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Queathem ED, Moazzami Z, Stagg DB, Nelson AB, Fulghum K, Hayir A, Seay A, Gillingham JR, d'Avignon DA, Han X, Ruan HB, Crawford PA, Puchalska P. Ketogenesis supports hepatic polyunsaturated fatty acid homeostasis via fatty acid elongation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.09.602593. [PMID: 39026753 PMCID: PMC11257565 DOI: 10.1101/2024.07.09.602593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Therapeutic interventions targeting hepatic lipid metabolism in metabolic dysfunction-associated steatotic liver disease (MASLD) and steatohepatitis (MASH) remain elusive. Using mass spectrometry-based stable isotope tracing and shotgun lipidomics, we established a novel link between ketogenesis and MASLD pathophysiology. Our findings show that mouse liver and primary hepatocytes consume ketone bodies to support fatty acid (FA) biosynthesis via both de novo lipogenesis (DNL) and FA elongation. Analysis of 13 C-labeled FAs in hepatocytes lacking mitochondrial D-β-hydroxybutyrate dehydrogenase (BDH1) revealed a partial reliance on mitochondrial conversion of D-βOHB to acetoacetate (AcAc) for cytoplasmic DNL contribution, whereas FA elongation from ketone bodies was fully dependent on cytosolic acetoacetyl-CoA synthetase (AACS). Ketone bodies were essential for polyunsaturated FA (PUFA) homeostasis in hepatocytes, as loss of AACS diminished both free and esterified PUFAs. Ketogenic insufficiency depleted liver PUFAs and increased triacylglycerols, mimicking human MASLD, suggesting that ketogenesis supports PUFA homeostasis, and may mitigate MASLD-MASH progression in humans.
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Elnwasany A, Ewida HA, Menendez-Montes I, Mizerska M, Fu X, Kim CW, Horton JD, Burgess SC, Rothermel BA, Szweda PA, Szweda LI. Reciprocal regulation of cardiac β-oxidation and pyruvate dehydrogenase by insulin. J Biol Chem 2024; 300:107412. [PMID: 38796064 PMCID: PMC11231754 DOI: 10.1016/j.jbc.2024.107412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 05/09/2024] [Accepted: 05/17/2024] [Indexed: 05/28/2024] Open
Abstract
The heart alters the rate and relative oxidation of fatty acids and glucose based on availability and energetic demand. Insulin plays a crucial role in this process diminishing fatty acid and increasing glucose oxidation when glucose availability increases. Loss of insulin sensitivity and metabolic flexibility can result in cardiovascular disease. It is therefore important to identify mechanisms by which insulin regulates substrate utilization in the heart. Mitochondrial pyruvate dehydrogenase (PDH) is the key regulatory site for the oxidation of glucose for ATP production. Nevertheless, the impact of insulin on PDH activity has not been fully delineated, particularly in the heart. We sought in vivo evidence that insulin stimulates cardiac PDH and that this process is driven by the inhibition of fatty acid oxidation. Mice injected with insulin exhibited dephosphorylation and activation of cardiac PDH. This was accompanied by an increase in the content of malonyl-CoA, an inhibitor of carnitine palmitoyltransferase 1 (CPT1), and, thus, mitochondrial import of fatty acids. Administration of the CPT1 inhibitor oxfenicine was sufficient to activate PDH. Malonyl-CoA is produced by acetyl-CoA carboxylase (ACC). Pharmacologic inhibition or knockout of cardiac ACC diminished insulin-dependent production of malonyl-CoA and activation of PDH. Finally, circulating insulin and cardiac glucose utilization exhibit daily rhythms reflective of nutritional status. We demonstrate that time-of-day-dependent changes in PDH activity are mediated, in part, by ACC-dependent production of malonyl-CoA. Thus, by inhibiting fatty acid oxidation, insulin reciprocally activates PDH. These studies identify potential molecular targets to promote cardiac glucose oxidation and treat heart disease.
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Affiliation(s)
- Abdallah Elnwasany
- Division of Cardiology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Heba A Ewida
- Department of Pharmaceutical Sciences, Jerry H. Hodge School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas, USA; Faculty of Pharmacy, Future University in Egypt (FUE), Cairo, Egypt
| | - Ivan Menendez-Montes
- Division of Cardiology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Monika Mizerska
- Department of Pharmacology, Center for Human Nutrition, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Xiaorong Fu
- Department of Pharmacology, Center for Human Nutrition, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Chai-Wan Kim
- Departments of Internal Medicine and Molecular Genetics, Center for Human Nutrition, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Jay D Horton
- Departments of Internal Medicine and Molecular Genetics, Center for Human Nutrition, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Shawn C Burgess
- Department of Pharmacology, Center for Human Nutrition, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Beverly A Rothermel
- Division of Cardiology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Pamela A Szweda
- Division of Cardiology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Luke I Szweda
- Division of Cardiology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA.
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Eller MM, Zuberi AR, Fu X, Burgess SC, Lutz CM, Bailey RM. Valine and Inflammation Drive Epilepsy in a Mouse Model of ECHS1 Deficiency. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.13.598697. [PMID: 38915588 PMCID: PMC11195255 DOI: 10.1101/2024.06.13.598697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
ECHS1 Deficiency (ECHS1D) is a rare and devastating pediatric disease that currently has no defined treatments. This disorder results from missense loss-of-function mutations in the ECHS1 gene that result in severe developmental delays, encephalopathy, hypotonia, and early death. ECHS1 enzymatic activity is necessary for the beta-oxidation of fatty acids and the oxidation of branched-chain amino acids within the inner mitochondrial matrix. The pathogenesis of disease remains unknown, however it is hypothesized that disease is driven by an accumulation of toxic metabolites from impaired valine oxidation. To expand our knowledge on disease mechanisms, a novel mouse model of ECHS1D was generated that possesses a disease-associated knock-in (KI) allele and a knock-out (KO) allele. To investigate the behavioral phenotype, a battery of testing was performed at multiple time points, which included assessments of learning, motor function, endurance, sensory responses, and anxiety. Neurological abnormalities were assessed using wireless telemetry EEG recordings, pentylenetetrazol (PTZ) seizure induction, and immunohistochemistry. Metabolic perturbations were measured within the liver, serum, and brain using mass spectrometry and magnetic resonance spectroscopy. To test disease mechanisms, mice were subjected to disease pathway stressors and then survival, body weight gain, and epilepsy were assessed. Mice containing KI/KI or KI/KO alleles were viable with normal development and survival, and the presence of KI and KO alleles resulted in a significant reduction in ECHS1 protein. ECHS1D mice displayed reduced exercise capacity and pain sensation. EEG analysis revealed increased slow wave power that was associated with perturbations in sleep. ECHS1D mice had significantly increased epileptiform EEG discharges, and were sensitive to seizure induction, which resulted in death of 60% of ECHS1D mice. Under basal conditions, brain structure was grossly normal, although histological analysis revealed increased microglial activation in aged ECHS1D mice. Increased dietary valine only affected ECHS1D mice, which significantly exacerbated seizure susceptibility and resulted in death. Lastly, acute inflammatory challenge drove regression and early lethality in ECHS1D mice. In conclusion, we developed a novel model of ECHS1D that may be used to further knowledge on disease mechanisms and to develop therapeutics. Our data suggests altered metabolic signaling and inflammation may contribute to epilepsy in ECHS1D, and these alterations may be attributed to impaired valine metabolism.
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Affiliation(s)
- Meghan M. Eller
- Graduate School of Biomedical Sciences, University of Texas Southwestern Medical School, 5323 Harry Hines Blvd, Dallas, TX 75235
- Center for Alzheimer’s and Neurodegenerative Diseases, University of Texas Southwestern Medical School, 5323 Harry Hines Blvd, Dallas, TX 75235
| | - Aamir R. Zuberi
- The Jackson Laboratory Center for Precision Genetics, The Jackson Laboratory, Bar Harbor, ME 04609
| | - Xiaorong Fu
- Center for Human Nutrition, University of Texas Southwestern Medical School, 5323 Harry Hines Blvd, Dallas, TX 75235
| | - Shawn C. Burgess
- Center for Human Nutrition, University of Texas Southwestern Medical School, 5323 Harry Hines Blvd, Dallas, TX 75235
- Department of Pharmacology, University of Texas Southwestern Medical School, 5323 Harry Hines Blvd, Dallas, TX 75235
| | - Cathleen M. Lutz
- The Jackson Laboratory Center for Precision Genetics, The Jackson Laboratory, Bar Harbor, ME 04609
| | - Rachel M. Bailey
- Center for Alzheimer’s and Neurodegenerative Diseases, University of Texas Southwestern Medical School, 5323 Harry Hines Blvd, Dallas, TX 75235
- Department of Pediatrics, University of Texas Southwestern Medical School, 5323 Harry Hines Blvd, Dallas, TX 75235
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Deja S, Fletcher JA, Kim CW, Kucejova B, Fu X, Mizerska M, Villegas M, Pudelko-Malik N, Browder N, Inigo-Vollmer M, Menezes CJ, Mishra P, Berglund ED, Browning JD, Thyfault JP, Young JD, Horton JD, Burgess SC. Hepatic malonyl-CoA synthesis restrains gluconeogenesis by suppressing fat oxidation, pyruvate carboxylation, and amino acid availability. Cell Metab 2024; 36:1088-1104.e12. [PMID: 38447582 PMCID: PMC11081827 DOI: 10.1016/j.cmet.2024.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 12/10/2023] [Accepted: 02/09/2024] [Indexed: 03/08/2024]
Abstract
Acetyl-CoA carboxylase (ACC) promotes prandial liver metabolism by producing malonyl-CoA, a substrate for de novo lipogenesis and an inhibitor of CPT-1-mediated fat oxidation. We report that inhibition of ACC also produces unexpected secondary effects on metabolism. Liver-specific double ACC1/2 knockout (LDKO) or pharmacologic inhibition of ACC increased anaplerosis, tricarboxylic acid (TCA) cycle intermediates, and gluconeogenesis by activating hepatic CPT-1 and pyruvate carboxylase flux in the fed state. Fasting should have marginalized the role of ACC, but LDKO mice maintained elevated TCA cycle intermediates and preserved glycemia during fasting. These effects were accompanied by a compensatory induction of proteolysis and increased amino acid supply for gluconeogenesis, which was offset by increased protein synthesis during feeding. Such adaptations may be related to Nrf2 activity, which was induced by ACC inhibition and correlated with fasting amino acids. The findings reveal unexpected roles for malonyl-CoA synthesis in liver and provide insight into the broader effects of pharmacologic ACC inhibition.
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Affiliation(s)
- Stanislaw Deja
- Center for Human Nutrition, University of Texas Southwestern Medical Center, Dallas, TX 75390-9046, USA; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390-9046, USA
| | - Justin A Fletcher
- Center for Human Nutrition, University of Texas Southwestern Medical Center, Dallas, TX 75390-9046, USA; Department of Clinical Nutrition, University of Texas Southwestern Medical Center, Dallas, TX 75390-9046, USA
| | - Chai-Wan Kim
- Center for Human Nutrition, University of Texas Southwestern Medical Center, Dallas, TX 75390-9046, USA
| | - Blanka Kucejova
- Center for Human Nutrition, University of Texas Southwestern Medical Center, Dallas, TX 75390-9046, USA
| | - Xiaorong Fu
- Center for Human Nutrition, University of Texas Southwestern Medical Center, Dallas, TX 75390-9046, USA; Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX 75390-9046, USA
| | - Monika Mizerska
- Center for Human Nutrition, University of Texas Southwestern Medical Center, Dallas, TX 75390-9046, USA
| | - Morgan Villegas
- Center for Human Nutrition, University of Texas Southwestern Medical Center, Dallas, TX 75390-9046, USA
| | - Natalia Pudelko-Malik
- Center for Human Nutrition, University of Texas Southwestern Medical Center, Dallas, TX 75390-9046, USA; Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wroclaw, Poland
| | - Nicholas Browder
- Center for Human Nutrition, University of Texas Southwestern Medical Center, Dallas, TX 75390-9046, USA
| | - Melissa Inigo-Vollmer
- Center for Human Nutrition, University of Texas Southwestern Medical Center, Dallas, TX 75390-9046, USA
| | - Cameron J Menezes
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390-9046, USA
| | - Prashant Mishra
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390-9046, USA
| | - Eric D Berglund
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390-9046, USA
| | - Jeffrey D Browning
- Department of Clinical Nutrition, University of Texas Southwestern Medical Center, Dallas, TX 75390-9046, USA; Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390-9046, USA
| | - John P Thyfault
- Departments of Cell Biology and Physiology, Internal Medicine and KU Diabetes Institute, Kansas Medical Center, Kansas City, KS, USA
| | - Jamey D Young
- Department of Chemical and Biomolecular Engineering, Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37235, USA
| | - Jay D Horton
- Center for Human Nutrition, University of Texas Southwestern Medical Center, Dallas, TX 75390-9046, USA; Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390-9046, USA; Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX 75390-9046, USA.
| | - Shawn C Burgess
- Center for Human Nutrition, University of Texas Southwestern Medical Center, Dallas, TX 75390-9046, USA; Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9046, USA.
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Li X, Liu Z, Li Z, Xiong X, Zhang X, Yang C, Zhao L, Zhao R. A simple, rapid and sensitive HILIC LC-MS/MS method for simultaneous determination of 16 purine metabolites in plasma and urine. Talanta 2024; 267:125171. [PMID: 37696233 DOI: 10.1016/j.talanta.2023.125171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 08/23/2023] [Accepted: 09/05/2023] [Indexed: 09/13/2023]
Abstract
Purine intermediates play important roles in physiological function and participate in the kidney disorders, while a targeted quantification of the metabolic alterations in the purine metabolism in acute kidney injury (AKI) individuals has not been conducted. In the study, a novel, rapid and sensitive LC-MS method for simultaneous quantification of 16 purine metabolites was developed using hydrophilic interaction separation mode in human plasma and urine. The developed method was validated by using charcoal-stripped plasma and urine as blank matrix. The results showed that the method was good linear (R2 > 0.99) and the lower limit of quantification (LLOQ) ranged from 0.833 ng/mL to 800 ng/mL. The recovery and matrix effect were repeatable and stable. The intraday precision ranged from 0.7% to 12.7%, while the inter-day precision ranged from 1.6% to 18.5%. Most analytes were stable in the autosampler and could subject three freeze-thaw cycles. The method provided a wider coverage of purine metabolites and completed good separation of interfering compounds of nucleosides, deoxynucleosides and their corresponding nucleobases without derivatization, which was time-saving and labor-saving for the large-scale analysis. Furthermore, the method was successfully applied to plasma and urine samples of hospitalized patients without and with AKI. The results showed certain purine intermediates were up-regulated in plasma and down-regulated in urine of AKI inpatients, indicating that AKI stress may associate with inflammatory responses. The novel method can facilitate the quantitative analysis of purine metabolites in biological fluids, and exhibit great prospects in providing more information on the pathogenesis of AKI.
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Affiliation(s)
- Xiaona Li
- Department of Pharmacy, Peking University Third Hospital, Beijing, 100191, China; Therapeutic Drug Monitoring and Clinical Toxicology Center of Peking University, Beijing, 100191, China
| | - Zhini Liu
- Department of Pharmacy, Peking University Third Hospital, Beijing, 100191, China; School of Basic Medical and Clinical Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu Province 211198, China
| | - Zhuo Li
- Department of Pharmacy, Peking University Third Hospital, Beijing, 100191, China; School of Basic Medical and Clinical Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu Province 211198, China
| | - Xin Xiong
- Department of Pharmacy, Peking University Third Hospital, Beijing, 100191, China; Therapeutic Drug Monitoring and Clinical Toxicology Center of Peking University, Beijing, 100191, China
| | - Xianhua Zhang
- Department of Pharmacy, Peking University Third Hospital, Beijing, 100191, China; Therapeutic Drug Monitoring and Clinical Toxicology Center of Peking University, Beijing, 100191, China
| | - Changqing Yang
- School of Basic Medical and Clinical Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu Province 211198, China.
| | - Libo Zhao
- Department of Pharmacy, Peking University Third Hospital, Beijing, 100191, China; Therapeutic Drug Monitoring and Clinical Toxicology Center of Peking University, Beijing, 100191, China.
| | - Rongsheng Zhao
- Department of Pharmacy, Peking University Third Hospital, Beijing, 100191, China; Therapeutic Drug Monitoring and Clinical Toxicology Center of Peking University, Beijing, 100191, China.
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Nestor L, De Bundel D, Vander Heyden Y, Smolders I, Van Eeckhaut A. Unravelling the brain metabolome: A review of liquid chromatography - mass spectrometry strategies for extracellular brain metabolomics. J Chromatogr A 2023; 1712:464479. [PMID: 37952387 DOI: 10.1016/j.chroma.2023.464479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 10/27/2023] [Accepted: 10/29/2023] [Indexed: 11/14/2023]
Abstract
The analysis of the brain extracellular metabolome is of interest for numerous subdomains within neuroscience. Not only does it provide information about normal physiological functions, it is even more of interest for biomarker discovery and target discovery in disease. The extracellular analysis of the brain is particularly interesting as it provides information about the release of mediators in the brain extracellular fluid to look at cellular signaling and metabolic pathways through the release, diffusion and re-uptake of neurochemicals. In vivo samples are obtained through microdialysis, cerebral open-flow microperfusion or solid-phase microextraction. The analytes of potential interest are typically low in concentration and can have a wide range of physicochemical properties. Liquid chromatography coupled to mass spectrometry has proven its usefulness in brain metabolomics. It allows sensitive and specific analysis of low sample volumes, obtained through different approaches. Several strategies for the analysis of the extracellular fluid have been proposed. The most widely used approaches apply sample derivatization, specific stationary phases and/or hydrophilic interaction liquid chromatography. Miniaturization of these methods allows an even higher sensitivity. The development of chiral metabolomics is indispensable, as it allows to compare the enantiomeric ratio of compounds and provides even more challenges. Some limitations continue to exist for the previously developed methods and the development of new, more sensitive methods remains needed. This review provides an overview of the methods developed for sampling and liquid chromatography-mass spectrometry analysis of the extracellular metabolome.
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Affiliation(s)
- Liam Nestor
- Research group Experimental Pharmacology (EFAR), Center for Neurosciences (C4N), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Dimitri De Bundel
- Research group Experimental Pharmacology (EFAR), Center for Neurosciences (C4N), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Yvan Vander Heyden
- Department of Analytical Chemistry, Applied Chemometrics and Molecular Modelling (FABI), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Ilse Smolders
- Research group Experimental Pharmacology (EFAR), Center for Neurosciences (C4N), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Ann Van Eeckhaut
- Research group Experimental Pharmacology (EFAR), Center for Neurosciences (C4N), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Brussels, Belgium.
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7
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Ji T, Fang B, Zhang M, Liu Y. Succinate Enhances Lipolysis and Decreases Adipocytes Size in Both Subcutaneous and Visceral Adipose Tissue from High-Fat-Diet-Fed Obese Mice. Foods 2023; 12:4285. [PMID: 38231706 DOI: 10.3390/foods12234285] [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: 11/08/2023] [Revised: 11/15/2023] [Accepted: 11/22/2023] [Indexed: 01/19/2024] Open
Abstract
Obesity is a risk factor for many chronic diseases related to the overexpansion of adipose tissue during obesity, leading to metabolic dysfunction and ectopic lipids. Previous studies reported a close relationship between succinate and obesity and its co-morbidities, and studies have also reported on its anti-obesity potential. To confirm its efficacy in obesity interventions, we supplemented mice with obesity induced by a high-fat diet with succinate (1.5% m/v in drinking water) for 11 weeks without changing the diet. After succinate supplementation, the changes in body weight, adipose tissue deposition, glucose tolerance, energy expenditure and lipid metabolism were evaluated. It was found that succinate supplementation significantly decreased subcutaneous adipose tissue (HFD: 4239.3 ± 211.2 mg; HFD-SA: 3268.9 ± 265.7 mg. p < 0.05), triglyceride contents (decreased by 1.53 mmol/g and 0.39 mmol/g in eWAT and ingWAT, respectively, p < 0.05) and NEFA (decreased by 1.41 μmol/g and 1.31 μmol/g in eWAT and ingWAT, respectively, p < 0.05). The adipocytes' sizes all significantly decreased in both subcutaneous and visceral adipose tissue (the proportion of adipocytes with diameters larger than 100 μm in eWAT and ingWAT decreased by 16.83% and 11.96%, respectively. p < 0.05). Succinate significantly enhanced lipolysis in adipose tissue (eWAT: Adrb3, Hsl and Plin1; ingWAT: Hsl and CPT1a; p < 0.05), whereas the expression of lipogenesis-related genes remained unchanged (p > 0.05). Succinate supplementation also enhanced the activity of BAT by stimulating the expression of Ucp1 and Cidea (p < 0.05). Our results reported that succinate has a potential beneficial effect on obesity pathogenesis but cannot efficiently decrease bodyweight.
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Affiliation(s)
- Tengteng Ji
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100083, China
| | - Bing Fang
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100083, China
| | - Ming Zhang
- School of Food Science and Chemical Engineering, Beijing Technology and Business University, Beijing 100048, China
| | - Yaqiong Liu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100083, China
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Tokarska-Schlattner M, Zeaiter N, Cunin V, Attia S, Meunier C, Kay L, Achouri A, Hiriart-Bryant E, Couturier K, Tellier C, El Harras A, Elena-Herrmann B, Khochbin S, Le Gouellec A, Schlattner U. Multi-Method Quantification of Acetyl-Coenzyme A and Further Acyl-Coenzyme A Species in Normal and Ischemic Rat Liver. Int J Mol Sci 2023; 24:14957. [PMID: 37834405 PMCID: PMC10573920 DOI: 10.3390/ijms241914957] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 09/29/2023] [Accepted: 09/30/2023] [Indexed: 10/15/2023] Open
Abstract
Thioesters of coenzyme A (CoA) carrying different acyl chains (acyl-CoAs) are central intermediates of many metabolic pathways and donor molecules for protein lysine acylation. Acyl-CoA species largely differ in terms of cellular concentrations and physico-chemical properties, rendering their analysis challenging. Here, we compare several approaches to quantify cellular acyl-CoA concentrations in normal and ischemic rat liver, using HPLC and LC-MS/MS for multi-acyl-CoA analysis, as well as NMR, fluorimetric and spectrophotometric techniques for the quantification of acetyl-CoAs. In particular, we describe a simple LC-MS/MS protocol that is suitable for the relative quantification of short and medium-chain acyl-CoA species. We show that ischemia induces specific changes in the short-chain acyl-CoA relative concentrations, while mild ischemia (1-2 min), although reducing succinyl-CoA, has little effects on acetyl-CoA, and even increases some acyl-CoA species upstream of the tricarboxylic acid cycle. In contrast, advanced ischemia (5-6 min) also reduces acetyl-CoA levels. Our approach provides the keys to accessing the acyl-CoA metabolome for a more in-depth analysis of metabolism, protein acylation and epigenetics.
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Affiliation(s)
- Malgorzata Tokarska-Schlattner
- University Grenoble Alpes, Inserm U1055, Laboratory of Fundamental and Applied Bioenergetics (LBFA), 38058 Grenoble, France; (N.Z.); (S.A.); (L.K.); (A.A.); (E.H.-B.); (K.C.); (C.T.)
| | - Nour Zeaiter
- University Grenoble Alpes, Inserm U1055, Laboratory of Fundamental and Applied Bioenergetics (LBFA), 38058 Grenoble, France; (N.Z.); (S.A.); (L.K.); (A.A.); (E.H.-B.); (K.C.); (C.T.)
| | - Valérie Cunin
- University Grenoble Alpes, CNRS UMR 5525, Laboratory TIMC—Translational Microbiology, Evolution, Engineering (TREE), Service de Biochimie, Biologie Moléculaire et Toxicologie Environnementale, CHU Grenoble-Alpes, 38058 Grenoble, France; (V.C.); (C.M.); (A.L.G.)
| | - Stéphane Attia
- University Grenoble Alpes, Inserm U1055, Laboratory of Fundamental and Applied Bioenergetics (LBFA), 38058 Grenoble, France; (N.Z.); (S.A.); (L.K.); (A.A.); (E.H.-B.); (K.C.); (C.T.)
| | - Cécile Meunier
- University Grenoble Alpes, CNRS UMR 5525, Laboratory TIMC—Translational Microbiology, Evolution, Engineering (TREE), Service de Biochimie, Biologie Moléculaire et Toxicologie Environnementale, CHU Grenoble-Alpes, 38058 Grenoble, France; (V.C.); (C.M.); (A.L.G.)
| | - Laurence Kay
- University Grenoble Alpes, Inserm U1055, Laboratory of Fundamental and Applied Bioenergetics (LBFA), 38058 Grenoble, France; (N.Z.); (S.A.); (L.K.); (A.A.); (E.H.-B.); (K.C.); (C.T.)
| | - Amel Achouri
- University Grenoble Alpes, Inserm U1055, Laboratory of Fundamental and Applied Bioenergetics (LBFA), 38058 Grenoble, France; (N.Z.); (S.A.); (L.K.); (A.A.); (E.H.-B.); (K.C.); (C.T.)
| | - Edwige Hiriart-Bryant
- University Grenoble Alpes, Inserm U1055, Laboratory of Fundamental and Applied Bioenergetics (LBFA), 38058 Grenoble, France; (N.Z.); (S.A.); (L.K.); (A.A.); (E.H.-B.); (K.C.); (C.T.)
| | - Karine Couturier
- University Grenoble Alpes, Inserm U1055, Laboratory of Fundamental and Applied Bioenergetics (LBFA), 38058 Grenoble, France; (N.Z.); (S.A.); (L.K.); (A.A.); (E.H.-B.); (K.C.); (C.T.)
| | - Cindy Tellier
- University Grenoble Alpes, Inserm U1055, Laboratory of Fundamental and Applied Bioenergetics (LBFA), 38058 Grenoble, France; (N.Z.); (S.A.); (L.K.); (A.A.); (E.H.-B.); (K.C.); (C.T.)
| | - Abderrafek El Harras
- University Grenoble Alpes, Inserm U1209 and CNRS UMR5309, Institute for Advanced Biosciences (IAB), 38058 Grenoble, France; (A.E.H.); (B.E.-H.); (S.K.)
| | - Bénédicte Elena-Herrmann
- University Grenoble Alpes, Inserm U1209 and CNRS UMR5309, Institute for Advanced Biosciences (IAB), 38058 Grenoble, France; (A.E.H.); (B.E.-H.); (S.K.)
| | - Saadi Khochbin
- University Grenoble Alpes, Inserm U1209 and CNRS UMR5309, Institute for Advanced Biosciences (IAB), 38058 Grenoble, France; (A.E.H.); (B.E.-H.); (S.K.)
| | - Audrey Le Gouellec
- University Grenoble Alpes, CNRS UMR 5525, Laboratory TIMC—Translational Microbiology, Evolution, Engineering (TREE), Service de Biochimie, Biologie Moléculaire et Toxicologie Environnementale, CHU Grenoble-Alpes, 38058 Grenoble, France; (V.C.); (C.M.); (A.L.G.)
| | - Uwe Schlattner
- University Grenoble Alpes, Inserm U1055, Laboratory of Fundamental and Applied Bioenergetics (LBFA), 38058 Grenoble, France; (N.Z.); (S.A.); (L.K.); (A.A.); (E.H.-B.); (K.C.); (C.T.)
- Institut Universitaire de France (IUF), 75231 Paris, France
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9
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Klabunde B, Wesener A, Bertrams W, Beinborn I, Paczia N, Surmann K, Blankenburg S, Wilhelm J, Serrania J, Knoops K, Elsayed EM, Laakmann K, Jung AL, Kirschbaum A, Hammerschmidt S, Alshaar B, Gisch N, Abu Mraheil M, Becker A, Völker U, Vollmeister E, Benedikter BJ, Schmeck B. NAD + metabolism is a key modulator of bacterial respiratory epithelial infections. Nat Commun 2023; 14:5818. [PMID: 37783679 PMCID: PMC10545792 DOI: 10.1038/s41467-023-41372-w] [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: 03/29/2023] [Accepted: 08/30/2023] [Indexed: 10/04/2023] Open
Abstract
Lower respiratory tract infections caused by Streptococcus pneumoniae (Spn) are a leading cause of death globally. Here we investigate the bronchial epithelial cellular response to Spn infection on a transcriptomic, proteomic and metabolic level. We found the NAD+ salvage pathway to be dysregulated upon infection in a cell line model, primary human lung tissue and in vivo in rodents, leading to a reduced production of NAD+. Knockdown of NAD+ salvage enzymes (NAMPT, NMNAT1) increased bacterial replication. NAD+ treatment of Spn inhibited its growth while growth of other respiratory pathogens improved. Boosting NAD+ production increased NAD+ levels in immortalized and primary cells and decreased bacterial replication upon infection. NAD+ treatment of Spn dysregulated the bacterial metabolism and reduced intrabacterial ATP. Enhancing the bacterial ATP metabolism abolished the antibacterial effect of NAD+. Thus, we identified the NAD+ salvage pathway as an antibacterial pathway in Spn infections, predicting an antibacterial mechanism of NAD+.
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Affiliation(s)
- Björn Klabunde
- Institute for Lung Research, Universities of Giessen and Marburg Lung Center (UGMLC), German Center for Lung Research (DZL), Philipps-Universität Marburg, Marburg, Germany
| | - André Wesener
- Institute for Lung Research, Universities of Giessen and Marburg Lung Center (UGMLC), German Center for Lung Research (DZL), Philipps-Universität Marburg, Marburg, Germany
| | - Wilhelm Bertrams
- Institute for Lung Research, Universities of Giessen and Marburg Lung Center (UGMLC), German Center for Lung Research (DZL), Philipps-Universität Marburg, Marburg, Germany
| | - Isabell Beinborn
- Institute for Lung Research, Universities of Giessen and Marburg Lung Center (UGMLC), German Center for Lung Research (DZL), Philipps-Universität Marburg, Marburg, Germany
| | - Nicole Paczia
- Core Facility for Metabolomics and Small Molecule Mass Spectrometry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Kristin Surmann
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Sascha Blankenburg
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Jochen Wilhelm
- Institute for Lung Health (ILH), Giessen, Germany
- Universities of Giessen and Marburg Lung Center (UGMLC), Justus-Liebig-Universität Giessen, German Center for Lung Research (DZL), Giessen, Germany
| | - Javier Serrania
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany
| | - Kèvin Knoops
- Microscopy CORE Lab, Maastricht Multimodal Molecular Imaging Institute (M4I), Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands
| | - Eslam M Elsayed
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany
- Department of Biology, Philipps-Universität Marburg, Marburg, Germany
- Department of Microbiology and Immunology, Faculty of Pharmacy, Zagazig University, Zagazig, Egypt
| | - Katrin Laakmann
- Institute for Lung Research, Universities of Giessen and Marburg Lung Center (UGMLC), German Center for Lung Research (DZL), Philipps-Universität Marburg, Marburg, Germany
| | - Anna Lena Jung
- Institute for Lung Research, Universities of Giessen and Marburg Lung Center (UGMLC), German Center for Lung Research (DZL), Philipps-Universität Marburg, Marburg, Germany
- Core Facility Flow Cytometry - Bacterial Vesicles, Philipps-Universität Marburg, Marburg, Germany
| | - Andreas Kirschbaum
- Department of Visceral, Thoracic and Vascular Surgery, University Hospital Gießen and Marburg (UKGM), Marburg, Germany
| | - Sven Hammerschmidt
- Department of Molecular Genetics and Infection Biology, Interfaculty Institute for Genetics and Functional Genomics, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany
| | - Belal Alshaar
- Division of Bioanalytical Chemistry, Priority Area Infections, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Nicolas Gisch
- Division of Bioanalytical Chemistry, Priority Area Infections, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Mobarak Abu Mraheil
- Institute for Medical Microbiology, Justus-Liebig Universität Giessen, Giessen, Germany
| | - Anke Becker
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany
| | - Uwe Völker
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Evelyn Vollmeister
- Institute for Lung Research, Universities of Giessen and Marburg Lung Center (UGMLC), German Center for Lung Research (DZL), Philipps-Universität Marburg, Marburg, Germany
| | - Birke J Benedikter
- Institute for Lung Research, Universities of Giessen and Marburg Lung Center (UGMLC), German Center for Lung Research (DZL), Philipps-Universität Marburg, Marburg, Germany.
- University Eye Clinic Maastricht, Maastricht University Medical Center (MUMC+), School for Mental Health and Neuroscience, Maastricht University, P. Debyelaan 25, 6229 HX, Maastricht, The Netherlands.
| | - Bernd Schmeck
- Institute for Lung Research, Universities of Giessen and Marburg Lung Center (UGMLC), German Center for Lung Research (DZL), Philipps-Universität Marburg, Marburg, Germany.
- Institute for Lung Health (ILH), Giessen, Germany.
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany.
- Core Facility Flow Cytometry - Bacterial Vesicles, Philipps-Universität Marburg, Marburg, Germany.
- Department of Medicine, Pulmonary and Critical Care Medicine, University Medical Center Marburg, Philipps-Universität Marburg, Marburg, Germany.
- Member of the German Center for Infectious Disease Research (DZIF), Marburg, Germany.
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10
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Hiefner J, Rische J, Bunders MJ, Worthmann A. A liquid chromatography-tandem mass spectrometry based method for the quantification of adenosine nucleotides and NAD precursors and products in various biological samples. Front Immunol 2023; 14:1250762. [PMID: 37799723 PMCID: PMC10548204 DOI: 10.3389/fimmu.2023.1250762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 08/18/2023] [Indexed: 10/07/2023] Open
Abstract
Adenine nucleotides (AN) are ubiquitous metabolites that regulate cellular energy metabolism and modulate cell communication and inflammation. To understand how disturbances in AN balance arise and affect cellular function, robust quantification techniques for these metabolites are crucial. However, due to their hydrophilicity, simultaneous quantification of AN across various biological samples has been challenging. Here we present a hydrophilic interaction high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) based method for the quantification of 26 adenosine nucleotides and precursors as well as metabolic products of nicotinamide adenine dinucleotide (NAD) in plasma, liver, and adipose tissue samples as well as cell culture supernatants and cells. Method validation was performed with regard to linearity, accuracy, precision, matrix effects, and carryover. Finally, analysis of cell culture supernatants derived from intestinal organoids and RAW 264.7 cells illustrates that the here described method is a reliable and easy-to-use tool to quantify AN and opens up new avenues to understand the role of AN generation and breakdown for cellular functions.
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Affiliation(s)
- Johanna Hiefner
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Johann Rische
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Madeleine J. Bunders
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Department of Virus Immunology, Leibniz Institute of Virology, Hamburg, Germany
- Hamburg Center of Translational Immunology, Hamburg, Germany
| | - Anna Worthmann
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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11
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Wang W, Ruan S, Su Z, Xu P, Chen Y, Lin Z, Chen J, Lu Y. A novel "on-off" SERS nanoprobe based on sulfonated cellulose nanofiber-Ag composite for selective determination of NADH in human serum. Mikrochim Acta 2023; 190:254. [PMID: 37294367 DOI: 10.1007/s00604-023-05809-9] [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: 02/15/2023] [Accepted: 04/19/2023] [Indexed: 06/10/2023]
Abstract
A novel S-CNF-based nanocomposite was created using sulfonated cellulose nanofiber (S-CNF) to enable the detection of NADH in serum by surface-enhanced Raman spectroscopy (SERS). The numerous hydroxyl and sulfonic acid groups on the S-CNF surface absorbed silver ions and converted them to silver seeds, which formed the load fulcrum. After adding a reducing agent, silver nanoparticles (Ag NPs) were firmly adhered to the S-CNF surface to form stable 1D "hot spots." The S-CNF-Ag NP substrate demonstrated outstanding SERS performance, including good uniformity with an RSD of 6.88% and an enhancement factor (EF) of 1.23 × 107. Owing to the anionic charge repulsion effect, the S-CNF-Ag NP substrate still maintains remarkable dispersion stability after 12 months of preservation. Finally, S-CNF-Ag NPs' surface was modified with 4-mercaptophenol (4-MP), a special redox Raman signal molecule, to detect reduced nicotinamide adenine dinucleotide (NADH). The results showed that the detection limit (LOD) of NADH was 0.75 μM; a good linear relationship (R2 = 0.993) was established in the concentration range 10-6 - 10-2 M. The SERS nanoprobe enabled rapid detection of NADH in human serum without any complicated sample pretreatment and provides a new potential to detect biomarkers.
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Affiliation(s)
- Wenxi Wang
- College of Chemistry and Materials Science, Fujian Provincial Key Laboratory of Advanced Oriented Chemical Engineer, Fujian Key Laboratory of Polymer Materials, Engineering Research Center of Industrial Biocatalysis, Fujian Province Higher Education Institutes, Fujian Normal University, Fuzhou, 350007, Fujian, China
| | - Shuyan Ruan
- College of Chemistry and Materials Science, Fujian Provincial Key Laboratory of Advanced Oriented Chemical Engineer, Fujian Key Laboratory of Polymer Materials, Engineering Research Center of Industrial Biocatalysis, Fujian Province Higher Education Institutes, Fujian Normal University, Fuzhou, 350007, Fujian, China
| | - Zhixiong Su
- Department of Oncology, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, 350001, Fujian, China
| | - Peipei Xu
- College of Chemistry and Materials Science, Fujian Provincial Key Laboratory of Advanced Oriented Chemical Engineer, Fujian Key Laboratory of Polymer Materials, Engineering Research Center of Industrial Biocatalysis, Fujian Province Higher Education Institutes, Fujian Normal University, Fuzhou, 350007, Fujian, China
| | - Yujia Chen
- College of Chemistry and Materials Science, Fujian Provincial Key Laboratory of Advanced Oriented Chemical Engineer, Fujian Key Laboratory of Polymer Materials, Engineering Research Center of Industrial Biocatalysis, Fujian Province Higher Education Institutes, Fujian Normal University, Fuzhou, 350007, Fujian, China
| | - Zheng Lin
- College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China.
| | - Jingbo Chen
- Department of Oncology, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, 350001, Fujian, China.
| | - Yudong Lu
- College of Chemistry and Materials Science, Fujian Provincial Key Laboratory of Advanced Oriented Chemical Engineer, Fujian Key Laboratory of Polymer Materials, Engineering Research Center of Industrial Biocatalysis, Fujian Province Higher Education Institutes, Fujian Normal University, Fuzhou, 350007, Fujian, China.
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12
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Mahr RM, Jena S, Nashif SK, Nelson AB, Rauckhorst AJ, Rome FI, Sheldon RD, Hughey CC, Puchalska P, Gearhart MD, Taylor EB, Crawford PA, Wernimont SA. Mitochondrial citrate metabolism and efflux regulate BeWo differentiation. Sci Rep 2023; 13:7387. [PMID: 37149697 PMCID: PMC10164164 DOI: 10.1038/s41598-023-34435-x] [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: 02/01/2023] [Accepted: 04/29/2023] [Indexed: 05/08/2023] Open
Abstract
Cytotrophoblasts fuse to form and renew syncytiotrophoblasts necessary to maintain placental health throughout gestation. During cytotrophoblast to syncytiotrophoblast differentiation, cells undergo regulated metabolic and transcriptional reprogramming. Mitochondria play a critical role in differentiation events in cellular systems, thus we hypothesized that mitochondrial metabolism played a central role in trophoblast differentiation. In this work, we employed static and stable isotope tracing untargeted metabolomics methods along with gene expression and histone acetylation studies in an established BeWo cell culture model of trophoblast differentiation. Differentiation was associated with increased abundance of the TCA cycle intermediates citrate and α-ketoglutarate. Citrate was preferentially exported from mitochondria in the undifferentiated state but was retained to a larger extent within mitochondria upon differentiation. Correspondingly, differentiation was associated with decreased expression of the mitochondrial citrate transporter (CIC). CRISPR/Cas9 disruption of the mitochondrial citrate carrier showed that CIC is required for biochemical differentiation of trophoblasts. Loss of CIC resulted in broad alterations in gene expression and histone acetylation. These gene expression changes were partially rescued through acetate supplementation. Taken together, these results highlight a central role for mitochondrial citrate metabolism in orchestrating histone acetylation and gene expression during trophoblast differentiation.
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Affiliation(s)
- Renee M Mahr
- Department of Obstetrics, Gynecology and Women's Health, University of Minnesota, 420 Delaware Street SE, Minneapolis, MN, 55455, USA
| | - Snehalata Jena
- Department of Obstetrics, Gynecology and Women's Health, University of Minnesota, 420 Delaware Street SE, Minneapolis, MN, 55455, USA
| | - Sereen K Nashif
- Department of Obstetrics, Gynecology and Women's Health, University of Minnesota, 420 Delaware Street SE, Minneapolis, MN, 55455, USA
| | - Alisa B Nelson
- Division of Molecular Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Adam J Rauckhorst
- Fraternal Order of Eagles Diabetes Research Center, University of Iowa, Iowa City, IA, USA
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA, USA
| | - Ferrol I Rome
- Division of Molecular Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Ryan D Sheldon
- Department of Biochemistry, University of Iowa, Iowa City, IA, USA
| | - Curtis C Hughey
- Division of Molecular Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Patrycja Puchalska
- Division of Molecular Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Micah D Gearhart
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Eric B Taylor
- Fraternal Order of Eagles Diabetes Research Center, University of Iowa, Iowa City, IA, USA
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA, USA
| | - Peter A Crawford
- Division of Molecular Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Sarah A Wernimont
- Department of Obstetrics, Gynecology and Women's Health, University of Minnesota, 420 Delaware Street SE, Minneapolis, MN, 55455, USA.
- Division of Molecular Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN, USA.
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13
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Lin YT, Chan SA, Chen YJ, Chung KP, Kuo CH. Using an In-Sample Addition of Medronic Acid for the Analysis of Purine- and Pyrimidine-Related Derivatives and Its Application in the Study of Lung Adenocarcinoma A549 Cell Lines by LC-MS/MS. J Proteome Res 2023; 22:1434-1445. [PMID: 36930966 DOI: 10.1021/acs.jproteome.2c00736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
Abstract
Intracellular purine- and pyrimidine-related derivatives are vital molecules for preserving genetic information and are essential for cellular bioenergetics and signal transduction. This study developed a practical liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for quantifying intracellular purine- and pyrimidine-related derivatives. To solve the distorted peak shape related to di- and triphosphate nucleotides, in-sample addition of medronic acid and ammonium phosphate was performed. Using the BEH-amide column, the results showed that adding 0.5 mM medronic acid to the sample significantly improved the peak shape without causing an obvious ion suppressive effect. Method validation confirmed that the coefficients of determination (R2) values for linearity evaluation were above 0.94 for all analytes. The intraday and interday accuracies ranged from 85.1 to 128.4%, with the precision below 16.6%. The validated method was successfully applied in characterizing the alterations of purine- and pyrimidine-related derivatives in the A549 cell line with perturbed mitochondrial fission or blockade of the electron transport chain. Collectively, this study demonstrates that the strategy of in-sample medronic acid addition is effective in improving the quantification of intracellular purine- and pyrimidine-related derivatives. We believe that our proposed platform can facilitate the development of novel drugs targeting purine and pyrimidine metabolism in the future.
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Affiliation(s)
- Ya-Ting Lin
- School of Pharmacy, College of Medicine, National Taiwan University, Taipei 100, Taiwan.,The Metabolomics Core Laboratory, Center of Genomic and Precision Medicine, National Taiwan University, Taipei 100, Taiwan
| | | | - Yi-Jung Chen
- Department of Laboratory Medicine, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Kuei-Pin Chung
- Department of Laboratory Medicine, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Ching-Hua Kuo
- School of Pharmacy, College of Medicine, National Taiwan University, Taipei 100, Taiwan.,The Metabolomics Core Laboratory, Center of Genomic and Precision Medicine, National Taiwan University, Taipei 100, Taiwan.,Department of Pharmacy, National Taiwan University Hospital, Taipei 100, Taiwan
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14
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Mahr RM, Jena S, Nashif SK, Nelson AB, Rauckhorst AJ, Rome FI, Sheldon RD, Hughey CC, Puchalska P, Gearhart MD, Taylor EB, Crawford PA, Wernimont SA. Mitochondrial citrate metabolism and efflux regulates trophoblast differentiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.22.525071. [PMID: 36711862 PMCID: PMC9882289 DOI: 10.1101/2023.01.22.525071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Cytotrophoblasts fuse to form and renew syncytiotrophoblasts necessary to maintain placental health throughout gestation. During cytotrophoblast to syncytiotrophoblast differentiation, cells undergo regulated metabolic and transcriptional reprogramming. Mitochondria play a critical role in differentiation events in cellular systems, thus we hypothesized that mitochondrial metabolism played a central role in trophoblast differentiation. In this work, we employed static and stable isotope tracing untargeted metabolomics methods along with gene expression and histone acetylation studies in an established cell culture model of trophoblast differentiation. Trophoblast differentiation was associated with increased abundance of the TCA cycle intermediates citrate and α-ketoglutarate. Citrate was preferentially exported from mitochondria in the undifferentiated state but was retained to a larger extent within mitochondria upon differentiation. Correspondingly, differentiation was associated with decreased expression of the mitochondrial citrate transporter (CIC). CRISPR/Cas9 disruption of the mitochondrial citrate carrier showed that CIC is required for biochemical differentiation of trophoblasts. Loss of CIC resulted in broad alterations in gene expression and histone acetylation. These gene expression changes were partially rescued through acetate supplementation. Taken together, these results highlight a central role for mitochondrial citrate metabolism in orchestrating histone acetylation and gene expression during trophoblast differentiation.
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15
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Ngere J, Ebrahimi KH, Williams R, Pires E, Walsby-Tickle J, McCullagh JSO. Ion-Exchange Chromatography Coupled to Mass Spectrometry in Life Science, Environmental, and Medical Research. Anal Chem 2023; 95:152-166. [PMID: 36625129 PMCID: PMC9835059 DOI: 10.1021/acs.analchem.2c04298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Judith
B. Ngere
- Department
of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - Kourosh H. Ebrahimi
- Institute
of Pharmaceutical Science, King’s
College London, London SE1 9NH, U.K.
| | - Rachel Williams
- Department
of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - Elisabete Pires
- Department
of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - John Walsby-Tickle
- Department
of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - James S. O. McCullagh
- Department
of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.,
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16
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Wang Y, Fan P, Zhang S, Wang L, Li X, Jia W, Liu Y, Wang K, Du X, Zhang P, Huang S. Discrimination of Ribonucleoside Mono-, Di-, and Triphosphates Using an Engineered Nanopore. ACS NANO 2022; 16:21356-21365. [PMID: 36475606 DOI: 10.1021/acsnano.2c09662] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Ribonucleotides, which widely exist in all living organisms and are essential to both physiological and pathological processes, can naturally appear as ribonucleoside mono-, di-, and triphosphates. Natural ribonucleotides can also dynamically switch between different phosphorylated forms, posing a great challenge for sensing. A specially engineered nanopore sensor is promising for full discrimination of all canonical ribonucleoside mono-, di-, and triphosphates. However, such a demonstration has never been reported, due to the lack of a suitable nanopore sensor that has a sufficient resolution. In this work, we utilized a phenylboronic acid (PBA) modified Mycobacterium smegmatis porin A (MspA) hetero-octamer for ribonucleotide sensing. Twelve types of ribonucleotides, including mono-, di-, and triphosphates of cytidine (CMP, CDP, CTP), uridine (UMP, UDP, UTP), adenosine (AMP, ADP, ATP), and guanosine (GMP, GDP, GTP) were simultaneously discriminated. A machine-learning algorithm was also developed, which achieved a general accuracy of 99.9% for ribonucleotide sensing. This strategy was also further applied to identify ribonucleotide components in ATP tablets and injections. This sensing strategy provides a direct, accurate, easy, and rapid solution to characterize ribonucleotide components in different phosphorylated forms.
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Affiliation(s)
- Yuqin Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, People's Republic of China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, People's Republic of China
| | - Pingping Fan
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, People's Republic of China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, People's Republic of China
| | - Shanyu Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, People's Republic of China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, People's Republic of China
| | - Liying Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, People's Republic of China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, People's Republic of China
| | - Xinyue Li
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, People's Republic of China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, People's Republic of China
| | - Wendong Jia
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, People's Republic of China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, People's Republic of China
| | - Yao Liu
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, People's Republic of China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, People's Republic of China
| | - Kefan Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, People's Republic of China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, People's Republic of China
| | - Xiaoyu Du
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, People's Republic of China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, People's Republic of China
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, People's Republic of China
| | - Shuo Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, People's Republic of China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, People's Republic of China
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17
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Ley-Ngardigal S, Bertolin G. Approaches to monitor ATP levels in living cells: where do we stand? FEBS J 2022; 289:7940-7969. [PMID: 34437768 DOI: 10.1111/febs.16169] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/30/2021] [Accepted: 08/25/2021] [Indexed: 01/14/2023]
Abstract
ATP is the most universal and essential energy molecule in cells. This is due to its ability to store cellular energy in form of high-energy phosphate bonds, which are extremely stable and readily usable by the cell. This energy is key for a variety of biological functions such as cell growth and division, metabolism, and signaling, and for the turnover of biomolecules. Understanding how ATP is produced and hydrolyzed with a spatiotemporal resolution is necessary to understand its functions both in physiological and in pathological contexts. In this review, first we will describe the organization of the electron transport chain and ATP synthase, the main molecular motor for ATP production in mitochondria. Second, we will review the biochemical assays currently available to estimate ATP quantities in cells, and we will compare their readouts, strengths, and weaknesses. Finally, we will explore the palette of genetically encoded biosensors designed for microscopy-based approaches, and show how their spatiotemporal resolution opened up the possibility to follow ATP levels in living cells.
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Affiliation(s)
- Seyta Ley-Ngardigal
- CNRS, Univ Rennes, IGDR (Genetics and Development Institute of Rennes), Rennes, France.,LVMH Research Perfumes and Cosmetics, Saint-Jean-de-Braye, France
| | - Giulia Bertolin
- CNRS, Univ Rennes, IGDR (Genetics and Development Institute of Rennes), Rennes, France
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18
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Targeted profiling of polar metabolites in cancer metabolic reprogramming by hydrophilic interaction liquid chromatography-tandem mass spectrometry. J Chromatogr A 2022; 1686:463654. [DOI: 10.1016/j.chroma.2022.463654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/09/2022] [Accepted: 11/16/2022] [Indexed: 11/19/2022]
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19
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Ahmed LR, Chuang CH, Lüder J, Yang HW, EL-Mahdy AFM. Direct Metal-Free Synthesis of Uracil- and Pentaazaphenalene-Functionalized Porous Organic Polymers via Quadruple Mannich Cyclization and Their Nucleobase Recognition Activities. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c01627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lamiaa Reda Ahmed
- Department of Materials and Optoelectronic Science, National Sun Yat-Sen University, Kaohsiung 80424, Taiwan
- Institute of Medical Science and Technology, National Sun Yat-Sen University, Kaohsiung 80424, Taiwan
| | - Cheng-Hsin Chuang
- Institute of Medical Science and Technology, National Sun Yat-Sen University, Kaohsiung 80424, Taiwan
| | - Johann Lüder
- Department of Materials and Optoelectronic Science, National Sun Yat-Sen University, Kaohsiung 80424, Taiwan
- Center for Theoretical and computational Physics, National Sun Yat-Sen University, Kaohsiung 80424, Taiwan
| | - Hung-Wei Yang
- Institute of Medical Science and Technology, National Sun Yat-Sen University, Kaohsiung 80424, Taiwan
| | - Ahmed F. M. EL-Mahdy
- Department of Materials and Optoelectronic Science, National Sun Yat-Sen University, Kaohsiung 80424, Taiwan
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20
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Rauckhorst AJ, Borcherding N, Pape DJ, Kraus AS, Scerbo DA, Taylor EB. Mouse tissue harvest-induced hypoxia rapidly alters the in vivo metabolome, between-genotype metabolite level differences, and 13C-tracing enrichments. Mol Metab 2022; 66:101596. [PMID: 36100179 PMCID: PMC9589196 DOI: 10.1016/j.molmet.2022.101596] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/17/2022] [Accepted: 09/06/2022] [Indexed: 12/29/2022] Open
Abstract
OBJECTIVE Metabolomics as an approach to solve biological problems is exponentially increasing in use. Thus, this a pivotal time for the adoption of best practices. It is well known that disrupted tissue oxygen supply rapidly alters cellular energy charge. However, the speed and extent to which delayed mouse tissue freezing after dissection alters the broad metabolome is not well described. Furthermore, how tissue genotype may modulate such metabolomic drift and the degree to which traced 13C-isotopologue distributions may change have not been addressed. METHODS By combined liquid chromatography (LC)- and gas chromatography (GC)-mass spectrometry (MS), we measured how levels of 255 mouse liver metabolites changed following 30-second, 1-minute, 3-minute, and 10-minute freezing delays. We then performed test-of-concept delay-to-freeze experiments evaluating broad metabolomic drift in mouse heart and skeletal muscle, differential metabolomic change between wildtype (WT) and mitochondrial pyruvate carrier (MPC) knockout mouse livers, and shifts in 13C-isotopologue abundances and enrichments traced from 13C-labled glucose into mouse liver. RESULTS Our data demonstrate that delayed mouse tissue freezing after dissection leads to rapid hypoxia-driven remodeling of the broad metabolome, induction of both false-negative and false-positive between-genotype differences, and restructuring of 13C-isotopologue distributions. Notably, we show that increased purine nucleotide degradation products are an especially high dynamic range marker of delayed liver and heart freezing. CONCLUSIONS Our findings provide a previously absent, systematic illustration of the extensive, multi-domain metabolomic changes occurring within the early minutes of delayed tissue freezing. They also provide a novel, detailed resource of mouse liver ex vivo, hypoxic metabolomic remodeling.
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Affiliation(s)
- Adam J Rauckhorst
- Department of Molecular Physiology and Biophysics, University of Iowa Carver College of Medicine, Iowa City, IA 52240, USA; Fraternal Order of Eagles Diabetes Research Center (FOEDRC), University of Iowa Carver College of Medicine, Iowa City, IA 52240, USA; FOEDRC Metabolomics Core Research Facility, University of Iowa Carver College of Medicine, Iowa City, IA 52240, USA
| | - Nicholas Borcherding
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Daniel J Pape
- Department of Molecular Physiology and Biophysics, University of Iowa Carver College of Medicine, Iowa City, IA 52240, USA
| | - Alora S Kraus
- Department of Molecular Physiology and Biophysics, University of Iowa Carver College of Medicine, Iowa City, IA 52240, USA
| | - Diego A Scerbo
- Department of Molecular Physiology and Biophysics, University of Iowa Carver College of Medicine, Iowa City, IA 52240, USA; Fraternal Order of Eagles Diabetes Research Center (FOEDRC), University of Iowa Carver College of Medicine, Iowa City, IA 52240, USA
| | - Eric B Taylor
- Department of Molecular Physiology and Biophysics, University of Iowa Carver College of Medicine, Iowa City, IA 52240, USA; Fraternal Order of Eagles Diabetes Research Center (FOEDRC), University of Iowa Carver College of Medicine, Iowa City, IA 52240, USA; Holden Comprehensive Cancer Center, University of Iowa Carver College of Medicine, Iowa City, IA 52240, USA; Abboud Cardiovascular Research Center, University of Iowa Carver College of Medicine, Iowa City, IA 52240, USA; Pappajohn Biomedical Institute, University of Iowa Carver College of Medicine, Iowa City, IA 52240, USA; FOEDRC Metabolomics Core Research Facility, University of Iowa Carver College of Medicine, Iowa City, IA 52240, USA.
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21
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Pachnis P, Wu Z, Faubert B, Tasdogan A, Gu W, Shelton S, Solmonson A, Rao AD, Kaushik AK, Rogers TJ, Ubellacker JM, LaVigne CA, Yang C, Ko B, Ramesh V, Sudderth J, Zacharias LG, Martin-Sandoval MS, Do D, Mathews TP, Zhao Z, Mishra P, Morrison SJ, DeBerardinis RJ. In vivo isotope tracing reveals a requirement for the electron transport chain in glucose and glutamine metabolism by tumors. SCIENCE ADVANCES 2022; 8:eabn9550. [PMID: 36044570 PMCID: PMC9432826 DOI: 10.1126/sciadv.abn9550] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 07/15/2022] [Indexed: 05/05/2023]
Abstract
In mice and humans with cancer, intravenous 13C-glucose infusion results in 13C labeling of tumor tricarboxylic acid (TCA) cycle intermediates, indicating that pyruvate oxidation in the TCA cycle occurs in tumors. The TCA cycle is usually coupled to the electron transport chain (ETC) because NADH generated by the cycle is reoxidized to NAD+ by the ETC. However, 13C labeling does not directly report ETC activity, and other pathways can oxidize NADH, so the ETC's role in these labeling patterns is unverified. We examined the impact of the ETC complex I inhibitor IACS-010759 on tumor 13C labeling. IACS-010759 suppresses TCA cycle labeling from glucose or lactate and increases labeling from glutamine. Cancer cells expressing yeast NADH dehydrogenase-1, which recycles NADH to NAD+ independently of complex I, display normalized labeling when complex I is inhibited, indicating that cancer cell ETC activity regulates TCA cycle metabolism and 13C labeling from multiple nutrients.
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Affiliation(s)
- Panayotis Pachnis
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Zheng Wu
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Brandon Faubert
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Alpaslan Tasdogan
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Wen Gu
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Spencer Shelton
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ashley Solmonson
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Aparna D. Rao
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Akash K. Kaushik
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Thomas J. Rogers
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jessalyn M. Ubellacker
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Collette A. LaVigne
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Chendong Yang
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Bookyung Ko
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Vijayashree Ramesh
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jessica Sudderth
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lauren G. Zacharias
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Misty S. Martin-Sandoval
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Duyen Do
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Thomas P. Mathews
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Zhiyu Zhao
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Prashant Mishra
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sean J. Morrison
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ralph J. DeBerardinis
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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22
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GAO R, FU Q, LUO D, LIU B. Multi-signal information increment sensing system for point-of-care testing of NADH based on cobalt oxyhydroxide nanoflakes. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2022. [DOI: 10.1016/j.cjac.2022.100154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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23
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Mo3+ hydride as the common origin of H2 evolution and selective NADH regeneration in molybdenum sulfide electrocatalysts. Nat Catal 2022. [DOI: 10.1038/s41929-022-00781-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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24
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Kim J, Jung I, Cheong YE, Kim KH. Evaluation and optimization of quantitative analysis of cofactors from yeast by liquid chromatography/mass spectrometry. Anal Chim Acta 2022; 1211:339890. [DOI: 10.1016/j.aca.2022.339890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 04/17/2022] [Accepted: 04/28/2022] [Indexed: 11/01/2022]
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25
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Nelson AB, Chow LS, Hughey CC, Crawford PA, Puchalska P. Artifactual FA dimers mimic FAHFA signals in untargeted metabolomics pipelines. J Lipid Res 2022; 63:100201. [PMID: 35315332 PMCID: PMC9034316 DOI: 10.1016/j.jlr.2022.100201] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 12/01/2022] Open
Abstract
FA esters of hydroxy FAs (FAHFAs) are lipokines with extensive structural and regional isomeric diversity that impact multiple physiological functions, including insulin sensitivity and glucose homeostasis. Because of their low molar abundance, FAHFAs are typically quantified using highly sensitive LC-MS/MS methods. Numerous relevant MS databases house in silico-spectra that allow identification and speciation of FAHFAs. These provisional chemical feature assignments provide a useful starting point but could lead to misidentification. To address this possibility, we analyzed human serum with a commonly applied high-resolution LC-MS untargeted metabolomics platform. We found that many chemical features are putatively assigned to the FAHFA lipid class based on exact mass and fragmentation patterns matching spectral databases. Careful validation using authentic standards revealed that many investigated signals provisionally assigned as FAHFAs are in fact FA dimers formed in the LC-MS pipeline. These isobaric FA dimers differ structurally only by the presence of an olefinic bond. Furthermore, stable isotope-labeled oleic acid spiked into human serum at subphysiological concentrations showed concentration-dependent formation of a diverse repertoire of FA dimers that analytically mimicked FAHFAs. Conversely, validated FAHFA species did not form spontaneously in the LC-MS pipeline. Together, these findings underscore that FAHFAs are endogenous lipid species. However, nonbiological FA dimers forming in the setting of high concentrations of FFAs can be misidentified as FAHFAs. Based on these results, we assembled a FA dimer database to identify nonbiological FA dimers in untargeted metabolomics datasets.
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Affiliation(s)
- Alisa B Nelson
- Division of Molecular Medicine; Department of Medicine, University of Minnesota, Minneapolis, MN, USA; Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, MN, USA
| | - Lisa S Chow
- Division of Diabetes, Endocrinology and Metabolism; Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Curtis C Hughey
- Division of Molecular Medicine; Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Peter A Crawford
- Division of Molecular Medicine; Department of Medicine, University of Minnesota, Minneapolis, MN, USA; Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, MN, USA; Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN, USA; Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA.
| | - Patrycja Puchalska
- Division of Molecular Medicine; Department of Medicine, University of Minnesota, Minneapolis, MN, USA.
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26
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Irie K, Hiramoto N, Ishikawa T, Fukushima S. Use of liquid chromatography-tandem mass spectrometry for foscarnet quantification in human serum and cerebrospinal fluid. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2022; 36:e9255. [PMID: 35001441 DOI: 10.1002/rcm.9255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/27/2021] [Accepted: 01/05/2022] [Indexed: 06/14/2023]
Abstract
RATIONALE Foscarnet (FCV) is used to treat cytomegalovirus, human herpesvirus, and human immunodeficiency virus infections. It is a low-molecular-weight compound containing carboxylate and phosphate groups. There are no reports on the use of liquid chromatography-tandem mass spectrometry (LC/MS/MS) to analyze FCV via bioanalysis. In the present study, we developed the ion-pair LC/MS/MS method to analyze FCV in human serum and cerebrospinal fluid (CSF). METHODS FCV was extracted from human serum and CSF by weak anion exchange (WAX) solid-phase extraction. The LC/MS/MS systems were coated with 0.1% phosphoric acid in methanol to avoid nonspecific absorption. FCV was detected using ion-pair LC/MS/MS with dibutylammonium acetate. Selected reaction monitoring transition of FCV in the negative ion mode was selected at m/z 125.1 → 62.9. RESULTS FCV was selectively detected in human serum and CSF, and the liner range was 5-1000 μM (R2 = 0.99). The intraday and interday accuracy and precision were within ±15%. FCV was constantly extracted from human serum and CSF by WAX solid-phase extraction (recovery ratio = 76.0-77.9%). No matrix effect was observed. CONCLUSIONS A robust LC/MS/MS method to analyze FCV was successfully developed. FCV was selectively measured using LC/MS/MS in very low extract volumes (20 μL). The method will be useful in evaluating the FCV level in human serum and CSF.
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Affiliation(s)
- Kei Irie
- Faculty of Pharmaceutical Science, Kobe Gakuin University, Kobe, Japan
- Department of Pharmacy, Kobe City Hospital Organization, Kobe City Medical Center General Hospital, Kobe, Japan
| | - Nobuhiro Hiramoto
- Department of Hematology, Kobe City Hospital Organization, Kobe City Medical Center General Hospital, Kobe, Japan
| | - Takayuki Ishikawa
- Department of Hematology, Kobe City Hospital Organization, Kobe City Medical Center General Hospital, Kobe, Japan
| | - Shoji Fukushima
- Faculty of Pharmaceutical Science, Kobe Gakuin University, Kobe, Japan
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27
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Zhang W, Ramautar R. Assessing the Energy Status of Low Numbers of Mammalian Cells by Capillary Electrophoresis-Mass Spectrometry. Methods Mol Biol 2022; 2531:203-209. [PMID: 35941487 DOI: 10.1007/978-1-0716-2493-7_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Capillary electrophoresis-mass spectrometry (CE-MS) employing a sheathless porous tip interface has become a strong analytical tool for the efficient profiling of highly polar and charged metabolites in volume/material-restricted biological samples. As more and more metabolomics studies are (intrinsically) dealing with low numbers of mammalian cells, it would be important to use an additional performance metric to effectively evaluate the sampling and sample preparation procedure, in particular quenching. An established parameter to assess the sampling and sample preparation quality when working with cell cultures is the adenylate energy charge (AEC), which represents an index of the energy state of a cell. In this protocol, a CE-MS strategy is proposed for the reliable determination of the adenylate energy charge (AEC) in metabolomics studies dealing with low numbers of mammalian cells.
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Affiliation(s)
- Wei Zhang
- Biomedical Microscale Analytics, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - Rawi Ramautar
- Biomedical Microscale Analytics, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands.
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28
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Cuny H, Kristianto E, Hodson MP, Dunwoodie SL. Simultaneous quantification of 26 NAD-related metabolites in plasma, blood, and liver tissue using UHPLC-MS/MS. Anal Biochem 2021; 633:114409. [PMID: 34648806 DOI: 10.1016/j.ab.2021.114409] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 09/15/2021] [Accepted: 10/07/2021] [Indexed: 01/23/2023]
Abstract
Nicotinamide adenine dinucleotide (NAD) is a key metabolic intermediate found in all cells and involved in numerous cellular functions. Perturbances in the NAD metabolome are linked to various diseases such as diabetes and schizophrenia, and to congenital malformations and recurrent miscarriage. Mouse models are central to the investigation of these and other NAD-related conditions because mice can be readily genetically modified and treated with diets with altered concentrations of NAD precursors. Simultaneous quantification of as many metabolites of the NAD metabolome as possible is required to understand which pathways are affected in these disease conditions and what are the functional consequences. Here, we report the development of a fit-for-purpose method to simultaneously quantify 26 NAD-related metabolites and creatinine in mouse plasma, whole blood, and liver tissue using ultra-high performance liquid chromatography - tandem mass spectrometry (UHPLC-MS/MS). The included metabolites represent dietary precursors, intermediates, enzymatic cofactors, and excretion products. Sample preparation was optimized for each matrix and included 21 isotope-labeled internal standards. The method reached adequate precision and accuracy for the intended context of use of exploratory pathway-related biomarker discovery in mouse models. The method was tested by determining metabolite concentrations in mice fed a special diet with defined precursor content.
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Affiliation(s)
- Hartmut Cuny
- Developmental and Stem Cell Biology Division, Victor Chang Cardiac Research Institute, Sydney, New South Wales, 2010, Australia; Faculty of Medicine, University of New South Wales, Sydney, New South Wales, 2052, Australia.
| | - Esther Kristianto
- Victor Chang Cardiac Research Institute Innovation Centre, Sydney, New South Wales, 2010, Australia.
| | - Mark P Hodson
- Victor Chang Cardiac Research Institute Innovation Centre, Sydney, New South Wales, 2010, Australia; School of Pharmacy, University of Queensland, Woolloongabba, Queensland, 4102, Australia.
| | - Sally L Dunwoodie
- Developmental and Stem Cell Biology Division, Victor Chang Cardiac Research Institute, Sydney, New South Wales, 2010, Australia; Faculty of Medicine, University of New South Wales, Sydney, New South Wales, 2052, Australia; Faculty of Science, University of New South Wales, Sydney, New South Wales, 2052, Australia.
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29
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Osada Y, Nakagawa S, Ishibe K, Takao S, Shimazaki A, Itohara K, Imai S, Yonezawa A, Nakagawa T, Matsubara K. Antibiotic-induced microbiome depletion alters renal glucose metabolism and exacerbates renal injury after ischemia-reperfusion injury in mice. Am J Physiol Renal Physiol 2021; 321:F455-F465. [PMID: 34423680 DOI: 10.1152/ajprenal.00111.2021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Recent studies have revealed the impact of antibiotic-induced microbiome depletion (AIMD) on host glucose homeostasis. The kidney has a critical role in systemic glucose homeostasis; however, information regarding the association between AIMD and renal glucose metabolism remains limited. Hence, we aimed to determine the effects of AIMD on renal glucose metabolism by inducing gut microbiome depletion using an antibiotic cocktail (ABX) composed of ampicillin, vancomycin, and levofloxacin in mice. The results showed that bacterial 16s rRNA expression, luminal concentrations of short-chain fatty acids and bile acids, and plasma glucose levels were significantly lower in ABX-treated mice than in vehicle-treated mice. In addition, ABX treatment significantly reduced renal glucose and pyruvate levels. mRNA expression levels of glucose-6-phosphatase and phosphoenolpyruvate carboxykinase in the renal cortex were significantly higher in ABX-treated mice than in vehicle-treated mice. We further examined the impact of AIMD on the altered metabolic status in mice after ischemia-induced kidney injury. After exposure to ischemia for 60 min, renal pyruvate concentrations were significantly lower in ABX-treated mice than in vehicle-treated mice. ABX treatment caused a more severe tubular injury after ischemia-reperfusion. Our findings confirm that AIMD is associated with decreased pyruvate levels in the kidney, which may have been caused by the activation of renal gluconeogenesis. Thus, we hypothesized that AIMD would increase the vulnerability of the kidney to ischemia-reperfusion injury.NEW & NOTEWORTHY This study aimed to determine the impact of antibiotic-induced microbiome depletion (AIMD) on renal glucose metabolism in mice. This is the first report confirming that AIMD is associated with decreased levels of pyruvate, a key intermediate in glucose metabolism, which may have been caused by activation of renal gluconeogenesis. We hypothesized that AIMD can increase the susceptibility of the kidney to ischemia-reperfusion injury.
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Affiliation(s)
- Yuika Osada
- Department of Clinical Pharmacology and Therapeutics, Kyoto University Hospital, Kyoto, Japan
| | - Shunsaku Nakagawa
- Department of Clinical Pharmacology and Therapeutics, Kyoto University Hospital, Kyoto, Japan
| | - Kanako Ishibe
- Department of Clinical Pharmacology and Therapeutics, Kyoto University Hospital, Kyoto, Japan
| | - Shota Takao
- Department of Clinical Pharmacology and Therapeutics, Kyoto University Hospital, Kyoto, Japan
| | - Aimi Shimazaki
- Department of Clinical Pharmacology and Therapeutics, Kyoto University Hospital, Kyoto, Japan
| | - Kotaro Itohara
- Department of Clinical Pharmacology and Therapeutics, Kyoto University Hospital, Kyoto, Japan
| | - Satoshi Imai
- Department of Clinical Pharmacology and Therapeutics, Kyoto University Hospital, Kyoto, Japan
| | - Atsushi Yonezawa
- Department of Clinical Pharmacology and Therapeutics, Kyoto University Hospital, Kyoto, Japan
| | - Takayuki Nakagawa
- Department of Clinical Pharmacology and Therapeutics, Kyoto University Hospital, Kyoto, Japan
| | - Kazuo Matsubara
- Department of Clinical Pharmacology and Therapeutics, Kyoto University Hospital, Kyoto, Japan
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30
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Jun S, Mahesula S, Mathews TP, Martin-Sandoval MS, Zhao Z, Piskounova E, Agathocleous M. The requirement for pyruvate dehydrogenase in leukemogenesis depends on cell lineage. Cell Metab 2021; 33:1777-1792.e8. [PMID: 34375613 DOI: 10.1016/j.cmet.2021.07.016] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 05/19/2021] [Accepted: 07/19/2021] [Indexed: 12/20/2022]
Abstract
Cancer cells are metabolically similar to their corresponding normal tissues. Differences between cancers and normal tissues may reflect reprogramming during transformation or maintenance of the metabolism of the specific normal cell type that originated the cancer. Here, we compare glucose metabolism in hematopoiesis and leukemia. Thymus T cell progenitors were glucose avid and oxidized more glucose in the tricarboxylic acid cycle through pyruvate dehydrogenase (PDH) as compared with other hematopoietic cells. PDH deletion decreased double-positive T cell progenitor cells but had no effect on hematopoietic stem cells, myeloid progenitors, or other hematopoietic cells. PDH deletion blocked the development of Pten-deficient T cell leukemia, but not the development of a Pten-deficient myeloid neoplasm. Therefore, the requirement for PDH in leukemia reflected the metabolism of the normal cell of origin independently of the driver genetic lesion. PDH was required to prevent pyruvate accumulation and maintain glutathione levels and redox homeostasis.
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Affiliation(s)
- Sojeong Jun
- Children's Medical Center Research Institute and Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Swetha Mahesula
- Children's Medical Center Research Institute and Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Thomas P Mathews
- Children's Medical Center Research Institute and Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Misty S Martin-Sandoval
- Children's Medical Center Research Institute and Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Zhiyu Zhao
- Children's Medical Center Research Institute and Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Elena Piskounova
- Sandra and Edward Meyer Cancer Center and Department of Dermatology, Weill Cornell Medicine, New York, NY, USA
| | - Michalis Agathocleous
- Children's Medical Center Research Institute and Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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31
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Stagg DB, Gillingham JR, Nelson AB, Lengfeld JE, d'Avignon DA, Puchalska P, Crawford PA. Diminished ketone interconversion, hepatic TCA cycle flux, and glucose production in D-β-hydroxybutyrate dehydrogenase hepatocyte-deficient mice. Mol Metab 2021; 53:101269. [PMID: 34116232 PMCID: PMC8259407 DOI: 10.1016/j.molmet.2021.101269] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/28/2021] [Accepted: 06/03/2021] [Indexed: 12/20/2022] Open
Abstract
Objective Throughout the last decade, interest has intensified in intermittent fasting, ketogenic diets, and exogenous ketone therapies as prospective health-promoting, therapeutic, and performance-enhancing agents. However, the regulatory roles of ketogenesis and ketone metabolism on liver homeostasis remain unclear. Therefore, we sought to develop a better understanding of the metabolic consequences of hepatic ketone body metabolism by focusing on the redox-dependent interconversion of acetoacetate (AcAc) and D-β-hydroxybutyrate (D-βOHB). Methods Using targeted and isotope tracing high-resolution liquid chromatography-mass spectrometry, dual stable isotope tracer nuclear magnetic resonance spectroscopy-based metabolic flux modeling, and complementary physiological approaches in novel cell type-specific knockout mice, we quantified the roles of hepatocyte D-β-hydroxybutyrate dehydrogenase (BDH1), a mitochondrial enzyme required for NAD+/NADH-dependent oxidation/reduction of ketone bodies. Results Exogenously administered AcAc is reduced to D-βOHB, which increases hepatic NAD+/NADH ratio and reflects hepatic BDH1 activity. Livers of hepatocyte-specific BDH1-deficient mice did not produce D-βOHB, but owing to extrahepatic BDH1, these mice nonetheless remained capable of AcAc/D-βOHB interconversion. Compared to littermate controls, hepatocyte-specific BDH1 deficient mice exhibited diminished liver tricarboxylic acid (TCA) cycle flux and impaired gluconeogenesis, but normal hepatic energy charge overall. Glycemic recovery after acute insulin challenge was impaired in knockout mice, but they were not more susceptible to starvation-induced hypoglycemia. Conclusions Ketone bodies influence liver homeostasis. While liver BDH1 is not required for whole body equilibration of AcAc and D-βOHB, loss of the ability to interconvert these ketone bodies in hepatocytes results in impaired TCA cycle flux and glucose production. Therefore, through oxidation/reduction of ketone bodies, BDH1 is a significant contributor to hepatic mitochondrial redox, liver physiology, and organism-wide ketone body homeostasis. Exogenously administered acetoacetate is reduced to D-β-hydroxybutyrate, increasing hepatic NAD+/NADH ratio. Liver BDH1 is not required for whole body equilibration of acetoacetate and D-β-hydroxybutyrate. Hepatocyte-specific loss of BDH1 reduces hepatic TCA cycle flux, and TCA-cycle sourced gluconeogenesis. Hepatocyte-specific loss of BDH1 impairs glycemic recovery without provoking starvation-induced hypoglycemia.
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Affiliation(s)
- David B Stagg
- Division of Molecular Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN, USA; Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Jacob R Gillingham
- Division of Molecular Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Alisa B Nelson
- Division of Molecular Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN, USA; Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, MN, USA
| | - Justin E Lengfeld
- Division of Molecular Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - D André d'Avignon
- Division of Molecular Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Patrycja Puchalska
- Division of Molecular Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Peter A Crawford
- Division of Molecular Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN, USA; Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA; Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, MN, USA.
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32
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Rampler E, Abiead YE, Schoeny H, Rusz M, Hildebrand F, Fitz V, Koellensperger G. Recurrent Topics in Mass Spectrometry-Based Metabolomics and Lipidomics-Standardization, Coverage, and Throughput. Anal Chem 2021; 93:519-545. [PMID: 33249827 PMCID: PMC7807424 DOI: 10.1021/acs.analchem.0c04698] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Evelyn Rampler
- Department of Analytical
Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Althanstraße 14, 1090 Vienna, Austria
- University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Yasin El Abiead
- Department of Analytical
Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria
| | - Harald Schoeny
- Department of Analytical
Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria
| | - Mate Rusz
- Department of Analytical
Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria
- Institute of Inorganic
Chemistry, University of Vienna, Währinger Straße 42, 1090 Vienna, Austria
| | - Felina Hildebrand
- Department of Analytical
Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria
| | - Veronika Fitz
- Department of Analytical
Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria
| | - Gunda Koellensperger
- Department of Analytical
Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Althanstraße 14, 1090 Vienna, Austria
- University of Vienna, Althanstraße 14, 1090 Vienna, Austria
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Olkowicz M, Tomczyk M, Debski J, Tyrankiewicz U, Przyborowski K, Borkowski T, Zabielska-Kaczorowska M, Szupryczynska N, Kochan Z, Smeda M, Dadlez M, Chlopicki S, Smolenski RT. Enhanced cardiac hypoxic injury in atherogenic dyslipidaemia results from alterations in the energy metabolism pattern. Metabolism 2021; 114:154400. [PMID: 33058853 DOI: 10.1016/j.metabol.2020.154400] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/22/2020] [Accepted: 09/24/2020] [Indexed: 12/17/2022]
Abstract
OBJECTIVE Dyslipidaemia is a major risk factor for myocardial infarction that is known to correlate with atherosclerosis in the coronary arteries. We sought to clarify whether metabolic alterations induced by dyslipidaemia in cardiomyocytes collectively constitute an alternative pathway that escalates myocardial injury. METHODS Dyslipidaemic apolipoprotein E and low-density lipoprotein receptor (ApoE/LDLR) double knockout (ApoE-/-/LDLR-/-) and wild-type C57BL/6 (WT) mice aged six months old were studied. Cardiac injury under reduced oxygen supply was evaluated by 5 min exposure to 5% oxygen in the breathing air under electrocardiogram (ECG) recording and with the assessment of troponin I release. To address the mechanisms LC/MS was used to analyse the cardiac proteome pattern or in vivo metabolism of stable isotope-labelled substrates and HPLC was applied to measure concentrations of cardiac high-energy phosphates. Furthermore, the effect of blocking fatty acid use with ranolazine on the substrate preference and cardiac hypoxic damage was studied in ApoE-/-/LDLR-/- mice. RESULTS Hypoxia induced profound changes in ECG ST-segment and troponin I leakage in ApoE-/-/LDLR-/- mice but not in WT mice. The evaluation of the cardiac proteomic pattern revealed that ApoE-/-/LDLR-/- as compared with WT mice were characterised by coordinated increased expression of mitochondrial proteins, including enzymes of fatty acids' and branched-chain amino acids' oxidation, accompanied by decreased expression levels of glycolytic enzymes. These findings correlated with in vivo analysis, revealing a reduction in the entry of glucose and enhanced entry of leucine into the cardiac Krebs cycle, with the cardiac high-energy phosphates pool maintained. These changes were accompanied by the activation of molecular targets controlling mitochondrial metabolism. Ranolazine reversed the oxidative metabolic shift in ApoE-/-/LDLR-/- mice and reduced cardiac damage induced by hypoxia. CONCLUSIONS We suggest a novel mechanism for myocardial injury in dyslipidaemia that is consequent to an increased reliance on oxidative metabolism in the heart. The alterations in the metabolic pattern that we identified constitute an adaptive mechanism that facilitates maintenance of metabolic equilibrium and cardiac function under normoxia. However, this adaptation could account for myocardial injury even in a mild reduction of oxygen supply.
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Affiliation(s)
- Mariola Olkowicz
- Department of Biochemistry, Faculty of Medicine, Medical University of Gdansk, 1 Debinki St., 80-211 Gdansk, Poland; Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, 14 Bobrzynskiego St., 30-348 Krakow, Poland
| | - Marta Tomczyk
- Department of Biochemistry, Faculty of Medicine, Medical University of Gdansk, 1 Debinki St., 80-211 Gdansk, Poland
| | - Janusz Debski
- Mass Spectrometry Laboratory, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 5a Pawinskiego St., 02-106 Warsaw, Poland
| | - Urszula Tyrankiewicz
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, 14 Bobrzynskiego St., 30-348 Krakow, Poland
| | - Kamil Przyborowski
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, 14 Bobrzynskiego St., 30-348 Krakow, Poland
| | - Tomasz Borkowski
- Department of Biochemistry, Faculty of Medicine, Medical University of Gdansk, 1 Debinki St., 80-211 Gdansk, Poland
| | - Magdalena Zabielska-Kaczorowska
- Department of Biochemistry, Faculty of Medicine, Medical University of Gdansk, 1 Debinki St., 80-211 Gdansk, Poland; Department of Physiology, Faculty of Medicine, Medical University of Gdansk, 1 Debinki St., 80-211 Gdansk, Poland
| | - Natalia Szupryczynska
- Department of Nutritional Biochemistry, Faculty of Health Sciences, Medical University of Gdansk, 7 Debinki St., 80-211 Gdansk, Poland
| | - Zdzislaw Kochan
- Department of Nutritional Biochemistry, Faculty of Health Sciences, Medical University of Gdansk, 7 Debinki St., 80-211 Gdansk, Poland
| | - Marta Smeda
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, 14 Bobrzynskiego St., 30-348 Krakow, Poland
| | - Michal Dadlez
- Mass Spectrometry Laboratory, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 5a Pawinskiego St., 02-106 Warsaw, Poland
| | - Stefan Chlopicki
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, 14 Bobrzynskiego St., 30-348 Krakow, Poland; Chair of Pharmacology, Jagiellonian University Medical College, 16 Grzegorzecka St., 31-531 Krakow, Poland.
| | - Ryszard T Smolenski
- Department of Biochemistry, Faculty of Medicine, Medical University of Gdansk, 1 Debinki St., 80-211 Gdansk, Poland.
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Walsby-Tickle J, Gannon J, Hvinden I, Bardella C, Abboud MI, Nazeer A, Hauton D, Pires E, Cadoux-Hudson T, Schofield CJ, McCullagh JSO. Anion-exchange chromatography mass spectrometry provides extensive coverage of primary metabolic pathways revealing altered metabolism in IDH1 mutant cells. Commun Biol 2020; 3:247. [PMID: 32433536 PMCID: PMC7239943 DOI: 10.1038/s42003-020-0957-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 04/21/2020] [Indexed: 12/19/2022] Open
Abstract
Altered central carbon metabolism is a hallmark of many diseases including diabetes, obesity, heart disease and cancer. Identifying metabolic changes will open opportunities for better understanding aetiological processes and identifying new diagnostic, prognostic, and therapeutic targets. Comprehensive and robust analysis of primary metabolic pathways in cells, tissues and bio-fluids, remains technically challenging. We report on the development and validation of a highly reproducible and robust untargeted method using anion-exchange tandem mass spectrometry (IC-MS) that enables analysis of 431 metabolites, providing detailed coverage of central carbon metabolism. We apply the method in an untargeted, discovery-driven workflow to investigate the metabolic effects of isocitrate dehydrogenase 1 (IDH1) mutations in glioblastoma cells. IC-MS provides comprehensive coverage of central metabolic pathways revealing significant elevation of 2-hydroxyglutarate and depletion of 2-oxoglutarate. Further analysis of the data reveals depletion in additional metabolites including previously unrecognised changes in lysine and tryptophan metabolism.
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Affiliation(s)
- John Walsby-Tickle
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Joan Gannon
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Ingvild Hvinden
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Chiara Bardella
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Martine I Abboud
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Areesha Nazeer
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - David Hauton
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Elisabete Pires
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Tom Cadoux-Hudson
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | | | - James S O McCullagh
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK.
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Røst LM, Shafaei A, Fuchino K, Bruheim P. Zwitterionic HILIC tandem mass spectrometry with isotope dilution for rapid, sensitive and robust quantification of pyridine nucleotides in biological extracts. J Chromatogr B Analyt Technol Biomed Life Sci 2020; 1144:122078. [PMID: 32222674 DOI: 10.1016/j.jchromb.2020.122078] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 03/15/2020] [Accepted: 03/19/2020] [Indexed: 12/13/2022]
Abstract
The pyridine nucleotides nicotineamide adenine dinucleotide (NAD) and nicotineamide adenine dinucleotide phosphate (NADP) are conserved coenzymes across all domains of life, and are involved in more than 200 different hydride transfer reactions supporting essential catabolic and anabolic functions. The intracellular levels of these metabolites, and the ratio of their oxidized to reduced forms regulate an extensive network of reactions ranging beyond metabolism. Hence, monitoring their intracellular levels provides information about, but not limited to, the metabolic state of a cell or tissue. Interconversion between oxidized and reduced forms, varying pH liability and varying intracellular concentrations of the different species leaves absolute quantification of the pyridine nucleotides analytically challenging. These polar metabolites are poorly retained on conventional reverseed-phase stationary phases without ion-pair reagents that contaminates the LC-system. Herein we demonstrate that zwitterionic HILIC-tandem mass spectroemtry can be applied to successfully resolve the pyridine nucleotides in biological extracts in a fast, robust and highly sensitive way. The presented method applies isotope dilution to compensate potential loss of these labile metabolites and is validated for low, medium and high biomass samples of two popular biological model systems; Escherichia coli and the human cell line JJN-3. High stability and rapid sample preparation without solvent removal allows for long sequence runs, making this method ideal for high-throughput analysis of biological extracts.
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Affiliation(s)
- Lisa M Røst
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, NTNU Norwegian University of Science and Technology, NO-7481 Trondheim, Norway
| | - Armaghan Shafaei
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, NTNU Norwegian University of Science and Technology, NO-7481 Trondheim, Norway
| | - Katsuya Fuchino
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, NTNU Norwegian University of Science and Technology, NO-7481 Trondheim, Norway
| | - Per Bruheim
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, NTNU Norwegian University of Science and Technology, NO-7481 Trondheim, Norway.
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36
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Lin CH, Lee C, Wu YC, Lu IC. New Strategy to Preserve Phosphate by Ionic Liquid Matrices in Matrix-Assisted Laser Desorption/Ionization: A Case of Adenosine Nucleotides. Molecules 2020; 25:molecules25051217. [PMID: 32182713 PMCID: PMC7179418 DOI: 10.3390/molecules25051217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 03/06/2020] [Accepted: 03/07/2020] [Indexed: 11/16/2022] Open
Abstract
Adenosine -5′-triphosphate (ATP) plays a valuable role in metabolic activity to produce adequate energy in a biosystem. A high ATP/AMP ratio has a correlation with diabetes that induces suppression of AMP-activated protein kinase (AMPK). Matrix-assisted laser desorption/ionization (MALDI)–mass spectrometry (MS) has outstanding potential in determining the ratio of several types of adenosine phosphates in a sample to rapidly understand the primary energy transfer in metabolism. Although MALDI is viewed as a soft ionization technique for MS analysis, excess photon energy might crack the phosphate bonds leading to misinterpretation of the ATP level. In this work, ionic liquid matrices (ILMs) were employed to reduce fragmentation and increase the detection efficiency during the MALDI process. This study demonstrated for the first time that 2,5-dihydroxybenzoic acid pyridine (DHBP) is one of the most effective matrices for further quantitative analysis of adenosine nucleotides. This systematic screening of ILMs also enhances the fundamental understanding of MALDI.
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Affiliation(s)
- Chih-Hao Lin
- Department of Chemistry, National Chung Hsing University, Taichung City 40227, Taiwan; (C.-H.L.); (Y.-C.W.)
| | - Chuping Lee
- Department of Applied Chemistry, National Chiayi University, Chiayi City 60004, Taiwan;
| | - Yu-Cheng Wu
- Department of Chemistry, National Chung Hsing University, Taichung City 40227, Taiwan; (C.-H.L.); (Y.-C.W.)
| | - I-Chung Lu
- Department of Chemistry, National Chung Hsing University, Taichung City 40227, Taiwan; (C.-H.L.); (Y.-C.W.)
- Correspondence: ; Tel.: +886-4-22840411 (ext. 502); Fax: +886-4-22862547
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Zhang W, Guled F, Hankemeier T, Ramautar R. Profiling nucleotides in low numbers of mammalian cells by sheathless CE-MS in positive ion mode: Circumventing corona discharge. Electrophoresis 2020; 41:360-369. [PMID: 31907937 DOI: 10.1002/elps.201900417] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/16/2019] [Accepted: 12/20/2019] [Indexed: 12/26/2022]
Abstract
Negative ion mode nano-ESI-MS is often considered for the analysis of acidic compounds, including nucleotides. However, under high aqueous separation conditions, corona discharge is frequently observed at emitter tips, which may result in low ion abundances and reduced nano-ESI needle emitter lifetimes. In this work, we introduce a sheathless CE-MS method for the highly efficient and sensitive analysis of nucleotides employing ESI in positive ion mode, thereby fully circumventing corona discharge. By using a background electrolyte of 16 mM ammonium acetate (pH 9.7) a mixture of 12 nucleotides, composed of mono-, di-, and tri-phosphates, could be efficiently analyzed with plate numbers per meter above 220 000 and with LODs in the range from 0.06 to 1.3 nM, corresponding to 0.4 to 8.6 attomole, when using an injection volume of about 6.5 nL only. The utility of the method was demonstrated for the profiling of nucleotides in low numbers of mammalian cells using HepG2 cells as a model system. Endogenous nucleotides could be efficiently analyzed in extracts from 50 000 down to 500 HepG2 cells only. Moreover, apart from nucleotides, also some nicotinamide-adenine dinucleotides and amino acids could be analyzed under these conditions, thereby clearly illustrating the utility of this approach for metabolic profiling of low amounts of biological material.
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Affiliation(s)
- Wei Zhang
- Biomedical Microscale Analytics, Division of Systems Biomedicine and Pharmacology, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands
| | - Faisa Guled
- Biomedical Microscale Analytics, Division of Systems Biomedicine and Pharmacology, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands
| | - Thomas Hankemeier
- Biomedical Microscale Analytics, Division of Systems Biomedicine and Pharmacology, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands.,Netherlands Metabolomics Centre, Leiden, The Netherlands
| | - Rawi Ramautar
- Biomedical Microscale Analytics, Division of Systems Biomedicine and Pharmacology, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands
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38
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Deja S, Fu X, Fletcher JA, Kucejova B, Browning JD, Young JD, Burgess SC. Simultaneous tracers and a unified model of positional and mass isotopomers for quantification of metabolic flux in liver. Metab Eng 2019; 59:1-14. [PMID: 31891762 DOI: 10.1016/j.ymben.2019.12.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 12/12/2019] [Accepted: 12/21/2019] [Indexed: 12/23/2022]
Abstract
Computational models based on the metabolism of stable isotope tracers can yield valuable insight into the metabolic basis of disease. The complexity of these models is limited by the number of tracers and the ability to characterize tracer labeling in downstream metabolites. NMR spectroscopy is ideal for multiple tracer experiments since it precisely detects the position of tracer nuclei in molecules, but it lacks sensitivity for detecting low-concentration metabolites. GC-MS detects stable isotope mass enrichment in low-concentration metabolites, but lacks nuclei and positional specificity. We performed liver perfusions and in vivo infusions of 2H and 13C tracers, yielding complex glucose isotopomers that were assigned by NMR and fit to a newly developed metabolic model. Fluxes regressed from 2H and 13C NMR positional isotopomer enrichments served to validate GC-MS-based flux estimates obtained from the same experimental samples. NMR-derived fluxes were largely recapitulated by modeling the mass isotopomer distributions of six glucose fragment ions measured by GC-MS. Modest differences related to limited fragmentation coverage of glucose C1-C3 were identified, but fluxes such as gluconeogenesis, glycogenolysis, cataplerosis and TCA cycle flux were tightly correlated between the methods. Most importantly, modeling of GC-MS data could assign fluxes in primary mouse hepatocytes, an experiment that is impractical by 2H or 13C NMR.
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Affiliation(s)
- Stanislaw Deja
- Center for Human Nutrition, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Xiaorong Fu
- Center for Human Nutrition, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Justin A Fletcher
- Center for Human Nutrition, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Blanka Kucejova
- Center for Human Nutrition, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Jeffrey D Browning
- Department of Clinical Nutrition, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Jamey D Young
- Department of Chemical and Biomolecular Engineering, Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37235, USA.
| | - Shawn C Burgess
- Center for Human Nutrition, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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