1
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Kantner DS, Megill E, Bostwick A, Yang V, Bekeova C, Van Scoyk A, Seifert EL, Deininger MW, Snyder NW. Comparison of colorimetric, fluorometric, and liquid chromatography-mass spectrometry assays for acetyl-coenzyme A. Anal Biochem 2024; 685:115405. [PMID: 38016493 PMCID: PMC10955768 DOI: 10.1016/j.ab.2023.115405] [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: 08/18/2023] [Revised: 11/08/2023] [Accepted: 11/17/2023] [Indexed: 11/30/2023]
Abstract
Acetyl-Coenzyme A is a central metabolite in catabolic and anabolic pathways as well as the acyl donor for acetylation reactions. Multiple quantitative measurement techniques for acetyl-CoA have been reported, including commercially available kits. Comparisons between techniques for acetyl-CoA measurement have not been reported. This lack of comparability between assays makes context-specific assay selection and interpretation of results reporting changes in acetyl-CoA metabolism difficult. We compared commercially available colorimetric ELISA and fluorometric enzymatic-based kits to liquid chromatography-mass spectrometry-based assays using tandem mass spectrometry (LC-MS/MS) and high-resolution mass spectrometry (LC-HRMS). The colorimetric ELISA kit did not produce interpretable results even with commercially available pure standards. The fluorometric enzymatic kit produced comparable results to the LC-MS-based assays depending on matrix and extraction. LC-MS/MS and LC-HRMS assays produced well-aligned results, especially when incorporating stable isotope-labeled internal standards. In addition, we demonstrated the multiplexing capability of the LC-HRMS assay by measuring a suite of short-chain acyl-CoAs in a variety of acute myeloid leukemia cell lines and patient cells.
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Affiliation(s)
- Daniel S Kantner
- Lewis Katz School of Medicine at Temple University, Department of Cardiovascular Sciences, Aging + Cardiovascular Discovery Center, Philadelphia, PA, 19140, USA
| | - Emily Megill
- Lewis Katz School of Medicine at Temple University, Department of Cardiovascular Sciences, Aging + Cardiovascular Discovery Center, Philadelphia, PA, 19140, USA
| | - Anna Bostwick
- Lewis Katz School of Medicine at Temple University, Department of Cardiovascular Sciences, Aging + Cardiovascular Discovery Center, Philadelphia, PA, 19140, USA
| | - Vicky Yang
- Lewis Katz School of Medicine at Temple University, Department of Cardiovascular Sciences, Aging + Cardiovascular Discovery Center, Philadelphia, PA, 19140, USA
| | - Carmen Bekeova
- MitoCare Center, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | | | - Erin L Seifert
- MitoCare Center, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Michael W Deininger
- Versiti Blood Research Institute and Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Nathaniel W Snyder
- Lewis Katz School of Medicine at Temple University, Department of Cardiovascular Sciences, Aging + Cardiovascular Discovery Center, Philadelphia, PA, 19140, USA.
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2
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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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3
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Kantner DS, Megill E, Bostwick A, Yang V, Bekeova C, Van Scoyk A, Seifert E, Deininger MW, Snyder NW. Comparison of colorimetric, fluorometric, and liquid chromatography-mass spectrometry assays for acetyl-coenzyme A. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.01.543311. [PMID: 37398224 PMCID: PMC10312605 DOI: 10.1101/2023.06.01.543311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Acetyl-Coenzyme A is a central metabolite in catabolic and anabolic pathways as well as the acyl donor for acetylation reactions. Multiple quantitative measurement techniques for acetyl-CoA have been reported, including commercially available kits. Comparisons between techniques for acetyl-CoA measurement have not been reported. This lack of comparability between assays makes context-specific assay selection and interpretation of results reporting changes in acetyl-CoA metabolism difficult. We compared commercially available colorimetric ELISA and fluorometric enzymatic-based kits to liquid chromatography-mass spectrometry-based assays using tandem mass spectrometry (LC-MS/MS) and high-resolution mass spectrometry (LC-HRMS). The colorimetric ELISA kit did not produce interpretable results even with commercially available pure standards. The fluorometric enzymatic kit produced comparable results to the LC-MS-based assays depending on matrix and extraction. LC-MS/MS and LC-HRMS assays produced well-aligned results, especially when incorporating stable isotope-labeled internal standards. In addition, we demonstrated the multiplexing capability of the LC-HRMS assay by measuring a suite of short-chain acyl-CoAs in a variety of acute myeloid leukemia cell lines and patient cells.
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Affiliation(s)
- Daniel S Kantner
- Lewis Katz School of Medicine at Temple University, Department of Cardiovascular Sciences, Center for Metabolic Disease Research, Philadelphia, PA 19140, USA
| | - Emily Megill
- Lewis Katz School of Medicine at Temple University, Department of Cardiovascular Sciences, Center for Metabolic Disease Research, Philadelphia, PA 19140, USA
| | - Anna Bostwick
- Lewis Katz School of Medicine at Temple University, Department of Cardiovascular Sciences, Center for Metabolic Disease Research, Philadelphia, PA 19140, USA
| | - Vicky Yang
- Lewis Katz School of Medicine at Temple University, Department of Cardiovascular Sciences, Center for Metabolic Disease Research, Philadelphia, PA 19140, USA
| | - Carmen Bekeova
- MitoCare Center, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | | | - Erin Seifert
- MitoCare Center, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Michael W Deininger
- Versiti Blood Research Institute and Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Nathaniel W Snyder
- Lewis Katz School of Medicine at Temple University, Department of Cardiovascular Sciences, Center for Metabolic Disease Research, Philadelphia, PA 19140, USA
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4
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Garcia AM, Toni LS, Miyano CA, Sparagna GC, Jonscher R, Phillips EK, Karimpour-Fard A, Chapman HL, Baybayon-Grandgeorge AN, Pietra AE, Selner E, Chatfield KC, Stauffer BL, Sucharov CC, Miyamoto SD. Cardiac Transcriptome Remodeling and Impaired Bioenergetics in Single-Ventricle Congenital Heart Disease. JACC Basic Transl Sci 2023; 8:258-279. [PMID: 37034285 PMCID: PMC10077120 DOI: 10.1016/j.jacbts.2022.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 09/28/2022] [Accepted: 09/28/2022] [Indexed: 01/13/2023]
Abstract
The mechanisms responsible for heart failure in single-ventricle congenital heart disease are unknown. Using explanted heart tissue, we showed that failing single-ventricle hearts have dysregulated metabolic pathways, impaired mitochondrial function, decreased activity of carnitine palmitoyltransferase activity, and altered functioning of the tricarboxylic acid cycle. Interestingly, nonfailing single-ventricle hearts demonstrated an intermediate metabolic phenotype suggesting that they are vulnerable to development of heart failure in the future. Mitochondrial targeted therapies and treatments aimed at normalizing energy generation could represent a novel approach to the treatment or prevention of heart failure in this vulnerable group of patients.
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Affiliation(s)
- Anastacia M. Garcia
- Division of Cardiology, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Children’s Hospital Colorado, Aurora, Colorado, USA
| | - Lee S. Toni
- Division of Cardiology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Carissa A. Miyano
- Division of Cardiology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Genevieve C. Sparagna
- Division of Cardiology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Raleigh Jonscher
- Division of Cardiology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Elisabeth K. Phillips
- Division of Cardiology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Anis Karimpour-Fard
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Hailey L. Chapman
- Division of Cardiology, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Children’s Hospital Colorado, Aurora, Colorado, USA
| | | | - Ashley E. Pietra
- Division of Cardiology, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Children’s Hospital Colorado, Aurora, Colorado, USA
| | - Emma Selner
- Division of Cardiology, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Children’s Hospital Colorado, Aurora, Colorado, USA
| | - Kathryn C. Chatfield
- Division of Cardiology, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Children’s Hospital Colorado, Aurora, Colorado, USA
| | - Brian L. Stauffer
- Division of Cardiology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Division of Cardiology, Department of Medicine, Denver Health and Hospital Authority, Denver, Colorado, USA
| | - Carmen C. Sucharov
- Division of Cardiology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Shelley D. Miyamoto
- Division of Cardiology, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Children’s Hospital Colorado, Aurora, Colorado, USA
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5
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Schonbrun AR, Resh MD. Hedgehog acyltransferase catalyzes a random sequential reaction and utilizes multiple fatty acyl-CoA substrates. J Biol Chem 2022; 298:102422. [PMID: 36030053 PMCID: PMC9513256 DOI: 10.1016/j.jbc.2022.102422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/17/2022] [Accepted: 08/19/2022] [Indexed: 11/17/2022] Open
Abstract
Sonic hedgehog (Shh) signaling is a key component of embryonic development and is a driving force in several cancers. Hedgehog acyltransferase (Hhat), a member of the membrane-bound O-acyltransferase family of enzymes, catalyzes the attachment of palmitate to the N-terminal cysteine of Shh, a posttranslation modification critical for Shh signaling. The activity of Hhat has been assayed in cells and in vitro, and cryo-EM structures of Hhat have been reported, yet several unanswered questions remain regarding the enzyme’s reaction mechanism, substrate specificity, and the impact of the latter on Shh signaling. Here, we present an in vitro acylation assay with purified Hhat that directly monitors attachment of a fluorescently tagged fatty acyl chain to Shh. Our kinetic analyses revealed that the reaction catalyzed by Hhat proceeds through a random sequential mechanism. We also determined that Hhat can utilize multiple fatty acyl-CoA substrates for fatty acid transfer to Shh, with comparable affinities and turnover rates for myristoyl-CoA, palmitoyl-CoA, palmitoleoyl-CoA, and oleoyl-CoA. Furthermore, we investigated the functional consequence of differential fatty acylation of Shh in a luciferase-based Shh reporter system. We found that the potency of the signaling response in cells was higher for Shh acylated with saturated fatty acids compared to monounsaturated fatty acids. These findings demonstrate that Hhat can attach fatty acids other than palmitate to Shh and suggest that heterogeneous fatty acylation has the potential to impact Shh signaling in the developing embryo and/or cancer cells.
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Affiliation(s)
- Adina R Schonbrun
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY; Gerstner Sloan Kettering Graduate School
| | - Marilyn D Resh
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY; Gerstner Sloan Kettering Graduate School; Biochemistry, Cell Biology and Molecular Biology Graduate Program, Weill-Cornell Graduate School of Medical Sciences, New York, NY.
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6
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James AM, Norman AAI, Houghton JW, Prag HA, Logan A, Antrobus R, Hartley RC, Murphy MP. Native chemical ligation approach to sensitively probe tissue acyl-CoA pools. Cell Chem Biol 2022; 29:1232-1244.e5. [PMID: 35868236 DOI: 10.1016/j.chembiol.2022.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 01/29/2022] [Accepted: 04/18/2022] [Indexed: 11/16/2022]
Abstract
During metabolism, carboxylic acids are often activated by conjugation to the thiol of coenzyme A (CoA). The resulting acyl-CoAs comprise a group of ∼100 thioester-containing metabolites that could modify protein behavior through non-enzymatic N-acylation of lysine residues. However, the importance of many potential acyl modifications remains unclear because antibody-based methods to detect them are unavailable and the in vivo concentrations of their respective acyl-CoAs are poorly characterized. Here, we develop cysteine-triphenylphosphonium (CysTPP), a mass spectrometry probe that uses "native chemical ligation" to sensitively detect the major acyl-CoAs present in vivo through irreversible modification of its amine via a thioester intermediate. Using CysTPP, we show that longer-chain (C13-C22) acyl-CoAs often constitute ∼60% of the acyl-CoA pool in rat tissues. These hydrophobic longer-chain fatty acyl-CoAs have the potential to non-enzymatically modify protein residues.
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Affiliation(s)
- Andrew M James
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK.
| | - Abigail A I Norman
- School of Chemistry, University of Glasgow, Glasgow G12 8QQ, Scotland, UK
| | - Jack W Houghton
- Cambridge Institute of Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - Hiran A Prag
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Angela Logan
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Robin Antrobus
- Cambridge Institute of Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - Richard C Hartley
- School of Chemistry, University of Glasgow, Glasgow G12 8QQ, Scotland, UK
| | - Michael P Murphy
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK.
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7
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Pearce RW, Kodger JV, Sandlers YI. A liquid chromatography tandem mass spectrometry method for a semiquantitative screening of cellular acyl-CoA. Anal Biochem 2022; 640:114430. [PMID: 34688603 DOI: 10.1016/j.ab.2021.114430] [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: 06/21/2021] [Revised: 09/28/2021] [Accepted: 10/17/2021] [Indexed: 01/10/2023]
Abstract
This study describes LC-ESI-MS/MS method that covers the analysis of various cellular acyl-CoA in a single injection. The method is based on a quick extraction step eliminating LLE/SPE clean up. Method performance characteristics were determined after spiking acyl-CoA standards in different concentrations into a surrogate matrix. The extensive matrix effect for most acyl-CoA except for palmitoyl-CoA was compensated by using isotopically labeled internal standard and matrix-matched calibration. As a result of the high matrix effect, the accuracy for palmitoyl-CoA at the low concentration deviated from the target range of ±20%. The developed method was applied to identify twenty-one cellular acyl-CoA in SK-HEP-1 cells and screening for alterations in acyl-CoA levels post Mito Q antioxidant intervention.
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Affiliation(s)
- Ryan W Pearce
- Cleveland State University, Department of Chemistry, United States
| | - Jillian V Kodger
- Cleveland State University, Department of Chemistry, United States
| | - Yana I Sandlers
- Cleveland State University, Department of Chemistry, United States.
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8
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Chatfield KC, Sparagna GC, Specht KS, Whitcomb LA, Omar AK, Miyamoto SD, Wolfe LM, Chicco AJ. Long-chain fatty acid oxidation and respiratory complex I deficiencies distinguish Barth Syndrome from idiopathic pediatric cardiomyopathy. J Inherit Metab Dis 2022; 45:111-124. [PMID: 34821394 DOI: 10.1002/jimd.12459] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 11/14/2021] [Accepted: 11/23/2021] [Indexed: 12/16/2022]
Abstract
Barth syndrome (BTHS) is an X-linked disorder that results from mutations in the TAFAZZIN gene, which encodes a phospholipid transacylase responsible for generating the mature form of cardiolipin in inner mitochondrial membranes. BTHS patients develop early onset cardiomyopathy and a derangement of intermediary metabolism consistent with mitochondrial disease, but the precise alterations in cardiac metabolism that distinguish BTHS from idiopathic forms of cardiomyopathy are unknown. We performed the first metabolic analysis of myocardial tissue from BTHS cardiomyopathy patients compared to age- and sex-matched patients with idiopathic dilated cardiomyopathy (DCM) and nonfailing controls. Results corroborate previous evidence for deficiencies in cardiolipin content and its linoleoyl enrichment as defining features of BTHS cardiomyopathy, and reveal a dramatic accumulation of hydrolyzed (monolyso-) cardiolipin molecular species. Respiratory chain protein deficiencies were observed in both BTHS and DCM, but a selective depletion of complex I was seen only in BTHS after controlling for an apparent loss of mitochondrial density in cardiomyopathic hearts. Distinct shifts in the expression of long-chain fatty acid oxidation enzymes and the tissue acyl-CoA profile of BTHS hearts suggest a specific block in mitochondrial fatty acid oxidation upstream of the conventional matrix beta-oxidation cycle, which may be compensated for by a greater reliance upon peroxisomal fatty acid oxidation and the catabolism of ketones, amino acids, and pyruvate to meet cardiac energy demands. These results provide a comprehensive foundation for exploring novel therapeutic strategies that target the adaptive and maladaptive metabolic features of BTHS cardiomyopathy.
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Affiliation(s)
- Kathryn C Chatfield
- Department of Pediatrics, University of Colorado School of Medicine, Children's Hospital of Colorado, Aurora, Colorado, USA
| | - Genevieve C Sparagna
- Division of Cardiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Kalyn S Specht
- Department of Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Luke A Whitcomb
- Department of Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Asma K Omar
- Department of Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Shelley D Miyamoto
- Department of Pediatrics, University of Colorado School of Medicine, Children's Hospital of Colorado, Aurora, Colorado, USA
| | - Lisa M Wolfe
- Proteomics and Metabolomics Facility, Colorado State University, Fort Collins, Colorado, USA
| | - Adam J Chicco
- Department of Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA
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9
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Smith SA, Ogawa SA, Chau L, Whelan KA, Hamilton KE, Chen J, Tan L, Chen EZ, Keilbaugh S, Fogt F, Bewtra M, Braun J, Xavier RJ, Clish CB, Slaff B, Weljie AM, Bushman FD, Lewis JD, Li H, Master SR, Bennett MJ, Nakagawa H, Wu GD. Mitochondrial dysfunction in inflammatory bowel disease alters intestinal epithelial metabolism of hepatic acylcarnitines. J Clin Invest 2021; 131:133371. [PMID: 33141762 DOI: 10.1172/jci133371] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 10/09/2020] [Indexed: 12/26/2022] Open
Abstract
As the interface between the gut microbiota and the mucosal immune system, there has been great interest in the maintenance of colonic epithelial integrity through mitochondrial oxidation of butyrate, a short-chain fatty acid produced by the gut microbiota. Herein, we showed that the intestinal epithelium could also oxidize long-chain fatty acids, and that luminally delivered acylcarnitines in bile could be consumed via apical absorption by the intestinal epithelium, resulting in mitochondrial oxidation. Finally, intestinal inflammation led to mitochondrial dysfunction in the apical domain of the surface epithelium that may reduce the consumption of fatty acids, contributing to higher concentrations of fecal acylcarnitines in murine Citrobacter rodentium-induced colitis and human inflammatory bowel disease. These results emphasized the importance of both the gut microbiota and the liver in the delivery of energy substrates for mitochondrial metabolism by the intestinal epithelium.
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Affiliation(s)
- Sarah A Smith
- Department of Medicine, Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Sayaka A Ogawa
- Department of Medicine, Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Lillian Chau
- Department of Medicine, Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kelly A Whelan
- Fels Institute for Cancer Research and Molecular Biology, Department of Pathology and Laboratory Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania, USA
| | - Kathryn E Hamilton
- Division of Gastroenterology, Hepatology and Nutrition, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jie Chen
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Lu Tan
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Eric Z Chen
- Department of Informatics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Sue Keilbaugh
- Department of Medicine, Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Franz Fogt
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Meenakshi Bewtra
- Department of Medicine, Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jonathan Braun
- Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Ramnik J Xavier
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, Massachusetts, USA.,Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Clary B Clish
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, Massachusetts, USA
| | - Barry Slaff
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Aalim M Weljie
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Frederic D Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - James D Lewis
- Department of Medicine, Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Hongzhe Li
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Stephen R Master
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Michael J Bennett
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Hiroshi Nakagawa
- Division of Digestive and Liver Diseases, Department of Medicine, Herbert Irving Comprehensive Cancer Research Center, Columbia University Irving Medical Center, New York, New York, USA
| | - Gary D Wu
- Department of Medicine, Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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10
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Jones AE, Arias NJ, Acevedo A, Reddy ST, Divakaruni AS, Meriwether D. A Single LC-MS/MS Analysis to Quantify CoA Biosynthetic Intermediates and Short-Chain Acyl CoAs. Metabolites 2021; 11:metabo11080468. [PMID: 34436409 PMCID: PMC8401288 DOI: 10.3390/metabo11080468] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 07/09/2021] [Accepted: 07/14/2021] [Indexed: 12/11/2022] Open
Abstract
Coenzyme A (CoA) is an essential cofactor for dozens of reactions in intermediary metabolism. Dysregulation of CoA synthesis or acyl CoA metabolism can result in metabolic or neurodegenerative disease. Although several methods use liquid chromatography coupled with mass spectrometry/mass spectrometry (LC-MS/MS) to quantify acyl CoA levels in biological samples, few allow for simultaneous measurement of intermediates in the CoA biosynthetic pathway. Here we describe a simple sample preparation and LC-MS/MS method that can measure both short-chain acyl CoAs and biosynthetic precursors of CoA. The method does not require use of a solid phase extraction column during sample preparation and exhibits high sensitivity, precision, and accuracy. It reproduces expected changes from known effectors of cellular CoA homeostasis and helps clarify the mechanism by which excess concentrations of etomoxir reduce intracellular CoA levels.
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Affiliation(s)
- Anthony E. Jones
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, 650 Charles E Young Dr. South, Los Angeles, CA 90095, USA; (A.E.J.); (N.J.A.); (A.A.); (S.T.R.)
| | - Nataly J. Arias
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, 650 Charles E Young Dr. South, Los Angeles, CA 90095, USA; (A.E.J.); (N.J.A.); (A.A.); (S.T.R.)
| | - Aracely Acevedo
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, 650 Charles E Young Dr. South, Los Angeles, CA 90095, USA; (A.E.J.); (N.J.A.); (A.A.); (S.T.R.)
| | - Srinivasa T. Reddy
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, 650 Charles E Young Dr. South, Los Angeles, CA 90095, USA; (A.E.J.); (N.J.A.); (A.A.); (S.T.R.)
- Department of Medicine, Division of Cardiology, David Geffen School of Medicine, University of California, Los Angeles, 10833 Le Conte Avenue, Los Angeles, CA 90095, USA
| | - Ajit S. Divakaruni
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, 650 Charles E Young Dr. South, Los Angeles, CA 90095, USA; (A.E.J.); (N.J.A.); (A.A.); (S.T.R.)
- Correspondence: (A.S.D.); (D.M.)
| | - David Meriwether
- Department of Medicine, Division of Cardiology, David Geffen School of Medicine, University of California, Los Angeles, 10833 Le Conte Avenue, Los Angeles, CA 90095, USA
- Department of Medicine, Division of Digestive Diseases, David Geffen School of Medicine, University of California, Los Angeles, 10833 Le Conte Avenue, Los Angeles, CA 90095, USA
- Correspondence: (A.S.D.); (D.M.)
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11
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Trefely S, Lovell CD, Snyder NW, Wellen KE. Compartmentalised acyl-CoA metabolism and roles in chromatin regulation. Mol Metab 2020; 38:100941. [PMID: 32199817 PMCID: PMC7300382 DOI: 10.1016/j.molmet.2020.01.005] [Citation(s) in RCA: 137] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 01/03/2020] [Accepted: 01/07/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Many metabolites serve as important signalling molecules to adjust cellular activities and functions based on nutrient availability. Links between acetyl-CoA metabolism, histone lysine acetylation, and gene expression have been documented and studied over the past decade. In recent years, several additional acyl modifications to histone lysine residues have been identified, which depend on acyl-coenzyme A thioesters (acyl-CoAs) as acyl donors. Acyl-CoAs are intermediates of multiple distinct metabolic pathways, and substantial evidence has emerged that histone acylation is metabolically sensitive. Nevertheless, the metabolic sources of acyl-CoAs used for chromatin modification in most cases remain poorly understood. Elucidating how these diverse chemical modifications are coupled to and regulated by cellular metabolism is important in deciphering their functional significance. SCOPE OF REVIEW In this article, we review the metabolic pathways that produce acyl-CoAs, as well as emerging evidence for functional roles of diverse acyl-CoAs in chromatin regulation. Because acetyl-CoA has been extensively reviewed elsewhere, we will focus on four other acyl-CoA metabolites integral to major metabolic pathways that are also known to modify histones: succinyl-CoA, propionyl-CoA, crotonoyl-CoA, and butyryl-CoA. We also briefly mention several other acyl-CoA species, which present opportunities for further research; malonyl-CoA, glutaryl-CoA, 3-hydroxybutyryl-CoA, 2-hydroxyisobutyryl-CoA, and lactyl-CoA. Each acyl-CoA species has distinct roles in metabolism, indicating the potential to report shifts in the metabolic status of the cell. For each metabolite, we consider the metabolic pathways in which it participates and the nutrient sources from which it is derived, the compartmentalisation of its metabolism, and the factors reported to influence its abundance and potential nuclear availability. We also highlight reported biological functions of these metabolically-linked acylation marks. Finally, we aim to illuminate key questions in acyl-CoA metabolism as they relate to the control of chromatin modification. MAJOR CONCLUSIONS A majority of acyl-CoA species are annotated to mitochondrial metabolic processes. Since acyl-CoAs are not known to be directly transported across mitochondrial membranes, they must be synthesized outside of mitochondria and potentially within the nucleus to participate in chromatin regulation. Thus, subcellular metabolic compartmentalisation likely plays a key role in the regulation of histone acylation. Metabolite tracing in combination with targeting of relevant enzymes and transporters will help to map the metabolic pathways that connect acyl-CoA metabolism to chromatin modification. The specific function of each acyl-CoA may be determined in part by biochemical properties that affect its propensity for enzymatic versus non-enzymatic protein modification, as well as the various enzymes that can add, remove and bind each modification. Further, competitive and inhibitory effects of different acyl-CoA species on these enzymes make determining the relative abundance of acyl-CoA species in specific contexts important to understand the regulation of chromatin acylation. An improved and more nuanced understanding of metabolic regulation of chromatin and its roles in physiological and disease-related processes will emerge as these questions are answered.
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Affiliation(s)
- Sophie Trefely
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Metabolic Disease Research, Department of Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Claudia D Lovell
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nathaniel W Snyder
- Center for Metabolic Disease Research, Department of Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA.
| | - Kathryn E Wellen
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
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12
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Le CH, Benage LG, Specht KS, Li Puma LC, Mulligan CM, Heuberger AL, Prenni JE, Claypool SM, Chatfield KC, Sparagna GC, Chicco AJ. Tafazzin deficiency impairs CoA-dependent oxidative metabolism in cardiac mitochondria. J Biol Chem 2020; 295:12485-12497. [PMID: 32665401 DOI: 10.1074/jbc.ra119.011229] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 07/07/2020] [Indexed: 12/20/2022] Open
Abstract
Barth syndrome is a mitochondrial myopathy resulting from mutations in the tafazzin (TAZ) gene encoding a phospholipid transacylase required for cardiolipin remodeling. Cardiolipin is a phospholipid of the inner mitochondrial membrane essential for the function of numerous mitochondrial proteins and processes. However, it is unclear how tafazzin deficiency impacts cardiac mitochondrial metabolism. To address this question while avoiding confounding effects of cardiomyopathy on mitochondrial phenotype, we utilized Taz-shRNA knockdown (TazKD ) mice, which exhibit defective cardiolipin remodeling and respiratory supercomplex instability characteristic of human Barth syndrome but normal cardiac function into adulthood. Consistent with previous reports from other models, mitochondrial H2O2 emission and oxidative damage were greater in TazKD than in wild-type (WT) hearts, but there were no differences in oxidative phosphorylation coupling efficiency or membrane potential. Fatty acid and pyruvate oxidation capacities were 40-60% lower in TazKD mitochondria, but an up-regulation of glutamate oxidation supported respiration rates approximating those with pyruvate and palmitoylcarnitine in WT. Deficiencies in mitochondrial CoA and shifts in the cardiac acyl-CoA profile paralleled changes in fatty acid oxidation enzymes and acyl-CoA thioesterases, suggesting limitations of CoA availability or "trapping" in TazKD mitochondrial metabolism. Incubation of TazKD mitochondria with exogenous CoA partially rescued pyruvate and palmitoylcarnitine oxidation capacities, implicating dysregulation of CoA-dependent intermediary metabolism rather than respiratory chain defects in the bioenergetic impacts of tafazzin deficiency. These findings support links among cardiolipin abnormalities, respiratory supercomplex instability, and mitochondrial oxidant production and shed new light on the distinct metabolic consequences of tafazzin deficiency in the mammalian heart.
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Affiliation(s)
- Catherine H Le
- Cell and Molecular Biology Program, Colorado State University, Fort Collins, Colorado, USA
| | - Lindsay G Benage
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Kalyn S Specht
- Department of Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Lance C Li Puma
- Department of Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Christopher M Mulligan
- Department of Food Science and Human Nutrition, Colorado State University, Fort Collins, Colorado, USA
| | - Adam L Heuberger
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, Colorado, USA
| | - Jessica E Prenni
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, Colorado, USA
| | - Steven M Claypool
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Kathryn C Chatfield
- Department of Pediatrics, University of Colorado School of Medicine, Children's Hospital Colorado, Aurora, Colorado, USA
| | - Genevieve C Sparagna
- Division of Cardiology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Adam J Chicco
- Cell and Molecular Biology Program, Colorado State University, Fort Collins, Colorado, USA .,Department of Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA.,Department of Food Science and Human Nutrition, Colorado State University, Fort Collins, Colorado, USA
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13
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Wang HYJ, Hsu FF. Revelation of Acyl Double Bond Positions on Fatty Acyl Coenzyme A Esters by MALDI/TOF Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1047-1057. [PMID: 32167298 DOI: 10.1021/jasms.9b00139] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Fatty acyl coenzyme A esters (FA-CoAs) are important crossroad intermediates in lipid catabolism and anabolism, and the structures are complicated. Several mass spectrometric approaches have been previously described to elucidate their structures. However, a direct mass spectrometric approach toward a complete identification of the molecule, including the location of unsaturated bond(s) in the fatty acid chain has not been reported. In this study, we applied a simple MALDI/TOF mass spectrometric method to a near-complete characterization of long-chain FA-CoAs, including the location(s) of the double bond in the fatty acyl chain, and the common structural features that recognize FA-CoAs. Negative ion mass spectra of saturated, monounsaturated, and polyunsaturated FA-CoAs were acquired with a MALDI/TOF mass spectrometer using 2,5-dihydroxybenzoic acid as the matrix and ionized with a laser fluence two folds of the threshold to induce the in-source fragmentation (ISF) of the analytes. The resulting ISF spectra contained fragment ions arising from specific cleavages of the C-C bond immediate adjacent to the acyl double-bond. This structural feature affords locating the double-bond position(s) of the fatty acyl substituent. Thereby, positional isomer such as 18:3(n - 3) and 18:3(n - 6) FA-CoA can be differentiated without applying tandem mass spectrometry.
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Affiliation(s)
- Hay-Yan J Wang
- Department of Biological Sciences, National Sun Yat-Sen University, Kaohsiung 80424, Taiwan
| | - Fong-Fu Hsu
- Mass Spectrometry Resource, Division of Endocrinology, Diabetes, Metabolism, and Lipid Research, Washington University School of Medicine Box 8127, 660 S Euclid Ave., St. Louis, Missouri 63110, United States
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14
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Chen Y, Chen J, Zhang C, Yang S, Zhang X, Liu Y, Su Z. Deficiency in the short-chain acyl-CoA dehydrogenase protects mice against diet-induced obesity and insulin resistance. FASEB J 2019; 33:13722-13733. [PMID: 31585505 DOI: 10.1096/fj.201901474rr] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Yulong Chen
- Molecular Medicine Research Center and National Clinical Research Center for Geriatrics, West China Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Jinglu Chen
- Molecular Medicine Research Center and National Clinical Research Center for Geriatrics, West China Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Caixia Zhang
- Molecular Medicine Research Center and National Clinical Research Center for Geriatrics, West China Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Shanshan Yang
- Molecular Medicine Research Center and National Clinical Research Center for Geriatrics, West China Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Xueping Zhang
- Molecular Medicine Research Center and National Clinical Research Center for Geriatrics, West China Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Yin Liu
- Molecular Medicine Research Center and National Clinical Research Center for Geriatrics, West China Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Zhiguang Su
- Molecular Medicine Research Center and National Clinical Research Center for Geriatrics, West China Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
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15
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Bloom K, Mohsen AW, Karunanidhi A, El Demellawy D, Reyes-Múgica M, Wang Y, Ghaloul-Gonzalez L, Otsubo C, Tobita K, Muzumdar R, Gong Z, Tas E, Basu S, Chen J, Bennett M, Hoppel C, Vockley J. Investigating the link of ACAD10 deficiency to type 2 diabetes mellitus. J Inherit Metab Dis 2018; 41:49-57. [PMID: 28120165 PMCID: PMC5524623 DOI: 10.1007/s10545-017-0013-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 11/27/2016] [Accepted: 01/03/2017] [Indexed: 12/12/2022]
Abstract
The Native American Pima population has the highest incidence of insulin resistance (IR) and type 2 diabetes mellitus (T2DM) of any reported population, but the pathophysiologic mechanism is unknown. Genetic studies in Pima Indians have linked acyl-CoA dehydrogenase 10 (ACAD10) gene polymorphisms, among others, to this predisposition. The gene codes for a protein with a C-terminus region that is structurally similar to members of a family of flavoenzymes-the acyl-CoA dehydrogenases (ACADs)-that catalyze α,β-dehydrogenation reactions, including the first step in mitochondrial FAO (FAO), and intermediary reactions in amino acids catabolism. Dysregulation of FAO and an increase in plasma acylcarnitines are recognized as important in the pathophysiology of IR and T2DM. To investigate the deficiency of ACAD10 as a monogenic risk factor for T2DM in human, an Acad-deficient mouse was generated and characterized. The deficient mice exhibit an abnormal glucose tolerance test and elevated insulin levels. Blood acylcarnitine analysis shows an increase in long-chain species in the older mice. Nonspecific variable pattern of elevated short-terminal branch-chain acylcarnitines in a variety of tissues was also observed. Acad10 mice accumulate excess abdominal adipose tissue, develop an early inflammatory liver process, exhibit fasting rhabdomyolysis, and have abnormal skeletal muscle mitochondria. Our results identify Acad10 as a genetic determinant of T2DM in mice and provide a model to further investigate genetic determinants for insulin resistance in humans.
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MESH Headings
- Abdominal Fat/enzymology
- Abdominal Fat/physiopathology
- Acyl-CoA Dehydrogenase/genetics
- Adiposity
- Animals
- Blood Glucose/metabolism
- Diabetes Mellitus, Type 2/genetics
- Diabetes Mellitus, Type 2/pathology
- Diabetes Mellitus, Type 2/physiopathology
- Disease Models, Animal
- Genetic Predisposition to Disease
- Insulin/blood
- Insulin Resistance/genetics
- Lipid Metabolism, Inborn Errors/enzymology
- Lipid Metabolism, Inborn Errors/genetics
- Lipid Metabolism, Inborn Errors/pathology
- Lipid Metabolism, Inborn Errors/physiopathology
- Liver/enzymology
- Liver/pathology
- Mice, 129 Strain
- Mice, Inbred C57BL
- Mice, Knockout
- Mitochondria, Muscle/enzymology
- Mitochondria, Muscle/pathology
- Muscle, Skeletal/enzymology
- Muscle, Skeletal/pathology
- Non-alcoholic Fatty Liver Disease/enzymology
- Non-alcoholic Fatty Liver Disease/genetics
- Non-alcoholic Fatty Liver Disease/pathology
- Obesity, Abdominal/enzymology
- Obesity, Abdominal/genetics
- Obesity, Abdominal/physiopathology
- Phenotype
- Rhabdomyolysis/enzymology
- Rhabdomyolysis/genetics
- Rhabdomyolysis/pathology
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Affiliation(s)
- Kaitlyn Bloom
- Department of Pediatrics, School of Medicine, University of Pittsburgh, 4401 Penn Avenue, Pittsburgh, PA, 15224, USA
- Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Al-Walid Mohsen
- Department of Pediatrics, School of Medicine, University of Pittsburgh, 4401 Penn Avenue, Pittsburgh, PA, 15224, USA
| | - Anuradha Karunanidhi
- Department of Pediatrics, School of Medicine, University of Pittsburgh, 4401 Penn Avenue, Pittsburgh, PA, 15224, USA
| | - Dina El Demellawy
- Department of Pediatrics, School of Medicine, University of Pittsburgh, 4401 Penn Avenue, Pittsburgh, PA, 15224, USA
| | - Miguel Reyes-Múgica
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yudong Wang
- Department of Pediatrics, School of Medicine, University of Pittsburgh, 4401 Penn Avenue, Pittsburgh, PA, 15224, USA
| | - Lina Ghaloul-Gonzalez
- Department of Pediatrics, School of Medicine, University of Pittsburgh, 4401 Penn Avenue, Pittsburgh, PA, 15224, USA
| | - Chikara Otsubo
- Department of Pediatrics, School of Medicine, University of Pittsburgh, 4401 Penn Avenue, Pittsburgh, PA, 15224, USA
| | - Kimi Tobita
- Department of Pediatrics, School of Medicine, University of Pittsburgh, 4401 Penn Avenue, Pittsburgh, PA, 15224, USA
| | - Radhika Muzumdar
- Department of Pediatrics, School of Medicine, University of Pittsburgh, 4401 Penn Avenue, Pittsburgh, PA, 15224, USA
| | - Zhenwei Gong
- Department of Pediatrics, School of Medicine, University of Pittsburgh, 4401 Penn Avenue, Pittsburgh, PA, 15224, USA
| | - Emir Tas
- Department of Pediatrics, School of Medicine, University of Pittsburgh, 4401 Penn Avenue, Pittsburgh, PA, 15224, USA
| | - Shrabani Basu
- Department of Pediatrics, School of Medicine, University of Pittsburgh, 4401 Penn Avenue, Pittsburgh, PA, 15224, USA
| | - Jie Chen
- Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Michael Bennett
- Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Charles Hoppel
- School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Jerry Vockley
- Department of Pediatrics, School of Medicine, University of Pittsburgh, 4401 Penn Avenue, Pittsburgh, PA, 15224, USA.
- Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA.
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16
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Abrankó L, Williamson G, Gardner S, Kerimi A. Comprehensive quantitative analysis of fatty-acyl-Coenzyme A species in biological samples by ultra-high performance liquid chromatography-tandem mass spectrometry harmonizing hydrophilic interaction and reversed phase chromatography. J Chromatogr A 2017; 1534:111-122. [PMID: 29290399 DOI: 10.1016/j.chroma.2017.12.052] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 12/18/2017] [Accepted: 12/19/2017] [Indexed: 02/07/2023]
Abstract
Fatty acyl-Coenzyme A species (acyl-CoAs) are key biomarkers in studies focusing on cellular energy metabolism. Existing analytical approaches are unable to simultaneously detect the full range of short-, medium-, and long-chain acyl-CoAs, while chromatographic limitations encountered in the analysis of limited amounts of biological samples are an often overlooked problem. We report the systematic development of a UHPLC-ESI-MS/MS method which incorporates reversed phase (RP) and hydrophilic interaction liquid chromatography (HILIC) separations in series, in an automated mode. The protocol outlined encompasses quantification of acyl-CoAs of varying hydrophobicity from C2 to C20 with recoveries in the range of 90-111 % and limit of detection (LOD) 1-5 fmol, which is substantially lower than previously published methods. We demonstrate that the poor chromatographic performance and signal losses in MS detection, typically observed for phosphorylated organic molecules, can be avoided by the incorporation of a 0.1% phosphoric acid wash step between injections. The methodological approach presented here permits a highly reliable, sensitive and precise analysis of small amounts of tissues and cell samples as demonstrated in mouse liver, human hepatic (HepG2) and skeletal muscle (LHCNM2) cells. The considerable improvements discussed pave the way for acyl-CoAs to be incorporated in routine targeted lipid biomarker profile studies.
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Affiliation(s)
- László Abrankó
- University of Leeds, School of Food Science and Nutrition, Leeds, LS2 9JT, UK
| | - Gary Williamson
- University of Leeds, School of Food Science and Nutrition, Leeds, LS2 9JT, UK
| | - Samantha Gardner
- University of Leeds, School of Food Science and Nutrition, Leeds, LS2 9JT, UK
| | - Asimina Kerimi
- University of Leeds, School of Food Science and Nutrition, Leeds, LS2 9JT, UK.
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17
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Kebede AF, Nieborak A, Shahidian LZ, Le Gras S, Richter F, Gómez DA, Baltissen MP, Meszaros G, Magliarelli HDF, Taudt A, Margueron R, Colomé-Tatché M, Ricci R, Daujat S, Vermeulen M, Mittler G, Schneider R. Histone propionylation is a mark of active chromatin. Nat Struct Mol Biol 2017; 24:1048-1056. [PMID: 29058708 DOI: 10.1038/nsmb.3490] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 09/22/2017] [Indexed: 12/17/2022]
Abstract
Histones are highly covalently modified, but the functions of many of these modifications remain unknown. In particular, it is unclear how histone marks are coupled to cellular metabolism and how this coupling affects chromatin architecture. We identified histone H3 Lys14 (H3K14) as a site of propionylation and butyrylation in vivo and carried out the first systematic characterization of histone propionylation. We found that H3K14pr and H3K14bu are deposited by histone acetyltransferases, are preferentially enriched at promoters of active genes and are recognized by acylation-state-specific reader proteins. In agreement with these findings, propionyl-CoA was able to stimulate transcription in an in vitro transcription system. Notably, genome-wide H3 acylation profiles were redefined following changes to the metabolic state, and deletion of the metabolic enzyme propionyl-CoA carboxylase altered global histone propionylation levels. We propose that histone propionylation, acetylation and butyrylation may act in combination to promote high transcriptional output and to couple cellular metabolism with chromatin structure and function.
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Affiliation(s)
- Adam F Kebede
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Anna Nieborak
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Lara Zorro Shahidian
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Stephanie Le Gras
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
| | - Florian Richter
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.,Goethe-Universität Fachbereich Medizin, Frankfurt, Germany
| | - Diana Aguilar Gómez
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany.,Undergraduate Program in Genomic Sciences, National Autonomous University of Mexico, Mexico City, Mexico
| | - Marijke P Baltissen
- Radboud University Nijmegen, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Gergo Meszaros
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Université de Strasbourg, Strasbourg, France.,Laboratoire de Biochimie et de Biologie Moléculaire, Nouvel Hôpital Civil, Strasbourg, France
| | | | - Aaron Taudt
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | | | - Maria Colomé-Tatché
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Technical University Munich, Freising, Germany
| | - Romeo Ricci
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Université de Strasbourg, Strasbourg, France.,Laboratoire de Biochimie et de Biologie Moléculaire, Nouvel Hôpital Civil, Strasbourg, France
| | - Sylvain Daujat
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
| | - Michiel Vermeulen
- Radboud University Nijmegen, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Gerhard Mittler
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Robert Schneider
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany.,Ludwig-Maximilains-Universität München, Faculty of Biology, Munich, Germany
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18
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Carrer A, Parris JLD, Trefely S, Henry RA, Montgomery DC, Torres A, Viola JM, Kuo YM, Blair IA, Meier JL, Andrews AJ, Snyder NW, Wellen KE. Impact of a High-fat Diet on Tissue Acyl-CoA and Histone Acetylation Levels. J Biol Chem 2017; 292:3312-3322. [PMID: 28077572 PMCID: PMC5336165 DOI: 10.1074/jbc.m116.750620] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 01/06/2017] [Indexed: 11/06/2022] Open
Abstract
Cellular metabolism dynamically regulates the epigenome via availability of the metabolite substrates of chromatin-modifying enzymes. The impact of diet on the metabolism-epigenome axis is poorly understood but could alter gene expression and influence metabolic health. ATP citrate-lyase produces acetyl-CoA in the nucleus and cytosol and regulates histone acetylation levels in many cell types. Consumption of a high-fat diet (HFD) results in suppression of ATP citrate-lyase levels in tissues such as adipose and liver, but the impact of diet on acetyl-CoA and histone acetylation in these tissues remains unknown. Here we examined the effects of HFD on levels of acyl-CoAs and histone acetylation in mouse white adipose tissue (WAT), liver, and pancreas. We report that mice consuming a HFD have reduced levels of acetyl-CoA and/or acetyl-CoA:CoA ratio in these tissues. In WAT and the pancreas, HFD also impacted the levels of histone acetylation; in particular, histone H3 lysine 23 acetylation was lower in HFD-fed mice. Genetic deletion of Acly in cultured adipocytes also suppressed acetyl-CoA and histone acetylation levels. In the liver, no significant effects on histone acetylation were observed with a HFD despite lower acetyl-CoA levels. Intriguingly, acetylation of several histone lysines correlated with the acetyl-CoA: (iso)butyryl-CoA ratio in liver. Butyryl-CoA and isobutyryl-CoA interacted with the acetyltransferase P300/CBP-associated factor (PCAF) in liver lysates and inhibited its activity in vitro This study thus provides evidence that diet can impact tissue acyl-CoA and histone acetylation levels and that acetyl-CoA abundance correlates with acetylation of specific histone lysines in WAT but not in the liver.
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Affiliation(s)
- Alessandro Carrer
- Department of Cancer Biology, Abramson Family Cancer Research Institute
| | - Joshua L D Parris
- Department of Cancer Biology, Abramson Family Cancer Research Institute
| | - Sophie Trefely
- Department of Cancer Biology, Abramson Family Cancer Research Institute; A. J. Drexel Autism Institute, Drexel University, Philadelphia, Pennsylvania 19104
| | - Ryan A Henry
- Department of Cancer Biology, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111
| | - David C Montgomery
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702
| | - AnnMarie Torres
- Department of Cancer Biology, Abramson Family Cancer Research Institute
| | - John M Viola
- Department of Cancer Biology, Abramson Family Cancer Research Institute
| | - Yin-Ming Kuo
- Department of Cancer Biology, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111
| | - Ian A Blair
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Jordan L Meier
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702
| | - Andrew J Andrews
- Department of Cancer Biology, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111
| | - Nathaniel W Snyder
- A. J. Drexel Autism Institute, Drexel University, Philadelphia, Pennsylvania 19104
| | - Kathryn E Wellen
- Department of Cancer Biology, Abramson Family Cancer Research Institute.
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Ringel AE, Wolberger C. Structural basis for acyl-group discrimination by human Gcn5L2. Acta Crystallogr D Struct Biol 2016; 72:841-8. [PMID: 27377381 PMCID: PMC4932917 DOI: 10.1107/s2059798316007907] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 05/13/2016] [Indexed: 11/10/2022] Open
Abstract
Gcn5 is a conserved acetyltransferase that regulates transcription by acetylating the N-terminal tails of histones. Motivated by recent studies identifying a chemically diverse array of lysine acyl modifications in vivo, the acyl-chain specificity of the acetyltransferase human Gcn5 (Gcn5L2) was examined. Whereas Gcn5L2 robustly catalyzes lysine acetylation, the acyltransferase activity of Gcn5L2 becomes progressively weaker with increasing acyl-chain length. To understand how Gcn5 discriminates between different acyl-CoA molecules, structures of the catalytic domain of human Gcn5L2 bound to propionyl-CoA and butyryl-CoA were determined. Although the active site of Gcn5L2 can accommodate propionyl-CoA and butyryl-CoA without major structural rearrangements, butyryl-CoA adopts a conformation incompatible with catalysis that obstructs the path of the incoming lysine residue and acts as a competitive inhibitor of Gcn5L2 versus acetyl-CoA. These structures demonstrate how Gcn5L2 discriminates between acyl-chain donors and explain why Gcn5L2 has weak activity for acyl moieties that are larger than an acetyl group.
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Affiliation(s)
- Alison E. Ringel
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, USA
| | - Cynthia Wolberger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, USA
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Ganetzky RD, Bloom K, Ahrens-Nicklas R, Edmondson A, Deardorff MA, Bennett MJ, Ficicioglu C. ECHS1 Deficiency as a Cause of Severe Neonatal Lactic Acidosis. JIMD Rep 2016; 30:33-37. [PMID: 26920905 DOI: 10.1007/8904_2016_538] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 01/11/2016] [Accepted: 01/13/2016] [Indexed: 12/02/2022] Open
Abstract
Mitochondrial short-chain enoyl-CoA hydratase deficiency (ECHS1D) is caused by mutations in ECHS1 (OMIM 602292) and is a recently identified inborn error of valine and fatty acid metabolism. This defect leads to secondary mitochondrial dysfunction. The majority of previously reported patients had the Leigh syndrome, with a median life expectancy of approximately 2 years. We report two siblings born 3 years apart with prenatal findings including facial dysmorphia, oligohydramnios, intrauterine growth restriction, and premature delivery. They had severe lactic acidosis with onset within the first hours of life, had congenital dilated cardiomyopathy, and died at 16 h of life and 2 days of life, respectively.Biochemical evaluation of these patients showed elevated butyryl-carnitine in the blood and elevated methylmalonyl/succinyl-CoA and decreased hydroxybutyryl-CoA in frozen liver of patient 2, confirming abnormal short-chain fatty acid metabolism. Elevated butyryl-carnitine has been reported only in a single previous case of ECHS1 deficiency, which also had neonatal onset. Pyruvate and lactate levels were both elevated with a normal pyruvate-lactate ratio. This supports the previous hypothesis that lactic acidosis in these patients results from secondary inhibition of the pyruvate dehydrogenase complex. The biomarker 2,3-dihydroxy-2-methylbutyric acid was detected in patient 2, but at lower levels than in previously reported cases.These cases extend our understanding of the severe end of the phenotypic spectrum of ECHS1 deficiency, clarify the range of biochemical abnormalities associated with this new disorder, and highlight the need to suspect this disease in patients presenting with comparable metabolic derangements and dysmorphic features.
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Affiliation(s)
- Rebecca D Ganetzky
- Department of Pediatrics, Division of Human Genetics, The Children's Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, 3501 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Kaitlyn Bloom
- Department of Pathology and Laboratory Medicine, Michael Palmieri Metabolic Disease Laboratory, The Children's Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Rebecca Ahrens-Nicklas
- Department of Pediatrics, Division of Human Genetics, The Children's Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, 3501 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Andrew Edmondson
- Department of Pediatrics, Division of Human Genetics, The Children's Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, 3501 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Matthew A Deardorff
- Department of Pediatrics, Division of Human Genetics, The Children's Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, 3501 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Michael J Bennett
- Department of Pathology and Laboratory Medicine, Michael Palmieri Metabolic Disease Laboratory, The Children's Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Can Ficicioglu
- Department of Pediatrics, Division of Human Genetics, The Children's Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, 3501 Civic Center Blvd, Philadelphia, PA, 19104, USA.
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21
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Ferdinandusse S, Friederich MW, Burlina A, Ruiter JPN, Coughlin CR, Dishop MK, Gallagher RC, Bedoyan JK, Vaz FM, Waterham HR, Gowan K, Chatfield K, Bloom K, Bennett MJ, Elpeleg O, Van Hove JLK, Wanders RJA. Clinical and biochemical characterization of four patients with mutations in ECHS1. Orphanet J Rare Dis 2015; 10:79. [PMID: 26081110 PMCID: PMC4474341 DOI: 10.1186/s13023-015-0290-1] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 05/29/2015] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Short-chain enoyl-CoA hydratase (SCEH, encoded by ECHS1) catalyzes hydration of 2-trans-enoyl-CoAs to 3(S)-hydroxy-acyl-CoAs. SCEH has a broad substrate specificity and is believed to play an important role in mitochondrial fatty acid oxidation and in the metabolism of branched-chain amino acids. Recently, the first patients with SCEH deficiency have been reported revealing only a defect in valine catabolism. We investigated the role of SCEH in fatty acid and branched-chain amino acid metabolism in four newly identified patients. In addition, because of the Leigh-like presentation, we studied enzymes involved in bioenergetics. METHODS Metabolite, enzymatic, protein and genetic analyses were performed in four patients, including two siblings. Palmitate loading studies in fibroblasts were performed to study mitochondrial β-oxidation. In addition, enoyl-CoA hydratase activity was measured with crotonyl-CoA, methacrylyl-CoA, tiglyl-CoA and 3-methylcrotonyl-CoA both in fibroblasts and liver to further study the role of SCEH in different metabolic pathways. Analyses of pyruvate dehydrogenase and respiratory chain complexes were performed in multiple tissues of two patients. RESULTS All patients were either homozygous or compound heterozygous for mutations in the ECHS1 gene, had markedly reduced SCEH enzymatic activity and protein level in fibroblasts. All patients presented with lactic acidosis. The first two patients presented with vacuolating leukoencephalopathy and basal ganglia abnormalities. The third patient showed a slow neurodegenerative condition with global brain atrophy and the fourth patient showed Leigh-like lesions with a single episode of metabolic acidosis. Clinical picture and metabolite analysis were not consistent with a mitochondrial fatty acid oxidation disorder, which was supported by the normal palmitate loading test in fibroblasts. Patient fibroblasts displayed deficient hydratase activity with different substrates tested. Pyruvate dehydrogenase activity was markedly reduced in particular in muscle from the most severely affected patients, which was caused by reduced expression of E2 protein, whereas E2 mRNA was increased. CONCLUSIONS Despite its activity towards substrates from different metabolic pathways, SCEH appears to be only crucial in valine metabolism, but not in isoleucine metabolism, and only of limited importance for mitochondrial fatty acid oxidation. In severely affected patients SCEH deficiency can cause a secondary pyruvate dehydrogenase deficiency contributing to the clinical presentation.
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Affiliation(s)
- Sacha Ferdinandusse
- Departments of Clinical Chemistry and Pediatrics, Laboratory Genetic Metabolic Diseases, Academic Medical Center, University of Amsterdam, Amsterdam, AZ, 1105, The Netherlands.
| | - Marisa W Friederich
- Department of Pediatrics, Section of Genetics, University of Colorado, Aurora, CO, 80045, USA.
| | - Alberto Burlina
- Department of Paediatrics, Division of Metabolic Diseases, University Hospital of Padua, Padua, Italy.
| | - Jos P N Ruiter
- Departments of Clinical Chemistry and Pediatrics, Laboratory Genetic Metabolic Diseases, Academic Medical Center, University of Amsterdam, Amsterdam, AZ, 1105, The Netherlands.
| | - Curtis R Coughlin
- Department of Pediatrics, Section of Genetics, University of Colorado, Aurora, CO, 80045, USA.
| | - Megan K Dishop
- Department of Pathology, University of Colorado, Aurora, CO, 80045, USA.
| | - Renata C Gallagher
- Department of Pediatrics, Section of Genetics, University of Colorado, Aurora, CO, 80045, USA.
| | - Jirair K Bedoyan
- Center for Inherited Disorders of Energy Metabolism (CIDEM), University Hospitals Case Medical Center, Cleveland, OH, 44106, USA. .,Departments of Genetics and Pediatrics, Case Western Reserve University, Cleveland, OH, 44106, USA.
| | - Frédéric M Vaz
- Departments of Clinical Chemistry and Pediatrics, Laboratory Genetic Metabolic Diseases, Academic Medical Center, University of Amsterdam, Amsterdam, AZ, 1105, The Netherlands.
| | - Hans R Waterham
- Departments of Clinical Chemistry and Pediatrics, Laboratory Genetic Metabolic Diseases, Academic Medical Center, University of Amsterdam, Amsterdam, AZ, 1105, The Netherlands.
| | - Katherine Gowan
- Department of Biochemistry and Molecular Genetics, University of Colorado, Aurora, CO, 80045, USA.
| | - Kathryn Chatfield
- Department of Pediatrics, Section of Genetics, University of Colorado, Aurora, CO, 80045, USA. .,Department of Pediatrics, Section of Pediatric Cardiology, University of Colorado, Aurora, CO, 80045, USA.
| | - Kaitlyn Bloom
- Department of Pathology & Laboratory Medicine, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, U74SA, USA.
| | - Michael J Bennett
- Department of Pathology & Laboratory Medicine, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, U74SA, USA.
| | - Orly Elpeleg
- Monique and Jacques Roboh Department of Genetic Research, Hadassah, Hebrew University Medical Center, Jerusalem, Israel.
| | - Johan L K Van Hove
- Department of Pediatrics, Section of Genetics, University of Colorado, Aurora, CO, 80045, USA.
| | - Ronald J A Wanders
- Departments of Clinical Chemistry and Pediatrics, Laboratory Genetic Metabolic Diseases, Academic Medical Center, University of Amsterdam, Amsterdam, AZ, 1105, The Netherlands.
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22
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Dittenhafer-Reed KE, Richards AL, Fan J, Smallegan MJ, Fotuhi Siahpirani A, Kemmerer ZA, Prolla TA, Roy S, Coon JJ, Denu JM. SIRT3 mediates multi-tissue coupling for metabolic fuel switching. Cell Metab 2015; 21:637-46. [PMID: 25863253 PMCID: PMC4393847 DOI: 10.1016/j.cmet.2015.03.007] [Citation(s) in RCA: 141] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 12/17/2014] [Accepted: 03/09/2015] [Indexed: 02/07/2023]
Abstract
SIRT3 is a member of the Sirtuin family of NAD(+)-dependent deacylases and plays a critical role in metabolic regulation. Organism-wide SIRT3 loss manifests in metabolic alterations; however, the coordinating role of SIRT3 among metabolically distinct tissues is unknown. Using multi-tissue quantitative proteomics comparing fasted wild-type mice to mice lacking SIRT3, innovative bioinformatic analysis, and biochemical validation, we provide a comprehensive view of mitochondrial acetylation and SIRT3 function. We find SIRT3 regulates the acetyl-proteome in core mitochondrial processes common to brain, heart, kidney, liver, and skeletal muscle, but differentially regulates metabolic pathways in fuel-producing and fuel-utilizing tissues. We propose an additional maintenance function for SIRT3 in liver and kidney where SIRT3 expression is elevated to reduce the acetate load on mitochondrial proteins. We provide evidence that SIRT3 impacts ketone body utilization in the brain and reveal a pivotal role for SIRT3 in the coordination between tissues required for metabolic homeostasis.
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Affiliation(s)
| | - Alicia L Richards
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53715, USA; The Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin 53715, USA
| | - Jing Fan
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin 53715, USA
| | - Michael J Smallegan
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin 53715, USA
| | | | - Zachary A Kemmerer
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53715, USA
| | - Tomas A Prolla
- Department of Genetics and Medical Genetics, University of Wisconsin, Madison, Wisconsin 53715, USA
| | - Sushmita Roy
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, Wisconsin 53715, USA
| | - Joshua J Coon
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin 53715, USA; Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53715, USA; The Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin 53715, USA
| | - John M Denu
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin 53715, USA.
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23
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Human platelets as a platform to monitor metabolic biomarkers using stable isotopes and LC-MS. Bioanalysis 2014; 5:3009-21. [PMID: 24320127 DOI: 10.4155/bio.13.269] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Intracellular metabolites such as CoA thioesters are modulated in a number of clinical settings. Their accurate measurement from surrogate tissues such as platelets may provide additional information to current serum and urinary biomarkers. METHODS Freshly isolated platelets from healthy volunteers were treated with rotenone, propionate or isotopically labeled metabolic tracers. Using a recently developed LC-MS-based methodology, absolute changes in short-chain acyl-CoA thioesters were monitored, as well as relative metabolic labeling using isotopomer distribution analysis. RESULTS Consistent with in vitro experiments, isolated platelets treated with rotenone showed decreased intracellular succinyl-CoA and increased β-hydroxybutyryl-CoA, while propionate treatment resulted in increased propionyl-CoA. In addition, isotopomers of the CoAs were readily detected in platelets treated with the [(13)C]- or [(13)C(15)N]-labeled metabolic precursors. CONCLUSION Here, we show that human platelets can provide a powerful ex vivo challenge platform with potential clinical diagnostic and biomarker discovery applications.
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24
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Rogers GW, Nadanaciva S, Swiss R, Divakaruni AS, Will Y. Assessment of fatty acid beta oxidation in cells and isolated mitochondria. ACTA ACUST UNITED AC 2014; 60:25.3.1-19. [PMID: 24865647 DOI: 10.1002/0471140856.tx2503s60] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Fatty acid beta oxidation is a major pathway of energy metabolism and occurs primarily in mitochondria. Drug-induced modulation of this pathway can cause adverse effects such as liver injury, or be beneficial for treating heart failure, type 2 diabetes, and obesity. Hence, in vitro assays that are able to identify compounds that affect fatty acid oxidation are of value for toxicity assessments, as well as for efficacy assessments. Here, we describe two high-throughput assays, one for assessing fatty acid oxidation in cells and the other for assessing fatty acid oxidation in isolated rat liver mitochondria. Both assays measure fatty acid-driven oxygen consumption and can be used for rapid and robust screening of compounds that modulate fatty acid oxidation.
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25
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Bennett MJ, Palladino A, Kallish S, Chen J. Novel biomarkers for diagnosing and understanding pathophysiology of metabolic diseases. Clin Biochem 2014; 47:706-7. [PMID: 24854684 DOI: 10.1016/j.clinbiochem.2014.05.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Michael J Bennett
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Metabolic Disease Laboratory, Children's Hospital of Philadelphia, 5NW58, 34th Street & Civic Center Blvd, Philadelphia, PA 19104, USA.
| | - Andrew Palladino
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Metabolic Disease Laboratory, Children's Hospital of Philadelphia, 5NW58, 34th Street & Civic Center Blvd, Philadelphia, PA 19104, USA
| | - Stacy Kallish
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Metabolic Disease Laboratory, Children's Hospital of Philadelphia, 5NW58, 34th Street & Civic Center Blvd, Philadelphia, PA 19104, USA
| | - Jie Chen
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Metabolic Disease Laboratory, Children's Hospital of Philadelphia, 5NW58, 34th Street & Civic Center Blvd, Philadelphia, PA 19104, USA
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Siegel D, Permentier H, Reijngoud DJ, Bischoff R. Chemical and technical challenges in the analysis of central carbon metabolites by liquid-chromatography mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2013; 966:21-33. [PMID: 24326023 DOI: 10.1016/j.jchromb.2013.11.022] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 11/10/2013] [Accepted: 11/12/2013] [Indexed: 11/18/2022]
Abstract
This review deals with chemical and technical challenges in the analysis of small-molecule metabolites involved in central carbon and energy metabolism via liquid-chromatography mass-spectrometry (LC-MS). The covered analytes belong to the prominent pathways in biochemical carbon oxidation such as glycolysis or the tricarboxylic acid cycle and, for the most part, share unfavorable properties such as a high polarity, chemical instability or metal-affinity. The topic is introduced by selected examples on successful applications of metabolomics in the clinic. In the core part of the paper, the structural features of important analyte classes such as nucleotides, coenzyme A thioesters or carboxylic acids are linked to "problematic hotspots" along the analytical chain (sample preparation and-storage, separation and detection). We discuss these hotspots from a chemical point of view, covering issues such as analyte degradation or interactions with metals and other matrix components. Based on this understanding we propose solutions wherever available. A major notion derived from these considerations is that comprehensive carbon metabolomics inevitably requires multiple, complementary analytical approaches covering different chemical classes of metabolites.
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Affiliation(s)
- David Siegel
- University of Groningen, Department of Pharmacy, Analytical Biochemistry, Antonius-Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Hjalmar Permentier
- University of Groningen, Department of Pharmacy, Mass Spectrometry Core Facility, Antonius-Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Dirk-Jan Reijngoud
- University Medical Center Groningen, Department of Pediatrics, Center for Liver, Digestive and Metabolic Diseases, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Rainer Bischoff
- University of Groningen, Department of Pharmacy, Analytical Biochemistry, Antonius-Deusinglaan 1, 9713 AV Groningen, The Netherlands.
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A liver-specific defect of Acyl-CoA degradation produces hyperammonemia, hypoglycemia and a distinct hepatic Acyl-CoA pattern. PLoS One 2013; 8:e60581. [PMID: 23861731 PMCID: PMC3702508 DOI: 10.1371/journal.pone.0060581] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Accepted: 05/06/2013] [Indexed: 01/15/2023] Open
Abstract
Most conditions detected by expanded newborn screening result from deficiency of one of the enzymes that degrade acyl-coenzyme A (CoA) esters in mitochondria. The role of acyl-CoAs in the pathophysiology of these disorders is poorly understood, in part because CoA esters are intracellular and samples are not generally available from human patients. We created a mouse model of one such condition, deficiency of 3-hydroxy-3-methylglutaryl-CoA lyase (HL), in liver (HLLKO mice). HL catalyses a reaction of ketone body synthesis and of leucine degradation. Chronic HL deficiency and acute crises each produced distinct abnormal liver acyl-CoA patterns, which would not be predictable from levels of urine organic acids and plasma acylcarnitines. In HLLKO hepatocytes, ketogenesis was undetectable. Carboxylation of [2-(14)C] pyruvate diminished following incubation of HLLKO hepatocytes with the leucine metabolite 2-ketoisocaproate (KIC). HLLKO mice also had suppression of the normal hyperglycemic response to a systemic pyruvate load, a measure of gluconeogenesis. Hyperammonemia and hypoglycemia, cardinal features of many inborn errors of acyl-CoA metabolism, occurred spontaneously in some HLLKO mice and were inducible by administering KIC. KIC loading also increased levels of several leucine-related acyl-CoAs and reduced acetyl-CoA levels. Ultrastructurally, hepatocyte mitochondria of KIC-treated HLLKO mice show marked swelling. KIC-induced hyperammonemia improved following administration of carglumate (N-carbamyl-L-glutamic acid), which substitutes for the product of an acetyl-CoA-dependent reaction essential for urea cycle function, demonstrating an acyl-CoA-related mechanism for this complication.
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