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An J, Astapova I, Zhang G, Cangelosi AL, Ilkayeva O, Marchuk H, Muehlbauer MJ, George T, Brozinick J, Herman MA, Newgard CB. Integration of metabolomic and transcriptomic analyses reveals novel regulatory functions of the ChREBP transcription factor in energy metabolism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.17.613577. [PMID: 39345566 PMCID: PMC11429843 DOI: 10.1101/2024.09.17.613577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Carbohydrate Response Element-Binding Protein (ChREBP) is a transcription factor that activates key genes involved in glucose, fructose, and lipid metabolism in response to carbohydrate feeding, but its other potential roles in metabolic homeostasis have not been as well studied. We used liver-selective GalNAc-siRNA technology to suppress expression of ChREBP in rats fed a high fat/high sucrose diet and characterized hepatic and systemic responses by integrating transcriptomic and metabolomic analyses. GalNAc-siChREBP-treated rats had lower levels of multiple short-chain acyl CoA metabolites compared to rats treated with GalNAc-siCtrl containing a non-targeting siRNA sequence. These changes were related to a sharp decrease in free CoA levels in GalNAc-siChREBP treated-rats, accompanied by lower expression of transcripts encoding enzymes and transporters involved in CoA biosynthesis. These activities of ChREBP likely contribute to its complex effects on hepatic lipid and energy metabolism. While core enzymes of fatty acid (FA) oxidation are induced by ChREBP knockdown, accumulation of liver acylcarnitines and circulating ketones indicate diversion of acetyl CoA to ketone production rather than complete oxidation in the TCA cycle. Despite strong suppression of pyruvate kinase and activation of pyruvate dehydrogenase, pyruvate levels were maintained, likely via increased expression of pyruvate transporters, and decreased expression of lactate dehydrogenase and alanine transaminase. GalNAc-siChREBP treatment increased hepatic citrate and isocitrate levels while decreasing levels of distal TCA cycle intermediates. The drop in free CoA levels, needed for the 2-ketoglutarate dehydrogenase reaction, as well as a decrease in transcripts encoding the anaplerotic enzymes pyruvate carboxylase, glutamate dehydrogenase, and aspartate transaminase likely contributed to these effects. GalNAc-siChREBP treatment caused striking increases in PRPP and ZMP/AICAR levels, and decreases in GMP, IMP, AMP, NaNM, NAD(P), and NAD(P)H levels, accompanied by reduced expression of enzymes that catalyze late steps in purine and NAD synthesis. ChREBP suppression also increased expression of a set of plasma membrane amino acid transporters, possibly as an attempt to replenish TCA cycle intermediates. In sum, combining transcriptomic and metabolomic analyses has revealed regulatory functions of ChREBP that go well beyond its canonical roles in control of carbohydrate and lipid metabolism to now include mitochondrial metabolism and cellular energy balance.
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Affiliation(s)
- Jie An
- Sarah W. Stedman Nutrition and Metabolism Center & Duke Molecular Physiology Institute, Duke University Medical Center
| | - Inna Astapova
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Baylor College of Medicine
| | - Guofang Zhang
- Sarah W. Stedman Nutrition and Metabolism Center & Duke Molecular Physiology Institute, Duke University Medical Center
- Division of Endocrinology, Metabolism and Nutrition, Department of Medicine, Duke University Medical Center
| | - Andrew L. Cangelosi
- Sarah W. Stedman Nutrition and Metabolism Center & Duke Molecular Physiology Institute, Duke University Medical Center
| | - Olga Ilkayeva
- Sarah W. Stedman Nutrition and Metabolism Center & Duke Molecular Physiology Institute, Duke University Medical Center
- Division of Endocrinology, Metabolism and Nutrition, Department of Medicine, Duke University Medical Center
| | - Hannah Marchuk
- Sarah W. Stedman Nutrition and Metabolism Center & Duke Molecular Physiology Institute, Duke University Medical Center
| | - Michael J. Muehlbauer
- Sarah W. Stedman Nutrition and Metabolism Center & Duke Molecular Physiology Institute, Duke University Medical Center
| | - Tabitha George
- Sarah W. Stedman Nutrition and Metabolism Center & Duke Molecular Physiology Institute, Duke University Medical Center
| | | | - Mark A. Herman
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Baylor College of Medicine
| | - Christopher B. Newgard
- Sarah W. Stedman Nutrition and Metabolism Center & Duke Molecular Physiology Institute, Duke University Medical Center
- Division of Endocrinology, Metabolism and Nutrition, Department of Medicine, Duke University Medical Center
- Department of Pharmacology & Cancer Biology, Duke University Medical Center
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Lu J, Li XQ, Chen PP, Zhang JX, Liu L, Wang GH, Liu XQ, Jiang TT, Wang MY, Liu WT, Ruan XZ, Ma KL. Activation of acetyl-CoA synthetase 2 mediates kidney injury in diabetic nephropathy. JCI Insight 2023; 8:e165817. [PMID: 37870960 PMCID: PMC10619493 DOI: 10.1172/jci.insight.165817] [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: 10/06/2022] [Accepted: 09/05/2023] [Indexed: 10/25/2023] Open
Abstract
Albuminuria and podocyte injury are the key cellular events in the progression of diabetic nephropathy (DN). Acetyl-CoA synthetase 2 (ACSS2) is a nucleocytosolic enzyme responsible for the regulation of metabolic homeostasis in mammalian cells. This study aimed to investigate the possible roles of ACSS2 in kidney injury in DN. We constructed an ACSS2-deleted mouse model to investigate the role of ACSS2 in podocyte dysfunction and kidney injury in diabetic mouse models. In vitro, podocytes were chosen and transfected with ACSS2 siRNA and ACSS2 inhibitor and treated with high glucose. We found that ACSS2 expression was significantly elevated in the podocytes of patients with DN and diabetic mice. ACSS2 upregulation promoted phenotype transformation and inflammatory cytokine expression while inhibiting podocytes' autophagy. Conversely, ACSS2 inhibition improved autophagy and alleviated podocyte injury. Furthermore, ACSS2 epigenetically activated raptor expression by histone H3K9 acetylation, promoting activation of the mammalian target of rapamycin complex 1 (mTORC1) pathway. Pharmacological inhibition or genetic depletion of ACSS2 in the streptozotocin-induced diabetic mouse model greatly ameliorated kidney injury and podocyte dysfunction. To conclude, ACSS2 activation promoted podocyte injury in DN by raptor/mTORC1-mediated autophagy inhibition.
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Affiliation(s)
- Jian Lu
- Department of Nephrology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, China
- Institute of Nephrology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Xue Qi Li
- Institute of Nephrology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Pei Pei Chen
- Institute of Nephrology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Jia Xiu Zhang
- Institute of Nephrology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Liang Liu
- Department of Intensive Care Unit, People’s Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Gui Hua Wang
- Institute of Nephrology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Xiao Qi Liu
- Institute of Nephrology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Ting Ting Jiang
- Institute of Nephrology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Meng Ying Wang
- Institute of Nephrology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Wen Tao Liu
- Institute of Nephrology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Xiong Zhong Ruan
- John Moorhead Research Laboratory, Department of Renal Medicine, University College London Medical School, Royal Free Campus, London, United Kingdom
| | - Kun Ling Ma
- Department of Nephrology, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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Rehan M, Deskin B, Kurundkar AR, Yadav S, Matsunaga Y, Manges J, Smith N, Dsouza KG, Burow ME, Thannickal VJ. Nicotinamide N-methyltransferase mediates lipofibroblast-myofibroblast transition and apoptosis resistance. J Biol Chem 2023; 299:105027. [PMID: 37423298 PMCID: PMC10413354 DOI: 10.1016/j.jbc.2023.105027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 06/01/2023] [Accepted: 06/23/2023] [Indexed: 07/11/2023] Open
Abstract
Metabolism controls cellular phenotype and fate. In this report, we demonstrate that nicotinamide N-methyltransferase (NNMT), a metabolic enzyme that regulates developmental stem cell transitions and tumor progression, is highly expressed in human idiopathic pulmonary fibrosis (IPF) lungs, and is induced by the pro-fibrotic cytokine, transforming growth factor-β1 (TGF-β1) in lung fibroblasts. NNMT silencing reduces the expression of extracellular matrix proteins, both constitutively and in response to TGF-β1. Furthermore, NNMT controls the phenotypic transition from homeostatic, pro-regenerative lipofibroblasts to pro-fibrotic myofibroblasts. This effect of NNMT is mediated, in part, by the downregulation of lipogenic transcription factors, TCF21 and PPARγ, and the induction of a less proliferative but more differentiated myofibroblast phenotype. NNMT confers an apoptosis-resistant phenotype to myofibroblasts that is associated with the downregulation of pro-apoptotic members of the Bcl-2 family, including Bim and PUMA. Together, these studies indicate a critical role for NNMT in the metabolic reprogramming of fibroblasts to a pro-fibrotic and apoptosis-resistant phenotype and support the concept that targeting this enzyme may promote regenerative responses in chronic fibrotic disorders such as IPF.
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Affiliation(s)
- Mohammad Rehan
- John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, Louisiana, USA.
| | - Brian Deskin
- John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, Louisiana, USA; Southeast Louisiana Veterans Health Care System, New Orleans, Louisiana, USA
| | - Ashish R Kurundkar
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Santosh Yadav
- John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, Louisiana, USA; Southeast Louisiana Veterans Health Care System, New Orleans, Louisiana, USA
| | - Yasuka Matsunaga
- John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Justin Manges
- John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, Louisiana, USA; Southeast Louisiana Veterans Health Care System, New Orleans, Louisiana, USA
| | - Nia Smith
- John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, Louisiana, USA; Southeast Louisiana Veterans Health Care System, New Orleans, Louisiana, USA
| | - Kevin G Dsouza
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Matthew E Burow
- John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Victor J Thannickal
- John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, Louisiana, USA; Southeast Louisiana Veterans Health Care System, New Orleans, Louisiana, USA.
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Kuna RS, Kumar A, Wessendorf-Rodriguez KA, Galvez H, Green CR, McGregor GH, Cordes T, Shaw RJ, Svensson RU, Metallo CM. Inter-organelle cross-talk supports acetyl-coenzyme A homeostasis and lipogenesis under metabolic stress. SCIENCE ADVANCES 2023; 9:eadf0138. [PMID: 37134162 PMCID: PMC10156121 DOI: 10.1126/sciadv.adf0138] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [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
Proliferating cells rely on acetyl-CoA to support membrane biogenesis and acetylation. Several organelle-specific pathways are available for provision of acetyl-CoA as nutrient availability fluctuates, so understanding how cells maintain acetyl-CoA homeostasis under such stresses is critically important. To this end, we applied 13C isotope tracing cell lines deficient in these mitochondrial [ATP-citrate lyase (ACLY)]-, cytosolic [acetyl-CoA synthetase (ACSS2)]-, and peroxisomal [peroxisomal biogenesis factor 5 (PEX5)]-dependent pathways. ACLY knockout in multiple cell lines reduced fatty acid synthesis and increased reliance on extracellular lipids or acetate. Knockout of both ACLY and ACSS2 (DKO) severely stunted but did not entirely block proliferation, suggesting that alternate pathways can support acetyl-CoA homeostasis. Metabolic tracing and PEX5 knockout studies link peroxisomal oxidation of exogenous lipids as a major source of acetyl-CoA for lipogenesis and histone acetylation in cells lacking ACLY, highlighting a role for inter-organelle cross-talk in supporting cell survival in response to nutrient fluctuations.
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Affiliation(s)
- Ramya S. Kuna
- Department of Molecular and Cell Biology, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Avi Kumar
- Department of Molecular and Cell Biology, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Karl A. Wessendorf-Rodriguez
- Department of Molecular and Cell Biology, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Hector Galvez
- Department of Molecular and Cell Biology, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Courtney R. Green
- Department of Molecular and Cell Biology, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Grace H. McGregor
- Department of Molecular and Cell Biology, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Thekla Cordes
- Department of Molecular and Cell Biology, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig 38106, Germany
| | - Reuben J. Shaw
- Department of Molecular and Cell Biology, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | | | - Christian M. Metallo
- Department of Molecular and Cell Biology, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
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Roglans N, Laguna JC, Alegret M. Bempedoic acid for nonalcoholic fatty liver disease: evidence and mechanisms of action. Curr Opin Lipidol 2023:00041433-990000000-00034. [PMID: 36942869 DOI: 10.1097/mol.0000000000000878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
PURPOSE OF REVIEW Nonalcoholic fatty liver disease (NAFLD) is a highly prevalent progressive condition that lacks a specific pharmacological treatment. ATP-citrate lyase (ACLY) is one of the emergent targets for the treatment of NAFLD. This review aims to summarize the role of ACLY in NAFLD, provide evidences of the beneficial effects of the ACLY inhibitor bempedoic acid (BemA) in NAFLD and discuss the mechanisms involved. RECENT FINDINGS BemA is effective in reducing hepatic steatosis in several animal models that recapitulate different stages of the disease. Thus, in a dietary model of simple hepatic steatosis in female rats, BemA abrogates the accumulation of liver fat. Apart from ACLY inhibition, BemA has several functions in the liver that contribute to the antisteatotic effect: inhibition of ketohexokinase, induction of patatin-like phospholipase domain-containing protein 3 and increases in both fatty acid β-oxidation activity and hepatic H2S production. In models of the advanced phases of NAFLD, BemA reduces not only steatosis, but also ballooning, lobular inflammation and hepatic fibrosis, by mechanisms involving both hepatocytes and hepatic stellate cells. SUMMARY BemA, an ACLY inhibitor currently approved for the treatment of hypercholesterolemia, may be a useful drug to treat NAFLD through its antisteatotic, anti-inflammatory and antifibrotic effects.
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Affiliation(s)
- Núria Roglans
- Department of Pharmacology, Toxicology and Therapeutic Chemistry, School of Pharmacy and Food Science
- Institute of Biomedicine, University of Barcelona, Barcelona
- Spanish Biomedical Research Centre in Physiopathology of Obesity and Nutrition (CIBEROBN), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Juan Carlos Laguna
- Department of Pharmacology, Toxicology and Therapeutic Chemistry, School of Pharmacy and Food Science
- Institute of Biomedicine, University of Barcelona, Barcelona
- Spanish Biomedical Research Centre in Physiopathology of Obesity and Nutrition (CIBEROBN), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Marta Alegret
- Department of Pharmacology, Toxicology and Therapeutic Chemistry, School of Pharmacy and Food Science
- Institute of Biomedicine, University of Barcelona, Barcelona
- Spanish Biomedical Research Centre in Physiopathology of Obesity and Nutrition (CIBEROBN), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
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6
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Abstract
Few metabolites can claim a more central and versatile role in cell metabolism than acetyl coenzyme A (acetyl-CoA). Acetyl-CoA is produced during nutrient catabolism to fuel the tricarboxylic acid cycle and is the essential building block for fatty acid and isoprenoid biosynthesis. It also functions as a signalling metabolite as the substrate for lysine acetylation reactions, enabling the modulation of protein functions in response to acetyl-CoA availability. Recent years have seen exciting advances in our understanding of acetyl-CoA metabolism in normal physiology and in cancer, buoyed by new mouse models, in vivo stable-isotope tracing approaches and improved methods for measuring acetyl-CoA, including in specific subcellular compartments. Efforts to target acetyl-CoA metabolic enzymes are also advancing, with one therapeutic agent targeting acetyl-CoA synthesis receiving approval from the US Food and Drug Administration. In this Review, we give an overview of the regulation and cancer relevance of major metabolic pathways in which acetyl-CoA participates. We further discuss recent advances in understanding acetyl-CoA metabolism in normal tissues and tumours and the potential for targeting these pathways therapeutically. We conclude with a commentary on emerging nodes of acetyl-CoA metabolism that may impact cancer biology.
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Affiliation(s)
- David A Guertin
- Program in Molecular Medicine, UMass Chan Medical School, Worcester, MA, USA.
| | - Kathryn E Wellen
- Department of Cancer Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
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