1
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Zhang D, Gao J, Zhu Z, Mao Q, Xu Z, Singh PK, Rimayi CC, Moreno-Yruela C, Xu S, Li G, Sin YC, Chen Y, Olsen CA, Snyder NW, Dai L, Li L, Zhao Y. Lysine L-lactylation is the dominant lactylation isomer induced by glycolysis. Nat Chem Biol 2024:10.1038/s41589-024-01680-8. [PMID: 39030363 DOI: 10.1038/s41589-024-01680-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 06/13/2024] [Indexed: 07/21/2024]
Abstract
Lysine L-lactylation (Kl-la) is a novel protein posttranslational modification (PTM) driven by L-lactate. This PTM has three isomers: Kl-la, N-ε-(carboxyethyl)-lysine (Kce) and D-lactyl-lysine (Kd-la), which are often confused in the context of the Warburg effect and nuclear presence. Here we introduce two methods to differentiate these isomers: a chemical derivatization and high-performance liquid chromatography analysis for efficient separation, and isomer-specific antibodies for high-selectivity identification. We demonstrated that Kl-la is the primary lactylation isomer on histones and dynamically regulated by glycolysis, not Kd-la or Kce, which are observed when the glyoxalase system was incomplete. The study also reveals that lactyl-coenzyme A, a precursor in L-lactylation, correlates positively with Kl-la levels. This work not only provides a methodology for distinguishing other PTM isomers, but also highlights Kl-la as the primary responder to glycolysis and the Warburg effect.
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Affiliation(s)
- Di Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
| | - Jinjun Gao
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL, USA
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
- Shenzhen Bay Laboratory, Shenzhen, China
| | - Zhijun Zhu
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Qianying Mao
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Zhiqiang Xu
- National Clinical Research Center for Geriatrics and General Practice Ward/International Medical Center Ward, General Practice Medical Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Pankaj K Singh
- Lewis Katz School of Medicine at Temple University, Department of Cardiovascular Sciences, Center for Metabolic Disease Research, Philadelphia, PA, USA
| | - Cornelius C Rimayi
- Lewis Katz School of Medicine at Temple University, Department of Cardiovascular Sciences, Center for Metabolic Disease Research, Philadelphia, PA, USA
| | - Carlos Moreno-Yruela
- Center for Biopharmaceuticals and Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Shuling Xu
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
| | - Gongyu Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
- Research Center for Analytical Science and Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, China
| | - Yi-Cheng Sin
- Department of Biochemistry, Molecular Biology and Biophysics, The University of Minnesota at Twin Cities, Minneapolis, MN, USA
| | - Yue Chen
- Department of Biochemistry, Molecular Biology and Biophysics, The University of Minnesota at Twin Cities, Minneapolis, MN, USA
| | - Christian A Olsen
- Center for Biopharmaceuticals and Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nathaniel W Snyder
- Lewis Katz School of Medicine at Temple University, Department of Cardiovascular Sciences, Center for Metabolic Disease Research, Philadelphia, PA, USA
| | - Lunzhi Dai
- National Clinical Research Center for Geriatrics and General Practice Ward/International Medical Center Ward, General Practice Medical Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China.
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA.
| | - Yingming Zhao
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL, USA.
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2
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Sharrow AC, Megill E, Chen AJ, Farooqi A, McGonigal S, Hempel N, Snyder NW, Buckanovich RJ, Aird KM. Acetate drives ovarian cancer quiescence via ACSS2-mediated acetyl-CoA production. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.12.603313. [PMID: 39026889 PMCID: PMC11257583 DOI: 10.1101/2024.07.12.603313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Quiescence is a reversible cell cycle exit traditionally thought to be associated with a metabolically inactive state. Recent work in muscle cells indicates that metabolic reprogramming is associated with quiescence. Whether metabolic changes occur in cancer to drive quiescence is unclear. Using a multi-omics approach, we found that the metabolic enzyme ACSS2, which converts acetate into acetyl-CoA, is both highly upregulated in quiescent ovarian cancer cells and required for their survival. Indeed, quiescent ovarian cancer cells have increased levels of acetate-derived acetyl-CoA, confirming increased ACSS2 activity in these cells. Furthermore, either inducing ACSS2 expression or supplementing cells with acetate was sufficient to induce a reversible quiescent cell cycle exit. RNA-Seq of acetate treated cells confirmed negative enrichment in multiple cell cycle pathways as well as enrichment of genes in a published G0 gene signature. Finally, analysis of patient data showed that ACSS2 expression is upregulated in tumor cells from ascites, which are thought to be more quiescent, compared to matched primary tumors. Additionally, high ACSS2 expression is associated with platinum resistance and worse outcomes. Together, this study points to a previously unrecognized ACSS2-mediated metabolic reprogramming that drives quiescence in ovarian cancer. As chemotherapies to treat ovarian cancer, such as platinum, have increased efficacy in highly proliferative cells, our data give rise to the intriguing question that metabolically-driven quiescence may affect therapeutic response.
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Affiliation(s)
- Allison C. Sharrow
- Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA
- UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Magee-Womens Research Institute, Pittsburgh, PA
| | - Emily Megill
- Center for Metabolic Disease Research, Department of Cardiovascular Sciences, Temple University, Philadelphia, PA
| | - Amanda J. Chen
- UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Afifa Farooqi
- UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | | | - Nadine Hempel
- UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Division of Hematology/Oncology, Department of Medicine University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Nathaniel W. Snyder
- Center for Metabolic Disease Research, Department of Cardiovascular Sciences, Temple University, Philadelphia, PA
| | - Ronald J. Buckanovich
- UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Magee-Womens Research Institute, Pittsburgh, PA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Katherine M. Aird
- Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA
- UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA
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3
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Esquea EM, Ciraku L, Young RG, Merzy J, Talarico AN, Ahmed NN, Karuppiah M, Ramesh A, Chatoff A, Crispim CV, Rashad AA, Cocklin S, Snyder NW, Beld J, Simone NL, Reginato MJ, Dick A. Selective and brain-penetrant ACSS2 inhibitors target breast cancer brain metastatic cells. Front Pharmacol 2024; 15:1394685. [PMID: 38818373 PMCID: PMC11137182 DOI: 10.3389/fphar.2024.1394685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 04/24/2024] [Indexed: 06/01/2024] Open
Abstract
Breast cancer brain metastasis (BCBM) typically results in an end-stage diagnosis and is hindered by a lack of brain-penetrant drugs. Tumors in the brain rely on the conversion of acetate to acetyl-CoA by the enzyme acetyl-CoA synthetase 2 (ACSS2), a key regulator of fatty acid synthesis and protein acetylation. Here, we used a computational pipeline to identify novel brain-penetrant ACSS2 inhibitors combining pharmacophore-based shape screen methodology with absorption, distribution, metabolism, and excretion (ADME) property predictions. We identified compounds AD-5584 and AD-8007 that were validated for specific binding affinity to ACSS2. Treatment of BCBM cells with AD-5584 and AD-8007 leads to a significant reduction in colony formation, lipid storage, acetyl-CoA levels and cell survival in vitro. In an ex vivo brain-tumor slice model, treatment with AD-8007 and AD-5584 reduced pre-formed tumors and synergized with irradiation in blocking BCBM tumor growth. Treatment with AD-8007 reduced tumor burden and extended survival in vivo. This study identifies selective brain-penetrant ACSS2 inhibitors with efficacy towards breast cancer brain metastasis.
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Affiliation(s)
- Emily M. Esquea
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Lorela Ciraku
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Riley G. Young
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Jessica Merzy
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Alexandra N. Talarico
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Nusaiba N. Ahmed
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Mangalam Karuppiah
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Anna Ramesh
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Adam Chatoff
- Department of Cardiovascular Sciences, Temple University Lewis Katz School of Medicine, Philadelphia, PA, United States
| | - Claudia V. Crispim
- Department of Cardiovascular Sciences, Temple University Lewis Katz School of Medicine, Philadelphia, PA, United States
| | - Adel A. Rashad
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Simon Cocklin
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Nathaniel W. Snyder
- Department of Cardiovascular Sciences, Temple University Lewis Katz School of Medicine, Philadelphia, PA, United States
| | - Joris Beld
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Nicole L. Simone
- Department of Radiation Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, United States
- Cancer Risk and Control Program, Philadelphia, PA, United States
| | - Mauricio J. Reginato
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, United States
- Translational Cellular Oncology Program, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, United States
| | - Alexej Dick
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, United States
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4
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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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5
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Park KC, Crump NT, Louwman N, Krywawych S, Cheong YJ, Vendrell I, Gill EK, Gunadasa-Rohling M, Ford KL, Hauton D, Fournier M, Pires E, Watson L, Roseman G, Holder J, Koschinski A, Carnicer R, Curtis MK, Zaccolo M, Hulikova A, Fischer R, Kramer HB, McCullagh JSO, Trefely S, Milne TA, Swietach P. Disrupted propionate metabolism evokes transcriptional changes in the heart by increasing histone acetylation and propionylation. NATURE CARDIOVASCULAR RESEARCH 2023; 2:1221-1245. [PMID: 38500966 PMCID: PMC7615744 DOI: 10.1038/s44161-023-00365-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 10/15/2023] [Indexed: 03/20/2024]
Abstract
Propiogenic substrates and gut bacteria produce propionate, a post-translational protein modifier. In this study, we used a mouse model of propionic acidaemia (PA) to study how disturbances to propionate metabolism result in histone modifications and changes to gene expression that affect cardiac function. Plasma propionate surrogates were raised in PA mice, but female hearts manifested more profound changes in acyl-CoAs, histone propionylation and acetylation, and transcription. These resulted in moderate diastolic dysfunction with raised diastolic Ca2+, expanded end-systolic ventricular volume and reduced stroke volume. Propionate was traced to histone H3 propionylation and caused increased acetylation genome-wide, including at promoters of Pde9a and Mme, genes related to contractile dysfunction through downscaled cGMP signaling. The less severe phenotype in male hearts correlated with β-alanine buildup. Raising β-alanine in cultured myocytes treated with propionate reduced propionyl-CoA levels, indicating a mechanistic relationship. Thus, we linked perturbed propionate metabolism to epigenetic changes that impact cardiac function.
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Affiliation(s)
- Kyung Chan Park
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, UK
| | - Nicholas T. Crump
- MRC Molecular Haematology Unit, Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Present Address: Hugh and Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, UK
| | - Niamh Louwman
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, UK
| | - Steve Krywawych
- Department of Chemical Pathology, Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Yuen Jian Cheong
- Epigenetics & Signalling Programmes, Babraham Institute, Cambridge, UK
| | - Iolanda Vendrell
- Nuffield Department of Medicine, Target Discovery Institute, Oxford, UK
- Nuffield Department of Medicine, Chinese Academy for Medical Sciences Oxford Institute, University of Oxford, Oxford, UK
| | - Eleanor K. Gill
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, UK
| | | | - Kerrie L. Ford
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, UK
| | - David Hauton
- Department of Chemistry, University of Oxford, Oxford, UK
| | | | | | - Lydia Watson
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, UK
| | - Gerald Roseman
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, UK
| | - James Holder
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Andreas Koschinski
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, UK
| | - Ricardo Carnicer
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - M. Kate Curtis
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, UK
| | - Manuela Zaccolo
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, UK
| | - Alzbeta Hulikova
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, UK
| | - Roman Fischer
- Nuffield Department of Medicine, Target Discovery Institute, Oxford, UK
- Nuffield Department of Medicine, Chinese Academy for Medical Sciences Oxford Institute, University of Oxford, Oxford, UK
| | - Holger B. Kramer
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | | | - Sophie Trefely
- Epigenetics & Signalling Programmes, Babraham Institute, Cambridge, UK
| | - Thomas A. Milne
- MRC Molecular Haematology Unit, Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Pawel Swietach
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, UK
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6
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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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7
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Lieberman WK, Brown ZA, Kantner DS, Jing Y, Megill E, Evans ND, Crawford MC, Jhulki I, Grose C, Jones JE, Snyder NW, Meier JL. Chemoproteomics Yields a Selective Molecular Host for Acetyl-CoA. J Am Chem Soc 2023; 145:16899-16905. [PMID: 37486078 PMCID: PMC10696595 DOI: 10.1021/jacs.3c05489] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Chemoproteomic profiling is a powerful approach to define the selectivity of small molecules and endogenous metabolites with the human proteome. In addition to mechanistic studies, proteome specificity profiling also has the potential to identify new scaffolds for biomolecular sensing. Here, we report a chemoproteomics-inspired strategy for selective sensing of acetyl-CoA. First, we use chemoproteomic capture experiments to validate the N-terminal acetyltransferase NAA50 as a protein capable of differentiating acetyl-CoA and CoA. A Nanoluc-NAA50 fusion protein retains this specificity and can be used to generate a bioluminescence resonance energy transfer (BRET) signal in the presence of a CoA-linked fluorophore. This enables the development of a ligand displacement assay in which CoA metabolites are detected via their ability to bind the Nanoluc-NAA50 protein "host" and compete binding of the CoA-linked fluorophore "guest". We demonstrate that the specificity of ligand displacement reflects the molecular recognition of the NAA50 host, while the window of dynamic sensing can be controlled by tuning the binding affinity of the CoA-linked fluorophore guest. Finally, we show that the method's specificity for acetyl-CoA can be harnessed for gain-of-signal optical detection of enzyme activity and quantification of acetyl-CoA from cellular samples. Overall, our studies demonstrate the potential of harnessing insights from chemoproteomics for molecular sensing and provide a foundation for future applications in target engagement and selective metabolite detection.
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Affiliation(s)
- Whitney K Lieberman
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
| | - Zachary A Brown
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
| | - Daniel S Kantner
- Department of Cardiovascular Sciences, Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania 19140, United States
| | - Yihang Jing
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
| | - Emily Megill
- Department of Cardiovascular Sciences, Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania 19140, United States
| | - Nya D Evans
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
| | - McKenna C Crawford
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
| | - Isita Jhulki
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
| | - Carissa Grose
- Protein Expression Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland 21702, United States
| | - Jane E Jones
- Protein Expression Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland 21702, United States
| | - Nathaniel W Snyder
- Department of Cardiovascular Sciences, Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania 19140, United States
| | - Jordan L Meier
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
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8
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He H, Sugiyama A, Snyder NW, Teneche MG, Liu X, Maner-Smith KM, Goessling W, Hagen SJ, Ortlund EA, Najafi-Shoushtari SH, Acuña M, Cohen DE. Acyl-CoA thioesterase 12 suppresses YAP-mediated hepatocarcinogenesis by limiting glycerolipid biosynthesis. Cancer Lett 2023; 565:216210. [PMID: 37150501 DOI: 10.1016/j.canlet.2023.216210] [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: 12/21/2022] [Revised: 04/18/2023] [Accepted: 05/01/2023] [Indexed: 05/09/2023]
Abstract
Cancer cells use acetate to support the higher demand for energy and lipid biosynthesis during uncontrolled cell proliferation, as well as for acetylation of regulatory proteins. Acyl-CoA thioesterase 12 (Acot12) is the enzyme that hydrolyzes acetyl-CoA to acetate in liver cytosol and is downregulated in hepatocellular carcinoma (HCC). A mechanistic role for Acot12 in hepatocarcinogenesis was assessed in mice in response to treatment with diethylnitrosamine(DEN)/carbon tetrachloride (CCl4) administration or prolonged feeding of a diet that promotes non-alcoholic steatohepatitis (NASH). Relative to controls, Acot12-/- mice exhibited accelerated liver tumor formation that was characterized by the hepatic accumulation of glycerolipids, including lysophosphatidic acid (LPA), and that was associated with reduced Hippo signaling and increased yes-associated protein (YAP)-mediated transcriptional activity. In Acot12-/- mice, restoration of hepatic Acot12 expression inhibited hepatocarcinogenesis and YAP activation, as did knockdown of hepatic YAP expression. Excess LPA produced due to deletion of Acot12 signaled through LPA receptors (LPARs) coupled to Gα12/13 subunits to suppress YAP phosphorylation, thereby promoting its nuclear localization and transcriptional activity. These findings identify a protective role for Acot12 in suppressing hepatocarcinogenesis by limiting biosynthesis of glycerolipids including LPA, which preserves Hippo signaling.
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Affiliation(s)
- Haiyue He
- Division of Gastroenterology and Hepatology, Joan & Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY, 10021, USA; Department of Gastroenterology, Xiangya Hospital of Central South University, Hunan, China
| | - Akiko Sugiyama
- Division of Gastroenterology and Hepatology, Joan & Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY, 10021, USA; Division of Gastroenterology, Hepatology and Endoscopy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Nathaniel W Snyder
- Center for Metabolic Disease Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19104, USA
| | - Marcos G Teneche
- Center for Metabolic Disease Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19104, USA
| | - Xiaowei Liu
- Department of Gastroenterology, Xiangya Hospital of Central South University, Hunan, China
| | - Kristal M Maner-Smith
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Wolfram Goessling
- Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA; Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA, 02115, USA
| | - Susan J Hagen
- Division of Surgical Sciences, Department of Surgery, Beth Israel-Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Eric A Ortlund
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - S Hani Najafi-Shoushtari
- Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY, 10021, USA; Research Department, Weill Cornell Medicine-Qatar, Education City, Doha, Qatar
| | - Mariana Acuña
- Division of Gastroenterology and Hepatology, Joan & Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY, 10021, USA; Division of Gastroenterology, Hepatology and Endoscopy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
| | - David E Cohen
- Division of Gastroenterology and Hepatology, Joan & Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY, 10021, USA; Division of Gastroenterology, Hepatology and Endoscopy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA; Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA, 02115, USA.
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9
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Soaita I, Megill E, Kantner D, Chatoff A, Cheong YJ, Clarke P, Arany Z, Snyder NW, Wellen KE, Trefely S. Dynamic protein deacetylation is a limited carbon source for acetyl-CoA-dependent metabolism. J Biol Chem 2023; 299:104772. [PMID: 37142219 PMCID: PMC10244699 DOI: 10.1016/j.jbc.2023.104772] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 04/25/2023] [Accepted: 04/27/2023] [Indexed: 05/06/2023] Open
Abstract
The ability of cells to store and rapidly mobilize energy reserves in response to nutrient availability is essential for survival. Breakdown of carbon stores produces acetyl-CoA (AcCoA), which fuels essential metabolic pathways and is also the acyl donor for protein lysine acetylation. Histones are abundant and highly acetylated proteins, accounting for 40% to 75% of cellular protein acetylation. Notably, histone acetylation is sensitive to AcCoA availability, and nutrient replete conditions induce a substantial accumulation of acetylation on histones. Deacetylation releases acetate, which can be recycled to AcCoA, suggesting that deacetylation could be mobilized as an AcCoA source to feed downstream metabolic processes under nutrient depletion. While the notion of histones as a metabolic reservoir has been frequently proposed, experimental evidence has been lacking. Therefore, to test this concept directly, we used acetate-dependent, ATP citrate lyase-deficient mouse embryonic fibroblasts (Acly-/- MEFs), and designed a pulse-chase experimental system to trace deacetylation-derived acetate and its incorporation into AcCoA. We found that dynamic protein deacetylation in Acly-/- MEFs contributed carbons to AcCoA and proximal downstream metabolites. However, deacetylation had no significant effect on acyl-CoA pool sizes, and even at maximal acetylation, deacetylation transiently supplied less than 10% of cellular AcCoA. Together, our data reveal that although histone acetylation is dynamic and nutrient-sensitive, its potential for maintaining cellular AcCoA-dependent metabolic pathways is limited compared to cellular demand.
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Affiliation(s)
- Ioana Soaita
- Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Emily Megill
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, TempleUniversity, Philadelphia, Pennsylvania, USA
| | - Daniel Kantner
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, TempleUniversity, Philadelphia, Pennsylvania, USA
| | - Adam Chatoff
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, TempleUniversity, Philadelphia, Pennsylvania, USA
| | - Yuen Jian Cheong
- Epigenetics and Signalling Programs, Babraham Institute, Cambridge, UK
| | - Philippa Clarke
- Epigenetics and Signalling Programs, Babraham Institute, Cambridge, UK
| | - Zoltan Arany
- Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
| | - Nathaniel W Snyder
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, TempleUniversity, Philadelphia, Pennsylvania, USA.
| | - Kathryn E Wellen
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
| | - Sophie Trefely
- Epigenetics and Signalling Programs, Babraham Institute, Cambridge, UK.
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10
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Izzo LT, Trefely S, Demetriadou C, Drummond JM, Mizukami T, Kuprasertkul N, Farria AT, Nguyen PT, Murali N, Reich L, Kantner DS, Shaffer J, Affronti H, Carrer A, Andrews A, Capell BC, Snyder NW, Wellen KE. Acetylcarnitine shuttling links mitochondrial metabolism to histone acetylation and lipogenesis. SCIENCE ADVANCES 2023; 9:eadf0115. [PMID: 37134161 PMCID: PMC10156126 DOI: 10.1126/sciadv.adf0115] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 04/03/2023] [Indexed: 05/05/2023]
Abstract
The metabolite acetyl-CoA is necessary for both lipid synthesis in the cytosol and histone acetylation in the nucleus. The two canonical precursors to acetyl-CoA in the nuclear-cytoplasmic compartment are citrate and acetate, which are processed to acetyl-CoA by ATP-citrate lyase (ACLY) and acyl-CoA synthetase short-chain 2 (ACSS2), respectively. It is unclear whether other substantial routes to nuclear-cytosolic acetyl-CoA exist. To investigate this, we generated cancer cell lines lacking both ACLY and ACSS2 [double knockout (DKO) cells]. Using stable isotope tracing, we show that both glucose and fatty acids contribute to acetyl-CoA pools and histone acetylation in DKO cells and that acetylcarnitine shuttling can transfer two-carbon units from mitochondria to cytosol. Further, in the absence of ACLY, glucose can feed fatty acid synthesis in a carnitine responsive and carnitine acetyltransferase (CrAT)-dependent manner. The data define acetylcarnitine as an ACLY- and ACSS2-independent precursor to nuclear-cytosolic acetyl-CoA that can support acetylation, fatty acid synthesis, and cell growth.
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Affiliation(s)
- Luke T. Izzo
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - 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, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Christina Demetriadou
- 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, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Jack M. Drummond
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Takuya Mizukami
- Department of Cancer Epigenetics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Nina Kuprasertkul
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Aimee T. Farria
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Phuong T. T. Nguyen
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nivitha Murali
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lauren Reich
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Daniel S. Kantner
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Joshua Shaffer
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hayley Affronti
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alessandro Carrer
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrew Andrews
- Department of Cancer Epigenetics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC 28403, USA
| | - Brian C. Capell
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nathaniel W. Snyder
- Center for Metabolic Disease Research, 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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11
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Yuan H, Wu X, Wu Q, Chatoff A, Megill E, Gao J, Huang T, Duan T, Yang K, Jin C, Yuan F, Wang S, Zhao L, Zinn PO, Abdullah KG, Zhao Y, Snyder NW, Rich JN. Lysine catabolism reprograms tumour immunity through histone crotonylation. Nature 2023; 617:818-826. [PMID: 37198486 PMCID: PMC11089809 DOI: 10.1038/s41586-023-06061-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 04/06/2023] [Indexed: 05/19/2023]
Abstract
Cancer cells rewire metabolism to favour the generation of specialized metabolites that support tumour growth and reshape the tumour microenvironment1,2. Lysine functions as a biosynthetic molecule, energy source and antioxidant3-5, but little is known about its pathological role in cancer. Here we show that glioblastoma stem cells (GSCs) reprogram lysine catabolism through the upregulation of lysine transporter SLC7A2 and crotonyl-coenzyme A (crotonyl-CoA)-producing enzyme glutaryl-CoA dehydrogenase (GCDH) with downregulation of the crotonyl-CoA hydratase enoyl-CoA hydratase short chain 1 (ECHS1), leading to accumulation of intracellular crotonyl-CoA and histone H4 lysine crotonylation. A reduction in histone lysine crotonylation by either genetic manipulation or lysine restriction impaired tumour growth. In the nucleus, GCDH interacts with the crotonyltransferase CBP to promote histone lysine crotonylation. Loss of histone lysine crotonylation promotes immunogenic cytosolic double-stranded RNA (dsRNA) and dsDNA generation through enhanced H3K27ac, which stimulates the RNA sensor MDA5 and DNA sensor cyclic GMP-AMP synthase (cGAS) to boost type I interferon signalling, leading to compromised GSC tumorigenic potential and elevated CD8+ T cell infiltration. A lysine-restricted diet synergized with MYC inhibition or anti-PD-1 therapy to slow tumour growth. Collectively, GSCs co-opt lysine uptake and degradation to shunt the production of crotonyl-CoA, remodelling the chromatin landscape to evade interferon-induced intrinsic effects on GSC maintenance and extrinsic effects on immune response.
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Affiliation(s)
- Huairui Yuan
- Hillman Cancer Center and Department of Neurology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Xujia Wu
- Hillman Cancer Center and Department of Neurology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Qiulian Wu
- Hillman Cancer Center and Department of Neurology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Adam Chatoff
- Department of Cardiovascular Sciences, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
| | - Emily Megill
- Department of Cardiovascular Sciences, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
| | - Jinjun Gao
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL, USA
| | - Tengfei Huang
- Hillman Cancer Center and Department of Neurology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Tingting Duan
- Hillman Cancer Center and Department of Neurology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Kailin Yang
- Department of Radiation Oncology, Taussig Cancer Center, Cleveland Clinic, Cleveland, OH, USA
| | - Chunyu Jin
- Department and School of Medicine, University of California, San Diego, CA, USA
| | - Fanen Yuan
- Hillman Cancer Center and Department of Neurology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Shuai Wang
- Hillman Cancer Center and Department of Neurology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Linjie Zhao
- Hillman Cancer Center and Department of Neurology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Pascal O Zinn
- Hillman Cancer Center and Department of Neurology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
- Department of Neurosurgery, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Kalil G Abdullah
- Hillman Cancer Center and Department of Neurology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
- Department of Neurosurgery, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Yingming Zhao
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL, USA
| | - Nathaniel W Snyder
- Department of Cardiovascular Sciences, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
| | - Jeremy N Rich
- Hillman Cancer Center and Department of Neurology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA.
- Department of Neurology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA.
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12
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Wei X, Schultz K, Pepper HL, Megill E, Vogt A, Snyder NW, Marmorstein R. Allosteric role of the citrate synthase homology domain of ATP citrate lyase. Nat Commun 2023; 14:2247. [PMID: 37076498 PMCID: PMC10115795 DOI: 10.1038/s41467-023-37986-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 04/06/2023] [Indexed: 04/21/2023] Open
Abstract
ATP citrate lyase (ACLY) is the predominant nucleocytosolic source of acetyl-CoA and is aberrantly regulated in many diseases making it an attractive therapeutic target. Structural studies of ACLY reveal a central homotetrameric core citrate synthase homology (CSH) module flanked by acyl-CoA synthetase homology (ASH) domains, with ATP and citrate binding the ASH domain and CoA binding the ASH-CSH interface to produce acetyl-CoA and oxaloacetate products. The specific catalytic role of the CSH module and an essential D1026A residue contained within it has been a matter of debate. Here, we report biochemical and structural analysis of an ACLY-D1026A mutant demonstrating that this mutant traps a (3S)-citryl-CoA intermediate in the ASH domain in a configuration that is incompatible with the formation of acetyl-CoA, is able to convert acetyl-CoA and OAA to (3S)-citryl-CoA in the ASH domain, and can load CoA and unload acetyl-CoA in the CSH module. Together, this data support an allosteric role for the CSH module in ACLY catalysis.
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Affiliation(s)
- Xuepeng Wei
- Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Laboratory, Guangzhou Medical University, Guangzhou, China
| | - Kollin Schultz
- Graduate Group in Biochemistry & Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Hannah L Pepper
- Department of Cardiovascular Sciences, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA
| | - Emily Megill
- Department of Cardiovascular Sciences, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA
| | - Austin Vogt
- Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Nathaniel W Snyder
- Department of Cardiovascular Sciences, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA
| | - Ronen Marmorstein
- Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Graduate Group in Biochemistry & Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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13
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Flam E, Jang C, Murashige D, Yang Y, Morley MP, Jung S, Kantner DS, Pepper H, Bedi KC, Brandimarto J, Prosser BL, Cappola T, Snyder NW, Rabinowitz JD, Margulies KB, Arany Z. Integrated landscape of cardiac metabolism in end-stage human nonischemic dilated cardiomyopathy. NATURE CARDIOVASCULAR RESEARCH 2022; 1:817-829. [PMID: 36776621 PMCID: PMC9910091 DOI: 10.1038/s44161-022-00117-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 07/08/2022] [Indexed: 01/03/2023]
Abstract
Heart failure (HF) is a leading cause of mortality. Failing hearts undergo profound metabolic changes, but a comprehensive evaluation in humans is lacking. We integrate plasma and cardiac tissue metabolomics of 678 metabolites, genome-wide RNA-sequencing, and proteomic studies to examine metabolic status in 87 explanted human hearts from 39 patients with end-stage HF compared with 48 nonfailing donors. We confirm bioenergetic defects in human HF and reveal selective depletion of adenylate purines required for maintaining ATP levels. We observe substantial reductions in fatty acids and acylcarnitines in failing tissue, despite plasma elevations, suggesting defective import of fatty acids into cardiomyocytes. Glucose levels, in contrast, are elevated. Pyruvate dehydrogenase, which gates carbohydrate oxidation, is de-repressed, allowing increased lactate and pyruvate burning. Tricarboxylic acid cycle intermediates are significantly reduced. Finally, bioactive lipids are profoundly reprogrammed, with marked reductions in ceramides and elevations in lysoglycerophospholipids. These data unveil profound metabolic abnormalities in human failing hearts.
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Affiliation(s)
- Emily Flam
- Perelman School of Medicine, Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Cholsoon Jang
- Department of Chemistry and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Biological Chemistry, University of California Irvine, Irvine, CA, USA
| | - Danielle Murashige
- Perelman School of Medicine, Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Yifan Yang
- Perelman School of Medicine, Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael P. Morley
- Perelman School of Medicine, Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Sunhee Jung
- Department of Biological Chemistry, University of California Irvine, Irvine, CA, USA
| | - Daniel S. Kantner
- Center for Metabolic Disease Research, Department of Cardiovascular Science, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA
| | - Hannah Pepper
- Center for Metabolic Disease Research, Department of Cardiovascular Science, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA
| | - Kenneth C. Bedi
- Perelman School of Medicine, Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Jeff Brandimarto
- Perelman School of Medicine, Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Benjamin L. Prosser
- Perelman School of Medicine, Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA, USA
- Department of Physiology, Pennsylvania Muscle Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Thomas Cappola
- Perelman School of Medicine, Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Nathaniel W. Snyder
- Center for Metabolic Disease Research, Department of Cardiovascular Science, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA
| | - Joshua D. Rabinowitz
- Department of Chemistry and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Kenneth B. Margulies
- Perelman School of Medicine, Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Zolt Arany
- Perelman School of Medicine, Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA, USA
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14
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Rigaud VO, Zarka C, Kurian J, Harlamova D, Elia A, Kasatkin N, Johnson J, Behanan M, Kraus L, Pepper H, Snyder NW, Mohsin S, Houser S, Khan M. UCP2 modulates cardiomyocyte cell cycle activity, acetyl-CoA and histone acetylation in response to moderate hypoxia. JCI Insight 2022; 7:155475. [PMID: 35771638 PMCID: PMC9462500 DOI: 10.1172/jci.insight.155475] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 06/27/2022] [Indexed: 11/17/2022] Open
Abstract
Developmental cardiac tissue is regenerative while operating under low oxygen. After birth, ambient oxygen is associated with cardiomyocyte cell cycle exit and regeneration. Likewise, cardiac metabolism undergoes a shift with cardiac maturation. Whether there are common regulators of cardiomyocyte cell cycle linking metabolism to oxygen tension remains unknown. The objective of the study is to determine whether mitochondrial UCP2 is a metabolic oxygen sensor regulating cardiomyocyte cell cycle. Neonatal rat ventricular myocytes (NRVMs) under moderate hypoxia showed increased cell cycle activity and UCP2 expression. NRVMs exhibited a metabolic shift towards glycolysis, reduced citrate synthase, mtDNA, ΔΨm and DNA damage/oxidative stress while loss of UCP2 reversed this phenotype. Next, WT and UCP2KO mice kept under hypoxia for 4 weeks showed significant decline in cardiac function that was more pronounced in UCP2KO animals. Cardiomyocyte cell cycle activity was reduced while fibrosis and DNA damage was significantly increased in UCP2KO animals compared to WT under hypoxia. Mechanistically, UCP2 increased acetyl-CoA levels, histone acetylation and altered chromatin modifiers linking metabolism to cardiomyocyte cell cycle under hypoxia. Here, we show a novel role for mitochondrial UCP2 as an oxygen sensor regulating cardiomyocyte cell cycle activity, acetyl-CoA levels and histone acetylation in response to moderate hypoxia.
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Affiliation(s)
- Vagner Oc Rigaud
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, United States of America
| | - Clare Zarka
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, United States of America
| | - Justin Kurian
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, United States of America
| | - Daria Harlamova
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, United States of America
| | - Andrea Elia
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, United States of America
| | - Nicole Kasatkin
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, United States of America
| | - Jaslyn Johnson
- Cardiovascular Research Institute, Lewis Katz School of Medicine, Temple University, Philadelphia, United States of America
| | - Michael Behanan
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, United States of America
| | - Lindsay Kraus
- Cardiovascular Research Institute, Lewis Katz School of Medicine, Temple University, Philadelphia, United States of America
| | - Hannah Pepper
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, United States of America
| | - Nathaniel W Snyder
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, United States of America
| | - Sadia Mohsin
- Cardiovascular Research Institute, Lewis Katz School of Medicine, Temple University, Philadelphia, United States of America
| | - Steven Houser
- Cardiovascular Research Institute, Lewis Katz School of Medicine, Temple University, Philadelphia, United States of America
| | - Mohsin Khan
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, United States of America
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15
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Doan MT, Neinast MD, Varner EL, Bedi KC, Bartee D, Jiang H, Trefely S, Xu P, Singh JP, Jang C, Rame JE, Brady DC, Meier JL, Marguiles KB, Arany Z, Snyder NW. Direct anabolic metabolism of three carbon propionate to a six carbon metabolite occurs in vivo across tissues and species. J Lipid Res 2022; 63:100224. [PMID: 35568254 PMCID: PMC9189226 DOI: 10.1016/j.jlr.2022.100224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 04/20/2022] [Accepted: 05/07/2022] [Indexed: 12/12/2022] Open
Abstract
Anabolic metabolism of carbon in mammals is mediated via the one- and two-carbon carriers S-adenosyl methionine and acetyl-coenzyme A. In contrast, anabolic metabolism of three-carbon units via propionate has not been shown to extensively occur. Mammals are primarily thought to oxidize the three-carbon short chain fatty acid propionate by shunting propionyl-CoA to succinyl-CoA for entry into the TCA cycle. Here, we found that this may not be absolute as, in mammals, one nonoxidative fate of propionyl-CoA is to condense to two three-carbon units into a six-carbon trans-2-methyl-2-pentenoyl-CoA (2M2PE-CoA). We confirmed this reaction pathway using purified protein extracts provided limited substrates and verified the product via LC-MS using a synthetic standard. In whole-body in vivo stable isotope tracing following infusion of 13C-labeled valine at steady state, 2M2PE-CoA was found to form via propionyl-CoA in multiple murine tissues, including heart, kidney, and to a lesser degree, in brown adipose tissue, liver, and tibialis anterior muscle. Using ex vivo isotope tracing, we found that 2M2PE-CoA also formed in human myocardial tissue incubated with propionate to a limited extent. While the complete enzymology of this pathway remains to be elucidated, these results confirm the in vivo existence of at least one anabolic three- to six-carbon reaction conserved in humans and mice that utilizes propionate.
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Affiliation(s)
- Mary T Doan
- Center for Metabolic Disease Research, Department of Cardiovascular Sciences, Temple University Lewis Katz School of Medicine, Philadelphia, PA, USA
| | - Michael D Neinast
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Erika L Varner
- Center for Metabolic Disease Research, Department of Cardiovascular Sciences, Temple University Lewis Katz School of Medicine, Philadelphia, PA, USA
| | - Kenneth C Bedi
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - David Bartee
- Chemical Biology Laboratory, National Cancer Institute, Frederick MD, USA
| | - Helen Jiang
- Center for Metabolic Disease Research, Department of Cardiovascular Sciences, Temple University Lewis Katz School of Medicine, Philadelphia, PA, USA
| | - Sophie Trefely
- Center for Metabolic Disease Research, Department of Cardiovascular Sciences, Temple University Lewis Katz School of Medicine, Philadelphia, PA, USA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Peining Xu
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jay P Singh
- Center for Metabolic Disease Research, Department of Cardiovascular Sciences, Temple University Lewis Katz School of Medicine, Philadelphia, PA, USA
| | - Cholsoon Jang
- Lewis Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - J Eduardo Rame
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Donita C Brady
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jordan L Meier
- Chemical Biology Laboratory, National Cancer Institute, Frederick MD, USA
| | - Kenneth B Marguiles
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Zoltan Arany
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Nathaniel W Snyder
- Center for Metabolic Disease Research, Department of Cardiovascular Sciences, Temple University Lewis Katz School of Medicine, Philadelphia, PA, USA.
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16
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Hamsanathan S, Anthonymuthu T, Han S, Shinglot H, Siefken E, Sims A, Sen P, Pepper HL, Snyder NW, Bayir H, Kagan V, Gurkar AU. Integrated -omics approach reveals persistent DNA damage rewires lipid metabolism and histone hyperacetylation via MYS-1/Tip60. SCIENCE ADVANCES 2022; 8:eabl6083. [PMID: 35171671 PMCID: PMC8849393 DOI: 10.1126/sciadv.abl6083] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 12/23/2021] [Indexed: 06/14/2023]
Abstract
Although DNA damage is intricately linked to metabolism, the metabolic alterations that occur in response to DNA damage are not well understood. We use a DNA repair-deficient model of ERCC1-XPF in Caenorhabditis elegans to gain insights on how genotoxic stress drives aging. Using multi-omic approach, we discover that nuclear DNA damage promotes mitochondrial β-oxidation and drives a global loss of fat depots. This metabolic shift to β-oxidation generates acetyl-coenzyme A to promote histone hyperacetylation and an associated change in expression of immune-effector and cytochrome genes. We identify the histone acetyltransferase MYS-1, as a critical regulator of this metabolic-epigenetic axis. We show that in response to DNA damage, polyunsaturated fatty acids, especially arachidonic acid (AA) and AA-related lipid mediators, are elevated and this is dependent on mys-1. Together, these findings reveal that DNA damage alters the metabolic-epigenetic axis to drive an immune-like response that can promote age-associated decline.
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Affiliation(s)
- Shruthi Hamsanathan
- Aging Institute of UPMC and the University of Pittsburgh School of Medicine, 100 Technology Dr., Pittsburgh, PA 15219, USA
| | - Tamil Anthonymuthu
- Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
- Children’s Neuroscience Institute, Children’s Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA 15224, USA
- Adeptrix Corp., Beverly, MA 01915, USA
| | - Suhao Han
- Aging Institute of UPMC and the University of Pittsburgh School of Medicine, 100 Technology Dr., Pittsburgh, PA 15219, USA
| | - Himaly Shinglot
- Aging Institute of UPMC and the University of Pittsburgh School of Medicine, 100 Technology Dr., Pittsburgh, PA 15219, USA
| | - Ella Siefken
- Aging Institute of UPMC and the University of Pittsburgh School of Medicine, 100 Technology Dr., Pittsburgh, PA 15219, USA
| | - Austin Sims
- Aging Institute of UPMC and the University of Pittsburgh School of Medicine, 100 Technology Dr., Pittsburgh, PA 15219, USA
| | - Payel Sen
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Hannah L. Pepper
- Center for Metabolic Disease Research, Department of Cardiovascular Sciences, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Nathaniel W. Snyder
- Center for Metabolic Disease Research, Department of Cardiovascular Sciences, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Hulya Bayir
- Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
- Children’s Neuroscience Institute, Children’s Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA 15224, USA
- Department of Environmental Occupational Health, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Valerian Kagan
- Children’s Neuroscience Institute, Children’s Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA 15224, USA
- Department of Environmental Occupational Health, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Aditi U. Gurkar
- Aging Institute of UPMC and the University of Pittsburgh School of Medicine, 100 Technology Dr., Pittsburgh, PA 15219, USA
- Division of Geriatric Medicine, Department of Medicine, University of Pittsburgh School of Medicine, 3471 Fifth Avenue, Kaufmann Medical Building Suite 500, Pittsburgh, PA 15213, USA
- Geriatric Research, Education and Clinical Center, Veterans Affairs Pittsburgh Healthcare System, Pittsburgh, PA 15240, USA
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17
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Trefely S, Huber K, Liu J, Noji M, Stransky S, Singh J, Doan MT, Lovell CD, von Krusenstiern E, Jiang H, Bostwick A, Pepper HL, Izzo L, Zhao S, Xu JP, Bedi KC, Rame JE, Bogner-Strauss JG, Mesaros C, Sidoli S, Wellen KE, Snyder NW. Quantitative subcellular acyl-CoA analysis reveals distinct nuclear metabolism and isoleucine-dependent histone propionylation. Mol Cell 2022; 82:447-462.e6. [PMID: 34856123 PMCID: PMC8950487 DOI: 10.1016/j.molcel.2021.11.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 09/24/2021] [Accepted: 11/03/2021] [Indexed: 01/22/2023]
Abstract
Quantitative subcellular metabolomic measurements can explain the roles of metabolites in cellular processes but are subject to multiple confounding factors. We developed stable isotope labeling of essential nutrients in cell culture-subcellular fractionation (SILEC-SF), which uses isotope-labeled internal standard controls that are present throughout fractionation and processing to quantify acyl-coenzyme A (acyl-CoA) thioesters in subcellular compartments by liquid chromatography-mass spectrometry. We tested SILEC-SF in a range of sample types and examined the compartmentalized responses to oxygen tension, cellular differentiation, and nutrient availability. Application of SILEC-SF to the challenging analysis of the nuclear compartment revealed a nuclear acyl-CoA profile distinct from that of the cytosol, with notable nuclear enrichment of propionyl-CoA. Using isotope tracing, we identified the branched chain amino acid isoleucine as a major metabolic source of nuclear propionyl-CoA and histone propionylation, thus revealing a new mechanism of crosstalk between metabolism and the epigenome.
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Affiliation(s)
- Sophie Trefely
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA; Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Katharina Huber
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute of Biochemistry, Graz University of Technology, Graz 8010, Austria
| | - Joyce Liu
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael Noji
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Stephanie Stransky
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Jay Singh
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Mary T Doan
- Center for Metabolic Disease Research, 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; Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Eliana von Krusenstiern
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Helen Jiang
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Anna Bostwick
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Hannah L Pepper
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Luke Izzo
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Steven Zhao
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jimmy P Xu
- Department of Pharmacology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kenneth C Bedi
- Penn Medicine Heart Failure Mechanical Assist and Cardiac Transplant Center, Hospital of the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - J Eduardo Rame
- Penn Medicine Heart Failure Mechanical Assist and Cardiac Transplant Center, Hospital of the University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Clementina Mesaros
- Department of Pharmacology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, 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; Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Nathaniel W Snyder
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA.
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18
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Giblin W, Bringman-Rodenbarger L, Guo AH, Kumar S, Monovich AC, Mostafa AM, Skinner ME, Azar M, Mady AS, Chung CH, Kadambi N, Melong KA, Lee HJ, Zhang L, Sajjakulnukit P, Trefely S, Varner EL, Iyer S, Wang M, Wilmott JS, Soyer HP, Sturm RA, Pritchard AL, Andea AA, Scolyer RA, Stark MS, Scott DA, Fullen DR, Bosenberg MW, Chandrasekaran S, Nikolovska-Coleska Z, Verhaegen ME, Snyder NW, Rivera MN, Osterman AL, Lyssiotis CA, Lombard DB. The deacylase SIRT5 supports melanoma viability by influencing chromatin dynamics. J Clin Invest 2021; 131:138926. [PMID: 33945506 PMCID: PMC8203465 DOI: 10.1172/jci138926] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 04/29/2021] [Indexed: 12/13/2022] Open
Abstract
Cutaneous melanoma remains the most lethal skin cancer, and ranks third among all malignancies in terms of years of life lost. Despite the advent of immune checkpoint and targeted therapies, only roughly half of patients with advanced melanoma achieve a durable remission. Sirtuin 5 (SIRT5) is a member of the sirtuin family of protein deacylases that regulates metabolism and other biological processes. Germline Sirt5 deficiency is associated with mild phenotypes in mice. Here we showed that SIRT5 was required for proliferation and survival across all cutaneous melanoma genotypes tested, as well as uveal melanoma, a genetically distinct melanoma subtype that arises in the eye and is incurable once metastatic. Likewise, SIRT5 was required for efficient tumor formation by melanoma xenografts and in an autochthonous mouse Braf Pten-driven melanoma model. Via metabolite and transcriptomic analyses, we found that SIRT5 was required to maintain histone acetylation and methylation levels in melanoma cells, thereby promoting proper gene expression. SIRT5-dependent genes notably included MITF, a key lineage-specific survival oncogene in melanoma, and the c-MYC proto-oncogene. SIRT5 may represent a druggable genotype-independent addiction in melanoma.
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Affiliation(s)
- William Giblin
- Department of Pathology and
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | | | | | | | | | - Ahmed M. Mostafa
- Department of Pathology and
- Department of Biochemistry, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | | | | | | | | | | | | | - Ho-Joon Lee
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Li Zhang
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Peter Sajjakulnukit
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Sophie Trefely
- Department of Cancer Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Center for Metabolic Disease Research, Department of Microbiology and Immunology, Temple University, Lewis Katz School of Medicine, Philadelphia, Pennsylvania, USA
| | - Erika L. Varner
- Center for Metabolic Disease Research, Department of Microbiology and Immunology, Temple University, Lewis Katz School of Medicine, Philadelphia, Pennsylvania, USA
| | - Sowmya Iyer
- Department of Pathology and MGH Cancer Center, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | | | - James S. Wilmott
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia
| | - H. Peter Soyer
- The University of Queensland Diamantina Institute, The University of Queensland, Dermatology Research Centre, Brisbane, Australia
- Department of Dermatology, Princess Alexandra Hospital, Brisbane, Queensland, Australia
| | - Richard A. Sturm
- The University of Queensland Diamantina Institute, The University of Queensland, Dermatology Research Centre, Brisbane, Australia
| | - Antonia L. Pritchard
- Institute of Health Research and Innovation, University of the Highlands and Islands, An Lóchran, Inverness, United Kingdom
- Oncogenomics, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Aleodor A. Andea
- Department of Pathology and
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - Richard A. Scolyer
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia
- Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, and NSW Pathology, Sydney, New South Wales, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Mitchell S. Stark
- The University of Queensland Diamantina Institute, The University of Queensland, Dermatology Research Centre, Brisbane, Australia
| | - David A. Scott
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Douglas R. Fullen
- Department of Pathology and
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - Marcus W. Bosenberg
- Departments of Pathology and Dermatology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Sriram Chandrasekaran
- Department of Biomedical Engineering and
- Program in Chemical Biology
- Center for Computational Medicine and Bioinformatics, and
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Zaneta Nikolovska-Coleska
- Department of Pathology and
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | | | - Nathaniel W. Snyder
- Center for Metabolic Disease Research, Department of Microbiology and Immunology, Temple University, Lewis Katz School of Medicine, Philadelphia, Pennsylvania, USA
| | - Miguel N. Rivera
- Department of Pathology and MGH Cancer Center, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Andrei L. Osterman
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Costas A. Lyssiotis
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Division of Gastroenterology, Department of Internal Medicine and
| | - David B. Lombard
- Department of Pathology and
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Institute of Gerontology, University of Michigan, Ann Arbor, Michigan, USA
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19
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Varner EL, Trefely S, Bartee D, von Krusenstiern E, Izzo L, Bekeova C, O'Connor RS, Seifert EL, Wellen KE, Meier JL, Snyder NW. Quantification of lactoyl-CoA (lactyl-CoA) by liquid chromatography mass spectrometry in mammalian cells and tissues. Open Biol 2020; 10:200187. [PMID: 32961073 PMCID: PMC7536085 DOI: 10.1098/rsob.200187] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 08/25/2020] [Indexed: 12/15/2022] Open
Abstract
Lysine lactoylation is a recently described protein post-translational modification (PTM). However, the biochemical pathways responsible for this acylation remain unclear. Two metabolite-dependent mechanisms have been proposed: enzymatic histone lysine lactoylation derived from lactoyl-coenzyme A (lactoyl-CoA, also termed lactyl-CoA), and non-enzymatic lysine lactoylation resulting from acyl-transfer via lactoyl-glutathione. While the former has precedent in the form of enzyme-catalysed lysine acylation, the lactoyl-CoA metabolite has not been previously quantified in mammalian systems. Here, we use liquid chromatography-high-resolution mass spectrometry (LC-HRMS) together with a synthetic standard to detect and validate the presence of lactoyl-CoA in cell and tissue samples. Conducting a retrospective analysis of data from previously analysed samples revealed the presence of lactoyl-CoA in diverse cell and tissue contexts. In addition, we describe a biosynthetic route to generate 13C315N1-isotopically labelled lactoyl-CoA, providing a co-eluting internal standard for analysis of this metabolite. We estimate lactoyl-CoA concentrations of 1.14 × 10-8 pmol per cell in cell culture and 0.0172 pmol mg-1 tissue wet weight in mouse heart. These levels are similar to crotonyl-CoA, but between 20 and 350 times lower than predominant acyl-CoAs such as acetyl-, propionyl- and succinyl-CoA. Overall our studies provide the first quantitative measurements of lactoyl-CoA in metazoans, and provide a methodological foundation for the interrogation of this novel metabolite in biology and disease.
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Affiliation(s)
- Erika L. Varner
- Center for Metabolic Disease Research, Department of Microbiology and Immunology, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Sophie Trefely
- Center for Metabolic Disease Research, Department of Microbiology and Immunology, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
- Department of Cancer Biology and Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - David Bartee
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Eliana von Krusenstiern
- Center for Metabolic Disease Research, Department of Microbiology and Immunology, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Luke Izzo
- Department of Cancer Biology and Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Carmen Bekeova
- MitoCare Center, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Roddy S. O'Connor
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Center for Cellular Immunotherapies, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Erin L. Seifert
- MitoCare Center, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Kathryn E. Wellen
- Department of Cancer Biology and Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jordan L. Meier
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Nathaniel W. Snyder
- Center for Metabolic Disease Research, Department of Microbiology and Immunology, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
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20
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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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21
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Martinez Calejman C, Trefely S, Entwisle SW, Luciano A, Jung SM, Hsiao W, Torres A, Hung CM, Li H, Snyder NW, Villén J, Wellen KE, Guertin DA. mTORC2-AKT signaling to ATP-citrate lyase drives brown adipogenesis and de novo lipogenesis. Nat Commun 2020; 11:575. [PMID: 31996678 PMCID: PMC6989638 DOI: 10.1038/s41467-020-14430-w] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 12/10/2019] [Indexed: 01/09/2023] Open
Abstract
mTORC2 phosphorylates AKT in a hydrophobic motif site that is a biomarker of insulin sensitivity. In brown adipocytes, mTORC2 regulates glucose and lipid metabolism, however the mechanism has been unclear because downstream AKT signaling appears unaffected by mTORC2 loss. Here, by applying immunoblotting, targeted phosphoproteomics and metabolite profiling, we identify ATP-citrate lyase (ACLY) as a distinctly mTORC2-sensitive AKT substrate in brown preadipocytes. mTORC2 appears dispensable for most other AKT actions examined, indicating a previously unappreciated selectivity in mTORC2-AKT signaling. Rescue experiments suggest brown preadipocytes require the mTORC2/AKT/ACLY pathway to induce PPAR-gamma and establish the epigenetic landscape during differentiation. Evidence in mature brown adipocytes also suggests mTORC2 acts through ACLY to increase carbohydrate response element binding protein (ChREBP) activity, histone acetylation, and gluco-lipogenic gene expression. Substrate utilization studies additionally implicate mTORC2 in promoting acetyl-CoA synthesis from acetate through acetyl-CoA synthetase 2 (ACSS2). These data suggest that a principal mTORC2 action is controlling nuclear-cytoplasmic acetyl-CoA synthesis. mTORC2 activates Akt, a regulator of cell growth and metabolism, however, the role of mTORC2 in adipocytes is incompletely understood. Here the authors report that a mTORC2-Akt axis specifically activates ACLY to promote lipid synthesis and histone acetylation during brown adipocyte differentiation.
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Affiliation(s)
- C Martinez Calejman
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - S Trefely
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA, 19104, USA.,AJ Drexel Autism Institute, Drexel University, Philadelphia, PA, 19104, USA
| | - S W Entwisle
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA.,Program in Molecular and Cellular Biology, University of Washington, Seattle, WA, 98195, USA
| | - A Luciano
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - S M Jung
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - W Hsiao
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - A Torres
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - C M Hung
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - H Li
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - N W Snyder
- AJ Drexel Autism Institute, Drexel University, Philadelphia, PA, 19104, USA
| | - J Villén
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA.,Program in Molecular and Cellular Biology, University of Washington, Seattle, WA, 98195, USA
| | - K 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
| | - D A Guertin
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA. .,Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA.
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22
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Ecker C, Guo L, Voicu S, Gil-de-Gómez L, Medvec A, Cortina L, Pajda J, Andolina M, Torres-Castillo M, Donato JL, Mansour S, Zynda ER, Lin PY, Varela-Rohena A, Blair IA, Riley JL. Differential Reliance on Lipid Metabolism as a Salvage Pathway Underlies Functional Differences of T Cell Subsets in Poor Nutrient Environments. Cell Rep 2019; 23:741-755. [PMID: 29669281 PMCID: PMC5929999 DOI: 10.1016/j.celrep.2018.03.084] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 01/23/2018] [Accepted: 03/17/2018] [Indexed: 12/31/2022] Open
Abstract
T cells compete with malignant cells for limited nutrients within the solid tumor microenvironment. We found that effector memory CD4 T cells respond distinctly from other T cell subsets to limiting glucose and can maintain high levels of interferon-γ (IFN-γ) production in a nutrient-poor environment. Unlike naive (TN) or central memory T (TCM) cells, effector memory T (TEM) cells fail to upregulate fatty acid synthesis, oxidative phosphorylation, and reductive glutaminolysis in limiting glucose. Interference of fatty acid synthesis in naive T cells dramatically upregulates IFN-γ, while increasing exogenous lipids in media inhibits production of IFN-γ by all subsets, suggesting that relative ratio of fatty acid metabolism to glycolysis is a direct predictor of T cell effector activity. Together, these data suggest that effector memory T cells are programmed to have limited ability to synthesize and metabolize fatty acids, which allows them to maintain T cell function in nutrient-depleted microenvironments.
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Affiliation(s)
- Christopher Ecker
- Department of Microbiology and Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lili Guo
- Department of Pharmacology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Stefana Voicu
- Department of Microbiology and Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Luis Gil-de-Gómez
- Department of Pharmacology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrew Medvec
- Department of Microbiology and Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Luis Cortina
- Department of Microbiology and Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jackie Pajda
- Gibco BioProduction Cell Culture and Cell Therapy, Thermo Fisher Scientific, 3175 Staley Road, Grand Island, NY 14072, USA
| | - Melanie Andolina
- Gibco BioProduction Cell Culture and Cell Therapy, Thermo Fisher Scientific, 3175 Staley Road, Grand Island, NY 14072, USA
| | - Maria Torres-Castillo
- Gibco BioProduction Cell Culture and Cell Therapy, Thermo Fisher Scientific, 3175 Staley Road, Grand Island, NY 14072, USA
| | - Jennifer L Donato
- Gibco BioProduction Cell Culture and Cell Therapy, Thermo Fisher Scientific, 3175 Staley Road, Grand Island, NY 14072, USA
| | - Sarya Mansour
- Gibco BioProduction Cell Culture and Cell Therapy, Thermo Fisher Scientific, 3175 Staley Road, Grand Island, NY 14072, USA
| | - Evan R Zynda
- Gibco BioProduction Cell Culture and Cell Therapy, Thermo Fisher Scientific, 3175 Staley Road, Grand Island, NY 14072, USA
| | - Pei-Yi Lin
- Gibco BioProduction Cell Culture and Cell Therapy, Thermo Fisher Scientific, 3175 Staley Road, Grand Island, NY 14072, USA
| | - Angel Varela-Rohena
- Gibco BioProduction Cell Culture and Cell Therapy, Thermo Fisher Scientific, 3175 Staley Road, Grand Island, NY 14072, USA
| | - Ian A Blair
- Department of Pharmacology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James L Riley
- Department of Microbiology and Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Glycerol phosphate shuttle enzyme GPD2 regulates macrophage inflammatory responses. Nat Immunol 2019; 20:1186-1195. [PMID: 31384058 PMCID: PMC6707851 DOI: 10.1038/s41590-019-0453-7] [Citation(s) in RCA: 123] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 06/26/2019] [Indexed: 01/25/2023]
Abstract
Macrophages are activated during microbial infection to coordinate inflammatory responses and host defense. Here we find that in macrophages activated by bacterial lipopolysaccharide (LPS), mitochondrial glycerol 3-phosphate dehydrogenase (GPD2) regulates glucose oxidation to drive inflammatory responses. GPD2, a component of the glycerol phosphate shuttle, boosts glucose oxidation to fuel the production of acetyl coenzyme A, acetylation of histones and induction of genes encoding inflammatory mediators. While acute exposure to LPS drives macrophage activation, prolonged exposure to LPS triggers tolerance to LPS, where macrophages induce immunosuppression to limit the detrimental effects of sustained inflammation. The shift in the inflammatory response is modulated by GPD2, which coordinates a shutdown of oxidative metabolism; this limits the availability of acetyl coenzyme A for histone acetylation at genes encoding inflammatory mediators and thus contributes to the suppression of inflammatory responses. Therefore, GPD2 and the glycerol phosphate shuttle integrate the extent of microbial stimulation with glucose oxidation to balance the beneficial and detrimental effects of the inflammatory response.
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24
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Abstract
Dynamic interplay between cellular metabolism and histone acetylation is a key mechanism underlying metabolic control of epigenetics. In particular, the central metabolite acetyl-coenzyme A (acetyl-CoA) acts as the acetyl-donor for histone acetylation in both an enzymatic and non-enzymatic manner. Since members of the family of histone acetyl transferases (HATs) that catalyze the acetylation of histone tails possess a Michaelis constant (Km) within the range of physiological cellular acetyl-CoA concentrations, changing concentrations of acetyl-CoA can restrict or promote enzymatic histone acetylation. Likewise, non-enzymatic histone acetylation occurs at physiological concentrations. These concepts implicate acetyl-CoA as a rheostat for nutrient availability acting, in part, by controlling histone acetylation. Histone acetylation is an important epigenetic modification that controls gene expression and acetyl-CoA dependent changes in both histone acetylation and gene expression have been shown in yeast and mammalian systems. However, quantifying the metabolic conditions required to achieve specific changes in histone acetylation is a major challenge. The relationship between acetyl-CoA and histone acetylation may be influenced by a variety of factors including sub-cellular location of metabolites and enzymes, relative quantities of metabolites, and substrate availability/preference. A diversity of substrates can contribute the two-carbon acyl-chain to acetyl-CoA, a number of pathways can create or degrade acetyl-CoA, and only a handful of potential mechanisms for the crosstalk between metabolism and histone acetylation have been explored. The centrality of acetyl-CoA in intermediary metabolism means that acetyl-CoA levels may change, or be resistant to change, in unexpected ways. Thus, quantification of relevant metabolites is critical evidence in understanding how the nutrient rheostat is set in normal and pathological contexts. Coupling metabolite quantitation with isotope tracing to examine fate of specific metabolites is critical to the crosstalk between metabolism and histone acetylation, including but not limited to acetyl-CoA provides necessary context. This chapter provides guidance on experimental design of quantification with isotope dilution and/or tracing of acetyl-CoA within a targeted or highly multiplexed multi-analyte workflow.
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25
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Abstract
Diseases associated with mitochondrial DNA (mtDNA) mutations are highly variable in phenotype, in large part because of differences in the percentage of normal and mutant mtDNAs (heteroplasmy) present within the cell. For example, increasing heteroplasmy levels of the mtDNA tRNALeu(UUR) nucleotide (nt) 3243A > G mutation result successively in diabetes, neuromuscular degenerative disease, and perinatal lethality. These phenotypes are associated with differences in mitochondrial function and nuclear DNA (nDNA) gene expression, which are recapitulated in cybrid cell lines with different percentages of m.3243G mutant mtDNAs. Using metabolic tracing, histone mass spectrometry, and NADH fluorescence lifetime imaging microscopy in these cells, we now show that increasing levels of this single mtDNA mutation cause profound changes in the nuclear epigenome. At high heteroplasmy, mitochondrially derived acetyl-CoA levels decrease causing decreased histone H4 acetylation, with glutamine-derived acetyl-CoA compensating when glucose-derived acetyl-CoA is limiting. In contrast, α-ketoglutarate levels increase at midlevel heteroplasmy and are inversely correlated with histone H3 methylation. Inhibition of mitochondrial protein synthesis induces acetylation and methylation changes, and restoration of mitochondrial function reverses these effects. mtDNA heteroplasmy also affects mitochondrial NAD+/NADH ratio, which correlates with nuclear histone acetylation, whereas nuclear NAD+/NADH ratio correlates with changes in nDNA and mtDNA transcription. Thus, mutations in the mtDNA cause distinct metabolic and epigenomic changes at different heteroplasmy levels, potentially explaining transcriptional and phenotypic variability of mitochondrial disease.
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26
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Sidoli S, Trefely S, Garcia BA, Carrer A. Integrated Analysis of Acetyl-CoA and Histone Modification via Mass Spectrometry to Investigate Metabolically Driven Acetylation. Methods Mol Biol 2019; 1928:125-147. [PMID: 30725455 DOI: 10.1007/978-1-4939-9027-6_9] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Acetylation is a highly abundant and dynamic post-translational modification (PTM) on histone proteins which, when present on chromatin-bound histones, facilitates the accessibility of DNA for gene transcription. The central metabolite, acetyl-CoA, is a substrate for acetyltransferases, which catalyze protein acetylation. Acetyl-CoA is an essential intermediate in diverse metabolic pathways, and cellular acetyl-CoA levels fluctuate according to extracellular nutrient availability and the metabolic state of the cell. The Michaelis constant (Km) of most histone acetyltransferases (HATs), which specifically target histone proteins, falls within the range of cellular acetyl-CoA concentrations. As a consequence, global levels of histone acetylation are often restricted by availability of acetyl-CoA. Such metabolic regulation of histone acetylation is important for cell proliferation, differentiation, and a variety of cellular functions. In cancer, numerous oncogenic signaling events hijack cellular metabolism, ultimately inducing an extensive rearrangement of the epigenetic state of the cell. Understanding metabolic control of the epigenome through histone acetylation is essential to illuminate the molecular mechanisms by which cells sense, adapt, and occasionally disengage nutrient fluctuations and environmental cues from gene expression. In particular, targeting metabolic regulators or even dietary interventions to impact acetyl-CoA availability and histone acetylation is a promising target in cancer therapy. Liquid chromatography coupled to mass spectrometry (LC-MS) is the most accurate methodology to quantify protein PTMs and metabolites. In this chapter, we present state-of-the-art protocols to analyze histone acetylation and acetyl-CoA. Histones are extracted and digested into short peptides (4-20 aa) prior to LC-MS. Acetyl-CoA is extracted from cells and analyzed using an analogous mass spectrometry-based procedure. Model systems can be fed with isotopically labeled substrates to investigate the metabolic preference for acetyl-CoA production and the metabolic dependence and turnover of histone acetylation. We also present an example of data integration to correlate changes in acetyl-CoA production with histone acetylation.
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Affiliation(s)
- Simone Sidoli
- Department of Biochemistry and Biophysics, Perelman School of Medicine, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Sophie Trefely
- Department of Cancer Biology, Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA, USA.,A. J. Drexel Autism Institute, Drexel University, Philadelphia, PA, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, Perelman School of Medicine, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Alessandro Carrer
- Department of Cancer Biology, Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA, USA.
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27
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Huber K, Hofer DC, Trefely S, Pelzmann HJ, Madreiter-Sokolowski C, Duta-Mare M, Schlager S, Trausinger G, Stryeck S, Graier WF, Kolb D, Magnes C, Snyder NW, Prokesch A, Kratky D, Madl T, Wellen KE, Bogner-Strauss JG. N-acetylaspartate pathway is nutrient responsive and coordinates lipid and energy metabolism in brown adipocytes. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2019; 1866:337-348. [PMID: 30595160 PMCID: PMC6390944 DOI: 10.1016/j.bbamcr.2018.08.017] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 08/27/2018] [Indexed: 12/22/2022]
Abstract
The discovery of significant amounts of metabolically active brown adipose tissue (BAT) in adult humans renders it a promising target for anti-obesity therapies by inducing weight loss through increased energy expenditure. The components of the N-acetylaspartate (NAA) pathway are highly abundant in BAT. Aspartate N-acetyltransferase (Asp-NAT, encoded by Nat8l) synthesizes NAA from acetyl-CoA and aspartate and increases energy expenditure in brown adipocytes. However, the exact mechanism how the NAA pathway contributes to accelerated mobilization and oxidation of lipids and the physiological regulation of the NAA pathway remained elusive. Here, we demonstrate that the expression of NAA pathway genes corresponds to nutrient availability and specifically responds to changes in exogenous glucose. NAA is preferentially produced from glucose-derived acetyl-CoA and aspartate and its concentration increases during adipogenesis. Overexpression of Nat8l drains glucose-derived acetyl-CoA into the NAA pool at the expense of cellular lipids and certain amino acids. Mechanistically, we elucidated that a combined activation of neutral and lysosomal (acid) lipolysis is responsible for the increased lipid degradation. Specifically, translocation of the transcription factor EB to the nucleus activates the biosynthesis of autophagosomes and lysosomes. Lipid degradation within lysosomes accompanied by adipose triglyceride lipase-mediated lipolysis delivers fatty acids for the support of elevated mitochondrial respiration. Together, our data suggest a crucial role of the NAA pathway in energy metabolism and metabolic adaptation in BAT.
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Affiliation(s)
- Katharina Huber
- Institute of Biochemistry, Graz University of Technology, Graz, Austria; Department of Cancer Biology, University of Pennsylvania, Philadelphia, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, USA
| | - Dina C Hofer
- Institute of Biochemistry, Graz University of Technology, Graz, Austria
| | - Sophie Trefely
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, USA; AJ Drexel Autism Institute, Drexel University, Philadelphia, USA
| | - Helmut J Pelzmann
- Institute of Biochemistry, Graz University of Technology, Graz, Austria
| | - Corina Madreiter-Sokolowski
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Cell Biology, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Madalina Duta-Mare
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Cell Biology, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Stefanie Schlager
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Cell Biology, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Gert Trausinger
- HEALTH Institute for Biomedicine and Health Sciences, Joanneum Research, Graz, Austria
| | - Sarah Stryeck
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Cell Biology, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Wolfgang F Graier
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Cell Biology, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria; BioTechMed-Graz, Graz, Austria
| | - Dagmar Kolb
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Cell Biology, Histology and Embryology, Medical University of Graz, Graz, Austria
| | - Christoph Magnes
- HEALTH Institute for Biomedicine and Health Sciences, Joanneum Research, Graz, Austria
| | | | - Andreas Prokesch
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Cell Biology, Histology and Embryology, Medical University of Graz, Graz, Austria; BioTechMed-Graz, Graz, Austria
| | - Dagmar Kratky
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Cell Biology, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria; BioTechMed-Graz, Graz, Austria
| | - Tobias Madl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Cell Biology, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria; BioTechMed-Graz, Graz, Austria
| | - Kathryn E Wellen
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, USA
| | - Juliane G Bogner-Strauss
- Institute of Biochemistry, Graz University of Technology, Graz, Austria; BioTechMed-Graz, Graz, Austria.
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28
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Liu M, O'Connor RS, Trefely S, Graham K, Snyder NW, Beatty GL. Metabolic rewiring of macrophages by CpG potentiates clearance of cancer cells and overcomes tumor-expressed CD47-mediated 'don't-eat-me' signal. Nat Immunol 2019; 20:265-275. [PMID: 30664738 PMCID: PMC6380920 DOI: 10.1038/s41590-018-0292-y] [Citation(s) in RCA: 172] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 12/01/2018] [Indexed: 12/12/2022]
Abstract
Macrophages enforce anti-tumor immunity by engulfing and killing tumor cells. Although these functions are determined by a balance of stimulatory and inhibitory signals, the role of macrophage metabolism is unknown. Here, we study the capacity of macrophages to circumvent inhibitory activity mediated by CD47 on cancer cells. We show that stimulation with CpG, a TLR9 agonist, evokes changes in the central carbon metabolism of macrophages that enable anti-tumor activity, including engulfment of CD47+ cancer cells. CpG activation engenders a metabolic state, that requires fatty acid oxidation and shunting of tricarboxylic acid cycle intermediates for de novo lipid biosynthesis. This integration of metabolic inputs is underpinned by carnitine palmitoyltransferase 1A and ATP citrate lyase, which together, impart macrophages with anti-tumor potential capable of overcoming inhibitory CD47 on cancer cells. Our findings identify central carbon metabolism to be a novel determinant and potential therapeutic target for stimulating anti-tumor activity by macrophages.
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Affiliation(s)
- Mingen Liu
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Roddy S O'Connor
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sophie Trefely
- AJ Drexel Autism Institute, Drexel University, Philadelphia, PA, USA.,Department of Cancer Biology, Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Kathleen Graham
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Gregory L Beatty
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA. .,Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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29
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Frederick DW, Trefely S, Buas A, Goodspeed J, Singh J, Mesaros C, Baur JA, Snyder NW. Stable isotope labeling by essential nutrients in cell culture (SILEC) for accurate measurement of nicotinamide adenine dinucleotide metabolism. Analyst 2018; 142:4431-4437. [PMID: 29072717 DOI: 10.1039/c7an01378g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Nicotinamide adenine dinucleotide (NAD) and nicotinamide adenine dinucleotide phosphate (NADP) are conserved metabolic cofactors that mediate reduction-oxidation (redox) reactions throughout all domains of life. The diversity of synthetic routes and cellular processes involving the transfer of reducing equivalents to and from these cofactors makes the accurate quantitation and metabolic tracing of NAD(H) and NADP(H) of broad interest. However, current analytical techniques typically rely on standard curves that do not incorporate confounding effects of the sample matrix. We utilized the essential requirement of niacin and tryptophan for NAD synthesis in mammalian cells to devise a stable isotope labeling by essential nutrients in cell culture (SILEC) method for efficient labeling of intracellular NAD(H) and NADP(H) pools. Coupling this approach with detection by liquid chromatography-high resolution mass spectrometry (LC-HRMS), we demonstrate the utility of incorporating a [13C315N1]-nicotinamide moiety into a library of NAD-derived metabolites for use as internal standards in matrixed samples. Using a two-label system incorporating [13C315N1]-nicotinamide and [13C11]-tryptophan, we quantify the relative contribution of salvage and de novo NAD synthesis, respectively, in S. cerevisiae and HepG2 human hepatocellular carcinoma cells under basal conditions. As a further proof-of-principle, we demonstrate an improvement in the linear range for quantification of NAD and apply this method to analysis of NAD(H) in mouse liver. This method demonstrates the generalizability of SILEC, and provides a simple method for generating a library of stable isotope labeled internal standards for quantifying and tracing the metabolism of cellular and tissue NAD(H) and NADP(H).
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Affiliation(s)
- David W Frederick
- Department of Physiology and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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30
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Wei X, Tao J, Shen Y, Xiao S, Jiang S, Shang E, Zhu Z, Qian D, Duan J. Sanhuang Xiexin Tang Ameliorates Type 2 Diabetic Rats via Modulation of the Metabolic Profiles and NF-κB/PI-3K/Akt Signaling Pathways. Front Pharmacol 2018; 9:955. [PMID: 30210342 PMCID: PMC6121076 DOI: 10.3389/fphar.2018.00955] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 08/03/2018] [Indexed: 01/07/2023] Open
Abstract
Sanhuang Xiexin Tang (SXT), a classic prescription, has been clinically used to cure diabetes for thousands of years, but its mechanism remains unclear. Here, a systematic in-depth research was performed to unravel how it worked by the signaling pathway and metabonomics analysis. Our studies were conducted using high-fat diets (HFD) and streptozocin (STZ)-induced type 2 diabetes mellitus (T2DM) rats. The blood glucose was measured by a glucose-meter. Protein contents were determined by western blotting or ELISA and mRNA expression was identified by RT-PCR analysis. The pathological status of pancreas was assessed by histopathological analysis. Furthermore, Ultra Performance Liquid Chromatography-Quadrupole-Time of Flight/Mass Spectrometry (UPLC-Q-TOF/MS) coupled with multivariate statistical analysis was performed to discover potential biomarkers and the associated pathways. Hyperglycaemia, insulin resistance, dyslipidemia and inflammation in T2DM rats were significantly ameliorated after 7-week oral administration of SXT. The expressions of phosphatidylinositol-3-kinase (PI-3K), protein kinase B (Akt), glucose transporters-4 (GLUT4) Mrna, and p-PI-3K, p-Akt, GLUT4 protein involved in the PI-3K/Akt signaling pathway of T2DM were markedly up-regulated. Further investigation indicated that the perturbance of metabolic profiling in T2DM rats was obviously reversed by SXT and 38 potential biomarkers were screened and identified. Our study might help clarify the mechanism of SXT and provide some evidences for its clinical application in the future.
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Affiliation(s)
- Xiaoyan Wei
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jinhua Tao
- School of Pharmacy, Nantong University, Nantong, China
| | - Yumeng Shen
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing, China
| | - Suwei Xiao
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing, China
| | - Shu Jiang
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing, China
| | - Erxin Shang
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing, China
| | - Zhenhua Zhu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing, China
| | - Dawei Qian
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jinao Duan
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing, China
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31
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Tenopoulou M, Doulias PT, Nakamoto K, Berrios K, Zura G, Li C, Faust M, Yakovishina V, Evans P, Tan L, Bennett MJ, Snyder NW, Quinn WJ, Baur JA, Atochin DN, Huang PL, Ischiropoulos H. Oral nitrite restores age-dependent phenotypes in eNOS-null mice. JCI Insight 2018; 3:122156. [PMID: 30135317 DOI: 10.1172/jci.insight.122156] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 07/11/2018] [Indexed: 01/01/2023] Open
Abstract
Alterations in the synthesis and bioavailability of NO are central to the pathogenesis of cardiovascular and metabolic disorders. Although endothelial NO synthase-derived (eNOS-derived) NO affects mitochondrial long-chain fatty acid β-oxidation, the pathophysiological significance of this regulation remains unclear. Accordingly, we determined the contributions of eNOS/NO signaling in the adaptive metabolic responses to fasting and in age-induced metabolic dysfunction. Four-month-old eNOS-/- mice are glucose intolerant and exhibit serum dyslipidemia and decreased capacity to oxidize fatty acids. However, during fasting, eNOS-/- mice redirect acetyl-CoA to ketogenesis to elevate circulating levels of β-hydroxybutyrate similar to wild-type mice. Treatment of 4-month-old eNOS-/- mice with nitrite for 10 days corrected the hypertension and serum hyperlipidemia and normalized the rate of fatty acid oxidation. Fourteen-month-old eNOS-/- mice exhibited metabolic derangements, resulting in reduced utilization of fat to generate energy, lower resting metabolic activity, and diminished physical activity. Seven-month administration of nitrite to eNOS-/- mice reversed the age-dependent metabolic derangements and restored physical activity. While the eNOS/NO signaling is not essential for the metabolic adaptation to fasting, it is critical for regulating systemic metabolic homeostasis in aging. The development of age-dependent metabolic disorder is prevented by low-dose replenishment of bioactive NO.
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Affiliation(s)
- Margarita Tenopoulou
- Children's Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania, USA
| | | | - Kent Nakamoto
- Children's Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania, USA
| | - Kiara Berrios
- Children's Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania, USA
| | - Gabriella Zura
- Children's Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania, USA
| | - Chenxi Li
- Children's Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania, USA
| | - Michael Faust
- Children's Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania, USA
| | - Veronika Yakovishina
- Children's Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania, USA
| | - Perry Evans
- Children's Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania, USA
| | - Lu Tan
- Children's Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania, USA
| | - Michael J Bennett
- Children's Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania, USA
| | - Nathaniel W Snyder
- A.J. Drexel Autism Institute, Drexel University, Philadelphia, Pennsylvania, USA
| | - William J Quinn
- Department of Physiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Joseph A Baur
- Department of Physiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Dmitriy N Atochin
- Cardiovascular Research Center Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Paul L Huang
- Cardiovascular Research Center Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Harry Ischiropoulos
- Children's Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania, USA
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32
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Shrimp JH, Garlick JM, Tezil T, Sorum AW, Worth AJ, Blair IA, Verdin E, Snyder NW, Meier JL. Defining Metabolic and Nonmetabolic Regulation of Histone Acetylation by NSAID Chemotypes. Mol Pharm 2017; 15:729-736. [PMID: 29240439 DOI: 10.1021/acs.molpharmaceut.7b00943] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Nonsteroidal anti-inflammatory drugs (NSAIDs) are well-known for their effects on inflammatory gene expression. Although NSAIDs are known to impact multiple cellular signaling mechanisms, a recent finding is that the NSAID salicylate can disrupt histone acetylation, in part through direct inhibition of the lysine acetyltransferase (KAT) p300/CBP. While salicylate is a relatively weak KAT inhibitor, its CoA-linked metabolite is more potent; however, the ability of NSAID metabolites to inhibit KAT enzymes biochemically and in cells remains relatively unexplored. Here we define the role of metabolic and nonmetabolic mechanisms in inhibition of KAT activity by NSAID chemotypes. First, we screen a small panel of NSAIDs for biochemical inhibition of the prototypical KAT p300, leading to the finding that many carboxylate-containing NSAIDs, including ibuprofen, are able to function as weak inhibitors. Assessing the inhibition of p300 by ibuprofen-CoA, a known NSAID metabolite, reveals that linkage of ibuprofen to CoA increases its biochemical potency toward p300 and other KAT enzymes. In cellular studies, we find that carboxylate-containing NSAIDs inhibit histone acetylation. Finally, we exploit the stereoselective metabolism of ibuprofen to assess the role of its acyl-CoA metabolite in regulation of histone acetylation. This unique strategy reveals that formation of ibuprofen-CoA and histone acetylation are poorly correlated, suggesting metabolism may not be required for ibuprofen to inhibit histone acetylation. Overall, these studies provide new insights into the ability of NSAIDs to alter histone acetylation, and illustrate how selective metabolism may be leveraged as a tool to explore the influence of metabolic acyl-CoAs on cellular enzyme activity.
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Affiliation(s)
- Jonathan H Shrimp
- Chemical Biology Laboratory , National Cancer Institute , Frederick , Maryland 21702 , United States
| | - Julie M Garlick
- Chemical Biology Laboratory , National Cancer Institute , Frederick , Maryland 21702 , United States
| | - Tugsan Tezil
- Buck Institute for Research on Aging, Novato , California 94945 , United States
| | - Alexander W Sorum
- Chemical Biology Laboratory , National Cancer Institute , Frederick , Maryland 21702 , United States
| | - Andrew J Worth
- Penn SRP Center, Center of Excellence in Environmental Toxicology , University of Pennsylvania , Philadelphia Pennsylvania 19104 , United States
| | - Ian A Blair
- Penn SRP Center, Center of Excellence in Environmental Toxicology , University of Pennsylvania , Philadelphia Pennsylvania 19104 , United States
| | - Eric Verdin
- Buck Institute for Research on Aging, Novato , California 94945 , United States
| | - Nathaniel W Snyder
- Drexel University, A.J. Drexel Autism Institute , 3020 Market Street , Philadelphia Pennsylvania 19104 , United States
| | - Jordan L Meier
- Chemical Biology Laboratory , National Cancer Institute , Frederick , Maryland 21702 , United States
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33
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Zhao S, Torres A, Henry RA, Trefely S, Wallace M, Lee JV, Carrer A, Sengupta A, Campbell SL, Kuo YM, Frey AJ, Meurs N, Viola JM, Blair IA, Weljie AM, Metallo CM, Snyder NW, Andrews AJ, Wellen KE. ATP-Citrate Lyase Controls a Glucose-to-Acetate Metabolic Switch. Cell Rep 2017; 17:1037-1052. [PMID: 27760311 DOI: 10.1016/j.celrep.2016.09.069] [Citation(s) in RCA: 256] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 08/09/2016] [Accepted: 09/21/2016] [Indexed: 12/22/2022] Open
Abstract
Mechanisms of metabolic flexibility enable cells to survive under stressful conditions and can thwart therapeutic responses. Acetyl-coenzyme A (CoA) plays central roles in energy production, lipid metabolism, and epigenomic modifications. Here, we show that, upon genetic deletion of Acly, the gene coding for ATP-citrate lyase (ACLY), cells remain viable and proliferate, although at an impaired rate. In the absence of ACLY, cells upregulate ACSS2 and utilize exogenous acetate to provide acetyl-CoA for de novo lipogenesis (DNL) and histone acetylation. A physiological level of acetate is sufficient for cell viability and abundant acetyl-CoA production, although histone acetylation levels remain low in ACLY-deficient cells unless supplemented with high levels of acetate. ACLY-deficient adipocytes accumulate lipid in vivo, exhibit increased acetyl-CoA and malonyl-CoA production from acetate, and display some differences in fatty acid content and synthesis. Together, these data indicate that engagement of acetate metabolism is a crucial, although partial, mechanism of compensation for ACLY deficiency.
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Affiliation(s)
- Steven Zhao
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - AnnMarie Torres
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ryan A Henry
- Department of Cancer Biology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Sophie Trefely
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; A.J. Drexel Autism Institute, Drexel University, Philadelphia, PA 19104, USA
| | - Martina Wallace
- Department of Bioengineering and Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Joyce V Lee
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alessandro Carrer
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Arjun Sengupta
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sydney L Campbell
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yin-Ming Kuo
- Department of Cancer Biology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Alexander J Frey
- A.J. Drexel Autism Institute, Drexel University, Philadelphia, PA 19104, USA
| | - Noah Meurs
- Department of Bioengineering and Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - John M Viola
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ian A Blair
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Aalim M Weljie
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Christian M Metallo
- Department of Bioengineering and Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nathaniel W Snyder
- A.J. Drexel Autism Institute, Drexel University, Philadelphia, PA 19104, USA
| | - Andrew J Andrews
- Department of Cancer Biology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Kathryn E Wellen
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Simithy J, Sidoli S, Yuan ZF, Coradin M, Bhanu NV, Marchione DM, Klein BJ, Bazilevsky GA, McCullough CE, Magin RS, Kutateladze TG, Snyder NW, Marmorstein R, Garcia BA. Characterization of histone acylations links chromatin modifications with metabolism. Nat Commun 2017; 8:1141. [PMID: 29070843 PMCID: PMC5656686 DOI: 10.1038/s41467-017-01384-9] [Citation(s) in RCA: 140] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 09/14/2017] [Indexed: 12/30/2022] Open
Abstract
Over the last decade, numerous histone acyl post-translational modifications (acyl-PTMs) have been discovered, of which the functional significance is still under intense study. Here, we use high-resolution mass spectrometry to accurately quantify eight acyl-PTMs in vivo and after in vitro enzymatic assays. We assess the ability of seven histone acetyltransferases (HATs) to catalyze acylations on histones in vitro using short-chain acyl-CoA donors, proving that they are less efficient towards larger acyl-CoAs. We also observe that acyl-CoAs can acylate histones through non-enzymatic mechanisms. Using integrated metabolomic and proteomic approaches, we achieve high correlation (R 2 > 0.99) between the abundance of acyl-CoAs and their corresponding acyl-PTMs. Moreover, we observe a dose-dependent increase in histone acyl-PTM abundances in response to acyl-CoA supplementation in in nucleo reactions. This study represents a comprehensive profiling of scarcely investigated low-abundance histone marks, revealing that concentrations of acyl-CoAs affect histone acyl-PTM abundances by both enzymatic and non-enzymatic mechanisms.
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Affiliation(s)
- Johayra Simithy
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Simone Sidoli
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Zuo-Fei Yuan
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Mariel Coradin
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Natarajan V Bhanu
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Dylan M Marchione
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Brianna J Klein
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Gleb A Bazilevsky
- Graduate Group in Cell and Molecular Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Cheryl E McCullough
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Robert S Magin
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Nathaniel W Snyder
- AJ Drexel Autism Institute, Drexel University, 3020 Market Street Suite 560, Philadelphia, PA, 19104, USA
| | - Ronen Marmorstein
- Department of Biochemistry and Biophysics, Abramson Family Cancer Research Institute, and the Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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Schultz MC, Zhang J, Luo X, Savchenko O, Li L, Deyholos M, Chen J. Impact of Low-Intensity Pulsed Ultrasound on Transcript and Metabolite Abundance in Saccharomyces cerevisiae. J Proteome Res 2017; 16:2975-2982. [DOI: 10.1021/acs.jproteome.7b00273] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Michael C. Schultz
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2V4, Canada
| | - Jian Zhang
- InnTech Alberta, Vegreville, Alberta T6N 1E4, Canada
- Department
of Biology, University of British Columbia, Okanagan Campus, Kelowna, British Columbia V1V 1V7, Canada
| | - Xian Luo
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2V4, Canada
| | - Oleksandra Savchenko
- Department
of Biomedical Engineering, University of Alberta, Edmonton, Alberta T6G 2V4, Canada
| | - Liang Li
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2V4, Canada
| | - Michael Deyholos
- Department
of Biology, University of British Columbia, Okanagan Campus, Kelowna, British Columbia V1V 1V7, Canada
| | - Jie Chen
- Department
of Biomedical Engineering, University of Alberta, Edmonton, Alberta T6G 2V4, Canada
- Department
of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta T6G 2V4, Canada
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36
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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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Company profile: BluePen Biomarkers LLC – integrated biomarker solutions. Future Sci OA 2016; 2:FSO124. [PMID: 28031971 PMCID: PMC5137845 DOI: 10.4155/fsoa-2016-0031] [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: 05/04/2016] [Accepted: 05/06/2016] [Indexed: 11/17/2022] Open
Abstract
BluePen Biomarkers provides a unique comprehensive multi-omics biomarker discovery and validation platform. We can quantify, integrate and analyze genomics, proteomics, metabolomics and lipidomics biomarkers, alongside clinical data, demographics and other phenotypic data. A unique bio-inspired signal processing analytic approach is used that has the proven ability to identify biomarkers in a wide variety of diseases. The resulting biomarkers can be used for diagnosis, prognosis, mechanistic studies and predicting treatment response, in contexts from core research through clinical trials. BluePen Biomarkers provides an additional groundbreaking research goal: identifying surrogate biomarkers from different modalities. This not only provides new biological insights, but enables least invasive, least-cost tests that meet or exceed the predictive quality of current tests.
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38
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Worth AJ, Marchione DM, Parry RC, Wang Q, Gillespie KP, Saillant NN, Sims C, Mesaros C, Snyder NW, Blair IA. LC-MS Analysis of Human Platelets as a Platform for Studying Mitochondrial Metabolism. J Vis Exp 2016:e53941. [PMID: 27077278 DOI: 10.3791/53941] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Perturbed mitochondrial metabolism has received renewed interest as playing a causative role in a range of diseases. Probing alterations to metabolic pathways requires a model in which external factors can be well controlled, allowing for reproducible and meaningful results. Many studies employ transformed cellular models for these purposes; however, metabolic reprogramming that occurs in many cancer cell lines may introduce confounding variables. For this reason primary cells are desirable, though attaining adequate biomass for metabolic studies can be challenging. Here we show that human platelets can be utilized as a platform to carry out metabolic studies in combination with liquid chromatography-tandem mass spectrometry analysis. This approach is amenable to relative quantification and isotopic labeling to probe the activity of specific metabolic pathways. Availability of platelets from individual donors or from blood banks makes this model system applicable to clinical studies and feasible to scale up. Here we utilize isolated platelets to confirm previously identified compensatory metabolic shifts in response to the complex I inhibitor rotenone. More specifically, a decrease in glycolysis is accompanied by an increase in fatty acid oxidation to maintain acetyl-CoA levels. Our results show that platelets can be used as an easily accessible and medically relevant model to probe the effects of xenobiotics on cellular metabolism.
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Affiliation(s)
- Andrew J Worth
- Center for Cancer Pharmacology, University of Pennsylvania; Center for Excellence in Environmental Toxicology, University of Pennsylvania
| | - Dylan M Marchione
- Center for Excellence in Environmental Toxicology, University of Pennsylvania; Penn SRP and Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania
| | - Robert C Parry
- Center for Cancer Pharmacology, University of Pennsylvania; Center for Excellence in Environmental Toxicology, University of Pennsylvania
| | - Qingqing Wang
- Center for Excellence in Environmental Toxicology, University of Pennsylvania; Penn SRP and Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania
| | - Kevin P Gillespie
- Center for Excellence in Environmental Toxicology, University of Pennsylvania; Penn SRP and Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania
| | - Noelle N Saillant
- Division of Traumatology, Department of Surgery, Critical Care and Acute Care Surgery, University of Pennsylvania
| | - Carrie Sims
- Division of Traumatology, Department of Surgery, Critical Care and Acute Care Surgery, University of Pennsylvania
| | - Clementina Mesaros
- Center for Cancer Pharmacology, University of Pennsylvania; Center for Excellence in Environmental Toxicology, University of Pennsylvania
| | | | - Ian A Blair
- Center for Cancer Pharmacology, University of Pennsylvania; Center for Excellence in Environmental Toxicology, University of Pennsylvania;
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LC-quadrupole/Orbitrap high-resolution mass spectrometry enables stable isotope-resolved simultaneous quantification and ¹³C-isotopic labeling of acyl-coenzyme A thioesters. Anal Bioanal Chem 2016; 408:3651-8. [PMID: 26968563 DOI: 10.1007/s00216-016-9448-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 02/19/2016] [Accepted: 02/25/2016] [Indexed: 01/13/2023]
Abstract
Acyl-coenzyme A (acyl-CoA) thioesters are evolutionarily conserved, compartmentalized, and energetically activated substrates for biochemical reactions. The ubiquitous involvement of acyl-CoA thioesters in metabolism, including the tricarboxylic acid cycle, fatty acid metabolism, amino acid degradation, and cholesterol metabolism highlights the broad applicability of applied measurements of acyl-CoA thioesters. However, quantitation of acyl-CoA levels provides only one dimension of metabolic information and a more complete description of metabolism requires the relative contribution of different precursors to individual substrates and pathways. Using two distinct stable isotope labeling approaches, acyl-CoA thioesters can be labeled with either a fixed [(13)C3(15)N1] label derived from pantothenate into the CoA moiety or via variable [(13)C] labeling into the acyl chain from metabolic precursors. Liquid chromatography-hybrid quadrupole/Orbitrap high-resolution mass spectrometry using parallel reaction monitoring, but not single ion monitoring, allowed the simultaneous quantitation of acyl-CoA thioesters by stable isotope dilution using the [(13)C3(15)N1] label and measurement of the incorporation of labeled carbon atoms derived from [(13)C6]-glucose, [(13)C5(15)N2]-glutamine, and [(13)C3]-propionate. As a proof of principle, we applied this method to human B cell lymphoma (WSU-DLCL2) cells in culture to precisely describe the relative pool size and enrichment of isotopic tracers into acetyl-, succinyl-, and propionyl-CoA. This method will allow highly precise, multiplexed, and stable isotope-resolved determination of metabolism to refine metabolic models, characterize novel metabolism, and test modulators of metabolic pathways involving acyl-CoA thioesters.
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40
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Covarrubias AJ, Aksoylar HI, Yu J, Snyder NW, Worth AJ, Iyer SS, Wang J, Ben-Sahra I, Byles V, Polynne-Stapornkul T, Espinosa EC, Lamming D, Manning BD, Zhang Y, Blair IA, Horng T. Akt-mTORC1 signaling regulates Acly to integrate metabolic input to control of macrophage activation. eLife 2016; 5. [PMID: 26894960 PMCID: PMC4769166 DOI: 10.7554/elife.11612] [Citation(s) in RCA: 303] [Impact Index Per Article: 37.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 01/05/2016] [Indexed: 12/18/2022] Open
Abstract
Macrophage activation/polarization to distinct functional states is critically supported by metabolic shifts. How polarizing signals coordinate metabolic and functional reprogramming, and the potential implications for control of macrophage activation, remains poorly understood. Here we show that IL-4 signaling co-opts the Akt-mTORC1 pathway to regulate Acly, a key enzyme in Ac-CoA synthesis, leading to increased histone acetylation and M2 gene induction. Only a subset of M2 genes is controlled in this way, including those regulating cellular proliferation and chemokine production. Moreover, metabolic signals impinge on the Akt-mTORC1 axis for such control of M2 activation. We propose that Akt-mTORC1 signaling calibrates metabolic state to energetically demanding aspects of M2 activation, which may define a new role for metabolism in supporting macrophage activation.
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Affiliation(s)
- Anthony J Covarrubias
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, United States
| | - Halil Ibrahim Aksoylar
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, United States
| | - Jiujiu Yu
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, United States
| | - Nathaniel W Snyder
- Center of Excellence in Environmental Toxicology, University of Pennsylvania, Philadelphia, United States.,A.J. Drexel Autism Institute, Drexel University, Philadelphia, United States
| | - Andrew J Worth
- Center of Excellence in Environmental Toxicology, University of Pennsylvania, Philadelphia, United States
| | - Shankar S Iyer
- Department of Medicine, Brigham and Women's Hospital, Boston, United States
| | - Jiawei Wang
- Institute for Plant Physiology and Ecology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Issam Ben-Sahra
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, United States
| | - Vanessa Byles
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, United States
| | - Tiffany Polynne-Stapornkul
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, United States
| | - Erika C Espinosa
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, United States
| | - Dudley Lamming
- Department of Medicine, University of Wisconsin-Madison, Madison, United States
| | - Brendan D Manning
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, United States
| | - Yijing Zhang
- Institute for Plant Physiology and Ecology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ian A Blair
- Center of Excellence in Environmental Toxicology, University of Pennsylvania, Philadelphia, United States
| | - Tiffany Horng
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, United States
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Bedi KC, Snyder NW, Brandimarto J, Aziz M, Mesaros C, Worth AJ, Wang LL, Javaheri A, Blair IA, Margulies KB, Rame JE. Evidence for Intramyocardial Disruption of Lipid Metabolism and Increased Myocardial Ketone Utilization in Advanced Human Heart Failure. Circulation 2016; 133:706-16. [PMID: 26819374 DOI: 10.1161/circulationaha.115.017545] [Citation(s) in RCA: 434] [Impact Index Per Article: 54.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 12/28/2015] [Indexed: 12/16/2022]
Abstract
BACKGROUND The failing human heart is characterized by metabolic abnormalities, but these defects remains incompletely understood. In animal models of heart failure there is a switch from a predominance of fatty acid utilization to the more oxygen-sparing carbohydrate metabolism. Recent studies have reported decreases in myocardial lipid content, but the inclusion of diabetic and nondiabetic patients obscures the distinction of adaptations to metabolic derangements from adaptations to heart failure per se. METHODS AND RESULTS We performed both unbiased and targeted myocardial lipid surveys using liquid chromatography-mass spectroscopy in nondiabetic, lean, predominantly nonischemic, advanced heart failure patients at the time of heart transplantation or left ventricular assist device implantation. We identified significantly decreased concentrations of the majority of myocardial lipid intermediates, including long-chain acylcarnitines, the primary subset of energetic lipid substrate for mitochondrial fatty acid oxidation. We report for the first time significantly reduced levels of intermediate and anaplerotic acyl-coenzyme A (CoA) species incorporated into the Krebs cycle, whereas the myocardial concentration of acetyl-CoA was significantly increased in end-stage heart failure. In contrast, we observed an increased abundance of ketogenic β-hydroxybutyryl-CoA, in association with increased myocardial utilization of β-hydroxybutyrate. We observed a significant increase in the expression of the gene encoding succinyl-CoA:3-oxoacid-CoA transferase, the rate-limiting enzyme for myocardial oxidation of β-hydroxybutyrate and acetoacetate. CONCLUSIONS These findings indicate increased ketone utilization in the severely failing human heart independent of diabetes mellitus, and they support the role of ketone bodies as an alternative fuel and myocardial ketone oxidation as a key metabolic adaptation in the failing human heart.
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Affiliation(s)
- Kenneth C Bedi
- From Cardiovascular Institute University of Pennsylvania Perelman School of Medicine, Smilow Translational Research Center, Philadelphia, PA (K.C.B., J.B., A.J., K.B.M., J.E.R.); A.J. Drexel Autism Institute, Drexel University, Philadelphia, PA (N.W.S.); and Center of Cancer Pharmacology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA (M.A., C.M., A.J.W., L.L.W., I.A.B.)
| | - Nathaniel W Snyder
- From Cardiovascular Institute University of Pennsylvania Perelman School of Medicine, Smilow Translational Research Center, Philadelphia, PA (K.C.B., J.B., A.J., K.B.M., J.E.R.); A.J. Drexel Autism Institute, Drexel University, Philadelphia, PA (N.W.S.); and Center of Cancer Pharmacology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA (M.A., C.M., A.J.W., L.L.W., I.A.B.)
| | - Jeffrey Brandimarto
- From Cardiovascular Institute University of Pennsylvania Perelman School of Medicine, Smilow Translational Research Center, Philadelphia, PA (K.C.B., J.B., A.J., K.B.M., J.E.R.); A.J. Drexel Autism Institute, Drexel University, Philadelphia, PA (N.W.S.); and Center of Cancer Pharmacology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA (M.A., C.M., A.J.W., L.L.W., I.A.B.)
| | - Moez Aziz
- From Cardiovascular Institute University of Pennsylvania Perelman School of Medicine, Smilow Translational Research Center, Philadelphia, PA (K.C.B., J.B., A.J., K.B.M., J.E.R.); A.J. Drexel Autism Institute, Drexel University, Philadelphia, PA (N.W.S.); and Center of Cancer Pharmacology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA (M.A., C.M., A.J.W., L.L.W., I.A.B.)
| | - Clementina Mesaros
- From Cardiovascular Institute University of Pennsylvania Perelman School of Medicine, Smilow Translational Research Center, Philadelphia, PA (K.C.B., J.B., A.J., K.B.M., J.E.R.); A.J. Drexel Autism Institute, Drexel University, Philadelphia, PA (N.W.S.); and Center of Cancer Pharmacology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA (M.A., C.M., A.J.W., L.L.W., I.A.B.)
| | - Andrew J Worth
- From Cardiovascular Institute University of Pennsylvania Perelman School of Medicine, Smilow Translational Research Center, Philadelphia, PA (K.C.B., J.B., A.J., K.B.M., J.E.R.); A.J. Drexel Autism Institute, Drexel University, Philadelphia, PA (N.W.S.); and Center of Cancer Pharmacology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA (M.A., C.M., A.J.W., L.L.W., I.A.B.)
| | - Linda L Wang
- From Cardiovascular Institute University of Pennsylvania Perelman School of Medicine, Smilow Translational Research Center, Philadelphia, PA (K.C.B., J.B., A.J., K.B.M., J.E.R.); A.J. Drexel Autism Institute, Drexel University, Philadelphia, PA (N.W.S.); and Center of Cancer Pharmacology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA (M.A., C.M., A.J.W., L.L.W., I.A.B.)
| | - Ali Javaheri
- From Cardiovascular Institute University of Pennsylvania Perelman School of Medicine, Smilow Translational Research Center, Philadelphia, PA (K.C.B., J.B., A.J., K.B.M., J.E.R.); A.J. Drexel Autism Institute, Drexel University, Philadelphia, PA (N.W.S.); and Center of Cancer Pharmacology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA (M.A., C.M., A.J.W., L.L.W., I.A.B.)
| | - Ian A Blair
- From Cardiovascular Institute University of Pennsylvania Perelman School of Medicine, Smilow Translational Research Center, Philadelphia, PA (K.C.B., J.B., A.J., K.B.M., J.E.R.); A.J. Drexel Autism Institute, Drexel University, Philadelphia, PA (N.W.S.); and Center of Cancer Pharmacology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA (M.A., C.M., A.J.W., L.L.W., I.A.B.)
| | - Kenneth B Margulies
- From Cardiovascular Institute University of Pennsylvania Perelman School of Medicine, Smilow Translational Research Center, Philadelphia, PA (K.C.B., J.B., A.J., K.B.M., J.E.R.); A.J. Drexel Autism Institute, Drexel University, Philadelphia, PA (N.W.S.); and Center of Cancer Pharmacology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA (M.A., C.M., A.J.W., L.L.W., I.A.B.)
| | - J Eduardo Rame
- From Cardiovascular Institute University of Pennsylvania Perelman School of Medicine, Smilow Translational Research Center, Philadelphia, PA (K.C.B., J.B., A.J., K.B.M., J.E.R.); A.J. Drexel Autism Institute, Drexel University, Philadelphia, PA (N.W.S.); and Center of Cancer Pharmacology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA (M.A., C.M., A.J.W., L.L.W., I.A.B.).
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Neubauer S, Chu DB, Marx H, Sauer M, Hann S, Koellensperger G. LC-MS/MS-based analysis of coenzyme A and short-chain acyl-coenzyme A thioesters. Anal Bioanal Chem 2015; 407:6681-8. [PMID: 26168961 DOI: 10.1007/s00216-015-8825-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 06/03/2015] [Accepted: 06/03/2015] [Indexed: 11/27/2022]
Abstract
Absolute quantification of intracellular coenzyme A (CoA), coenzyme A disulfide, and short-chain acyl-coenzyme A thioesters was addressed by developing a tailored metabolite profiling method based on liquid chromatography in combination with tandem mass spectrometric detection (LC-MS/MS). A reversed phase chromatographic separation was established which is capable of separating a broad spectrum of CoA, its corresponding derivatives, and their isomers despite the fact that no ion-pairing reagent was used (which was considered as a key advantage of the method). Excellent analytical figures of merit such as high sensitivity (LODs in the nM to sub-nM range) and high repeatability (routinely 4 %; N = 15) were obtained. Method validation comprised a study on standard purity, stability, and recoveries during sample preparation. Uniformly labeled U(13)C yeast cell extracts offered ideal internal standards for validation purposes and for a quantification exercise in the rumen bacterium Megasphaera elsdenii.
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Affiliation(s)
- Stefan Neubauer
- Department of Chemistry, Division of Analytical Chemistry, University of Natural Resources and Life Sciences-BOKU, 1190, Vienna, Austria
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