); (S.C.); (S.B.); (C.C.)
| | - Simona Bartova
- Nestle Research, EPFL Innovation Park, H, 1015 Lausanne, Switzerland; (M.P.G.); (S.C.); (S.B.); (C.C.)
| | - Mikhail V. Makarov
- Mitchell Cancer Institute, University of South Alabama, 1660 Springhill Avenue, Mobile, AL 36604, USA; (M.V.M.); (M.E.M.)
- Olon Ricerca Bioscience, 7528 Auburn Road, Concord, OH 44077, USA
| | - Marie E. Migaud
- Mitchell Cancer Institute, University of South Alabama, 1660 Springhill Avenue, Mobile, AL 36604, USA; (M.V.M.); (M.E.M.)
| | - Carles Canto
- Nestle Research, EPFL Innovation Park, H, 1015 Lausanne, Switzerland; (M.P.G.); (S.C.); (S.B.); (C.C.)
| | - Sofia Moco
- Nestle Research, EPFL Innovation Park, H, 1015 Lausanne, Switzerland; (M.P.G.); (S.C.); (S.B.); (C.C.)
- Division of Molecular and Computational Toxicology, Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute for Molecular and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
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25
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Singh Y, Trautwein C, Fendel R, Krickeberg N, Berezhnoy G, Bissinger R, Ossowski S, Salker MS, Casadei N, Riess O. SARS-CoV-2 infection paralyzes cytotoxic and metabolic functions of the immune cells. Heliyon 2021; 7:e07147. [PMID: 34075347 PMCID: PMC8159709 DOI: 10.1016/j.heliyon.2021.e07147] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 03/10/2021] [Accepted: 05/24/2021] [Indexed: 12/29/2022] Open
Abstract
The SARS-CoV-2 virus is the causative agent of the global COVID-19 infectious disease outbreak, which can lead to acute respiratory distress syndrome (ARDS). However, it is still unclear how the virus interferes with immune cell and metabolic functions in the human body. In this study, we investigated the immune response in acute or convalescent COVID-19 patients. We characterized the peripheral blood mononuclear cells (PBMCs) using flow cytometry and found that CD8+ T cells were significantly subsided in moderate COVID-19 and convalescent patients. Furthermore, characterization of CD8+ T cells suggested that convalescent patients have significantly diminished expression of both perforin and granzyme A. Using 1H-NMR spectroscopy, we characterized the metabolic status of their autologous PBMCs. We found that fructose, lactate and taurine levels were elevated in infected (mild and moderate) patients compared with control and convalescent patients. Glucose, glutamate, formate and acetate levels were attenuated in COVID-19 (mild and moderate) patients. In summary, our report suggests that SARS-CoV-2 infection leads to disrupted CD8+ T cytotoxic functions and changes the overall metabolic functions of immune cells.
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Affiliation(s)
- Yogesh Singh
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Calwerstrasse 7, 72076, Tübingen, Germany
- NGS Competence Center Tübingen (NCCT), University of Tübingen, Calwerstrasse 7, 72076 Tübingen, Germany
- Research Institute of Women’s Health, University of Tübingen, Calwerstrasse 7/6, 72076, Tübingen, Germany
| | - Christoph Trautwein
- Werner Siemens Imaging Center, University of Tübingen, Röntgenweg 13, 72076, Tübingen, Germany
| | - Rolf Fendel
- Institute of Tropical Medicine, University Hospital of Tübingen, Wilhelmstrasse 27, 72076, Tübingen, Germany
| | - Naomi Krickeberg
- Institute of Tropical Medicine, University Hospital of Tübingen, Wilhelmstrasse 27, 72076, Tübingen, Germany
| | - Georgy Berezhnoy
- Werner Siemens Imaging Center, University of Tübingen, Röntgenweg 13, 72076, Tübingen, Germany
| | - Rosi Bissinger
- Department of Internal Medicine, Division of Endocrinology, Diabetology and Nephrology, University Hospital of Tübingen, Germany
| | - Stephan Ossowski
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Calwerstrasse 7, 72076, Tübingen, Germany
- NGS Competence Center Tübingen (NCCT), University of Tübingen, Calwerstrasse 7, 72076 Tübingen, Germany
| | - Madhuri S. Salker
- Research Institute of Women’s Health, University of Tübingen, Calwerstrasse 7/6, 72076, Tübingen, Germany
| | - Nicolas Casadei
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Calwerstrasse 7, 72076, Tübingen, Germany
- NGS Competence Center Tübingen (NCCT), University of Tübingen, Calwerstrasse 7, 72076 Tübingen, Germany
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Calwerstrasse 7, 72076, Tübingen, Germany
- NGS Competence Center Tübingen (NCCT), University of Tübingen, Calwerstrasse 7, 72076 Tübingen, Germany
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26
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Coulton JB, Edwards JL. Capillary flow-based sample preparation system for metabolomic analysis of mammalian cells in suspension. Anal Bioanal Chem 2021; 413:2493-2501. [PMID: 33665672 DOI: 10.1007/s00216-021-03204-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/16/2020] [Accepted: 01/27/2021] [Indexed: 11/25/2022]
Abstract
Sample preparation methodology is critical to obtaining reliable data for studying endogenous metabolites. Dependable preparation techniques require separation of cells from culture media, quenching of enzymatic activity, and extraction of metabolites from the cells. Presented here is a simple, rapid, semi-automated metabolomic sample preparation technique for 20 μL samples of RAW 264.7 cells suspended in culture media. This method uses online filter-assisted electroporation-based cell lysis and chilled organic solvent extraction to prepare metabolomic samples from cells in suspension in 2 min. Experiments using an isotopically labeled adenosine triphosphate internal standard were carried out to ensure enzymatic quenching by monitoring the ratio of labeled adenosine diphosphate to adenosine triphosphate. Cells were metabolically labeled with 13C-glucose concurrent with sampling aliquots of the cell suspension over the course of 24 h. Incorporation of 13C into organic acid metabolites such as itaconate Cell lysates was analyzed by nano-reverse-phase liquid chromatography-mass spectrometry (nano-RP-LC-MS), showing incorporation of 13C into organic acid metabolites such as itaconate.
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Affiliation(s)
- John B Coulton
- Department of Chemistry and Biochemistry, Saint Louis University, 3501 Laclede Ave., Saint Louis, MO, 63103, USA
| | - James L Edwards
- Department of Chemistry and Biochemistry, Saint Louis University, 3501 Laclede Ave., Saint Louis, MO, 63103, USA.
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27
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Zhu J, Zhang M, Guo J, Wu X, Wang S, Zhou Y, Liu H. Metabolite profiling of chondrosarcoma cells: A robust GC-MS method for the analysis of endogenous metabolome. J Chromatogr B Analyt Technol Biomed Life Sci 2021; 1169:122606. [PMID: 33684880 DOI: 10.1016/j.jchromb.2021.122606] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 02/14/2021] [Accepted: 02/16/2021] [Indexed: 11/28/2022]
Abstract
Chondrosarcoma is the 2nd most frequent bone sarcoma. In this study, the metabolic profiling of human chondrosarcoma SW-1353 cell line was investigated for the first time. To obtain more precise information about the metabolites from chondrosarcoma cells, pretreatment methods including washing steps/solvents, harvesting conditions, and extraction protocols for chondrosarcoma SW-1353 cells were evaluated in the context of metabolite profiling by GC-MS technique. In addition, a total of 32 representative metabolites (related to amino acid metabolism, TCA cycle, glycolysis, and fatty acid metabolism) were quantitatively determined. We found that a fast water rinse step before metabolic quenching, may reduce the contaminants and improve sensitivity. Trypsin/ethylene diamine tetraacetic acid treatment led to a large amount of metabolite leakage, which was not suitable for metabolomics research. Methanol was selected as a more suitable extraction solvent among four extraction approaches applied to SW-1353 cells. The final protocol can provide a simple, robust, and reproducible method to obtain precise information about the metabolites from chondrosarcoma cells, which is helpful to further understand the chondrosarcoma cell physiology and the mechanism of drug resistance in this disease, from the perspective of metabolomics.
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Affiliation(s)
- Jinfeng Zhu
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Mengmeng Zhang
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Jinxiu Guo
- Department of Pharmacy, the First Affiliated Hospital, Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Xueke Wu
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Shaomin Wang
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, Zhengzhou, Henan 450001, China.
| | - Yubing Zhou
- Department of Pharmacy, the First Affiliated Hospital, Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Hongmin Liu
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
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28
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Skolik RA, Solocinski J, Konkle ME, Chakraborty N, Menze MA. Global changes to HepG2 cell metabolism in response to galactose treatment. Am J Physiol Cell Physiol 2021; 320:C778-C793. [PMID: 33439775 DOI: 10.1152/ajpcell.00460.2020] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Tumor cell proliferation requires sufficient metabolic flux through the pentose phosphate pathway to meet the demand for biosynthetic precursors and to increase protection against oxidative stress which in turn requires an upregulation of substrate flow through glycolysis. This metabolic poise is often coupled with a shift in ATP production from mitochondrial OXPHOS to substrate-level phosphorylation. Despite major advances that were facilitated by using tumor-derived cell lines in research areas spanning from membrane to cytoskeletal biology, this distorted metabolic profile limits their impact as a model in physiology and toxicology. Substitution of glucose with galactose in the cell culture medium has been demonstrated to shift ATP production from substrate-level phosphorylation to mitochondrial OXPHOS. This increase in oxygen utilization is coupled to a global metabolic reorganization with potential impacts on macromolecule biosynthesis and cellular redox homeostasis, but a comprehensive analysis on the effects of sugar substitution in tumor-derived cells is still missing. To address this gap in knowledge we performed transcriptomic and metabolomic analyses on human hepatocellular carcinoma (HepG2) cells adapted to either glucose or galactose as the aldohexose source. We observed a shift toward oxidative metabolism in all primary metabolic pathways at both transcriptomic and metabolomic levels. We also observed a decrease in nicotinamide dinucleotide (NAD(P)) levels and subcellular NAD+-to-NADH ratios in cells cultured with galactose compared with glucose control cells. Our results suggest that galactose reduces both glycolytic and biosynthetic flux and restores a metabolic poise in HepG2 cells that closely reflects the metabolic state observed in primary hepatocytes.
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Affiliation(s)
- R A Skolik
- Department of Biology, University of Louisville, Louisville, Kentucky
| | - J Solocinski
- Department of Mechanical Engineering, University of Michigan, Dearborn, Michigan
| | - M E Konkle
- Department of Chemistry, Ball State University, Muncie, Indiana
| | - N Chakraborty
- Department of Mechanical Engineering, University of Michigan, Dearborn, Michigan
| | - M A Menze
- Department of Biology, University of Louisville, Louisville, Kentucky
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29
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Van Pelt DW, Kharaz YA, Sarver DC, Eckhardt LR, Dzierzawski JT, Disser NP, Piacentini AN, Comerford E, McDonagh B, Mendias CL. Multiomics analysis of the mdx/mTR mouse model of Duchenne muscular dystrophy. Connect Tissue Res 2021; 62:24-39. [PMID: 32664808 DOI: 10.1080/03008207.2020.1791103] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
PURPOSE/AIM Duchenne muscular dystrophy (DMD) is a progressive neuromuscular disease characterized by extensive muscle weakness. Patients with DMD lack a functional dystrophin protein, which transmits force and organizes the cytoskeleton of skeletal muscle. Multiomic studies have been proposed as a way to obtain novel insight about disease processes from preclinical models, and we used this approach to study pathological changes in dystrophic muscles. MATERIALS AND METHODS We evaluated hindlimb muscles of male mdx/mTR mice, which lack a functional dystrophin protein and have deficits in satellite cell abundance and proliferative capacity. Wild type (WT) C57BL/6 J mice served as controls. Muscle fiber contractility was measured, along with changes in the transcriptome using RNA sequencing, and in the proteome, metabolome, and lipidome using mass spectrometry. RESULTS While mdx/mTR mice displayed gross pathological changes and continued cycles of degeneration and regeneration, we found no differences in permeabilized fiber contractility between strains. However, there were numerous changes in the transcriptome and proteome related to protein balance, contractile elements, extracellular matrix, and metabolism. There was only a 53% agreement in fold-change data between the proteome and transcriptome. Numerous changes in markers of skeletal muscle metabolism were observed, with dystrophic muscles exhibiting elevated glycolytic metabolites such as 6-phosphoglycerate, fructose-6-phosphate and glucose-6-phosphate, fructose bisphosphate, phosphorylated hexoses, and phosphoenolpyruvate. CONCLUSIONS These findings highlight the utility of multiomics in studying muscle disease, and provide additional insight into the pathological changes in dystrophic muscles that might help to indirectly guide evidence-based nutritional or exercise prescription in DMD patients.
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Affiliation(s)
- Douglas W Van Pelt
- Department of Rehabilitation Sciences, College of Health Sciences, University of Kentucky , Lexington, KY, USA
| | - Yalda A Kharaz
- Department of Musculoskeletal Biology, Institute of Ageing and Chronic Disease, University of Liverpool , Liverpool, UK
| | - Dylan C Sarver
- Department of Orthopaedic Surgery, University of Michigan Medical School , Ann Arbor, MI, USA
| | - Logan R Eckhardt
- Department of Orthopaedic Surgery, University of Michigan Medical School , Ann Arbor, MI, USA
| | - Justin T Dzierzawski
- Department of Orthopaedic Surgery, University of Michigan Medical School , Ann Arbor, MI, USA
| | | | - Alex N Piacentini
- Research Institute, Hospital for Special Surgery , New York, NY, USA
| | - Eithne Comerford
- Department of Musculoskeletal Biology, Institute of Ageing and Chronic Disease, University of Liverpool , Liverpool, UK
| | - Brian McDonagh
- Department of Physiology, School of Medicine, National University of Ireland , Galway, Ireland
| | - Christopher L Mendias
- Department of Orthopaedic Surgery, University of Michigan Medical School , Ann Arbor, MI, USA.,Research Institute, Hospital for Special Surgery , New York, NY, USA.,Department of Physiology & Biophysics, Weill Cornell Medical College , New York, NY, USA
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30
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Roca M, Alcoriza MI, Garcia-Cañaveras JC, Lahoz A. Reviewing the metabolome coverage provided by LC-MS: Focus on sample preparation and chromatography-A tutorial. Anal Chim Acta 2020; 1147:38-55. [PMID: 33485584 DOI: 10.1016/j.aca.2020.12.025] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 12/11/2020] [Accepted: 12/14/2020] [Indexed: 12/11/2022]
Abstract
Metabolomics has become an invaluable tool for both studying metabolism and biomarker discovery. The great technical advances in analytical chemistry and bioinformatics have considerably increased the number of measurable metabolites, yet an important part of the human metabolome remains uncovered. Among the various MS hyphenated techniques available, LC-MS stands out as the most used. Here, we aimed to show the capabilities of LC-MS to uncover part of the metabolome and how to best proceed with sample preparation and LC to maximise metabolite detection. The analyses of various open metabolite databases served us to estimate the size of the already detected human metabolome, the expected metabolite composition of most used human biospecimens and which part of the metabolome can be detected when LC-MS is used. Based on an extensive review and on our experience, we have outlined standard procedures for LC-MS analysis of urine, cells, serum/plasma, tissues and faeces, to guide in the selection of the sample preparation method that best matches with one or more LC techniques in order to get the widest metabolome coverage. These standard procedures may be a useful tool to explore, at a glance, the wide spectrum of possibilities available, which can be a good starting point for most of the LC-MS metabolomic studies.
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Affiliation(s)
- Marta Roca
- Analytical Unit, Medical Research Institute-Hospital La Fe, Av. Fernando Abril Martorell 106, Valencia, 46026, Spain
| | - Maria Isabel Alcoriza
- Biomarkers and Precision Medicine Unit, Medical Research Institute-Hospital La Fe, Av. Fernando Abril Martorell 106, Valencia, 46026, Spain
| | - Juan Carlos Garcia-Cañaveras
- Biomarkers and Precision Medicine Unit, Medical Research Institute-Hospital La Fe, Av. Fernando Abril Martorell 106, Valencia, 46026, Spain
| | - Agustín Lahoz
- Analytical Unit, Medical Research Institute-Hospital La Fe, Av. Fernando Abril Martorell 106, Valencia, 46026, Spain; Biomarkers and Precision Medicine Unit, Medical Research Institute-Hospital La Fe, Av. Fernando Abril Martorell 106, Valencia, 46026, Spain.
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Balik K, Matulewicz K, Modrakowska P, Kozłowska J, Montane X, Tylkowski B, Bajek A. Advanced cell culture techniques for cancer research. PHYSICAL SCIENCES REVIEWS 2020. [DOI: 10.1515/psr-2019-0059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The incessant increase number of cancer cases, motivates scientists to constantly develop and search for new therapies. Along with the dynamic development of anti-cancer drugs and therapies, we are witnessing huge progress in the world of science - the development of personalized medicine. An inseparable element is also a very strong trend in the development of new in vitro animal models for chemotherapeutic research. Cell cultures are commonly undertaken by research models before animal testing. They are the basis for the development of new diagnostic and cancer treatments. It should be emphasized that basic research is a strong foundation for any therapy introduced. This chapter provides an overview of the modern cell culture techniques that are currently developing, which allow the introduction of modern models that reflect the organs and physiological system. Currently available cell culture methods are a key aspect of studying these interactions, however, a method that eliminates the limitations of standard methods is still being sought.
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Affiliation(s)
- Karolina Balik
- Department of Tissue Engineering Chair of Urology , Ludwik Rydygier Collegium Medicum in Bydgoszcz Nicolaus Copernicus University in Torun , Bydgoszcz , Poland
| | - Karolina Matulewicz
- Department of Tissue Engineering Chair of Urology , Ludwik Rydygier Collegium Medicum in Bydgoszcz Nicolaus Copernicus University in Torun , Bydgoszcz , Poland
| | - Paulina Modrakowska
- Department of Tissue Engineering Chair of Urology , Ludwik Rydygier Collegium Medicum in Bydgoszcz Nicolaus Copernicus University in Torun , Bydgoszcz , Poland
| | - Jolanta Kozłowska
- Department of Biological Pest Control and Organic Agriculture , Institute of Plant Protection, National Research Institute , Poznan , Poland
| | - Xavier Montane
- Department of Chemical Engineering , Universitat Rovira i Virgili , Tarragona , Spain
| | - Bartosz Tylkowski
- Chemical Technologies Unit , Eurecat, Centre Tecnològic de Catalunya , Tarragona , Spain
| | - Anna Bajek
- Department of Tissue Engineering Chair of Urology , Ludwik Rydygier Collegium Medicum in Bydgoszcz Nicolaus Copernicus University in Torun , Bydgoszcz , Poland
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Lopez R, Marzban B, Gao X, Lauinger E, Van den Bergh F, Whitesall SE, Converso-Baran K, Burant CF, Michele DE, Beard DA. Impaired Myocardial Energetics Causes Mechanical Dysfunction in Decompensated Failing Hearts. FUNCTION 2020; 1:zqaa018. [PMID: 33074265 PMCID: PMC7552914 DOI: 10.1093/function/zqaa018] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/11/2020] [Accepted: 09/21/2020] [Indexed: 01/06/2023] Open
Abstract
Cardiac mechanical function is supported by ATP hydrolysis, which provides the chemical-free energy to drive the molecular processes underlying cardiac pumping. Physiological rates of myocardial ATP consumption require the heart to resynthesize its entire ATP pool several times per minute. In the failing heart, cardiomyocyte metabolic dysfunction leads to a reduction in the capacity for ATP synthesis and associated free energy to drive cellular processes. Yet it remains unclear if and how metabolic/energetic dysfunction that occurs during heart failure affects mechanical function of the heart. We hypothesize that changes in phosphate metabolite concentrations (ATP, ADP, inorganic phosphate) that are associated with decompensation and failure have direct roles in impeding contractile function of the myocardium in heart failure, contributing to the whole-body phenotype. To test this hypothesis, a transverse aortic constriction (TAC) rat model of pressure overload, hypertrophy, and decompensation was used to assess relationships between metrics of whole-organ pump function and myocardial energetic state. A multiscale computational model of cardiac mechanoenergetic coupling was used to identify and quantify the contribution of metabolic dysfunction to observed mechanical dysfunction. Results show an overall reduction in capacity for oxidative ATP synthesis fueled by either fatty acid or carbohydrate substrates as well as a reduction in total levels of adenine nucleotides and creatine in myocardium from TAC animals compared to sham-operated controls. Changes in phosphate metabolite levels in the TAC rats are correlated with impaired mechanical function, consistent with the overall hypothesis. Furthermore, computational analysis of myocardial metabolism and contractile dynamics predicts that increased levels of inorganic phosphate in TAC compared to control animals kinetically impair the myosin ATPase crossbridge cycle in decompensated hypertrophy/heart failure.
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Affiliation(s)
- Rachel Lopez
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Bahador Marzban
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Xin Gao
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Ellen Lauinger
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Françoise Van den Bergh
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Steven E Whitesall
- Frankel Cardiovascular Center Physiology and Phenotyping Core, University of Michigan, Ann Arbor, MI, USA
| | - Kimber Converso-Baran
- Frankel Cardiovascular Center Physiology and Phenotyping Core, University of Michigan, Ann Arbor, MI, USA
| | - Charles F Burant
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA,Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Daniel E Michele
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA,Frankel Cardiovascular Center Physiology and Phenotyping Core, University of Michigan, Ann Arbor, MI, USA
| | - Daniel A Beard
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA,Address correspondence to D.A.B. (e-mail: )
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Rai SK, Bril F, Hatch HM, Xu Y, Shelton L, Kalavalapalli S, Click A, Lee D, Beecher C, Kirby A, Kong K, Trevino J, Jha A, Jatav S, Kriti K, Luthra S, Garrett TJ, Guingab-Cagmat J, Plant D, Bose P, Cusi K, Hromas RA, Tischler AS, Powers JF, Gupta P, Bibb J, Beuschlein F, Robledo M, Calsina B, Timmers H, Taieb D, Kroiss M, Richter S, Langton K, Eisenhofer G, Bergeron R, Pacak K, Tevosian SG, Ghayee HK. Targeting pheochromocytoma/paraganglioma with polyamine inhibitors. Metabolism 2020; 110:154297. [PMID: 32562798 PMCID: PMC7482423 DOI: 10.1016/j.metabol.2020.154297] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 06/12/2020] [Accepted: 06/17/2020] [Indexed: 12/15/2022]
Abstract
BACKGROUND Pheochromocytomas (PCCs) and paragangliomas (PGLs) are neuroendocrine tumors that are mostly benign. Metastatic disease does occur in about 10% of cases of PCC and up to 25% of PGL, and for these patients no effective therapies are available. Patients with mutations in the succinate dehydrogenase subunit B (SDHB) gene tend to have metastatic disease. We hypothesized that a down-regulation in the active succinate dehydrogenase B subunit should result in notable changes in cellular metabolic profile and could present a vulnerability point for successful pharmacological targeting. METHODS Metabolomic analysis was performed on human hPheo1 cells and shRNA SDHB knockdown hPheo1 (hPheo1 SDHB KD) cells. Additional analysis of 115 human fresh frozen samples was conducted. In vitro studies using N1,N11-diethylnorspermine (DENSPM) and N1,N12- diethylspermine (DESPM) treatments were carried out. DENSPM efficacy was assessed in human cell line derived mouse xenografts. RESULTS Components of the polyamine pathway were elevated in hPheo1 SDHB KD cells compared to wild-type cells. A similar observation was noted in SDHx PCC/PGLs tissues compared to their non-mutated counterparts. Specifically, spermidine, and spermine were significantly elevated in SDHx-mutated PCC/PGLs, with a similar trend in hPheo1 SDHB KD cells. Polyamine pathway inhibitors DENSPM and DESPM effectively inhibited growth of hPheo1 cells in vitro as well in mouse xenografts. CONCLUSIONS This study demonstrates overactive polyamine pathway in PCC/PGL with SDHB mutations. Treatment with polyamine pathway inhibitors significantly inhibited hPheo1 cell growth and led to growth suppression in xenograft mice treated with DENSPM. These studies strongly implicate the polyamine pathway in PCC/PGL pathophysiology and provide new foundation for exploring the role for polyamine analogue inhibitors in treating metastatic PCC/PGL. PRéCIS: Cell line metabolomics on hPheo1 cells and PCC/PGL tumor tissue indicate that the polyamine pathway is activated. Polyamine inhibitors in vitro and in vivo demonstrate that polyamine inhibitors are promising for malignant PCC/PGL treatment. However, further research is warranted.
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Affiliation(s)
- Sudhir Kumar Rai
- Department of Medicine, Division of Endocrinology, University of Florida, Gainesville, FL, USA
| | - Fernando Bril
- Department of Medicine, Division of Endocrinology, University of Florida and Malcom Randall VA Medical Center, Gainesville, FL, USA
| | - Heather M Hatch
- Department of Physiological Sciences, University of Florida, Gainesville, FL, USA
| | - Yiling Xu
- Department of Medicine, Division of Endocrinology, University of Florida, Gainesville, FL, USA
| | - Laura Shelton
- Scientific Project Development, Human Metabolome Technologies, Boston, MA, USA
| | - Srilaxmi Kalavalapalli
- Department of Medicine, Division of Endocrinology, University of Florida, Gainesville, FL, USA
| | - Arielle Click
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | | | - Austin Kirby
- Department of Medicine, University of Texas Health Science Center, San Antonio, TX, USA
| | - Kimi Kong
- Department of Medicine, University of Texas Health Science Center, San Antonio, TX, USA
| | - Jose Trevino
- Department of Surgery, University of Florida, Gainesville, FL, USA
| | | | | | | | | | - Timothy J Garrett
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, USA
| | - Joy Guingab-Cagmat
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, USA
| | - Daniel Plant
- Department of Physiological Sciences, University of Florida, Malcom Randall VA Medical Center, Gainesville, FL, USA
| | - Prodip Bose
- Department of Physiological Sciences, University of Florida, Malcom Randall VA Medical Center, Gainesville, FL, USA
| | - Kenneth Cusi
- Department of Medicine, Division of Endocrinology, University of Florida and Malcom Randall VA Medical Center, Gainesville, FL, USA
| | - Robert A Hromas
- Department of Medicine, University of Texas Health Science Center, San Antonio, TX, USA
| | - Arthur S Tischler
- Department of Pathology and Laboratory Medicine, Tufts Medical Center, Boston, MA, USA
| | - James F Powers
- Department of Pathology and Laboratory Medicine, Tufts Medical Center, Boston, MA, USA
| | - Priyanka Gupta
- Department of Surgery, University of Alabama, Birmingham, AL, USA
| | - James Bibb
- Department of Surgery, University of Alabama, Birmingham, AL, USA
| | - Felix Beuschlein
- Klinik für Endokrinologie, Diabetologie und Klinische Ernährung, UniversitätsSpital Zurich, Zurich, Switzerland
| | - Mercedes Robledo
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Center (CNIO), and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Bruna Calsina
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Center (CNIO), and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Henri Timmers
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | - David Taieb
- Department of Nuclear Medicine, La Timone University Hospital, European Center for Research in Medical Imaging, Aix Marseille Université, Marseille, France
| | - Matthias Kroiss
- Department of Internal Medicine, Division of Endocrinology and Diabetology, University Hospital Würzburg, University of Würzburg, Würzburg, Germany
| | - Susan Richter
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany
| | - Katharina Langton
- Department of Medicine III, University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany
| | - Graeme Eisenhofer
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany; Department of Medicine III, University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany; Division of Clinical Neurochemistry, Institute of Clinical Chemistry and Laboratory Medicine, and Department of Medicine, Faculty of Medicine, University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany
| | - Raymond Bergeron
- Department of Medicinal Chemistry, University of Florida, Gainesville, FL, USA
| | - Karel Pacak
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Sergei G Tevosian
- Department of Physiological Sciences, University of Florida, Gainesville, FL, USA.
| | - Hans K Ghayee
- Department of Medicine, Division of Endocrinology, University of Florida and Malcom Randall VA Medical Center, Gainesville, FL, USA.
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Kaiser L, Weinschrott H, Quint I, Blaess M, Csuk R, Jung M, Kohl M, Deigner HP. Metabolite Patterns in Human Myeloid Hematopoiesis Result from Lineage-Dependent Active Metabolic Pathways. Int J Mol Sci 2020; 21:ijms21176092. [PMID: 32847028 PMCID: PMC7504406 DOI: 10.3390/ijms21176092] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/18/2020] [Accepted: 08/21/2020] [Indexed: 12/18/2022] Open
Abstract
Assessment of hematotoxicity from environmental or xenobiotic compounds is of notable interest and is frequently assessed via the colony forming unit (CFU) assay. Identification of the mode of action of single compounds is of further interest, as this often enables transfer of results across different tissues and compounds. Metabolomics displays one promising approach for such identification, nevertheless, suitability with current protocols is restricted. Here, we combined a hematopoietic stem and progenitor cell (HSPC) expansion approach with distinct lineage differentiations, resulting in formation of erythrocytes, dendritic cells and neutrophils. We examined the unique combination of pathway activity in glycolysis, glutaminolysis, polyamine synthesis, fatty acid oxidation and synthesis, as well as glycerophospholipid and sphingolipid metabolism. We further assessed their interconnections and essentialness for each lineage formation. By this, we provide further insights into active metabolic pathways during the differentiation of HSPC into different lineages, enabling profound understanding of possible metabolic changes in each lineage caused by exogenous compounds.
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Affiliation(s)
- Lars Kaiser
- Institute of Precision Medicine, Medical and Life Sciences Faculty, Furtwangen University, Jakob-Kienzle-Straße 17, 78054 Villingen-Schwenningen, Germany; (L.K.); (H.W.); (I.Q.); (M.B.); (M.K.)
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstraße 25, 79104 Freiburg i. Br., Germany;
| | - Helga Weinschrott
- Institute of Precision Medicine, Medical and Life Sciences Faculty, Furtwangen University, Jakob-Kienzle-Straße 17, 78054 Villingen-Schwenningen, Germany; (L.K.); (H.W.); (I.Q.); (M.B.); (M.K.)
| | - Isabel Quint
- Institute of Precision Medicine, Medical and Life Sciences Faculty, Furtwangen University, Jakob-Kienzle-Straße 17, 78054 Villingen-Schwenningen, Germany; (L.K.); (H.W.); (I.Q.); (M.B.); (M.K.)
| | - Markus Blaess
- Institute of Precision Medicine, Medical and Life Sciences Faculty, Furtwangen University, Jakob-Kienzle-Straße 17, 78054 Villingen-Schwenningen, Germany; (L.K.); (H.W.); (I.Q.); (M.B.); (M.K.)
| | - René Csuk
- Organic Chemistry, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 2, 06120 Halle (Saale), Germany;
| | - Manfred Jung
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstraße 25, 79104 Freiburg i. Br., Germany;
- CIBSS—Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Matthias Kohl
- Institute of Precision Medicine, Medical and Life Sciences Faculty, Furtwangen University, Jakob-Kienzle-Straße 17, 78054 Villingen-Schwenningen, Germany; (L.K.); (H.W.); (I.Q.); (M.B.); (M.K.)
| | - Hans-Peter Deigner
- Institute of Precision Medicine, Medical and Life Sciences Faculty, Furtwangen University, Jakob-Kienzle-Straße 17, 78054 Villingen-Schwenningen, Germany; (L.K.); (H.W.); (I.Q.); (M.B.); (M.K.)
- Fraunhofer Institute IZI, Leipzig, EXIM Department, Schillingallee 68, 18057 Rostock, Germany
- Associated member of Tuebingen University, Faculty of Science, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Correspondence: ; Tel.: +49-7720-307-4232
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Pyridoxamine-phosphate oxidases and pyridoxamine-phosphate oxidase-related proteins catalyze the oxidation of 6-NAD(P)H to NAD(P). Biochem J 2020; 476:3033-3052. [PMID: 31657440 DOI: 10.1042/bcj20190602] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 09/30/2019] [Accepted: 10/03/2019] [Indexed: 11/17/2022]
Abstract
6-NADH and 6-NADPH are strong inhibitors of several dehydrogenases that may form spontaneously from NAD(P)H. They are known to be oxidized to NAD(P)+ by mammalian renalase, an FAD-linked enzyme mainly present in heart and kidney, and by related bacterial enzymes. We partially purified an enzyme oxidizing 6-NADPH from rat liver, and, surprisingly, identified it as pyridoxamine-phosphate oxidase (PNPO). This was confirmed by the finding that recombinant mouse PNPO oxidized 6-NADH and 6-NADPH with catalytic efficiencies comparable to those observed with pyridoxine- and pyridoxamine-5'-phosphate. PNPOs from Escherichia coli, Saccharomyces cerevisiae and Arabidopsis thaliana also displayed 6-NAD(P)H oxidase activity, indicating that this 'side-activity' is conserved. Remarkably, 'pyridoxamine-phosphate oxidase-related proteins' (PNPO-RP) from Nostoc punctiforme, A. thaliana and the yeast S. cerevisiae (Ygr017w) were not detectably active on pyridox(am)ine-5'-P, but oxidized 6-NADH, 6-NADPH and 2-NADH suggesting that this may be their main catalytic function. Their specificity profiles were therefore similar to that of renalase. Inactivation of renalase and of PNPO in mammalian cells and of Ygr017w in yeasts led to the accumulation of a reduced form of 6-NADH, tentatively identified as 4,5,6-NADH3, which can also be produced in vitro by reduction of 6-NADH by glyceraldehyde-3-phosphate dehydrogenase or glucose-6-phosphate dehydrogenase. As 4,5,6-NADH3 is not a substrate for renalase, PNPO or PNPO-RP, its accumulation presumably reflects the block in the oxidation of 6-NADH. These findings indicate that two different classes of enzymes using either FAD (renalase) or FMN (PNPOs and PNPO-RPs) as a cofactor play an as yet unsuspected role in removing damaged forms of NAD(P).
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Mili M, Panthu B, Madec AM, Berger MA, Rautureau GJP, Elena-Herrmann B. Fast and ergonomic extraction of adherent mammalian cells for NMR-based metabolomics studies. Anal Bioanal Chem 2020; 412:5453-5463. [PMID: 32556564 DOI: 10.1007/s00216-020-02764-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 05/08/2020] [Accepted: 06/08/2020] [Indexed: 11/29/2022]
Abstract
Cellular metabolomics has become key to elucidate mechanistic aspects in various fields such as cancerology or pharmacology, and is rapidly becoming a standard phenotyping tool accessible to the broad biological community. Acquisition of reliable spectroscopic datasets, such as nuclear magnetic resonance (NMR) spectra, to characterize biological systems depends on the elaboration of robust methods for cellular metabolites extraction. Previous studies have addressed many issues raised by these protocols, however with little pondering on ergonomic and practical aspects of the methods that impact their scalability, reproducibility and hence their suitability to high-throughput studies or their use by non-metabolomics experts. Here, we optimize a fast and ergonomic protocol for extraction of metabolites from adherent mammalian cells for NMR metabolomics studies. The proposed extraction protocol, including cell washing, metabolism quenching and actual extraction of intracellular metabolites, was first optimized on HeLa cells. Efficiency of the protocol, in its globality and for the different individual steps, was assessed by NMR quantification of 27 metabolites from cellular extracts. We show that a single PBS wash provides a seemly compromise between contamination from growth medium and leakage of intracellular metabolites. In HeLa cells, extraction using pure methanol, without cell scraping, recovered a higher amount of intracellular metabolites than the reference methanol/water/chloroform method with cell scraping, with yields varying across metabolite classes. Optimized and reference protocols were further tested on eight cell lines of miscellaneous nature, and inter-operator reproducibility was demonstrated. Our results stress the need for tailored extraction protocols and show that fast protocols minimizing time-consuming steps, without compromising extraction yields, are suitable for high-throughput metabolomics studies. Graphical abstract.
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Affiliation(s)
- Manhal Mili
- Institut des Sciences Analytiques UMR 5280, CRMN FRE 2034, Univ Lyon, CNRS, Université Claude Bernard Lyon 1, ENS de Lyon, 5 rue de la Doua, 69100, Villeurbanne, France
| | - Baptiste Panthu
- CarMeN laboratory, Univ Lyon, INSERM, INRA, INSA, Université Claude Bernard Lyon1, 69121, Oullins, France
| | - Anne-Marie Madec
- CarMeN laboratory, Univ Lyon, INSERM, INRA, INSA, Université Claude Bernard Lyon1, 69121, Oullins, France
| | - Marie-Agnès Berger
- CarMeN laboratory, Univ Lyon, INSERM, INRA, INSA, Université Claude Bernard Lyon1, 69121, Oullins, France
| | - Gilles J P Rautureau
- Institut des Sciences Analytiques UMR 5280, CRMN FRE 2034, Univ Lyon, CNRS, Université Claude Bernard Lyon 1, ENS de Lyon, 5 rue de la Doua, 69100, Villeurbanne, France
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Ulmer CZ, Koelmel JP, Jones CM, Garrett TJ, Aristizabal-Henao JJ, Vesper HW, Bowden JA. A Review of Efforts to Improve Lipid Stability during Sample Preparation and Standardization Efforts to Ensure Accuracy in the Reporting of Lipid Measurements. Lipids 2020; 56:3-16. [PMID: 32519378 DOI: 10.1002/lipd.12263] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 05/03/2020] [Accepted: 05/19/2020] [Indexed: 11/07/2022]
Abstract
Lipidomics is a rapidly growing field, fueled by developments in analytical instrumentation and bioinformatics. To date, most researchers and industries have employed their own lipidomics workflows without a consensus on best practices. Without a community-wide consensus on best practices for the prevention of lipid degradation and transformations through sample collection and analysis, it is difficult to assess the quality of lipidomics data and hence trust results. Clinical studies often rely on samples being stored for weeks or months until they are analyzed, but inappropriate sampling techniques, storage temperatures, and analytical protocols can result in the degradation of complex lipids and the generation of oxidized or hydrolyzed metabolite artifacts. While best practices for lipid stability are sample dependent, it is generally recommended that strategies during sample preparation capable of quenching enzymatic activity and preventing oxidation should be considered. In addition, after sample preparation, lipid extracts should be stored in organic solvents with antioxidants at -20 °C or lower in an airtight container without exposure to light or oxygen. This will reduce or eliminate sublimation, and chemically and physically induced molecular transformations such as oxidation, enzymatic transformation, and photon/heat-induced degradation. This review explores the available literature on lipid stability, with a particular focus on human health and/or clinical lipidomic applications. Specifically, this includes a description of known mechanisms of lipid degradation, strategies, and considerations for lipid storage, as well as current efforts for standardization and quality insurance of protocols.
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Affiliation(s)
- Candice Z Ulmer
- Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, 4770 Buford Hwy NE, MS F25, Atlanta, GA, 30341, USA
| | - Jeremy P Koelmel
- Department of Environmental Health Sciences, Yale School of Medicine, Yale University, 60 College Street, Room 510, New Haven, CT, 06520, USA
| | - Christina M Jones
- Chemical Sciences Division, Organic Chemical Metrology Group, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD, 20899, USA
| | - Timothy J Garrett
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Juan J Aristizabal-Henao
- Center for Environmental and Human Toxicology & Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Hubert W Vesper
- Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, 4770 Buford Hwy NE, MS F25, Atlanta, GA, 30341, USA
| | - John A Bowden
- Center for Environmental and Human Toxicology & Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32611, USA
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Li YY, Douillet C, Huang M, Beck R, Sumner SJ, Styblo M. Exposure to inorganic arsenic and its methylated metabolites alters metabolomics profiles in INS-1 832/13 insulinoma cells and isolated pancreatic islets. Arch Toxicol 2020; 94:1955-1972. [PMID: 32277266 PMCID: PMC8711643 DOI: 10.1007/s00204-020-02729-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 03/26/2020] [Indexed: 12/17/2022]
Abstract
Inorganic arsenic (iAs) is an environmental diabetogen, but mechanisms underlying its diabetogenic effects are poorly understood. Exposures to arsenite (iAsIII) and its methylated metabolites, methylarsonite (MAsIII) and dimethylarsinite (DMAsIII), have been shown to inhibit glucose-stimulated insulin secretion (GSIS) in pancreatic β-cells and isolated pancreatic islets. GSIS is regulated by complex mechanisms. Increase in ATP production through metabolism of glucose and other substrates is the ultimate trigger for GSIS in β-cells. In the present study, we used metabolomics to identify metabolites and pathways perturbed in cultured INS-1 832/13 rat insulinoma cells and isolated murine pancreatic islets by exposures to iAsIII, MAsIII and DMAsIII. We found that the exposures perturbed multiple metabolites, which were enriched primarily in the pathways of amino acid, carbohydrate, phospholipid and carnitine metabolism. However, the effects of arsenicals in INS-1 832/13 cells differed from those in the islets and were exposure specific with very few overlaps between the three arsenicals. In INS-1 832/13 cells, all three arsenicals decreased succinate, a metabolite of Krebs cycle, which provides substrates for ATP synthesis in mitochondria. Acetylcarnitine was decreased consistently by exposures to arsenicals in both the cells and the islets. Acetylcarnitine is usually found in equilibrium with acetyl-CoA, which is the central metabolite in the catabolism of macronutrients and the key substrate for Krebs cycle. It is also thought to play an antioxidant function in mitochondria. Thus, while each of the three trivalent arsenicals perturbed specific metabolic pathways, which may or may not be associated with GSIS, all three arsenicals appeared to impair mechanisms that support ATP production or antioxidant defense in mitochondria. These results suggest that impaired ATP production and/or mitochondrial dysfunction caused by oxidative stress may be the mechanisms underlying the inhibition of GSIS in β-cells exposed to trivalent arsenicals.
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Affiliation(s)
- Yuan-Yuan Li
- Department of Nutrition, Nutrition Research Institute, CB# 74612, University of North Carolina at Chapel Hill School of Public Health, Chapel Hill, NC, 27599-7461, USA
- Department of Nutrition, CB# 74612, University of North Carolina Gillings School of Global Public Health, Chapel Hill, NC, 27599-7461, USA
| | - Christelle Douillet
- Department of Nutrition, CB# 74612, University of North Carolina Gillings School of Global Public Health, Chapel Hill, NC, 27599-7461, USA
| | - Madelyn Huang
- Curriculum in Toxicology and Environmental Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA
- National Toxicology Program, National Institute of Environmental Health Science, Research Triangle Park, NC, USA
| | - Rowan Beck
- Curriculum in Genetics and Molecular Biology, School of Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Susan Jenkins Sumner
- Department of Nutrition, Nutrition Research Institute, CB# 74612, University of North Carolina at Chapel Hill School of Public Health, Chapel Hill, NC, 27599-7461, USA.
- Department of Nutrition, CB# 74612, University of North Carolina Gillings School of Global Public Health, Chapel Hill, NC, 27599-7461, USA.
| | - Miroslav Styblo
- Department of Nutrition, CB# 74612, University of North Carolina Gillings School of Global Public Health, Chapel Hill, NC, 27599-7461, USA.
- Curriculum in Toxicology and Environmental Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA.
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Iqbal MA, Chattopadhyay S, Siddiqui FA, Ur Rehman A, Siddiqui S, Prakasam G, Khan A, Sultana S, Bamezai RN. Silibinin induces metabolic crisis in triple-negative breast cancer cells by modulating EGFR-MYC-TXNIP axis: potential therapeutic implications. FEBS J 2020; 288:471-485. [PMID: 32356386 DOI: 10.1111/febs.15353] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 03/04/2020] [Accepted: 04/28/2020] [Indexed: 12/14/2022]
Abstract
Triple-negative breast cancer (TNBC) is an aggressive form of breast cancer with limited treatment modalities and poor prognosis. Metabolic reprogramming in cancer is considered a hallmark of therapeutic relevance. Here, we report disruption of metabolic reprogramming in TNBC cells by silibinin via modulation of EGFR-MYC-TXNIP signaling. Metabolic assays combined with LC-MS-based metabolomics revealed inhibition of glycolysis and other key biosynthetic pathways by silibinin, to induce metabolic catastrophe in TNBC cells. Silibinin-induced metabolic suppression resulted in decreased cell biomass, proliferation, and stem cell properties. Mechanistically, we identify EGFR-MYC-TXNIP as an important regulator of TNBC metabolism and mediator of inhibitory effects of silibinin. Highlighting the clinical relevance of our observations, the analysis of METABRIC dataset revealed deregulation of EGFR-MYC-TXNIP axis in TNBC and association of EGFRhigh -MYChigh -TXNIPlow signature with aggressive glycolytic metabolism and poor disease-specific and metastasis-free survival. Importantly, combination treatment of silibinin or 2-deoxyglucose (glycolysis inhibitor) with paclitaxel synergistically inhibited proliferation of TNBC cells. Together, our results highlight the importance of EGFR-MYC-TXNIP axis in regulating TNBC metabolism, demonstrate the anti-TNBC activity of silibinin, and argue in favor of targeting metabolic vulnerabilities of TNBC, at least in combination with mainstay chemotherapeutic drugs, to effectively treat TNBC patients.
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Affiliation(s)
- Mohammad Askandar Iqbal
- Department of Biotechnology, Faculty of Natural Sciences, Jamia Millia Islamia (A Central University), New Delhi, India
| | - Shilpi Chattopadhyay
- Department of Toxicology, School of Chemical and Life Sciences, Jamia Hamdard (Deemed University), New Delhi, India
| | - Farid Ahmad Siddiqui
- Department of Biotechnology, Faculty of Natural Sciences, Jamia Millia Islamia (A Central University), New Delhi, India.,Turku Centre for Biotechnology, University of Turku and Abo Akademi, Biocity, Finland
| | - Asad Ur Rehman
- Department of Biotechnology, Faculty of Natural Sciences, Jamia Millia Islamia (A Central University), New Delhi, India.,Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, India
| | - Shumaila Siddiqui
- Department of Biotechnology, Faculty of Natural Sciences, Jamia Millia Islamia (A Central University), New Delhi, India
| | - Gopinath Prakasam
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India.,Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Asifa Khan
- Department of Biotechnology, Faculty of Natural Sciences, Jamia Millia Islamia (A Central University), New Delhi, India.,Department of Biosciences, Faculty of Natural Sciences, Jamia Millia Islamia (A Central University), New Delhi, India
| | - Sarwat Sultana
- Department of Toxicology, School of Chemical and Life Sciences, Jamia Hamdard (Deemed University), New Delhi, India
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40
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Luo Y, Geng N, Zhang B, Chen J, Zhang H. Effects of harvesting and extraction methods on metabolite recovery from adherently growing mammalian cells. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:2491-2498. [PMID: 32930239 DOI: 10.1039/c9ay02753j] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
With the wide application of cell metabolomics in many research areas, there is a need to develop an effective procedure for adherent mammalian cell metabolomics that allows for accurate determination of intracellular metabolite levels and easy comparison between multiple studies of a similar application. Here we aimed to compare the efficiencies of different cell harvesting methods and metabolite extraction methods in sample preparation procedures, and to provide a cell sample processing protocol which focuses on maximizing metabolite recovery ranging from polar to lipidic ones. A systematical evaluation of 4 cell harvesting methods and 4 extraction methods was conducted based on human hepatoma HepG2 cells. The impact of different methods on the recoveries of 11 different categories of metabolites was further investigated. The water disruption sample harvesting method provided superior performance to the other 3 harvesting methods, trypsinization, scraping in phosphate buffered saline, and direct solvent scraping, with respect to the recoveries of polar metabolites and lipids. Among the 4 extraction methods, the novel two-phase solvent system extraction method with both methyl tert-butyl ether (MTBE) and 75% 9 : 1 methanol : chloroform showed an absolute advantage with high extraction efficiency for global metabolomics. We showed a metabolite-specific impact of the harvesting method and extraction method on metabolite concentrations. The water disruption sample collection combined with novel two-phase solvent system extraction enabled simultaneous profiling of lipids and metabolites with mixed polarity for sample preparation. Our approach may open up new perspectives toward large-scale comprehensive metabolomic analyses of adherent mammalian cell samples.
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Affiliation(s)
- Yun Luo
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ningbo Geng
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China.
| | - Baoqin Zhang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China.
| | - Jiping Chen
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China.
| | - Haijun Zhang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China.
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Abstract
Untargeted metabolomics aims to quantify the complete set of metabolites within a biological system, most commonly by liquid chromatography/mass spectrometry (LC/MS). Since nearly the inception of the field, compound identification has been widely recognized as the rate-limiting step of the experimental workflow. In spite of exponential increases in the size of metabolomic databases, which now contain experimental MS/MS spectra for over a half a million reference compounds, chemical structures still cannot be confidently assigned to many signals in a typical LC/MS dataset. The purpose of this Perspective is to consider why identification rates continue to be low in untargeted metabolomics. One rationalization is that many naturally occurring metabolites detected by LC/MS are true "novel" compounds that have yet to be incorporated into metabolomic databases. An alternative possibility, however, is that research data do not provide database matches because of informatic artifacts, chemical contaminants, and signal redundancies. Increasing evidence suggests that, for at least some sample types, many unidentifiable signals in untargeted metabolomics result from the latter rather than new compounds originating from the specimen being measured. The implications of these observations on chemical discovery in untargeted metabolomics are discussed.
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Affiliation(s)
- Miriam Sindelar
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Gary J. Patti
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
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42
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Talarek JR, Piacentini AN, Konja AC, Wada S, Swanson JB, Nussenzweig SC, Dines JS, Rodeo SA, Mendias CL. The MRL/MpJ Mouse Strain Is Not Protected From Muscle Atrophy and Weakness After Rotator Cuff Tear. J Orthop Res 2020; 38:811-822. [PMID: 31696955 PMCID: PMC7071998 DOI: 10.1002/jor.24516] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 11/04/2019] [Indexed: 02/04/2023]
Abstract
Chronic rotator cuff tears are a common source of shoulder pain and disability. Patients with rotator cuff tears often have substantial weakness, fibrosis, and fat accumulation, which limit successful surgical repair and postoperative rehabilitation. The Murphy Roths Large (MRL) strain of mice have demonstrated superior healing and protection against pathological changes in several disease and injury conditions. We tested the hypothesis that, compared with the commonly used C57Bl/6 (B6) strain, MRL mice would have less muscle fiber atrophy and fat accumulation, and be protected against the loss in force production that occurs after cuff tear. Adult male B6 and MRL mice were subjected to a rotator cuff tear, and changes in muscle fiber contractility and histology were measured. RNA sequencing and shotgun metabolomics and lipidomics were also performed. The muscles were harvested one month after tear. B6 and MRL mice had a 40% reduction in relative muscle force production after rotator cuff tear. RNA sequencing identified an increase in fibrosis-associated genes and a reduction in mitochondrial metabolism genes. The markers of glycolytic metabolism increased in B6 mice, while MRL mice appeared to increase amino acid metabolism after tear. There was an accumulation of lipid after injury, although there was a divergent response between B6 and MRL mice in the types of lipid species that accrued. There were strain-specific differences between the transcriptome, metabolome, and lipidome of B6 and MRL mice, but these differences did not protect MRL mice from weakness and pathological changes after rotator cuff tear. © 2019 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 38:811-822, 2020.
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Affiliation(s)
| | | | | | | | | | | | - Joshua S Dines
- Hospital for Special Surgery, New York, NY
- Department of Orthopaedic Surgery, Weill Cornell Medical College, New York, NY
| | - Scott A Rodeo
- Hospital for Special Surgery, New York, NY
- Department of Orthopaedic Surgery, Weill Cornell Medical College, New York, NY
| | - Christopher L Mendias
- Hospital for Special Surgery, New York, NY
- Department of Orthopaedic Surgery, Weill Cornell Medical College, New York, NY
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY
- Corresponding Author: Christopher Mendias, PhD, Hospital for Special Surgery, 535 E 70th St, New York, NY 10021, USA, +1 212-606-1785 office, +1 212-249-2373 fax,
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Nagao-Kitamoto H, Leslie JL, Kitamoto S, Jin C, Thomsson KA, Gillilland MG, Kuffa P, Goto Y, Jenq RR, Ishii C, Hirayama A, Seekatz AM, Martens EC, Eaton KA, Kao JY, Fukuda S, Higgins PDR, Karlsson NG, Young VB, Kamada N. Interleukin-22-mediated host glycosylation prevents Clostridioides difficile infection by modulating the metabolic activity of the gut microbiota. Nat Med 2020; 26:608-617. [PMID: 32066975 PMCID: PMC7160049 DOI: 10.1038/s41591-020-0764-0] [Citation(s) in RCA: 128] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 01/13/2020] [Indexed: 12/14/2022]
Abstract
The involvement of host immunity in the gut microbiota-mediated colonization resistance to Clostridioides difficile infection (CDI) is incompletely understood. Here, we show that interleukin (IL)-22, induced by colonization of the gut microbiota, is crucial for the prevention of CDI in human microbiota-associated (HMA) mice. IL-22 signaling in HMA mice regulated host glycosylation, which enabled the growth of succinate-consuming bacteria Phascolarctobacterium spp. within the gut microbiome. Phascolarctobacterium reduced the availability of luminal succinate, a crucial metabolite for the growth of C. difficile, and therefore prevented the growth of C. difficile. IL-22-mediated host N-glycosylation is likely impaired in patients with ulcerative colitis (UC) and renders UC-HMA mice more susceptible to CDI. Transplantation of healthy human-derived microbiota or Phascolarctobacterium reduced luminal succinate levels and restored colonization resistance in UC-HMA mice. IL-22-mediated host glycosylation thus fosters the growth of commensal bacteria that compete with C. difficile for the nutritional niche.
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Affiliation(s)
- Hiroko Nagao-Kitamoto
- Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Jhansi L Leslie
- Division of Infectious Disease, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
- The University of Virginia, Washington, VA, USA
| | - Sho Kitamoto
- Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Chunsheng Jin
- Institute of Biomedicine, Department of Medical Biochemistry, University of Gothenburg, Gothenburg, Sweden
| | - Kristina A Thomsson
- Institute of Biomedicine, Department of Medical Biochemistry, University of Gothenburg, Gothenburg, Sweden
| | - Merritt G Gillilland
- Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Peter Kuffa
- Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Yoshiyuki Goto
- Division of Molecular Immunology, Medical Mycology Research Center, Chiba University, Chiba, Japan
- Division of Mucosal Symbiosis, International Research and Development Center for Mucosal Vaccines, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- AMED-PRIME, Japan Agency for Medical Research and Development, Tokyo, Japan
| | - Robert R Jenq
- Department of Genomic Medicine, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston TX, USA
| | - Chiharu Ishii
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Akiyoshi Hirayama
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Anna M Seekatz
- Division of Infectious Disease, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Clemson University, Columbia, SC, USA
| | - Eric C Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Kathryn A Eaton
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - John Y Kao
- Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Shinji Fukuda
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Intestinal Microbiota Project, Kanagawa Institute of Industrial Science and Technology, Ebina, Japan
- Transborder Medical Research Center, University of Tsukuba, Tsukuba, Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Japan
| | - Peter D R Higgins
- Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Niclas G Karlsson
- Institute of Biomedicine, Department of Medical Biochemistry, University of Gothenburg, Gothenburg, Sweden
| | - Vincent B Young
- Division of Infectious Disease, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Nobuhiko Kamada
- Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI, USA.
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Abstract
Ex-situ perfusion (ESP) is a promising method in preserving vascularized composite tissue allografts (VCAs) with potential to widen donor procurement to larger geographic areas. To optimize the method of preservation, we developed a small animal model to conduct biomolecular investigations. Twenty rat hind limbs (18.2 ± 1.3 g) were procured and connected to our custom-made ESP system. Perfusion pressure and flow parameters were measured with hourly blood gas analysis under near-normothermic (30-35˚C) conditions. Perfusate was prepared with swine hemoglobin (6-9 g/dL) and STEEN Solution. After 6 hours of perfusion, gastrocnemius muscles were evaluated for their histology and metabolomic profiling. Following 3 sets of experiments, perfusion was maintained at an average flow of 0.9 ± 0.24 mL/min and resulted in lactate levels of 3.78 ± 1.02 mmol/L. Metabolomic analysis revealed maintained cellular energy stores (total adenylates perfusion 0.698 ± 0.052 versus baseline 0.685 ± 0.091 umols/ug, p = 0.831), and histologic analysis revealed no evidence of barotrauma or myodegeneration. Rat hind limbs were viable after 6 hours of ESP on our miniaturized ESP system. This study is the first to document the ex-situ hind limb perfusion platform on a rodent model. These experimental findings have potential to guide future research to extend the viable duration of VCA preservation.
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Important Considerations for Sample Collection in Metabolomics Studies with a Special Focus on Applications to Liver Functions. Metabolites 2020; 10:metabo10030104. [PMID: 32178364 PMCID: PMC7142637 DOI: 10.3390/metabo10030104] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 03/05/2020] [Accepted: 03/07/2020] [Indexed: 12/16/2022] Open
Abstract
Metabolomics has found numerous applications in the study of liver metabolism in health and disease. Metabolomics studies can be conducted in a variety of biological matrices ranging from easily accessible biofluids such as urine, blood or feces, to organs, tissues or even cells. Sample collection and storage are critical steps for which standard operating procedures must be followed. Inappropriate sample collection or storage can indeed result in high variability, interferences with instrumentation or degradation of metabolites. In this review, we will first highlight important general factors that should be considered when planning sample collection in the study design of metabolomic studies, such as nutritional status and circadian rhythm. Then, we will discuss in more detail the specific procedures that have been described for optimal pre-analytical handling of the most commonly used matrices (urine, blood, feces, tissues and cells).
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46
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Metabolomics Analysis of Nutrient Metabolism in β-Cells. J Mol Biol 2020; 432:1429-1445. [DOI: 10.1016/j.jmb.2019.07.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 07/03/2019] [Accepted: 07/11/2019] [Indexed: 01/05/2023]
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Elkin ER, Bridges D, Harris SM, Loch-Caruso RK. Exposure to Trichloroethylene Metabolite S-(1,2-Dichlorovinyl)-L-cysteine Causes Compensatory Changes to Macronutrient Utilization and Energy Metabolism in Placental HTR-8/SVneo Cells. Chem Res Toxicol 2020; 33:1339-1355. [PMID: 31951115 PMCID: PMC7299793 DOI: 10.1021/acs.chemrestox.9b00356] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
Trichloroethylene
(TCE) is a widespread environmental contaminant
following decades of use as an industrial solvent, improper disposal,
and remediation challenges. Consequently, TCE exposure continues to
constitute a risk to human health. Despite epidemiological evidence
associating exposure with adverse birth outcomes, the effects of TCE
and its metabolite S-(1, 2-dichlorovinyl)-L-cysteine
(DCVC) on the placenta remain undetermined. Flexible and efficient
macronutrient and energy metabolism pathway utilization is essential
for placental cell physiological adaptability. Because DCVC is known
to compromise cellular energy status and disrupt energy metabolism
in renal proximal tubular cells, this study investigated the effects
of DCVC on cellular energy status and energy metabolism pathways in
placental cells. Human extravillous trophoblast cells, HTR-8/SVneo,
were exposed to 5–20 μM DCVC for 6 or 12 h. After establishing
concentration and exposure duration thresholds for DCVC-induced cytotoxicity,
targeted metabolomics was used to evaluate overall energy status and
metabolite concentrations from energy metabolism pathways. The data
revealed glucose metabolism perturbations including a time-dependent
accumulation of glucose-6-phosphate+frutose-6-phosphate (G6P+F6P)
as well as independent shunting of glucose intermediates that diminished
with time, with modest energy status decline but in the absence of
significant changes in ATP concentrations. Furthermore, metabolic
profiling suggested that DCVC stimulated compensatory utilization
of glycerol, lipid, and amino acid metabolism to provide intermediate
substrates entering downstream in the glycolytic pathway or the tricarboxylic
acid cycle. Lastly, amino acid deprivation increased susceptibility
to DCVC-induced cytotoxicity. Taken together, these results suggest
that DCVC caused metabolic perturbations necessitating adaptations
in macronutrient and energy metabolism pathway utilization to maintain
adequate ATP levels.
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Affiliation(s)
- Elana R Elkin
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, Michigan 48109-2029, United States
| | - Dave Bridges
- Department of Nutritional Sciences, University of Michigan, Ann Arbor, Michigan 48109-2029, United States
| | - Sean M Harris
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, Michigan 48109-2029, United States
| | - Rita Karen Loch-Caruso
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, Michigan 48109-2029, United States
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Pezzatti J, Boccard J, Codesido S, Gagnebin Y, Joshi A, Picard D, González-Ruiz V, Rudaz S. Implementation of liquid chromatography-high resolution mass spectrometry methods for untargeted metabolomic analyses of biological samples: A tutorial. Anal Chim Acta 2020; 1105:28-44. [PMID: 32138924 DOI: 10.1016/j.aca.2019.12.062] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 11/18/2019] [Accepted: 12/20/2019] [Indexed: 12/23/2022]
Abstract
Untargeted metabolomics is now widely recognized as a useful tool for exploring metabolic changes taking place in biological systems under different conditions. By its nature, this is a highly interdisciplinary field of research, and mastering all of the steps comprised in the pipeline can be a challenging task, especially for those researchers new to the topic. In this tutorial, we aim to provide an overview of the most widely adopted methods of performing LC-HRMS-based untargeted metabolomics of biological samples. A detailed protocol is provided in the Supplementary Information for rapidly implementing a basic screening workflow in a laboratory setting. This tutorial covers experimental design, sample preparation and analysis, signal processing and data treatment, and, finally, data analysis and its biological interpretation. Each section is accompanied by up-to-date literature to guide readers through the preparation and optimization of such a workflow, as well as practical information for avoiding or fixing some of the most frequently encountered pitfalls.
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Affiliation(s)
- Julian Pezzatti
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Rue Michel-Servet 1, 1211, Geneva, Switzerland
| | - Julien Boccard
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Rue Michel-Servet 1, 1211, Geneva, Switzerland; Swiss Centre for Applied Human Toxicology (SCAHT), Switzerland
| | - Santiago Codesido
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Rue Michel-Servet 1, 1211, Geneva, Switzerland
| | - Yoric Gagnebin
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Rue Michel-Servet 1, 1211, Geneva, Switzerland
| | - Abhinav Joshi
- Department of Cell Biology, Faculty of Science, University of Geneva, 1211, Geneva, Switzerland
| | - Didier Picard
- Department of Cell Biology, Faculty of Science, University of Geneva, 1211, Geneva, Switzerland
| | - Víctor González-Ruiz
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Rue Michel-Servet 1, 1211, Geneva, Switzerland; Swiss Centre for Applied Human Toxicology (SCAHT), Switzerland
| | - Serge Rudaz
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Rue Michel-Servet 1, 1211, Geneva, Switzerland; Swiss Centre for Applied Human Toxicology (SCAHT), Switzerland.
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49
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Modified Protocol of Harvesting, Extraction, and Normalization Approaches for Gas Chromatography Mass Spectrometry-Based Metabolomics Analysis of Adherent Cells Grown Under High Fetal Calf Serum Conditions. Metabolites 2019; 10:metabo10010002. [PMID: 31861324 PMCID: PMC7023238 DOI: 10.3390/metabo10010002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 12/09/2019] [Accepted: 12/11/2019] [Indexed: 12/22/2022] Open
Abstract
A gas chromatography mass spectrometry (GC-MS) metabolomics protocol was modified for quenching, harvesting, and extraction of metabolites from adherent cells grown under high (20%) fetal calf serum conditions. The reproducibility of using either 50% or 80% methanol for quenching of cells was compared for sample harvest. To investigate the efficiency and reproducibility of intracellular metabolite extraction, different volumes and ratios of chloroform were tested. Additionally, we compared the use of total protein amount versus cell mass as normalization parameters. We demonstrate that the method involving 50% methanol as quenching buffer followed by an extraction step using an equal ratio of methanol:chloroform:water (1:1:1, v/v/v) followed by the collection of 6 mL polar phase for GC-MS measurement was superior to the other methods tested. Especially for large sample sets, its comparative ease of measurement leads us to recommend normalization to protein amount for the investigation of intracellular metabolites of adherent human cells grown under high (or standard) fetal calf serum conditions. To avoid bias, care should be taken beforehand to ensure that the ratio of total protein to cell number are consistent among the groups tested. For this reason, it may not be suitable where culture conditions or cell types have very different protein outputs (e.g., hypoxia vs. normoxia). The full modified protocol is available in the Supplementary Materials.
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Li J, Wang Q, Zheng Y, Zhou P, Xu X, Liu X, Zhao L, Liu H. Development of a mass spectrometry-based pseudotargeted metabolomics strategy to analyze hormone-stimulated gastric cancer cells. J Pharm Biomed Anal 2019; 180:113041. [PMID: 31855724 DOI: 10.1016/j.jpba.2019.113041] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 12/07/2019] [Accepted: 12/09/2019] [Indexed: 01/13/2023]
Abstract
Gastric cancer (GC) is the third most common cause of cancer death worldwide, and the incidence of GC is higher in males than females. To investigate the gastric cellular response to hormone therapy, we developed a cell pseudotargeted metabolomics method based on liquid chromatography-hybrid triple quadrupole linear ion trap mass spectrometry (LC-QTRAP MS). Chromatographic separation, sample analysis and metabolite extraction were optimized in an integrated manner. The established pseudotargeted method, which combined nontargeted and targeted analyses, exhibited high selectivity, good repeatability and wide metabolome coverage. The method was then applied to discover differential metabolites from hormone-stimulated gastric cancer cells compared with the controls for the first time. The results demonstrated that hormone had subtle but phenotypically important alterations in nucleotide metabolism, amino acid metabolism, glycolysis, tricarboxylic acid (TCA) cycle, aminoacyl-tRNA biosynthesis and so on, which indicate that the developed method is a powerful tool for effective screening of endogenous polar metabolites in cell samples.
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Affiliation(s)
- Juan Li
- School of Pharmaceutical Sciences, Institute of Drug Discovery & Development, Zhengzhou University, Zhengzhou, 450001, PR China; Key Laboratory of Advanced Drug Preparation Technologies (Zhengzhou University), Ministry of Education, PR China; Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, PR China; Key Laboratory of Henan Province for Drug Quality and Evaluation, PR China
| | - Qingli Wang
- School of Pharmaceutical Sciences, Institute of Drug Discovery & Development, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Yichao Zheng
- School of Pharmaceutical Sciences, Institute of Drug Discovery & Development, Zhengzhou University, Zhengzhou, 450001, PR China; Key Laboratory of Advanced Drug Preparation Technologies (Zhengzhou University), Ministry of Education, PR China; Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, PR China; Key Laboratory of Henan Province for Drug Quality and Evaluation, PR China
| | - Piao Zhou
- School of Pharmaceutical Sciences, Institute of Drug Discovery & Development, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Xia Xu
- School of Pharmaceutical Sciences, Institute of Drug Discovery & Development, Zhengzhou University, Zhengzhou, 450001, PR China; Key Laboratory of Advanced Drug Preparation Technologies (Zhengzhou University), Ministry of Education, PR China; Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, PR China; Key Laboratory of Henan Province for Drug Quality and Evaluation, PR China
| | - Xueqi Liu
- School of Pharmaceutical Sciences, Institute of Drug Discovery & Development, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Longfei Zhao
- School of Pharmaceutical Sciences, Institute of Drug Discovery & Development, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Hongmin Liu
- School of Pharmaceutical Sciences, Institute of Drug Discovery & Development, Zhengzhou University, Zhengzhou, 450001, PR China; Key Laboratory of Advanced Drug Preparation Technologies (Zhengzhou University), Ministry of Education, PR China; Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, PR China; Key Laboratory of Henan Province for Drug Quality and Evaluation, PR China.
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